# Patent

## Title
Immune cell compositions and methods of use for treating viral and other infections

## Abstract

Disclosed herein are cells that are immune cells, which cells recombinantly express a dominant negative form of an inhibitor of a cell-mediated immune response of the immune cell, and optionally recombinantly express a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen. In certain embodiments, the immune cell is an immunostimulatory cell, such as a T cell. In certain embodiments, the immune cell is an immunoinhibitory cell, such as a regulatory T cell. Also disclosed herein are immune cells that recognize and are sensitized to a viral antigen, which immune cells recombinantly express a dominant negative form of an inhibitor of a cell-mediated immune response of the immune cell. The cells can be sensitized to an antigen that is a viral antigen. Additionally provided are methods of using such cells to treat a viral infection in a subject in need thereof.

## Background
1. CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a national stage of International Patent Application No. PCT/US2017/049085, filed Aug. 29, 2017, which claims the benefit of U.S. Provisional application No. 62/381,219, filed Aug. 30, 2016, and U.S. Provisional application No. 62/468,881, filed Mar. 8, 2017; each Provisional application is incorporated by reference herein in its entirety.


2. REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY
This application incorporates by reference a Sequence Listing with this application as an ASCII text file entitled “13542-038-228_SL.TXT” created on Aug. 22, 2017, and having a size of 59,378 bytes.
3. FIELD
The present invention relates generally to treating viral infections, and more specifically to immunotherapy for treating viral infections.
4. BACKGROUND
Viral infections are known to cause a wide range of diseases. An acute viral infection is characterized by viral replication, spread, secondary replication, tissue damage and shedding (Virgin et al., Cell 138(1):30-50 (2009)). If the infected subject survives the acute viral infection, either the host immune system clears the infection, or the infection becomes persistent.
Persistent viral infections are characterized as viral infections that are not cleared from an individual but remain or persist in cells of the individual (see Boldogh et al., “Persistent Viral Infections” in Medical Microbiology, 4th ed., Baron, editor, Chapter 46, The University of Texas Medical Branch at Galveston (1996); Virgin et al., Cell 138(1):30-50 (2009)). Persistent viral infections can be classified as latent, chronic or slow infections (Boldogh et al., supra, 1996).
Latent infections lack demonstrable infectious virus between episodes of recurrent disease. In chronic infection, continued presence of infectious virus follows the primary infection and may include chronic or recurrent disease. Slow infection involves a prolonged incubation period followed by progressive disease (Boldogh et al., supra, 1996). Unlike latent and chronic infections, slow infection does not necessarily begin with an acute period of viral multiplication. During persistent infections, the viral genome can be stably integrated into the cellular DNA or maintained episomally (see Boldogh et al., supra, 1996).
A number of viral infections have a tendency to become persistent infections. Examples of such viral infections include infection with human immunodeficiency virus (HIV), hepatitis B virus (HBV) and hepatitis C virus (HCV). Infection with human immunodeficiency virus (HIV) can lead to acquired immunodeficiency syndrome (AIDS) and related medical conditions (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 1837-1891, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1791-1856, McGraw-Hill, San Francisco Calif. (1998)). Infection with hepatitis B virus (HBV), which predominantly affects the liver, can lead to progressive chronic liver disease with cirrhosis and, in some cases, hepatocellular carcinoma (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 762-767, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1677-1681, McGraw-Hill, San Francisco Calif. (1998)). Infection with hepatitis C virus (HCV), which also predominantly affects the liver, also can lead to progressive chronic liver disease with cirrhosis and, in some cases, hepatocellular carcinoma (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 762-764, 767-769, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1677, 1681-1682, McGraw-Hill, San Francisco Calif. (1998)). Such viral infections can lead to persistent infections.
Other viral infections include infection with herpes simplex virus (HSV), varicella zoster virus or (VZV), adenovirus, cytomegalovirus (CMV), and Epstein-Barr Virus (EBV). Infection with HSV can lead to gingivostomatitis, usually caused by HSV-1, for example, herpes simplex labialis (cold sores) (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 1770-1774, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1080-1086, McGraw-Hill, San Francisco Calif. (1998)). Infection with HSV can also cause genital herpes, most commonly caused by HSV-2; herpetic keratitis, usually caused by HSV-1 and often accompanied by conjunctivitis; neonatal HSV infection, usually caused by HSV-2; and herpes simplex encephalitis, usually caused by HSV-1. Infection with HSV can become a latent infection (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 1770-1774, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1080-1086, McGraw-Hill, San Francisco Calif. (1998)).
Infection with VZV can cause chickenpox (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 1763-1765, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1086-1089, McGraw-Hill, San Francisco Calif. (1998)). Latent infections can evolve to herpes zoster (shingles) caused by reactivation of VZV that is normally latent in sensory ganglia (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 2093-2095, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1086-1089, McGraw-Hill, San Francisco Calif. (1998)). Infection with adenovirus can cause disease in a variety of human epithelial tissues including the eye (pharyngoconjunctival fever; epidemic keratoconjunctivitis), respiratory tract, including upper respiratory tract illness (acute pharyngitis; exudative tonsillitis) and lower respiratory tract (pneumonia), urinary disease (hemorrhagic cystitis), and gastrointestinal disease (gastroenteritis) (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 1757-1759, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1104-1105, McGraw-Hill, San Francisco Calif. (1998)).
Infection with CMV can cause infectious mononucleosis and congenital infection (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 1774-1776, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1092-1095, McGraw-Hill, San Francisco Calif. (1998)). Infection with EBV can cause infectious mononucleosis, including chronic mononucleosis or chronic fatigue syndrome, and latent EBV infection is associated with B lymphomas in immunosuppressed patients (Bennett et al., Cecil Textbook of Medicine, 20th ed., pp. 1776-1779, W.B. Saunders, Philadelphia Pa. (1996); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1089-1091, McGraw-Hill, San Francisco Calif. (1998)).
Functional impairment of T cells is characteristic of many human viral infections (see Day et al., Nature 443:350-354 (2006) and references cited therein). PD-1 is a negative regulator of activated T cells, and is markedly upregulated on the surface of exhausted virus-specific CD8+ T cells (Ishida et al., EMBO J. 11:3887-3895 (1992); Noshimura et al., Immunity 11:141-151 (1999); Sharpe et al., Nat. Rev. Immunol. 2:116-126 (2002); Che, Nat. Rev. Immunol. 4:336-347 (2004); Barber et al., Nature 439:682-687 (2006)). Blockade of this pathway using antibodies against the PD ligand 1 (PD-L1, also known as CD274) restores CD8+ T-cell function and reduces viral load (Barber et al., Nature 439:682-687 (2006)). It was found that PD-1 is significantly upregulated on T cells, and expression correlates with impaired HIV-specific CD8+ T-cell function as well as predictors of disease progression: positively with plasma viral load and inversely with CD4+ T-cell count (Day et al., Nature 443:350-354 (2006)). PD-1 expression on CD4+ T cells likewise showed a positive correlation with viral load and an inverse correlation with CD4+ T-cell count, and blockade of the pathway augmented HIV-specific CD4+ and CD8+ T-cell function (Day et al., Nature 443:350-354 (2006)). The results described by Day et al. (supra, 2006) indicate that the immunoregulatory PD-1/PD-L1 pathway is operative during a persistent viral infection in humans, and define a reversible defect in HIV-specific T-cell function (Day et al., Nature 443:350-354 (2006)).
PD-1-mediated inhibitory signaling not only attenuates HBV-specific CD8+ T-cell effector function during the acute phase of infection but also correlates with the development of HBV-specific memory CD8+ T cells following disease resolution (Zhang et al., J. Hepatol. 50:1163-1173 (2009)). In a study of patients with hepatitis B, PD-1 was significantly upregulated and subsequently led to the functional suppression of HBV-specific effector CD8+ T cells, as blocking PD-1/PD-L1 interactions in vitro enhanced their proliferation and IFN-gamma production (Zhang et al., supra, 2009). Following disease resolution, HBV-specific effector CD8+ T cells developed into memory T cells. During this period, the dynamic PD-1 decrease was numerically correlated with the reduction of HBV-specific CD8+ T-cell frequency, phenotypically correlated with an acquisition of CCR7, CD45RA and CD127 expression, and functionally correlated with the increase in proliferation and IFN-gamma production of the memory T cells (Zhang et al., supra, 2009).
Chronic viral infection, unlike acute infection, leads to a large expansion of regulatory T cells (Treg cells) and their upregulation of PD-1 (Park et al., supra, J. Immunol. 194:5801-5811 (2015)). Treg cells from chronically infected mice (chronic Treg cells) displayed greater suppressive capacity for inhibiting both CD8+ and CD4+ T cell proliferation and for inhibiting subsequent cytokine production than those from naive or acutely infected mice (Park et al., supra, 2015). A contact between Treg and CD8+ T cells was necessary for the potent suppression of CD8+ T cell immune response. More importantly, the suppression required cell-specific expression and interaction of PD-1 on chronic Treg cells and PD-1 ligand on CD8+ T cells (Park et al., supra, 2015).
T cell therapy has been previously described, in which the host immune system is utilized to treat or eliminate cancer or viral infections (see “T Cell Therapies: An Overview” Catapult Cell and Gene Therapy, White Paper 1 (ct.catapult.org.uk/wp-content/uploads/2016/03/Review-of-T-cell-Receptor-Therapies-2014_v2.pdf) (2014); Rooney et al., Mol. Ther. Nucleic Acids 1:e55, doi: 10.1038/mtna.2012.49 (2012)). Such therapies include gene modified T cell receptor (TCR) therapies and chimeric antigen receptor (CAR) therapies (see “T Cell Therapies: An Overview” Catapult Cell and Gene Therapy, White Paper 1 (ct.catapult.org.uk/wp-content/uploads/2016/03/Review-of-T-cell-Receptor-Therapies-2014_v2.pdf) (2014)). The use of CAR therapy in the treatment of conditions such as cancer has been previously described (see, for example, Sadelain et al., Cancer Discov. 3(4):388-398 (2013); Jensen et al., Immunol. Rev. 257:127-133 (2014); Sharpe et al., Dis. Model Mech. 8(4):337-350 (2015); Brentjens et al., Clin. Cancer Res. 13:5426-5435 (2007); Gade et al., Cancer Res. 65:9080-9088 (2005); Maher et al., Nat. Biotechnol. 20:70-75 (2002); Kershaw et al., J. Immunol. 173:2143-2150 (2004); Sadelain et al., Curr. Opin. Immunol. 21(2):215-223 (2009); Hollyman et al., J. Immunother. 32:169-180 (2009); WO/2015/188141).
There exists a need for therapies to provide improved treatment of viral infections, such as chronic viral infections. The object of the present invention is to satisfy this need.
5. SUMMARY OF INVENTION
The present invention relates to cells that are immune cells, which cells recombinantly express a dominant negative form of an inhibitor of a cell-mediated immune response of the immune cell, and optionally recombinantly express a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen.
In one aspect, provided herein is a cell that is an immunostimulatory cell or precursor cell thereof, which cell recombinantly expresses (a) a chimeric antigen receptor (CAR), and (b) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the CAR binds to a viral antigen. In another aspect, provided herein is a population of immunostimulatory cells or precursor cells thereof, which cell population comprises cells that recombinantly express (a) a chimeric antigen receptor (CAR), and (b) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the CAR binds to a viral antigen. In certain embodiments, the immunostimulatory cell is a T cell. In certain embodiments, the precursor cell is a hematopoietic stem or hematopoietic progenitor cell. In a specific embodiment, the immunostimulatory cell is a cytotoxic T lymphocyte (CTL). In another specific embodiment, the cell is a T cell. In another specific embodiment, the cell is a Natural Killer (NK) cell. In another specific embodiment, the cell is a memory T cell. In another specific embodiment, the memory T cell is a memory CD8+ T cell.
In another aspect, provided herein is a T cell that recognizes and is sensitized to a viral antigen, which T cell recombinantly expresses a dominant negative form of an inhibitor of a T cell-mediated immune response. In certain embodiments, the T cell is immunostimulatory. In a specific embodiment, the T cell is CD4+. In another specific embodiment, the T cell is CD8+.
In another aspect, provided herein is a population of T cells, which cell population comprises T cells that recognize and are sensitized to a viral antigen and which recombinantly express a dominant negative form of an inhibitor of a T cell-mediated immune response. In certain embodiments, the T cells are immunostimulatory. In a specific embodiment, the T cells are CD4+. In another specific embodiment, the T cells are CD8+.
In certain embodiments of the invention, the cell or cell population is derived from a human. In certain embodiments of the invention, the viral antigen is of a virus that is a human pathogen. In certain embodiments of the invention, the viral antigen can elicit an immune response in a human subject infected with the virus.
In certain embodiments of the invention, the viral antigen is selected from the group consisting of a human immunodeficiency virus (HIV) antigen, a hepatitis B virus (HBV) antigen, a hepatitis C virus (HCV) antigen, a herpes simplex virus (HSV) antigen, a varicella zoster virus (VZV) antigen, an adenovirus antigen, a cytomegalovirus (CMV) antigen, and an Epstein-Barr virus (EBV) antigen. In a specific embodiment, the viral antigen is a HIV antigen selected from the group consisting of group-specific antigen (gag) protein, p55, p24, p18, envelope glycoprotein (env), gp160, gp120, gp41, reverse transcriptase (pol), p66, and p31. In another specific embodiment, the viral antigen is a HBV antigen selected from the group consisting of HBV envelope protein S, HBV envelope protein M, HBV envelope protein L, and the S domain of HBV envelope protein S, M or L. In another specific embodiment, the viral antigen is a HCV antigen selected from the group consisting of core protein, envelope protein E1, envelope protein E2, NS2, NS3, NS4 (e.g., NS4A or NS4B), and NS5 (e.g., NS5A or NS5B). In another specific embodiment, the viral antigen is a HSV antigen selected from the group consisting of gE, gI, gB, gD, gH, gL, gC, gG, gK, gM, and the extracellular domain of gE. In another specific embodiment, the viral antigen is a VZV antigen selected from the group consisting of gE and gI. In another specific embodiment, the viral antigen is an adenovirus antigen selected from the group consisting of hexon protein and penton protein. In another specific embodiment, the viral antigen is a CMV antigen selected from the group consisting of pp65, immediate early (IE) antigen, and IE1. In another specific embodiment, the viral antigen is an EBV antigen selected from the group consisting of latent membrane protein 2 (LMP2), Epstein-Barr nuclear antigen 1 (EBNA1), and BZLF1.
In certain embodiments of the invention, the inhibitor of a cell-mediated immune response is an immune checkpoint inhibitor. In certain embodiments, the immune checkpoint inhibitor is selected from the group consisting of programmed death 1 (PD-1), cytotoxic T lymphocyte antigen-4 (CTLA-4), B- and T-lymphocyte attenuator (BTLA), T cell immunoglobulin mucin-3 (TIM-3), lymphocyte-activation protein 3 (LAG-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), leukocyte-associated immunoglobulin-like receptor 1 (LAIR1), natural killer cell receptor 2B4 (2B4), and CD160. In a particular embodiment, the immune checkpoint inhibitor is PD-1. In another embodiment, the inhibitor of a cell-mediated immune response is transforming growth factor β (TGF-β) receptor.
In certain embodiments of the invention, the cell of the invention further recombinantly expresses a suicide gene. In a specific embodiment, the suicide gene comprises inducible Caspase 9.
In another aspect, provided herein is a regulatory T cell that recognizes and is sensitized to a viral antigen, which regulatory T cell recombinantly expresses a dominant negative form of an inhibitor of a regulatory T cell-mediated immune response. In another aspect, provided herein is a population of regulatory T cells, which cell population comprises T cells that recognize and are sensitized to a viral antigen and which recombinantly express a dominant negative form of an inhibitor of a regulatory T cell-mediated immune response. In certain embodiments of the invention, the regulatory T cell is isolated from a subject having a chronic viral infection.
In another aspect, provided herein is a regulatory T cell isolated from a subject having a viral infection, which regulatory T cell recombinantly expresses a dominant negative form of an inhibitor of a regulatory T cell-mediated immune response. In another aspect, provided herein is a population of regulatory T cells isolated from a subject having a viral infection, which cell population comprises regulatory T cells which recombinantly express a dominant negative form of an inhibitor of a regulatory T cell-mediated immune response. In certain embodiments, the cell or cell population is derived from a human. In certain embodiments, the viral infection is infection with a virus that is a human pathogen. In certain embodiments, the viral infection is a chronic viral infection. In certain embodiments, the viral infection is infection with HCV, HBV, HIV, HSV, VZV, adenovirus, CMV or EBV.
In another aspect, provided herein is an immunoinhibitory cell, which cell is isolated from a subject having a viral infection, which immunoinhibitory cell recombinantly expresses a dominant negative form of an inhibitor of an immunoinhibitory cell-mediated immune response. In another aspect, provided herein is a population of immunoinhibitory cells isolated from a subject having a viral infection, which cell population comprises immunoinhibitory cells which recombinantly express a dominant negative form of an inhibitor of an immunoinhibitory cell-mediated immune response. In certain embodiments, the cell or cell population is derived from a human. In certain embodiments, the viral infection is infection with a virus that is a human pathogen. In certain embodiments, the viral infection is a chronic viral infection. In certain embodiments, the immunoinhibitory cell is a regulatory T cell. In certain embodiments, the immunoinhibitory cell recognizes and is sensitized to a viral antigen of the virus of the viral infection. In certain embodiments, the immunoinhibitory cell recombinantly expresses a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen of the virus of the viral infection. In a specific embodiment, the regulatory T cell is a human CD4+CD25+ T cell. In another specific embodiment, the regulatory T cell is a human CD4+CD127lo/−CD25+ T cell.
In another aspect, provided herein is a polyclonal population of human regulatory T cells that are CD4+CD25+, are sensitized to a viral antigen, and recombinantly express a dominant negative form of an inhibitor of a regulatory T cell-mediated immune response. In certain embodiments, the human regulatory T cells are CD127lo/−.
In certain embodiments, the regulatory T cell or population of regulatory T cells is derived from a human. In certain embodiments, the viral antigen is of a virus that is a human pathogen. In certain embodiments, the viral antigen can elicit an immune response in a human subject infected with the virus.
In certain embodiments of the regulatory T cells or regulatory T cell population, the viral antigen is selected from the group consisting of a hepatitis C virus (HCV) antigen, a human immunodeficiency virus (HIV) antigen, a hepatitis B virus (HBV) antigen, a herpes simplex virus (HSV) antigen, a varicella zoster virus (VZV) antigen, an adenovirus antigen, a cytomegalovirus (CMV) antigen, and an Epstein-Barr virus (EBV) antigen. In a specific embodiment, the viral antigen is a HCV antigen selected from the group consisting of core protein, envelope protein E1, envelope protein E2, NS2, NS3, NS4 (e.g., NS4A or NS4B), and NS5 (e.g., NS5A or NS5B). In another specific embodiment, the viral antigen is a HIV antigen selected from the group consisting of group-specific antigen (gag) protein, p55, p24, p18, envelope glycoprotein (env), gp160, gp120, gp41, reverse transcriptase (pol), p66, and p31. In another specific embodiment, the viral antigen is a HBV antigen selected from the group consisting of HBV envelope protein S, HBV envelope protein M, HBV envelope protein L, and the S domain of HBV envelope protein S, M or L. In another specific embodiment, the viral antigen is a HSV antigen selected from the group consisting of gE, gI, gB, gD, gH, gL, gC, gG, gK, gM, and the extracellular domain of gE. In another specific embodiment, the viral antigen is a VZV antigen selected from the group consisting of gE and gI. In another specific embodiment, the viral antigen is an adenovirus antigen selected from the group consisting of hexon protein and penton protein. In another specific embodiment, the viral antigen is a CMV antigen selected from the group consisting of pp65, immediate early (IE) antigen, and IE1. In another specific embodiment, the viral antigen is an EBV antigen selected from the group consisting of latent membrane protein 2 (LMP2), Epstein-Barr nuclear antigen 1 (EBNA1), and BZLF1.
In certain embodiments of the invention relating to immunoinhibitory cells or regulatory T cells, the inhibitor of a cell-mediated immune response is an immune checkpoint inhibitor. In certain embodiments, the immune checkpoint inhibitor is selected from the group consisting of programmed death 1 (PD-1), cytotoxic T lymphocyte antigen-4 (CTLA-4), B- and T-lymphocyte attenuator (BTLA), T cell immunoglobulin mucin-3 (TIM-3), lymphocyte-activation protein 3 (LAG-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), leukocyte-associated immunoglobulin-like receptor 1 (LAIR1), natural killer cell receptor 2B4 (2B4), and CD160. In a specific embodiment, the immune checkpoint inhibitor is PD-1. In certain embodiments of the invention, the inhibitor of a cell-mediated immune response is transforming growth factor β (TGF-β) receptor. In certain embodiments, the immunoinhibitory cell or regulatory T cell, or population thereof, further recombinantly expresses a suicide gene. In a specific embodiment, the suicide gene comprises inducible Caspase 9.
In another aspect, provided herein is a cell that is an immunostimulatory cell or precursor cell thereof, which cell recombinantly expresses (a) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen; (b) a first dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the first dominant negative form lacks an intracellular signaling domain and is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, and (ii) a transmembrane domain; and (c) a second dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the second dominant negative form is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, (ii) a transmembrane domain, and (iii) a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form.
In another aspect, provided herein is a population of immunostimulatory cells or precursor cells thereof, which cell population comprises cells that recombinantly express (a) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen; (b) a first dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the first dominant negative form lacks an intracellular signaling domain and is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, and (ii) a transmembrane domain; and (c) a second dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the second dominant negative form is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, (ii) a transmembrane domain, and (iii) a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form.
In certain embodiments of such cells, the co-stimulatory signaling domain of the second dominant negative form is the intracellular signaling domain of 4-1BB. In certain embodiments of such cells, the CAR comprises a co-stimulatory signaling domain. In certain embodiments of such cells, the co-stimulatory signaling domain of the second dominant negative form is different from the co-stimulatory signaling domain of the CAR. In certain embodiments of such cells, the co-stimulatory signaling domain of the CAR is the intracellular signaling domain of CD28. In certain embodiments of such cells, the immunostimulatory cell is a T cell. In certain embodiments of such cells, the precursor cell is a hematopoietic stem or hematopoietic progenitor cell. In certain embodiments of such cells, the immunostimulatory cell is a cytotoxic T lymphocyte (CTL). In certain embodiments of such cells, the cell is a Natural Killer (NK) cell. In certain embodiments of such cells, the cell is a memory T cell. In certain embodiments of such cells, the memory T cell is a memory CD8+ T cell.
In another aspect, provided herein is an immunoinhibitory cell, which cell is isolated from a subject having a viral infection, which immunoinhibitory cell recombinantly expresses (a) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen of the virus of the viral infection; (b) a first dominant negative form of an inhibitor of a cell-mediated immune response of the immunoinhibitory cell, wherein the first dominant negative form lacks an intracellular signaling domain and is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, and (ii) a transmembrane domain; and (c) a second dominant negative form of an inhibitor of a cell-mediated immune response of the immunoinhibitory cell, wherein the second dominant negative form is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, (ii) a transmembrane domain, and (iii) a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form.
In another aspect, provided herein is a population of immunoinhibitory cells isolated from a subject having a viral infection, which cell population comprises immunoinhibitory cells which recombinantly express (a) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen of the virus of the viral infection; (b) a first dominant negative form of an inhibitor of a cell-mediated immune response of the immunoinhibitory cell, wherein the first dominant negative form lacks an intracellular signaling domain and is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, and (ii) a transmembrane domain; and (c) a second dominant negative form of an inhibitor of a cell-mediated immune response of the immunoinhibitory cell, wherein the second dominant negative form is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, (ii) a transmembrane domain, and (iii) a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form.
In certain embodiments of such cells, the co-stimulatory signaling domain is the intracellular signaling domain of 4-1BB. In certain embodiments of such cells, the CAR comprises a co-stimulatory signaling domain. In certain embodiments of such cells, the co-stimulatory signaling domain of the second dominant negative form is different from the co-stimulatory signaling domain of the CAR. In certain embodiments of such cells, the co-stimulatory signaling domain of the CAR is the intracellular signaling domain of CD28. In certain embodiments of such cells, the cell or cell population is derived from a human. In certain embodiments of such cells, the viral infection is infection with a virus that is a human pathogen. In certain embodiments of such cells, the viral infection is a chronic viral infection. In certain embodiments of such cells, the immunoinhibitory cell is a regulatory T cell. In certain embodiments of such cells, the regulatory T cell is a human CD4+ CD25+ T cell. In certain embodiments of such cells, the regulatory T cell is a human CD4+CD127lo/−CD25+ T cell.
In another aspect, provided herein is a cell that is an immunostimulatory cell or precursor cell thereof, which cell recombinantly expresses (a) a chimeric antigen receptor (CAR), and (b) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the CAR binds to an antigen of a pathogen. In another aspect, provided herein is a population of immunostimulatory cells or precursor cells thereof, which cell population comprises cells that recombinantly express (a) a chimeric antigen receptor (CAR), and (b) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the CAR binds to an antigen of a pathogen.
In certain embodiments of such a cell or cell population, the immunostimulatory cell is a T cell. In certain embodiments, the T cell is CD4+. In certain embodiments, the T cell is CD8+. In certain embodiments of such a cell or cell population, the precursor cell is a hematopoietic stem or hematopoietic progenitor cell. In certain embodiments of such a cell or cell population, the immunostimulatory cell is a cytotoxic T lymphocyte (CTL). In certain embodiments of such a cell or cell population, the cell is a Natural Killer (NK) cell. In certain embodiments of such a cell or cell population, the cell is a memory T cell. In a particular embodiment, the memory T cell is a memory CD8+ T cell.
In another aspect, provided herein is a T cell that recognizes and is sensitized to an antigen of a pathogen, which T cell recombinantly expresses a dominant negative form of an inhibitor of a T cell-mediated immune response. In certain embodiments of such a T cell, the T cell is immunostimulatory. In a particular embodiment, the T cell is CD4+. In another particular embodiment, the T cell is CD8+.
In another aspect, provided herein is a population of T cells, which cell population comprises T cells that recognize and are sensitized to an antigen of a pathogen and which recombinantly express a dominant negative form of an inhibitor of a T cell-mediated immune response. In certain embodiments of such a population of T cells, the T cells are immunostimulatory.
In a particular embodiment of such a T cell or such a population of T cells, the T cells are CD4+. In a particular embodiment of such a T cell or such a population of T cells, the T cells are CD8+. In certain embodiments of such a T cell or such a population of T cells, the cell or cell population is derived from a human. In a particular embodiment of such a T cell or such a population of T cells, the pathogen is a human pathogen. In a particular embodiment, the antigen of the pathogen can elicit an immune response in a human subject infected with the pathogen. In certain embodiments of such a T cell or such a population of T cells, the pathogen is selected from the group consisting of a bacterium, fungus and protozoan.
In certain embodiments of such a T cell or such a population of T cells, the inhibitor of a cell-mediated immune response is an immune checkpoint inhibitor. In certain embodiments, the immune checkpoint inhibitor is selected from the group consisting of programmed death 1 (PD-1), cytotoxic T lymphocyte antigen-4 (CTLA-4), B- and T-lymphocyte attenuator (BTLA), T cell immunoglobulin mucin-3 (TIM-3), lymphocyte-activation protein 3 (LAG-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), leukocyte-associated immunoglobulin-like receptor 1 (LAIR1), natural killer cell receptor 2B4 (2B4), and CD160. In a particular embodiment, the immune checkpoint inhibitor is PD-1. In certain embodiments, the inhibitor of a cell-mediated immune response is transforming growth factor β (TGF-β) receptor.
In certain embodiments of such a T cell or such a population of T cells, the cell further recombinantly expresses a suicide gene. In a particular embodiment, the suicide gene comprises inducible Caspase 9.
In another aspect, provided herein are pharmaceutical compositions comprising a therapeutically effective amount of the immune cells or population of immune cells of the invention; and a pharmaceutically acceptable carrier. In certain embodiments, the immune cells or population of immune cells are immunostimulatory cells described above. In certain embodiments, the immune cells or population of immune cells are T cells described above. In certain embodiments, the immune cells or population of immune cells are immunoinhibitory cells described above. In certain embodiments, the immune cells or population of immune cells are regulatory T cells described above.
In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an immune cell or cell population of the invention, wherein the viral antigen is an antigen associated with the viral infection. In certain embodiments, the immune cells or population of immune cells are immunostimulatory cells described above. In certain embodiments, the immune cells or population of immune cells are T cells described above. In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject a pharmaceutical composition comprising the immune cells or population of immune cells that are immunostimulatory cells described above, wherein the viral antigen is an antigen associated with the viral infection. In certain embodiments, the immune cells or population of immune cells are T cells described above. In certain embodiments of the methods, the subject is a human. In certain embodiments of the method, the viral infection is infection with a virus that is a human pathogen. In certain embodiments, the viral infection is infection with HIV, HBV, HCV, HSV, VZV, adenovirus, CMV or EBV. In certain embodiments, expression of the dominant negative form promotes production of virus-specific memory cells.
In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of the regulatory T cell or population of regulatory T cells described above, wherein the viral antigen is an antigen associated with the viral infection. In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject the pharmaceutical composition comprising the regulatory T cell or population of regulatory T cells described above, wherein the viral antigen is an antigen associated with the viral infection.
In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of the immunoinhibitory cell or population of immunoinhibitory cells described above. In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject the pharmaceutical composition comprising the immunoinhibitory cell or population of immunoinhibitory cells described above.
In certain embodiments of the methods of administering regulatory T cells or immunoinhibitory cells, or populations thereof, or pharmaceutical compositions comprising such cells or cell populations, the subject is a human. In certain of embodiments of the methods of administering regulatory T cells or immunoinhibitory cells, or populations thereof, or pharmaceutical compositions comprising such cells or cell populations, the viral infection is infection with a virus that is a human pathogen. In certain of embodiments of the methods of administering regulatory T cells or immunoinhibitory cells, or populations thereof, or pharmaceutical compositions comprising such cells or cell populations, the viral infection is a chronic viral infection. In certain of embodiments of the methods of administering regulatory T cells or immunoinhibitory cells, or populations thereof, or pharmaceutical compositions comprising such cells or cell populations, the viral infection is infection with HCV, HIV, HBV, HSV, VZV, adenovirus, CMV or EBV.
In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising: (a) isolating virus-specific T cells from the subject; (b) expressing in the cells a dominant negative form of PD-1; and (c) administering the cells to the subject. In a specific embodiment, the viral infection is infection with HIV. In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising: (a) isolating virus-specific T cells from the subject; (b) expressing in the cells a dominant negative form of PD-1, wherein expression of the dominant negative form of PD-1 promotes production of virus-specific memory cells; and (c) administering the cells to the subject. In a specific embodiment, the viral infection is infection with HBV. In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising: (a) isolating regulatory T cells from a subject having a chronic viral infection; (b) expressing in the cells a dominant negative form of PD-1; and (c) administering the cells to the subject. In a specific embodiment, the viral infection is infection with HCV. In certain embodiments of the methods, the subject is a human. In certain embodiments of the methods, the viral infection is infection with a virus that is a human pathogen. In certain embodiments of the methods, the viral infection is infection with HIV, HBV, HCV, HSV, VZV, adenovirus, CMV or EBV.
In certain embodiments of the methods of the invention, the administering of the immune cell or immune cell population, or pharmaceutical composition comprising the immune cells or immune cell populations, is by intrapleural administration, intravenous administration, subcutaneous administration, intranodal administration, intrahepatic administration, intrathecal administration, intraperitoneal administration, intracranial administration, or direct administration to the thymus. In certain embodiments of the methods of the invention, the cell is administered in a dose in the range of 104 to 1010 cells per kilogram of body weight. In a specific embodiment, the dose is in the range of 3×105 to 3×106 cells per kilogram of body weight. In certain embodiments of methods of the invention the cell or cell population is autologous to the subject.
In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of the cell or cell population, where the cell recombinantly expresses (a) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen; (b) a first dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the first dominant negative form lacks an intracellular signaling domain and is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, and (ii) a transmembrane domain; and (c) a second dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the second dominant negative form is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, (ii) a transmembrane domain, and (iii) a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form and wherein the viral antigen is an antigen associated with the viral infection. In another embodiment, the invention provides a method of treating a viral infection in a subject in need thereof, comprising administering to the subject the pharmaceutical composition of such cells, wherein the viral antigen is an antigen associated with the viral infection.
In certain embodiments of such methods of the invention, the subject is a human. In certain embodiments of such methods, the viral infection is infection with a virus that is a human pathogen. In certain embodiments, the viral infection is infection with HIV, HBV, HCV, HSV, VZV, adenovirus, CMV or EBV. In certain embodiments of such methods, expression of the first dominant negative form promotes production in the subject of virus-specific memory cells.
In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of the cell or cell population, wherein the cell is isolated from a subject having a viral infection, which immunoinhibitory cell recombinantly expresses (a) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen of the virus of the viral infection; (b) a first dominant negative form of an inhibitor of a cell-mediated immune response of the immunoinhibitory cell, wherein the first dominant negative form lacks an intracellular signaling domain and is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, and (ii) a transmembrane domain; and (c) a second dominant negative form of an inhibitor of a cell-mediated immune response of the immunoinhibitory cell, wherein the second dominant negative form is a polypeptide comprising (i) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, (ii) a transmembrane domain, and (iii) a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form; wherein the viral antigen is an antigen associated with the viral infection. In another embodiment, the provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject a pharmaceutical composition of such cells, wherein the viral antigen is an antigen associated with the viral infection.
In certain embodiments of such methods of the invention, the subject is a human. In certain embodiments of such methods of the invention, the viral infection is infection with a virus that is a human pathogen. In certain embodiments, the viral infection is infection with HIV, HBV, HCV, HSV, VZV, adenovirus, CMV or EBV. In certain embodiments of such methods of the invention, expression of the first dominant negative form promotes production in the subject of virus-specific memory cells.
In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of (a) a first cell or first population of said first cell, wherein the first cell is an immunostimulatory cell and recombinantly expresses (i) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen and wherein the viral antigen is an antigen associated with the viral infection, and (ii) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the dominant negative form lacks an intracellular signaling domain and is a polypeptide comprising (A) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, and (B) a transmembrane domain; and (b) a second cell or second population of said second cell, wherein the second cell is an immunostimulatory cell and recombinantly expresses (i) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen and wherein the viral antigen is an antigen associated with the viral infection, and (ii) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the dominant negative form is a polypeptide comprising (A) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, (B) a transmembrane domain, and (C) a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form. In certain embodiments of such methods, the subject is a human. In certain embodiments of such methods, the viral infection is infection with a virus that is a human pathogen. In certain embodiments, the viral infection is infection with HIV, HBV, HCV, HSV, VZV, adenovirus, CMV or EBV.
In another aspect, provided herein is a method of treating a viral infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of (a) a first cell or first population of said first cell, wherein the first cell is an immunoinhibitory cell and recombinantly expresses (i) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen and wherein the viral antigen is an antigen associated with the viral infection, and (ii) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunoinhibitory cell, wherein the dominant negative form lacks an intracellular signaling domain and is a polypeptide comprising (A) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, and (B) a transmembrane domain; and (b) a second cell or second population of said second cell, wherein the second cell is an immunoinhibitory cell and recombinantly expresses (i) a chimeric antigen receptor (CAR), wherein the CAR binds to a viral antigen and wherein the viral antigen is an antigen associated with the viral infection, and (ii) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunoinhibitory cell, wherein the dominant negative form is a polypeptide comprising (A) at least a portion of an extracellular domain of an immune checkpoint inhibitor, wherein the portion comprises the ligand binding region, (B) a transmembrane domain, and (C) a fusion to a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form.
In certain embodiments of such methods, the subject is a human. In certain embodiments of such methods, the viral infection is infection with a virus that is a human pathogen. In certain embodiments, the viral infection is infection with HIV, HBV, HCV, HSV, VZV, adenovirus, CMV or EBV. In certain embodiments of such methods, the cell or cell population is autologous to the subject.
In another aspect, provided herein is a method of treating an infection caused by a pathogen in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a cell or cell population, wherein the cell or cell population recombinantly expresses (a) a chimeric antigen receptor (CAR), and (b) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the CAR binds to an antigen of a pathogen, wherein the antigen of the pathogen to which the CAR binds is an antigen of the pathogen causing the infection. In another aspect, provided herein is a method of treating an infection caused a pathogen in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a cell or cell population, wherein the cell is, or cell population comprises, a T cell that recognizes and is sensitized to an antigen of a pathogen, which T cell recombinantly expresses a dominant negative form of an inhibitor of a T cell-mediated immune response, wherein the antigen of the pathogen to which the T cell is sensitized is an antigen of the pathogen causing the infection. In certain embodiments, the T cell is immunostimulatory. In certain embodiments, the T cell is CD4+. In certain embodiments, the T cell is CD8+.
In another aspect, provided herein is a method of treating an infection caused by a pathogen in a subject in need thereof, comprising administering to the subject a pharmaceutical composition comprising a cell or cell population, wherein the cell or cell population recombinantly expresses (a) a chimeric antigen receptor (CAR), and (b) a dominant negative form of an inhibitor of a cell-mediated immune response of the immunostimulatory cell, wherein the CAR binds to an antigen of a pathogen, wherein the antigen of the pathogen to which the CAR binds is an antigen of the pathogen causing the infection. In another aspect, provided herein is a method of treating an infection caused by a pathogen in a subject in need thereof, comprising administering to the subject a pharmaceutical composition comprising a T cell, or population of T cells, that recognizes and is sensitized to an antigen of the pathogen, which T cell recombinantly expresses a dominant negative form of an inhibitor of a T cell-mediated immune response, wherein the antigen of the pathogen to which the T cell is sensitized is an antigen of the pathogen causing the infection.
In certain embodiments of methods for treating an infection caused by a pathogen, the subject is a human. In certain embodiments of such methods, the pathogen is a human pathogen.



6. DESCRIPTION OF THE DRAWINGS
FIGS. 1A-1E show that chimeric antigen receptors (CARs) with CD28 or 4-1BB costimulation exhibit equivalent effector cytokine secretion and proliferation in vitro upon initial antigen stimulation. FIG. 1A. First- and second-generation CARs. FIG. 1B. Mesothelin (MSLN)-targeted CARs contain the CD3ζ endodomain either alone (Mz, first-generation CAR) or in combination with the CD28 (M28z) or 4-1BB (MBBz) costimulatory domain (second-generation CAR). A prostate-specific membrane antigen (PSMA)-directed CAR with CD28 costimulation (P28z) as well as PSMA-expressing targets (PSMA+) are included in experiments as negative controls. CYT, cytoplasmic domain; LS, leader sequence; LTR, long terminal repeat; SA, splice acceptor; SD, splice donor; TM, transmembrane. FIGS. 1C-1E. Antigen-specific effector functions of CAR-transduced T cells. FIG. 1C. Lysis of MSLN-expressing targets (MSLN+), but not PSMA+ targets, as measured by chromium-release assays. FIG. 1D. 4-1BB and CD28 costimulations enhance cytokine secretion, as assessed by Luminex assay, after coculture of CAR T cells with MSLN+ cells. FIG. 1E. M28z and MBBz CARs facilitate robust T-cell accumulation after stimulation with MSLN+ cells. Data represent the mean±SEM (FIGS. 1C, 1E) of three replicates or are plotted as individual points (FIG. 1D). ***P<0.001, comparing costimulated CAR T cells (M28z or MBBz) with the first-generation receptor (Mz), by Student's t test; significance was determined using the Bonferroni correction for multiple comparisons.
FIG. 2 shows efficient retroviral transduction of human T cells to express Mz, M28z, and MBBz CARs. (Top) Shown is representative FACS analysis 4 days after gene transfer. Fluorescence minus one staining was used to set positive gates after a live/dead stain excluded nonviable cells. All experiments used T cells with 50% to 70% CAR transduction efficiency; transduction percentages between T-cell groups were within 5% of each other. (Bottom) Both CD4+ and CD8+ T-cell subsets were efficiently transduced. CD4+ and CD8+ percentages after gating for CAR T cells are shown.
FIGS. 3A-3D show that CAR T cells become exhausted following in vivo antigen exposure, although MBBz CAR T cells preferentially retain effector cytokine secretion and cytotoxicity. FIG. 3A. Six days after intrapleural administration of CAR T cells, M28z and MBBz CAR T cells were isolated from the tumor and spleen and subjected to ex vivo antigen stimulation. FIG. 3B. Chromium-release assay upon ex vivo stimulation demonstrates a decrease in M28z but persistent MBBz cytolytic function (E:T ratio 1:5). FIG. 3C. Cytokine secretion measurements demonstrate decreases in effector cytokine secretion by CAR T cells, although MBBz CAR T cells are better able to retain secretion. FIG. 3D. RT-PCR measurements of GzB, IFN-γ, and TL-2 expression by harvested CAR T cells correlate well with protein level measurements. Data represent the fold-change relative to the mRNA expression of unstimulated M28z CAR T cell in vitro. Data represent the mean±SEM of three individual wells per condition. Student's t tests were performed, and statistical significance was determined using the Bonferroni correction for multiple comparisons (*P<0.05; **P<0.01; ***P<0.001). Results are reproduced in two separate cohorts of mice used for each of the two experiments. In each of FIGS. 3B-3D, each pair of bar graphs show, from left to right, M28z, MBBZ.
FIGS. 4A-4E show that CAR T cells become exhausted upon repeated antigen stimulation in vitro, although MBBz CAR T cells preferentially retain effector cytokine secretion and cytotoxicity in vitro and upon tumor rechallenge in vivo. FIG. 4A. Both M28z and MBBz CAR T cells retain proliferative capacity in vitro upon repeated antigen stimulation. T cells were also tested for cytotoxicity by chromium-release assay and for cytokine secretion by Luminex assay (FIGS. 4B-4D). FIG. 4B. CAR T cells demonstrate equal killing at the first stimulation (left) and loss of cytolytic function upon repeated antigen stimulation, although MBBz CAR T cells are better able to retain cytolytic function as measured by chromium-release assay (circles, MZ; triangles, M28z; diamonds, MBBz). FIG. 4C. Cytotoxic granule release as measured by CD107a expression (shown at the third stimulation) correlates with chromium release assay (FIG. 4B). Data represent the mean±SD (triplicates) of the fold-change relative to the CD107a MFI of unstimulated CAR T cells (each pair of bar graphs shows, from left to right, M28z, MBBz). FIG. 4D. Cytokine secretion measurements similarly demonstrate loss of CAR T-cell effector function upon repeated antigen encounter; again, MBBz CAR T cells are better able to preserve their function (each set of symbols above “Stim 1,” “Stim 2” and “Stim 3” are, from left to right, Mz, M28z, MBBz). FIG. 4E. Although equally persistent, MBBz CAR T cells demonstrate superior functional persistence. Twenty-eight days after pleural tumor eradication (following a single dose of 1e5 CAR T cells), 1e6 MSLN+ tumor cells were injected into the pleural cavity (tumor rechallenge). MBBz CAR T cells prevented tumor growth in all mice, whereas tumor growth and death were observed in 2 of 4 mice initially treated with M28z CAR T cells. Student's t tests were performed and statistical significance was determined using the Bonferroni correction (*P<0.05; ***P<0.001). Data represent the mean±SEM of three replicates or are plotted as individual points.
FIG. 5 shows that MBBz CAR T cells express a less exhausted, more potent phenotype compared to M28z CAR T cells. 4-1BB- and CD28-costimulated T cells were expanded with repeated antigen stimulation, and mRNA was extracted and subjected to RT-PCR analysis 20 h after the third stimulation. Data are represented in fold change relative to the mRNA expression of CD4+ unstransduced T cells. MBBz CAR T cells express higher levels of EOMES (Eomesodermin) and TBX21 (T-bet), and lower levels of PDCD1 (PD-1) and FOXP3 (Foxp3). All comparisons were significant at P<0.001. Results were similar in 3 separate experiments using different donors. Each group of bar graphs shows, left to right, UT (untransduced T cells used as a control), M28z, MBBz.
FIGS. 6A-6F show that PD-1 receptor and its ligands are upregulated in vivo (FIGS. 6A-6D, harvested T cells; FIGS. 6E-6F, tumor cells). FIG. 6A. Tumor-infiltrating M28z and MBBz CAR T cells express inhibitory receptors 6 days after their administration, but MBBz CAR T cells express lower levels of PD-1. FIG. 6B. Mean fluorescence intensity (MFI) of PD-1 receptor expression of tumor-infiltrating CAR T cells (TIL) 6 days after intrapleural administration. FIG. 6C. Relative expression of PD-1 mRNA in CD4 and CD8 subsets of tumor-infiltrating CAR T cells 6 days after intrapleural administration. Data are represented in fold-change relative to the PD-1 mRNA expression of unstimulated M28z T cells (for each pair of bar graphs, M28z, left, MBBz, right). FIG. 6D. Tumor-infiltrating M28z CAR T cells isolated from progressing tumors express inhibitory receptors PD-1, Tim-3, and Lag-3. FIG. 6E. Single-cell tumor suspensions harvested from mice treated with M28z CAR T cells express high levels of PD-1 binding ligands. FIG. 6F. In vitro cultured mesothelioma tumor cells express the ligands (PD-L1, PD-L2) for the PD-1 receptor, and expression is further upregulated following incubation for 24 h with IFN-γ and TNF-α.
FIG. 7 shows M28z and MBBz CAR T cells coexpress PD-1 along with other inhibitory receptors. Tumor-infiltrating M28z and MBBz CAR T cells were harvested 6 days following intrapleural administration to pleural tumor bearing mice. Cells were costained with antibodies for PD-1 and for either LAG-3 (left) or TIM-3 (right) and analyzed by flow cytometry. Isotype staining controls (top) were used to establish positive gates.
FIGS. 8A-8D show that PD-L1 inhibits CAR T-cell effector function. FIG. 8A. 3T3 fibroblasts were transduced to either express mesothelin alone (MSLN+, left) or coexpress MSLN in addition to PD-L1 (MSLN+PD-L1+, right). FIGS. 8B-8D. M28z and MBBz CAR T-cell effector functions were assessed after stimulation with 3T3 MSLN+ or MSLN+PD-L1+ targets. PD-L1 inhibits M28z and MBBz CAR T-cell accumulation upon repeated antigen stimulation (FIG. 8B), cytolytic function following two stimulations with MSLN+PD-L1+ tumor cells (FIG. 8C), and Th1 effector cytokine secretion upon the first stimulation (FIG. 8D). Data represent the mean±SEM of three replicates or are plotted as individual points.
FIGS. 9A-9E show that cotransduction of a PD-1 dominant negative receptor (PD-1 DNR) rescues M28z CAR T cells from PD-1 Ligand-mediated inhibition in vitro and in vivo. FIG. 9A. (Left) Schematic representations of CD28-costimulated T cells binding tumor ligand via the endogenous PD-1 receptor (transmitting a coinhibitory signal) or a cotransduced PD-1 DNR lacking an inhibitory signaling domain. (Right) For in vitro and in vivo experiments, M28z CAR T cells were cotransduced with either empty vector (EV; SFG-mCherry) or PD-1 DNR (SFG-2A-PD-1 DNR). CAR T cells sorted for mCherry expression were then incubated for 24 h with MSLN+ tumor cells that had been treated with IFN-γ and TNF-α to upregulate PD-1 ligands. M28z PD-1 DNR CAR T cells demonstrated a small but statistically significant enhancement in accumulation upon repeated antigen stimulation (FIG. 9B; triangles, M28z EV; squares, M28z PD-1 DNR), an enhanced cytolytic function, as measured by chromium release assay upon the 3rd stimulation with MSLN+PD-L1+ tumor cells (FIG. 9C; triangles, M28z EV; squares, M28z PD-1 DNR), and an increased expression of Th1 supernatant cytokines upon initial stimulation (FIG. 9D). Student's t tests were performed, and statistical significance was determined using the Bonferroni correction for multiple comparisons (*P<0.05; **P<0.01; ***P<0.001). Data represent the mean±SEM of triplicates or are plotted as individual points. FIG. 9E. Tumor BLI (left) and Kaplan-Meier survival analysis (right) comparing the in vivo efficacy of a single dose of 5e4 M28z EV (n=19) or M28z PD-1 DNR (n=16) plurally administrated. Data shown are a combination of two independent experiments. The (†) symbol indicates death. Median survival is shown in days. The survival curve was analyzed using the log-rank test (P=0.001). The log-rank test for each independent experiment was significant to the P<0.05 level; two experiments are combined for illustration. A cohort of the mice (M28z PD-1 DNR) in this experiment survived beyond 450 days in spite of repeated tumor rechallenge, demonstrating the “functional persistence” of CAR T cells transduced with PD-1 DNR.
FIGS. 10A-10E show that cotransduction of PD-1 receptor-targeting shRNAs rescues M28z CAR T cells from PD-L1/PD-1-mediated inhibition in vitro. FIG. 10A. (Left) Schematic representation of CD28-costimulated T cells binding tumor-expressed PD-L1 via endogenous PD-1 receptor, with or without coexpression of PD-1-targeting shRNA. (Right) All experiments included M28z CAR T cells cotransduced with one of two PD-1-targeting shRNAs (sh1 or sh2 coexpressing a dsRED reporter) or with an shRNA targeting a bacterial sequence (KanR). FIG. 10B. Compared with KanR-transduced cells, M28z CAR T cells cotransduced with PD-1-targeting shRNAs demonstrated a 60% to 70% knockdown in PD-1 receptor protein expression upon stimulation with phytohemagglutinin (graphs left to right correspond to 430, 722, 813 and 1411). Cells were incubated with either 3T3 fibroblasts overexpressing PD-L1 (3T3 MSLN+PD-L1+) or mesothelioma tumor cells that had been treated with IFN-γ and TNF-α in order to upregulate PD-L1 and PD-L2. M28z PD1 shRNA CAR T cells demonstrate enhanced accumulation upon repeated antigen stimulation (FIG. 10C), enhanced cytolytic function at low effector to target ratios, as measured by luciferase activity of remaining live tumor cells (FIG. 10D; each group of bar grafts, from left to right, Sh1, Sh2, ShK), and increased Th1 cytokine secretion (FIG. 10E; each group of bar grafts, from left to right, Sh1, Sh2, ShK) (**P<0.01; ***P<0.001). Student's t tests were performed and statistical significance was determined using the Bonferroni correction for multiple comparisons. Data represent the mean±SEM of three replicates.
FIG. 11 shows an adhesion assay of PD-1 DNR to PD-L1 and PD-L2 recombinant proteins fused to an Fc domain. T cells labeled with mCherry and transduced with PD-1 DNR were exposed to plates coated with PD-L1 fused to Fc (“PD-L1 Fc”), PD-L2 fused to Fc (“PD-L2 Fc”), or control isotype Fc (“Iso Fc”). T cells bound to the plates were measured as absolute mcherry+ T cell count in the presence (“+PD-1 Ab”) or absence of PD-1 antibody. The bar graphs show the binding for each of the respectively coated plates, from left to right, T cells alone (“T cells”), T cells in the presence of PD-1 antibody (T cells+PD-1 ab”), T cells transduced with PD-1 DNR (“PD-1 DNR T cells”), and T cells transduced with PD-1 DNR in the presence of PD-1 antibody (“PD-1 DNR T cells+PD-1 Ab”).
FIGS. 12A-12D show that a PD-1 DNR, which inhibits PD-L1- or PD-L2-mediated inhibition of T cell activation, can be converted into a positive co-stimulatory signal. FIG. 12A shows a schematic diagram illustrating co-expression of a CAR and a PD-1 DNR. FIG. 12B shows a schematic diagram illustrating co-expression of a CAR and a PD-1 DNR converted into a costimulatory construct by fusing a costimulatory domain, exemplified as 4-1 BB, to a transmembrane domain fused to the ligand binding domain of PD-1. FIG. 12C shows accumulation of CAR T cells at day 0 and day 7 in T cells transduced with M28z CAR, M28z CAR plus PD-1 DNR, or M28z CAR plus a PD-1 4-1BB switch receptor construct. Bars left to right respectively: M28z CAR, M28z CAR+PD-1 DNR, and M28z CAR+PD-1 4-1BB switch receptor construct. FIG. 12D shows cytokine secretion of interferon gamma (IFN-γ), interleukin 2 (IL-2), tumor necrosis factor alpha (TNF-α) and granulocyte-macrophage colony-stimulating factor (GM-CSF) in T cells transduced with M28z CAR, M28z CAR plus PD-1 DNR or M28z CAR plus a PD-1 4-1BB switch receptor construct. Bars left to right respectively: M28z CAR, M28z CAR+PD-1 DNR, and M28z CAR+PD-1 4-1BB switch receptor construct.



7. DETAILED DESCRIPTION OF THE INVENTION
The present invention relates to compositions and methods for treating viral infections. Such viral infections include, but are not limited to, infection with human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), and the like. As described herein, immunostimulatory immune cells can be genetically engineered to intrinsically express proteins that are dominant negative mutants and that inhibit blockades that limit the activity of the immune cells. By inhibiting the blockade, the genetically engineered immune cells that are immunostimulatory are permitted to provide a more effective immune response against a viral infection. In another embodiment, immunoinhibitory cells, such as regulatory T cells, that exhibit immunosuppression of the immune activity of immunostimulatory cells targeted to a viral antigen, such as CD8+ and/or CD4+ T cells, can be genetically engineered to intrinsically express proteins that are dominant negative mutants and that inhibit the immunosuppressive effect of the immunoinhibitory cells on immune stimulatory cells.
7.1 Cells
In one embodiment, the invention provides cells that are immune cells, in particular immunostimulatory cells, or precursor cells thereof, that recombinantly express (i) a CAR that binds to a viral antigen and (ii) a dominant negative form (hereinafter “DN form”) of an inhibitor of a cell-mediated immune response, preferably of the immune cell. The immune cells in such an embodiment are preferably CD4+ or CD8+ T cells or a combination thereof. In another embodiment, the invention provides an immune cell, such as a T cell, in particular, an immunostimulatory T cell, that is sensitized to a viral antigen, where the cell expresses a DN form of an inhibitor of a cell-mediated immune response, preferably of the T cell. In yet another embodiment, the invention provides an immune cell that is an immunoinhibitory cell, such as a regulatory T cell, where the cell expresses a DN form of an inhibitor of a cell-mediated immune response, preferably of the regulatory T cell. In a particular embodiment, the immunoinhibitory cells, such as regulatory T cells, are isolated from a subject having a chronic viral infection. The recombinant cells can be used to enhance or provide an immune response against a target such as a virus. Preferably, the cells are derived from a human (are of human origin prior to being made recombinant) (and human-derived cells are particularly preferred for administration to a human in the methods of treatment of the invention).
Immune Cells that are Immunostimulatory Cells. The immune cells of the invention can be immunostimulatory cells of the lymphoid lineage. The immunostimulatory cells mediate an immune response in a subject. Non-limiting examples of cells of the lymphoid lineage that can be used as immunostimulatory cells include T cells and Natural Killer (NK) cells. T cells express the T cell receptor (TCR), with most cells expressing α and β chains and a smaller population expressing γ and δ chains. T cells useful as immunostimulatory cells of the invention can be CD4+ or CD8+ and can include, but are not limited to, T helper cells (CD4+), cytotoxic T cells (also referred to as cytotoxic T lymphocytes, CTL; CD8+ T cells), and memory T cells, including central memory T cells, stem-cell-like memory T cells (or stem-like memory T cells), and effector memory T cells, for example, TEM cells and TEMRA (CD45RA+) cells, natural killer T cells, mucosal associated invariant T cells (MAIT), and γδ T cells. Other exemplary immunostimulatory cells include, but are not limited to, macrophages, antigen presenting cells (APCs) such as dendritic cells, or any immune cell that mediates an immune response and expresses an inhibitor of a cell-mediated immune response, for example, an immune checkpoint inhibitor pathway receptor, e.g., PD-1 (while not intending to be bound by mechanism, it is submitted that expression of the DN form in the cell inhibits the inhibitor of the cell-mediated immune response to promote sustained activation of the cell). Precursor cells of immunostimulatory cells that can be used according to the invention, which recombinantly express a DN form or co-express a CAR and a DN form, as described above, are, by way of example, hematopoietic stem and/or progenitor cells. Hematopoietic stem and/or progenitor cells can be derived from bone marrow, umbilical cord blood, adult peripheral blood after cytokine mobilization, and the like, by methods known in the art, and then are genetically engineered to recombinantly express a DN form or co-express a CAR and DN form. Particularly useful precursor cells are those that can differentiate into the lymphoid lineage, for example, hematopoietic stem cells or progenitor cells of the lymphoid lineage.
Immune cells that are immunostimulatory cells, and precursor cells thereof, can be isolated by methods well known in the art, including commercially available isolation methods (see, for example, Rowland-Jones et al., Lymphocytes: A Practical Approach, Oxford University Press, New York (1999)). Sources for the immune cells or precursor cells thereof include, but are not limited to, peripheral blood, umbilical cord blood, bone marrow, or other sources of hematopoietic cells. Various techniques can be employed to separate the cells to isolate or enrich for desired immune cells. For instance, negative selection methods can be used to remove cells that are not the desired immune cells. Additionally, positive selection methods can be used to isolate or enrich for desired immune cells or precursor cells thereof, or a combination of positive and negative selection methods can be employed. Monoclonal antibodies (MAbs) are particularly useful for identifying markers associated with particular cell lineages and/or stages of differentiation for both positive and negative selections. If a particular type of cell is to be isolated, for example, a particular type of T cell, various cell surface markers or combinations of markers, including but not limited to, CD3, CD4, CD8, CD34 (for hematopoietic stem and progenitor cells) and the like, can be used to separate the cells, as is well known in the art (see Kearse, T Cell Protocols: Development and Activation, Humana Press, Totowa N.J. (2000); De Libero, T Cell Protocols, Vol. 514 of Methods in Molecular Biology, Humana Press, Totowa N.J. (2009)).
Various methods for isolating immune cells that can be used for recombinant expression of a CAR have been described previously, and can be used, including but not limited to, using peripheral donor lymphocytes (Sadelain et al., Nat. Rev. Cancer 3:35-45 (2003); Morgan et al., Science 314:126-129 (2006), and using selectively in vitro-expanded antigen-specific peripheral blood leukocytes employing artificial antigen-presenting cells (AAPCs) or dendritic cells (Dupont et al., Cancer Res. 65:5417-5427 (2005); Papanicolaou et al., Blood 102:2498-2505 (2003)). In the case of using stem cells, the cells can be isolated by methods well known in the art (see, for example, Klug et al., Hematopoietic Stem Cell Protocols, Humana Press, New Jersey (2002); Freshney et al., Culture of Human Stem Cells, John Wiley & Sons (2007)).
In another embodiment, the invention provides immune cells, such as T cells, that recognize and are sensitized to a viral antigen, and also which recombinantly express a DN form of an inhibitor of an immune cell-mediated immune response, such as a T cell-mediated immune response in the case of a T cell. Such immune cells, such as T cells, can but need not express a CAR that binds to a viral antigen, since the cells already are viral antigen-specific so that their immune response (for example, cytotoxicity) is stimulated specifically by such viral antigen. Such immune cells, such as T cells, that recognize and are sensitized to a viral antigen can be obtained by known methods, by way of example, in vitro sensitization methods using naive T cells (see, for example, Wolfl et al., Nat. Protocols 9:950-966 (2014)) or hematopoietic progenitor cells (see van Lent et al., J. Immunol. 179:4959-4968 (2007)); or obtained from a subject that has been exposed to and is mounting an immune response against the viral antigen, such as a subject having a viral infection (i.e., in vivo sensitized immune cells). Methods for isolating an antigen-specific T cell from a subject are well known in the art. Such methods include, but are not limited to, a cytokine capture system or cytokine secretion assay, which is based on the secretion of cytokines from antigen stimulated T cells that can be used to identify and isolate antigen-specific, and expansion of cells in vitro (see Assenmacher et al., Cytometric Cytokine Secretion Assay, in Analyzing T Cell Responses: How to Analyze Cellular Immune Responses Against Tumor Associated Antigens, Nagorsen et al., eds., Chapter 10, pp. 183-195, Springer, The Netherlands (2005); Haney et al., J. Immunol. Methods 369:33-41 (2011); Bunos et al., Vox Sanguinis DOI: 10.1111/vox.12291 (2015); Montes et al., Clin. Exp. Immunol. 142:292-302 (2005); Adusumilli et al., Sci Transl Med. 6:261ra151 (2014)). Such cytokines include, but are not limited to interferon-γ and tumor necrosis factor-α. The antigen-specific T cells can be isolated using well known techniques as described above for isolating immune cells, which include, but are not limited to, flow cytometry, magnetic beads, panning on a solid phase, and so forth. Antigen-specific T cell isolation techniques are also commercially available, which can be used or adapted for clinical applications (see, for example, Miltenyi Biotec, Cambridge, Mass.; Proimmune, Oxford, UK; and the like).
Immune Cells that are Immunoinhibitory Cells. The immune cells of the invention that are immunoinhibitory cells can be cells of the lymphoid lineage. Non-limiting examples of cells of the lymphoid lineage that can be used as immunoinhibitory cells include regulatory T cells (Tregs), follicular regulatory T cells, regulatory B cells, and the like. The immunoinhibitory cells of the invention express an inhibitor of a cell-mediated immune response, for example, an immune checkpoint inhibitor pathway receptor, e.g., PD-1.
Immunoinhibitory cells that can be genetically engineered to recombinantly express a DN form of an inhibitor of a cell-mediated immune response can be isolated by methods well known in the art, including commercially available isolation methods (see, for example, Rowland-Jones et al., Lymphocytes: A Practical Approach, Oxford University Press, New York (1999)). Sources for the immunoinhibitory cells thereof include, but are not limited to, peripheral blood, umbilical cord blood, bone marrow, or other sources of cells of the lymphoid lineage. Various techniques can be employed to separate the cells to isolate or enrich for desired immunoinhibitory cells. For instance, negative selection methods can be used to remove cells that are not the desired immunoinhibitory cells. Additionally, positive selection methods can be used to isolate or enrich for desired immunoinhibitory cells, or a combination of positive and negative selection methods can be employed. Monoclonal antibodies (MAbs) are particularly useful for identifying markers associated with particular cell lineages and/or stages of differentiation and can be used as reagents for both positive and negative selections. A particular type of immunoinhibitory cell can be isolated based on various cell surface markers or combinations of markers, or the absence of markers, including but not limited to CD4 and/or CD8 for positive selection combined with CD127 for negative selection, as is well known in the art (see Kearse, T Cell Protocols: Development and Activation, Humana Press, Totowa N.J. (2000); De Libero, T Cell Protocols, Vol. 514 of Methods in Molecular Biology, Humana Press, Totowa N.J. (2009); Su et al., Methods Mol. Biol. 806:287-299 (2012); Bluestone et al., Sci. Transl. Med. 7(315) (doi: 10.1126/scitranslmed.aad4134)(2015); Miyara et al., Nat. Rev. Rheumatol. 10:543-551 (2014); Liu et al., J. Exp. Med. 203:1701-1711 (2006); Seddiki et al., J. Exp. Med. 203:1693-1700 (2006); Ukena et al., Exp. Hematol. 39:1152-1160 (2011); Chen et al., J. Immunol. 183:4094-4102 (2009); Putnam et al., Diabetes 58:652-662 (2009); Putnam et al., Am. J. Tranplant. 13:3010-3020 (2013)). In a specific embodiment, CD4+CD25+ regulatory T cells are isolated, for example, using a CD4+CD25+ Regulatory T Cell Isolation Kit (Dynal brand, Invitrogen, Carlsbad, Calif.) (see Lee et al., Cancer Res. 71:2871-2881 (2011)). In vitro generation of regulatory T cells (iTregs) have also been described (see, for example, Lan et al., J. Mol. Cell. Biol. 4:22-28 (2012); Yamagiwa et al., J. Immunol. 166:7282-7289 (2001); Zheng et al., J. Immunol. 169:4183-4189 (2002)). Various methods for isolating immune cells that can be used for recombinant expression of a CAR have been described previously (Sadelain et al., Nat. Rev. Cancer 3:35-45 (2003); Morgan et al., Science 314:126-129 (2006); Panelli et al., J. Immunol. 164:495-504 (2000); Panelli et al., J Immunol. 164:4382-4392 (2000); Dupont et al., Cancer Res. 65:5417-5427 (2005); Papanicolaou et al., Blood 102:2498-2505 (2003); MacDonald et al., J Clin. Invest. 126:1413-1424 (2016)). In a particular embodiment, the immunoinhibitory cells, in particular regulatory T cells, are isolated from a subject having a viral infection, e.g., a chronic viral infection, such as a chronic infection with HCV, HBV or HIV. In a specific embodiment, regulatory T cells are isolated from a patient with a chronic viral infection when the patient is in remission of acute infection. In the case of immunoinhibitory cells isolated from a patient having a viral infection, the immunoinhibitory cells, such as regulatory T cells, need not be, but can be, antigen specific for a viral antigen.
Optionally, the immunoinhibitory cells, such as regulatory T cells, can be sensitized to a viral antigen. Methods for isolating an antigen-specific immunoinhibitory cell, such as a regulatory T cell, from a subject are well known in the art (see, for example, Noyan et al., Eur. J. Immunol. 44:2592-2602 (2014); Brusko et al., PLoS One 5(7) e11726 (doi: 10.1371) (2010); Bacher et al., Mucosal Immunol. 7:916-928 (2014); Koenen et al., J. Immunol. 174:7573-7583 (2005)).
In one embodiment, immunoinhibitory cells, such as regulatory T cells, are isolated from a patient having a viral infection, e.g., a chronic viral infection. Such isolated cells or their progeny can optionally be genetically modified to express a CAR that binds to an antigen of the virus responsible for the viral infection.
Methods for isolating and expanding regulatory T cells are well known in the art (see, for example, Su et al., Methods Mol. Biol. 806:287-299 (2012); Bluestone et al., Sci. Transl. Med. 7(315) (doi: 10.1126/scitranslmed.aad4134)(2015); Miyara et al., Nat. Rev. Rheumatol. 10:543-551 (2014); Liu et al., J. Exp. Med. 203:1701-1711 (2006); Seddiki et al., J. Exp. Med. 203:1693-1700 (2006); Ukena et al., Exp. Hematol. 39:1152-1160 (2011); Chen et al., J. Immunol. 183:4094-4102 (2009); Putnam et al., Diabetes 58:652-662 (2009); Putnam et al., Am. J. Tranplant. 13:3010-3020 (2013); Lee et al., Cancer Res. 71:2871-2881 (2011); MacDonald et al., J Clin. Invest. 126:1413-1424 (2016)). In vitro generation of regulatory T cells (iTregs) has also been described (see, for example, Lan et al., J. Mol. Cell. Biol. 4:22-28 (2012); Yamagiwa et al., J. Immunol. 166:7282-7289 (2001); Zheng et al., J. Immunol. 169:4183-4189 (2002)). Generally, regulatory T cells of the invention are CD4+, for example, CD4+CD25+, and in particular CD4+CD127lo/−CD25+. Such regulatory T cells express Foxp3 (forkhead box P3), which is in the forkhead/winged-helix family of transcription factors (Bluestone et al., J. Clin. Invest. 125:2250-2260 (2015); Riley et al., Immunity 30:656-665 (2009)). A regulatory T cell that is an immunoinhibitory cell of the invention can also be a CD8+ regulatory T cell (Guillonneau et al., Curr. Opin. Organ Transplant. 15:751-756 (2010)). Methods for isolating and expanding regulatory T cells are also commercially available (see, for example, BD Biosciences, San Jose, Calif.; STEMCELL Technologies Inc., Vancouver, Canada; eBioscience, San Diego, Calif.; Invitrogen, Carlsbad, Calif.). An immunoinhibitory cell of the invention can also be a follicular regulatory T cell (T(FR)) (Sage et al., Nat. Immunol. 14:152-161 (2013)). In a particular embodiment, the follicular regulatory T cells of the invention are CD4+CXCR5+ and express Foxp3 (Sage et al., supra, 2013).
In some embodiments, the immunoinhibitory cells of the invention are regulatory B cells. Regulatory B cells have the unique ability in B cells to produce interleukin 10 (IL10) (see, for example, Lykken et al., International Immunol. 27:471-477 (2015); Miyagaki et al., International Immunol. 27:495-504 (2015)). Methods of isolating regulatory B cells have been described (see, for example, Masson et al., in Regulatory B Cells: Methods and Protocols, Vitale and Mion, eds., Chapter 4, pp. 45-52, Humana Press, New York (2014)). Such methods are based on the expression of cell surface markers, such as CD24highCD38high, and the expression of IL10 (Masson et al., supra, 2014). Other markers for regulatory B cells include CD24hiCD27+ (see Lykken et al., supra, 2015).
Procedures for separation of immune cells include, but are not limited to, density gradient centrifugation, coupling to particles that modify cell density, magnetic separation with antibody-coated magnetic beads, affinity chromatography; cytotoxic agents joined to or used in conjunction with a monoclonal antibody (mAb), including, but not limited to, complement and cytotoxins, and panning with an antibody attached to a solid matrix, for example, a plate or chip, elutriation, flow cytometry, or any other convenient technique (see, for example, Recktenwald et al., Cell Separation Methods and Applications, Marcel Dekker, Inc., New York (1998)). It is understood that the immune cells used in methods of the invention can be substantially pure cells or can be a polyclonal population. In some embodiments, a polyclonal population can be enriched for a desired immune cell. Such an enrichment can take place prior to or after genetically engineering the cells to express a DN form, or a CAR and DN form, as desired.
The immune cells, or precursor cells thereof, can be autologous or non-autologous to the subject to which they are administered in the methods of treatment of the invention. Autologous cells are isolated from the subject to which the engineered cells are to be administered. Optionally, the cells can be obtained by leukapheresis, where leukocytes are selectively removed from withdrawn blood, made recombinant, and then retransfused into the donor. Alternatively, allogeneic cells from a non-autologous donor that is not the subject can be used. In the case of a non-autologous donor, the cells are typed and matched for human leukocyte antigen (HLA) to determine an appropriate level of compatibility, as is well known in the art. For both autologous and non-autologous cells, the cells can optionally be cryopreserved until ready to be used for genetic manipulation and/or administration to a subject using methods well known in the art.
The immune cells, or precursor cells thereof, can be subjected to conditions that favor maintenance or expansion of the immune cells, or precursor cells thereof (see Kearse, T Cell Protocols: Development and Activation, Humana Press, Totowa N.J. (2000); De Libero, T Cell Protocols, Vol. 514 of Methods in Molecular Biology, Humana Press, Totowa N.J. (2009); Parente-Pereira et al., J. Biol. Methods 1(2) e7 (doi 10.14440/jbm.2014.30) (2014); Movassagh et al., Hum. Gene Ther. 11:1189-1200 (2000); Rettig et al., Mol. Ther. 8:29-41 (2003); Agarwal et al., J. Virol. 72:3720-3728 (1998); Pollok et al., Hum. Gene Ther. 10:2221-2236 (1999); Quinn et al., Hum. Gene Ther. 9:1457-1467 (1998); Su et al., Methods Mol. Biol. 806:287-299 (2012); Bluestone et al., Sci. Transl. Med. 7(315) (doi: 10.1126/scitranslmed.aad4134)(2015); Miyara et al., Nat. Rev. Rheumatol. 10:543-551 (2014); Liu et al., J. Exp. Med. 203:1701-1711 (2006); Seddiki et al., J. Exp. Med. 203:1693-1700 (2006); Ukena et al., Exp. Hematol. 39:1152-1160 (2011); Chen et al., J. Immunol. 183:4094-4102 (2009); Putnam et al., Diabetes 58:652-662 (2009); Putnam et al., Am. J. Tranplant. 13:3010-3020 (2013); Lee et al., Cancer Res. 71:2871-2881 (2011); MacDonald et al., J Clin. Invest. 126:1413-1424 (2016); see also commercially available methods such as DynabeadsTM human T cell activator products, Thermo Fisher Scientific, Waltham, Mass.)). The immune cells, or precursor cells thereof, or viral antigen sensitized immune cells, such as T cells, can optionally be expanded prior to or after ex vivo genetic engineering. Expansion of the cells is particularly useful to increase the number of cells for administration to a subject. Such methods for expansion of immune cells are well known in the art (see Kaiser et al., Cancer Gene Therapy 22:72-78 (2015); Wolfl et al., Nat. Protocols 9:950-966 (2014); Su et al., Methods Mol. Biol. 806:287-299 (2012); Bluestone et al., Sci. Transl. Med. 7(315) (doi: 10.1126/scitranslmed.aad4134)(2015); Miyara et al., Nat. Rev. Rheumatol. 10:543-551 (2014); Liu et al., J. Exp. Med. 203:1701-1711 (2006); Seddiki et al., J. Exp. Med. 203:1693-1700 (2006); Ukena et al., Exp. Hematol. 39:1152-1160 (2011); Chen et al., J. Immunol. 183:4094-4102 (2009); Putnam et al., Diabetes 58:652-662 (2009); Putnam et al., Am. J. Tranplant. 13:3010-3020 (2013); Lee et al., Cancer Res. 71:2871-2881 (2011)). Furthermore, the cells can optionally be cryopreserved after isolation and/or genetic engineering, and/or expansion of genetically engineered cells (see Kaiser et al., supra, 2015)). Methods for cyropreserving cells are well known in the art (see, for example, Freshney, Culture of Animal Cells: A Manual of Basic Techniques, 4th ed., Wiley-Liss, New York (2000); Harrison and Rae, General Techniques of Cell Culture, Cambridge University Press (1997)).
In a specific embodiment, isolated immune cells that are immunostimulatory cells, or precursor cells thereof, are genetically engineered ex vivo for recombinant expression of a DN form and a CAR. In a specific embodiment, isolated T cells are genetically engineered ex vivo for recombinant expression of a DN form. In a specific embodiment, immunoinhibitory cells, such as regulatory T cells, are genetically engineered ex vivo for recombinant expression of a DN form. The cells can be genetically engineered for recombinant expression by methods well known in the art.
In an embodiment where viral antigen sensitized immune cells, such as T cells, that recombinantly express a DN form are used, and wherein such cells are obtained by in vitro sensitization, the sensitization can occur before or after the immune cells are genetically engineered to recombinantly express a DN form. In an embodiment where the sensitized immune cells, such T cells, are isolated from in vivo sources, it will be self-evident that genetic engineering occurs of the already-sensitized immune cells.
With respect to generating cells recombinantly expressing a DN form or a CAR and DN form, one or more nucleic acids encoding the DN form or the CAR and DN form is introduced into the immune cell, or precursor cell thereof, using a suitable expression vector. The immune cells (for example, T cells or regulatory T cells), or precursor cells thereof, are preferably transduced with one or more nucleic acids encoding a DN form, or a CAR and DN form. In the case of expressing both a CAR and DN form, the CAR and DN form encoding nucleic acids can be on separate vectors or on the same vector, as desired. For example, a polynucleotide encoding a CAR or DN form of the invention can be cloned into a suitable vector, such as a retroviral vector, and introduced into the immune cell using well known molecular biology techniques (see Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1999)). Any vector suitable for expression in a cell of the invention, particularly a human immune cell or a precursor cell thereof, can be employed. The vectors contain suitable expression elements such as promoters that provide for expression of the encoded nucleic acids in the immune cell. In the case of a retroviral vector, cells can optionally be activated to increase transduction efficiency (see Parente-Pereira et al., J. Biol. Methods 1(2) e7 (doi 10.14440/jbm.2014.30) (2014); Movassagh et al., Hum. Gene Ther. 11:1189-1200 (2000); Rettig et al., Mol. Ther. 8:29-41 (2003); Agarwal et al., J. Virol. 72:3720-3728 (1998); Pollok et al., Hum. Gene Ther. 10:2221-2236 (1998); Quinn et al., Hum. Gene Ther. 9:1457-1467 (1998); see also commercially available methods such as DynabeadsTM human T cell activator products, Thermo Fisher Scientific, Waltham, Mass.). Methods for use in expressing a polypeptide, such as a CAR, in a regulatory T cell can be any known in the art, e.g., those described in Lee et al., Cancer Res. 71:2871-2881 (2011).
In one embodiment, the vector is a retroviral vector, for example, a gamma retroviral or lentiviral vector, which is employed for the introduction of a CAR or DN form into the immune cell, or precursor cell thereof. For genetic modification of the cells to express a CAR and/or DN form, a retroviral vector is generally employed for transduction. However, it is understood that any suitable viral vector or non-viral delivery system can be used. Combinations of a retroviral vector and an appropriate packaging line are also suitable, where the capsid proteins will be functional for infecting human cells. Various amphotropic virus-producing cell lines are known, including, but not limited to, PA12 (Miller et al., Mol. Cell. Biol. 5:431-437 (1985)); PA317 (Miller et al., Mol. Cell. Biol. 6:2895-2902(1986)); and CRIP (Danos et al., Proc. Natl. Acad. Sci. USA 85:6460-6464 (1988)). Non-amphotropic particles are suitable too, for example, particles pseudotyped with VSVG, RD114 or GALV envelope and any other known in the art (Relander et al., Mol. Therap. 11:452-459 (2005)). Possible methods of transduction also include direct co-culture of the cells with producer cells (for example, Bregni et al., Blood 80:1418-1422 (1992)), or culturing with viral supernatant alone or concentrated vector stocks with or without appropriate growth factors and polycations (see, for example, Xu et al., Exp. Hemat. 22:223-230 (1994); Hughes, et al. J. Clin. Invest. 89:1817-1824 (1992)).
Generally, the chosen vector exhibits high efficiency of infection and stable integration and expression (see, for example, Cayouette et al., Human Gene Therapy 8:423-430 (1997); Kido et al., Current Eye Research 15:833-844 (1996); Bloomer et al., J. Virol. 71:6641-6649 (1997); Naldini et al., Science 272:263 267 (1996); and Miyoshi et al., Proc. Natl. Acad. Sci. U.S.A. 94:10319-10323 (1997)). Other viral vectors that can be used include, for example, adenoviral, lentiviral, and adeno-associated viral vectors, vaccinia virus, a bovine papilloma virus derived vector, or a herpes virus, such as Epstein-Barr Virus (see, for example, Miller, Hum. Gene Ther. 1(1):5-14 (1990); Friedman, Science 244:1275-1281 (1989); Eglitis et al., BioTechniques 6:608-614 (1988); Tolstoshev et al., Current Opin. Biotechnol. 1:55-61 (1990); Sharp, Lancet 337:1277-1278 (1991); Cornetta et al., Prog. Nucleic Acid Res. Mol. Biol. 36:311-322 (1989); Anderson, Science 226:401-409 (1984); Moen, Blood Cells 17:407-416 (1991); Miller et al., Biotechnology 7:980-990 (1989); Le Gal La Salle et al., Science 259:988-990 (1993); and Johnson, Chest 107:775-83S (1995)). Retroviral vectors are particularly well developed and have been used in clinical settings (Rosenberg et al., N. Engl. J. Med. 323:370 (1990); Anderson et al., U.S. Pat. No. 5,399,346).
Particularly useful vectors for expressing a CAR and/or DN form of the invention include vectors that have been used in human gene therapy. In one non-limiting embodiment, a vector is a retroviral vector. The use of retroviral vectors for expression in T cells or other immune cells, including engineered CAR T cells, has been described (see Scholler et al., Sci. Transl. Med. 4:132-153 (2012; Parente-Pereira et al., J. Biol. Methods 1(2):e7 (1-9)(2014); Lamers et al., Blood 117(1):72-82 (2011); Reviere et al., Proc. Natl. Acad. Sci. USA 92:6733-6737 (1995)). In one embodiment, the vector is an SGF retroviral vector such as an SGF γ-retroviral vector, which is Moloney murine leukemia-based retroviral vector. SGF vectors have been described previously (see, for example, Wang et al., Gene Therapy 15:1454-1459 (2008)).
The vectors of the invention employ suitable promoters for expression in a particular host cell. The promoter can be an inducible promoter or a constitutive promoter. In a particular embodiment, the promoter of an expression vector provides expression in an immune cell, such as a T cell, or precursor cell thereof, or a regulatory T cell. Non-viral vectors can be used as well, so long as the vector contains suitable expression elements for expression in the immune cell, or precursor cell thereof. Some vectors, such as retroviral vectors, can integrate into the host genome. If desired, targeted integration can be implemented using technologies such as a nuclease, transcription activator-like effector nucleases (TALENs), Zinc-finger nucleases (ZFNs), and/or clustered regularly interspaced short palindromic repeats (CRISPRs), by homologous recombination, and the like (Gersbach et al., Nucl. Acids Res. 39:7868-7878 (2011); Vasileva, et al. Cell Death Dis. 6:e1831. (Jul. 23, 2015); Sontheimer, Hum. Gene Ther. 26(7):413-424 (2015)).
The vectors and constructs can optionally be designed to include a reporter. For example, the vector can be designed to express a reporter protein, which can be useful to identify cells comprising the vector or nucleic acids provided on the vector, such as nucleic acids that have integrated into the host chromosome. In one embodiment, the reporter can be expressed as a bicistronic or multicistronic expression construct with the CAR or DN form. Exemplary reporter proteins include, but are not limited to, fluorescent proteins, such as mCherry, green fluorescent protein (GFP), blue fluorescent protein, for example, EBFP, EBFP2, Azurite, and mKalamal, cyan fluorescent protein, for example, ECFP, Cerulean, and CyPet, and yellow fluorescent protein, for example, YFP, Citrine, Venus, and YPet. In an additional embodiment, a vector construct can comprise a P2A sequence, which provides for optional co-expression of a reporter molecule. P2A is a self-cleaving peptide sequence, which can be used for bicistronic or multicistronic expression of protein sequences (see Szymczak et al., Expert Opin. Biol. Therapy 5(5):627-638 (2005)).
Assays can be used to determine the transduction efficiency of a CAR and/or DN form using routine molecular biology techniques. If a marker has been included in the construct, such as a fluorescent protein, gene transfer efficiency can be monitored by FACS analysis to quantify the fraction of transduced (for example, GFP+) immune cells, such as T cells, or precursor cells thereof, or regulatory T cells, and/or by quantitative PCR. Using a well-established cocultivation system (Gade et al., Cancer Res. 65:9080-9088 (2005); Gong et al., Neoplasia 1:123-127 (1999); Latouche et al., Nat. Biotechnol. 18:405-409 (2000)) it can be determined whether fibroblast AAPCs expressing viral antigen (vs. controls) direct cytokine release from transduced immune cells, such as T cells, expressing a CAR (cell supernatant LUMINEX (Austin Tex.) assay for IL-2, IL-4, IL-10, IFN-γ, TNF-α, and GM-CSF), T cell proliferation (by carboxyfluorescein succinimidyl ester (CFSE) labeling), and T cell survival (by Annexin V staining). The influence of CD80 and/or 4-1BBL on T cell survival, proliferation, and efficacy can be evaluated. T cells can be exposed to repeated stimulation by viral antigen positive target cells, and it can be determined whether T cell proliferation and cytokine response remain similar or diminished with repeated stimulation. Cells with and without the viral antigen CAR constructs can be compared side by side under equivalent assay conditions. Cytotoxicity assays with multiple E:T ratios can be conducted using chromium-release assays.
If desired, a nucleic acid encoding a polypeptide for genetic engineering of a cell of the invention, such as a DN form or a CAR, can be codon optimized to increase efficiency of expression in an immune cell, or precursor cell thereof. Codon optimization can be used to achieve higher levels of expression in a given cell. Factors that are involved in different stages of protein expression include codon adaptability, mRNA structure, and various cis-elements in transcription and translation. Any suitable codon optimization methods or technologies that are known to one skilled in the art can be used to modify the polynucleotides encoding the polypeptides. Such codon optimization methods are well known, including commercially available codon optimization services, for example, OptimumGeneTM (GenScript; Piscataway, N.J.), Encor optimization (EnCor Biotechnology; Gainseville Fla.), Blue Heron (Blue Heron Biotech; Bothell, Wash.), and the like. Optionally, multiple codon optimizations can be performed based on different algorithms, and the optimization results blended to generate a codon optimized nucleic acid encoding a polypeptide.
Further modification can be introduced to the immune cells, or precursor cells thereof, of the invention. For example, the cells can be modified to address immunological complications and/or targeting of the immune cells to healthy or non-target tissues. For example, a suicide gene can be introduced into the cells to provide for depletion of the cells when desired. Suitable suicide genes include, but are not limited to, Herpes simplex virus thymidine kinase (hsv-tk), inducible Caspase 9 Suicide gene (iCasp-9), and a truncated human epidermal growth factor receptor (EGFRt) polypeptide. Agents are administered to the subject to which the cells containing the suicide genes have been administered, including but not limited to, gancilovir (GCV) for hsv-tk (Greco et al., Frontiers Pharmacol. 6:95 (2015); Barese et al., Mol. Therapy 20:1932-1943 (2012)), AP1903 for iCasp-9 (Di Stasi et al., N. Engl. J. Med. 365:1673-1683 (2011), and cetuximab for EGFRt (U.S. Pat. No. 8,802,374), to promote cell death. In one embodiment, administration of a prodrug designed to activate the suicide gene, for example, a prodrug such as AP1903 that can activate iCasp-9, triggers apoptosis in the suicide gene-activated cells. In one embodiment, iCasp9 consists of the sequence of the human FK506-binding protein (FKBP12; GenBank number, AH002818 (AH002818.2, GI:1036032368)) with an F36V mutation, connected through a Ser-Gly-Gly-Gly-Ser (SEQ ID NO:28) linker to the gene encoding human caspase 9 (CASP9; GenBank number, NM001229 (NM_001229.4, GI:493798577)), which has had its endogenous caspase activation and recruitment domain deleted. FKBP12-F36V binds with high affinity to an otherwise bioinert small-molecule dimerizing agent, AP1903. In the presence of AP1903, the iCasp9 promolecule dimerizes and activates the intrinsic apoptotic pathway, leading to cell death (Di Stasi et al., N. Engl. J. Med. 365:1673-1683 (2011)). In another embodiment, the suicide gene is an EGFRt polypeptide. The EGFRt polypeptide can provide for cell elimination by administering anti-EGFR monoclonal antibody, for example, cetuximab. The suicide gene can be expressed on a separate vector or, optionally, expressed within the vector encoding a CAR or DN form, and can be a bicistronic or multicistronic construct joined to a CAR or DN form encoding nucleic acid.
7.2 Chimeric Antigen Receptors (CARs)
The CAR that is recombinantly expressed by a cell of the invention has an antigen binding domain that binds to a viral antigen. In specific embodiments, the CAR can be a “first generation,” “second generation” or “third generation” CAR (see, for example, Sadelain et al., Cancer Discov. 3(4):388-398 (2013); Jensen et al., Immunol. Rev. 257:127-133 (2014); Sharpe et al., Dis. Model Mech. 8(4):337-350 (2015); Brentjens et al., Clin. Cancer Res. 13:5426-5435 (2007); Gade et al., Cancer Res. 65:9080-9088 (2005); Maher et al., Nat. Biotechnol. 20:70-75 (2002); Kershaw et al., J. Immunol. 173:2143-2150 (2004); Sadelain et al., Curr. Opin. Immunol. 21(2):215-223 (2009); Hollyman et al., J. Immunother. 32:169-180 (2009)).
“First generation” CARs are typically composed of an extracellular antigen binding domain, for example, a single-chain variable fragment (scFv), fused to a transmembrane domain, which is fused to a cytoplasmic/intracellular domain of the T cell receptor chain. “First generation” CARs typically have the intracellular domain from the CD3ζ-chain, which is the primary transmitter of signals from endogenous T cell receptors (TCRs) (see exemplary first generation CAR in FIG. 1A). “First generation” CARs can provide de novo antigen recognition and cause activation of T cells, including both CD4+ and CD8+ T cells, through their CD3ζ chain signaling domain in a single fusion molecule, independent of HLA-mediated antigen presentation. “Second-generation” CARs for use in the invention comprise a viral antigen-binding domain fused to an intracellular signaling domain capable of activating immune cells such as T cells and a co-stimulatory domain designed to augment immune cell, such as T cell, potency and persistence (Sadelain et al., Cancer Discov. 3:388-398 (2013)). CAR design can therefore combine antigen recognition with signal transduction, two functions that are physiologically borne by two separate complexes, the TCR heterodimer and the CD3 complex. “Second generation” CARs include an intracellular domain from various co-stimulatory molecules, for example, CD28, 4-1BB, ICOS, OX40, and the like, in the cytoplasmic tail of the CAR to provide additional signals to the cell (see exemplary second generation CAR in FIG. 1A). “Second generation” CARs provide both co-stimulation, for example, by CD28 or 4-1BB domains, and activation, for example, by a CD3ζ signaling domain. “Third generation” CARs provide multiple co-stimulation, for example, by comprising both CD28 and 4-1BB domains, and activation, for example, by comprising a CD3ζ activation domain.
In the embodiments disclosed herein, the CARs generally comprise an extracellular antigen binding domain, a transmembrane domain and an intracellular domain, as described above, where the extracellular antigen binding domain binds to a viral antigen. In a particular non-limiting embodiment, the extracellular antigen-binding domain is an scFv.
As disclosed herein, the methods of the invention can involve administering cells that have been engineered to co-express a viral antigen CAR and a dominant negative form (“DN form”) of an inhibitor of a cell-mediated immune response. The extracellular antigen-binding domain of a CAR is usually derived from a monoclonal antibody (mAb) or from receptors or their ligands.
The design of CARs is well known in the art (see, for example, reviews by Sadelain et al., Cancer Discov. 3(4):388-398 (2013); Jensen et al., Immunol. Rev. 257:127-133 (2014); Sharpe et al., Dis. Model Mech. 8(4):337-350 (2015), and references cited therein). A CAR directed to a desired viral antigen can be generated using well known methods for designing a CAR, including those as described herein. A CAR, whether a first, second or third generation CAR, can be readily designed by fusing a viral antigen binding activity, for example, an scFv antibody directed to the viral antigen, to an immune cell signaling domain, such as a T cell receptor cytoplasmic/intracellular domain. As described above, the CAR generally has the structure of a cell surface receptor, with the viral antigen binding activity, such as an scFv, as at least a portion of the extracellular domain, fused to a transmembrane domain, which is fused to an intracellular domain that has cell signaling activity in an immune cell, such as a T cell, or precursor cell thereof. The viral antigen CAR can include co-stimulatory molecules, as described herein. One skilled in the art can readily select appropriate transmembrane domains, as described herein and known in the art, and intracellular domains to provide the desired signaling capability in the immune cell, such as a T cell, or precursor cell thereof.
A CAR for use in the present invention comprises an extracellular domain that includes an antigen binding domain that binds to a viral antigen. The antigen binding domain binds to an antigen on the target virus, or to a viral antigen expressed in a target cell or tissue. Such an antigen binding domain is generally derived from an antibody. In one embodiment, the antigen binding domain can be an scFv or a Fab, or any suitable antigen binding fragment of an antibody (see Sadelain et al., Cancer Discov. 3:388-398 (2013)). Many antibodies or antigen binding domains derived from antibodies that bind to a viral antigen are known in the art. Alternatively, such antibodies or antigen binding domains can be produced by routine methods. Methods of generating an antibody are well known in the art, including methods of producing a monoclonal antibody or screening a library to obtain an antigen binding polypeptide, including screening a library of human Fabs (Winter and Harris, Immunol. Today 14:243-246 (1993); Ward et al., Nature 341:544-546 (1989); Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press (1988); Hilyard et al., Protein Engineering: A practical approach (IRL Press 1992); Borrabeck, Antibody Engineering, 2nd ed. (Oxford University Press 1995); Huse et al., Science 246:1275-1281 (1989)). For the CAR, the antigen binding domain derived from an antibody can be human, humanized, chimeric, CDR-grafted, and the like, as desired. For example, if a mouse monoclonal antibody is a source antibody for generating the antigen binding domain of a CAR, such an antibody can be humanized by grafting CDRs of the mouse antibody onto a human framework (see Borrabeck, supra, 1995), which can be beneficial for administering the CAR to a human subject. In a preferred embodiment, the antigen binding domain is an scFv. The generation of scFvs is well known in the art (see, for example, Huston, et al., Proc. Nat. Acad. Sci. USA 85:5879-5883 (1988); Ahmad et al., Clin. Dev. Immunol. 2012: ID980250 (2012); U.S. Pat. Nos. 5,091,513, 5,132,405 and 4,956,778; and U.S. Patent Publication Nos. 20050196754 and 20050196754)).
With respect to obtaining a viral antigen binding activity, one skilled in the art can readily obtain a suitable viral antigen binding activity, such as an antibody, using any of the well known methods for generating and screening for an antibody that binds to a desired antigen, as disclosed herein, including the generation of an scFv that binds to a viral antigen, which is particularly useful in a CAR. In addition, a number viral antigen antibodies, in particular monoclonal antibodies, are commercially available and can also be used as a source for a viral antigen binding activity, such as an scFv, to generate a CAR (see, for example, Sigma-Aldrich, St. Louis, Mo.; Meridian Life Science, Memphis, Tenn.; ProSpec-Tany Technogene, East Brunswick, N.J., and the like).
Alternatively to using an antigen binding domain derived from an antibody, a CAR extracellular domain can comprise a ligand or extracellular ligand binding domain of a receptor (see Sadelain et al., Cancer Discov. 3:388-398 (2013); Sharpe et al., Dis. Model Mech. 8:337-350 (2015)). In this case, the ligand or extracellular ligand binding domain of a receptor provides to the CAR the ability to target the cell expressing the CAR to the corresponding receptor or ligand. In the case of targeting a virus, an exemplary embodiment is the use of the gE/gI glycoprotein of herpes simplex virus (HSV) (see Polcicova et al., J. Virol. 79:11990-12001 (2005). The HSV gE/gI glycoprotein accumulates at cell junctions and mediates cell-to-cell spread of HSV (Polcicova et al., supra, 2005). In a specific embodiment, a CAR extracellular domain comprises the extracellular domain of HSV gE, so as to target the immune cell expressing the CAR to cell junctions, where HSV spreads from cell to cell.
For a CAR directed to a viral antigen, the antigen binding domain of the CAR is selected to bind to a viral antigen of the target virus or a viral antigen expressed on a cell containing the virus, for example, an infected cell expressing viral antigen on its cell surface. Such a viral antigen can be uniquely expressed on a virus, or the viral antigen can be overexpressed on a virus or in a virus infected tissue or cell relative to non-virally infected cells or tissues. Generally, a viral antigen is uniquely expressed by the virus or a virally infected cell or tissue and is not naturally expressed in an infected organism. The viral antigen to be bound by the CAR is chosen to provide targeting of the cell expressing the CAR over non-virally infected cells or tissues. In one embodiment of the methods of the invention for treating a viral infection, an immune cell or precursor cell thereof is designed to treat a patient with a viral infection by expressing in the cell a CAR that binds to a suitable viral antigen of the patient's viral infection, along with a DN form, as described herein.
Any suitable viral antigen can be chosen based on the type of viral infection exhibited by a subject (patient with a viral infection) to be treated. It is understood that the selected viral antigen is expressed in a manner such that the viral antigen is accessible for binding by the CAR. Generally, the viral antigen to be targeted by a cell expressing a CAR is expressed on the surface of the virus or the surface of a virally infected cell or tissue of the subject. However, it is understood that any viral antigen that is accessible for binding to a CAR is suitable for targeting the CAR expressing cell to the site of a viral infection or virally infected tissue. Preferred viruses include those that are pathogenic, particularly human pathogens, and that elicit a viral antigen-specific immune response. In a specific embodiment, the targeted viral antigen is of a virus that is a human pathogen, and in a particular embodiment, such a viral antigen of a human pathogen is one that can elicit an immune response in a human patient infected with the virus. Exemplary viruses and their viral antigens that can be targeted include, but are not limited to, those provided below in Table 1.







TABLE 1







Viruses and Viral Antigens









Virus
Viral Antigen
Reference1





human immunodeficiency
group-specific antigen (gag) protein (p55, p24,
Mitsuya, 1990;


virus (HIV)
or p18), envelope glycoprotein (env) (gp160,
Fauci, 1998;



gp120 or gp41) or reverse transcriptase (pol)
Fauci, 1988;



(p66 or p31)
Rosenberg,




1997


hepatitis B virus (HBV)
HBV envelope protein S, M or L
Krebs, 2013


hepatitis C virus (HCV)
core protein, envelope protein E1 or E2,
Ashfaq (2011);



nostructural protein NS2, NS3, NS4 (NS4A or
Sillanpää



NS4B), NS5 (NS5A or NS5B)
(2009);




Dawson (2012)


herpes simplex virus (HSV)
gE, gI, gB, gD, gH, gL, gC, gG, gK or gM
Polcicova,




2005; Bennett,




1996


varicella zoster virus or
gE or gI
Polcicova,


(VZV)

2005


adenovirus
hexon protein or penton protein
Gerdemann,




2013


cytomegalovirus (CMV)
pp65, immediate early (IE) antigen or IE1
Gerdemann,




2013; Rooney,




2012


Epstein-Barr virus (EBV)
LMP2 (latent membrane protein 2), EBNA1
Gerdemann,



(Epstein-Barr nuclear antigen 1) or immediate
2013; Rooney,



early protein BZLF1 (also known as Zta,
2012



ZEBRA, EB1)





1Mitsuya et al., Science 249: 1533-1544 (1990); Fauci et al., Harrison's Principles of Internal Medicine, 14th ed., pp. 1814-1816, McGraw-Hill, San Francisco CA (1998); Fauci, Science 239: 617-622 (1988); Rosenberg et al., Science 278: 1447-1450 (1997); Krebs et al., Gastroenterol. 145: 456-465 (2013); Ashfaq et al., Virol. J. 8: 161 (doi: 10.1186/1743-422X-8-161); Sillanpää et al., Virol. J. 6: 84 (doi: 10.1186/1743-422X-6-84); Dawson, Antiviral Therap. 17: 1431-1435 (2012); Polcicova et al., J. Virol. 79: 11990-12001 (2005); Bennett et al., Cecil Textbook of Medicine, 20th ed., p. 1770, W. B. Saunders, Philadelphia PA (1996); Gerdemann et al., Mol. Ther. 21: 2113-2121 (2013); Rooney et al., Mol. Ther. Nucleic Acids 1: e55, doi: 10.1038/mtna.2012.49 (2012)






In a specific embodiment in the case of HBV, the S domain of an S, M or L envelope protein is targeted (see Krebs et al., supra, 2013). In another specific embodiment in the case of HSV, the extracellular domain of gE is targeted (see Polcicova et al., supra, 2005). It is understood that a person skilled in the art can readily determine a viral antigen, or domain of a viral antigen, suitable for targeting by an immune cell of the invention.
It is further understood that reference to a virus, such as those listed in Table 1, includes different strains or types of the same virus. For example, HSV exists as herpes simplex virus type 1 (HSV-1) and herpes simplex virus type 2 (HSV-2), which can be distinguished by the respective glycoprotein G (gG) (Bennett et al., Cecil Textbook of Medicine, 20th ed., p. 1770, W.B. Saunders, Philadelphia Pa. (1996)). In a particular embodiment, the viral antigen can be selected such that the antigen is common to different strains or types of the same virus or is a distinct antigen specific to a particular strain or type of virus, such as for HSV-1 and HSV-2.
It is to be understood that any of the above-described viral antigens or epitopes thereof, as well as any known in the art, can be targeted by the immune cells of the invention (that express a DN form), for example, by using such an immune cell that recombinantly expresses a CAR that binds to such antigen or epitope, or using such an immune cell sensitized ex vivo to such antigen or epitope, or using such an immune cell that is in vivo sensitized to such antigen or epitope. In a specific embodiment, one or more nucleic acids encoding a CAR and a DN form are used to transduce both CD4+ and CD8+ T cells. In such an embodiment, administration of the transduced T cells to a subject should generate both helper and cytotoxic T lymphocyte (CTL) responses in the subject, resulting in a sustained anti-viral response.
It is further understood that embodiments described herein relating to immune cells for treating a viral infection and methods of using such cells for treating a viral infection can be modified and similarly applied to treating an infection by another pathogen, e.g., a pathogen that is a bacterium, fungus, or protozoan. In one embodiment, the pathogen is a human pathogen. It is additionally understood that an antigen of the pathogen can be targeted, for example, by targeting a cell surface antigen of the pathogen.
As described above, a CAR also contains a signaling domain that functions in the immune cell, or precursor cell thereof, expressing the CAR. Such a signaling domain can be, for example, derived from CDζ or Fc receptor γ (see Sadelain et al., Cancer Discov. 3:388-398 (2013)). In general, the signaling domain will induce persistence, trafficking and/or effector functions in the transduced immune cells such as T cells, or precursor cells thereof (Sharpe et al., Dis. Model Mech. 8:337-350 (2015); Finney et al., J. Immunol. 161:2791-2797 (1998); Krause et al., J. Exp. Med. 188:619-626 (1998)). In the case of CDζ or Fc receptor γ, the signaling domain corresponds to the intracellular domain of the respective polypeptides, or a fragment of the intracellular domain that is sufficient for signaling. Exemplary signaling domains are described below in more detail.
Exemplary polypeptides are described herein with reference to GenBank numbers, GI numbers and/or SEQ ID NOS. It is understood that one skilled in the art can readily identify homologous sequences by reference to sequence sources, including but not limited to GenBank (ncbi.nlm.nih.gov/genbank/) and EMBL (embl.org/).
CD3ζ. In a non-limiting embodiment, a CAR can comprise a signaling domain derived from a CD3ζ polypeptide, for example, a signaling domain derived from the intracellular domain of CD3ζ, which can activate or stimulate an immune cell, for example, a T cell, or precursor cell thereof. CD3ζ comprises 3 Immune-receptor-Tyrosine-based-Activation-Motifs (ITAMs), and transmits an activation signal to the cell, for example, a cell of the lymphoid lineage such as a T cell, after antigen is bound. A CD3ζ polypeptide can have an amino acid sequence corresponding to the sequence having GenBank No. NP_932170 (NP_932170.1, GI:37595565; see below), or fragments thereof. In one embodiment, the CD3ζ polypeptide has an amino acid sequence of amino acids 52 to 164 of the CD3ζ polypeptide sequence provided below, or a fragment thereof that is sufficient for signaling activity. An exemplary CAR is Mz, which has an intracellular domain comprising a CD3ζ polypeptide comprising amino acids 52 to 164 of the CD3ζ polypeptide sequence provided below. Another exemplary CAR is M28z, which has an intracellular domain comprising a CD3ζ polypeptide comprising amino acids 52 to 164 of the CD3ζ polypeptide provided below. Still another exemplary CAR is MBBz, which has an intracellular domain comprising a CD3ζ polypeptide comprising amino acids 52 to 164 of the CD3ζ polypeptide provided below. Yet another exemplary CAR is P28z, which has an intracellular domain derived from a CD3ζ polypeptide. See GenBank NP_932170 for reference to domains within CD3ζ, for example, signal peptide, amino acids 1 to 21; extracellular domain, amino acids 22 to 30; transmembrane domain, amino acids 31 to 51; intracellular domain, amino acids 52 to 164.









1
MKWKALFTAA ILQAQLPITE AQSFGLLDPK LCYLLDGILF IYGVILTALF LRVKFSRSAD



 


61
APAYQQGQNQ LYNELNLGRR EEYDVLDKRR GRDPEMGGKP QRRKNPQEGL YNELQKDKMA


 


121
EAYSEIGMKG ERRRGKGHDG LYQGLSTATK DTYDALHMQA LPPR 


 








(NP_932170; SEQ ID NO: 1)







It is understood that a “CD3ζ nucleic acid molecule” refers to a polynucleotide encoding a CD3ζ polypeptide. In one embodiment, the CD3ζ nucleic acid molecule encoding the CD3ζ polypeptide comprised in the intracellular domain of a CAR, including exemplary CARs Mz, M28z, or MBBz, comprises a nucleotide sequence as set forth below.







(SEQ ID NO:2)


AGAGTGAAGTTCAGCAGGAGCGCAGACGCCCCCGCGTACCAGCAGGGCC


 


AGAACCAGCTCTATAACGAGCTCAATCTAGGACGAAGAGAGGAGTACGA


 


TGTTTTGGACAAGAGACGTGGCCGGGACCCTGAGATGGGGGGAAAGCCG


 


AGAAGGAAGAACCCTCAGGAAGGCCTGTACAATGAACTGCAGAAAGATA


 


AGATGGCGGAGGCCTACAGTGAGATTGGGATGAAAGGCGAGCGCCGGAG


 


GGGCAAGGGGCACGATGGCCTTTACCAGGGTCTCAGTACAGCCACCAAG


 


GACACCTACGACGCCCTTCACATGCAGGCCCTGCCCCCTCGCTAA 






In certain non-limiting embodiments, an intracellular domain of a CAR can further comprise at least one co-stimulatory signaling domain. Such a co-stimulatory signaling domain can provide increased activation of an immune cell, or precursor cell thereof. A co-stimulatory signaling domain can be derived from a CD28 polypeptide, a 4-1BB polypeptide, an OX40 polypeptide, an ICOS polypeptide, a DAP10 polypeptide, a 2B4 polypeptide, and the like. CARs comprising an intracellular domain that comprises a co-stimulatory signaling region comprising 4-1BB, ICOS or DAP-10 have been described previously (see U.S. Pat. No. 7,446,190, which is incorporated herein by reference, which also describes representative sequences for 4-1BB, ICOS and DAP-10). In some embodiments, the intracellular domain of a CAR can comprise a co-stimulatory signaling region that comprises two co-stimulatory molecules, such as CD28 and 4-1BB (see Sadelain et al., Cancer Discov. 3(4):388-398 (2013)), or CD28 and OX40, or other combinations of co-stimulatory ligands, as disclosed herein.
CD28. Cluster of Differentiation 28 (CD28) is a protein expressed on T cells that provides co-stimulatory signals for T cell activation and survival. CD28 is the receptor for CD80 (B7.1) and CD86 (B7.2) proteins. In one embodiment, a CAR can comprise a co-stimulatory signaling domain derived from CD28. For example, as disclosed herein, a CAR can include at least a portion of an intracellular/cytoplasmic domain of CD28, for example an intracellular/cytoplasmic domain that can function as a co-stimulatory signaling domain (see FIG. 1B). A CD28 polypeptide can have an amino acid sequence corresponding to the sequence having GenBank No. P10747 (P10747.1, GI:115973) or NP_006130 (NP_006130.1, GI:5453611), as provided below, or fragments thereof. If desired, CD28 sequences additional to the intracellular domain can be included in a CAR of the invention. For example, a CAR can comprise the transmembrane of a CD28 polypeptide. In one embodiment, a CAR can have an amino acid sequence comprising the intracellular domain of CD28 corresponding to amino acids 180 to 220 of CD28, or a fragment thereof. In another embodiment, a CAR can have an amino acid sequence comprising the transmembrane domain of CD28 corresponding to amino acids 153 to 179, or a fragment thereof. M28z is an exemplary CAR, which comprises a co-stimulatory signaling domain corresponding to an intracellular domain of CD28 (see FIG. 1B). M28z also comprises a transmembrane domain derived from CD28 (see FIG. 1B). Thus, M28z exemplifies a CAR that comprises two domains from CD28, a co-stimulatory signaling domain and a transmembrane domain. In one embodiment, a CAR has an amino acid sequence comprising the transmembrane domain and the intracellular domain of CD28 and comprises amino acids 153 to 220 of CD28. In another embodiment, a CAR is exemplified by M28z CAR and comprises amino acids 117 to 220 of CD28. Another exemplary CAR having a transmembrane domain and intracellular domain of CD28 is P28z (see FIG. 1B). In one embodiment, a CAR can comprise a transmembrane domain derived from a CD28 polypeptide comprising amino acids 153 to 179 of the CD28 polypeptide provided below. See GenBank NP_006130 for reference to domains within CD28, for example, signal peptide, amino acids 1 to 18; extracellular domain, amino acids 19 to 152; transmembrane domain, amino acids 153 to 179; intracellular domain, amino acids 180 to 220. It is understood that sequences of CD28 that are shorter or longer than a specific delineated domain can be included in a CAR, if desired.









1
MLRLLLALNL FPSIQVTGNK ILVKQSPMLV AYDNAVNLSC KYSYNLFSRE FRASLHKGLD



 


61
SAVEVCVVYG NYSQQLQVYS KTGFNCDGKL GNESVTFYLQ NLYVNQTDIY FCKIEVMYPP


 


121
PYLDNEKSNG TIIHVKGKHL CPSPLFPGPS KPFWVLVVVG GVLACYSLLV TVAFIIFWVR


 


181
SKRSRLLHSD YMNMTPRRPG PTRKHYQPYA PPRDFAAYRS (NP_006130; SEQ ID NO:3)






It is understood that a “CD28 nucleic acid molecule” refers to a polynucleotide encoding a CD28 polypeptide. In one embodiment, the CD28 nucleic acid molecule encoding the CD28 polypeptide of M28z comprising the transmembrane domain and the intracellular domain, for example, the co-stimulatory signaling region, comprises a nucleotide sequence as set forth below.







(SEQ ID NO:4)


ATTGAAGTTATGTATCCTCCTCCTTACCTAGACAATGAGAAGAGCAATG


 


GAACCATTATCCATGTGAAAGGGAAACACCTTTGTCCAAGTCCCCTATT


 


TCCCGGACCTTCTAAGCCCTTTTGGGTGCTGGTGGTGGTTGGTGGAGTC


 


CTGGCTTGCTATAGCTTGCTAGTAACAGTGGCCTTTATTATTTTCTGGG


 


TGAGGAGTAAGAGGAGCAGGCTCCTGCACAGTGACTACATGAACATGAC


 


TCCCCGCCGCCCCGGGCCCACCCGCAAGCATTACCAGCCCTATGCCCCA


 


CCACGCGACTTCGCAGCCTATCGCTCC 






4-1BB. 4-1BB, also referred to as tumor necrosis factor receptor superfamily member 9, can act as a tumor necrosis factor (TNF) ligand and have stimulatory activity. In one embodiment, a CAR can comprise a co-stimulatory signaling domain derived from 4-1BB. A 4-1BB polypeptide can have an amino acid sequence corresponding to the sequence having GenBank No. P41273 (P41273.1, GI:728739) or NP_001552 (NP_001552.2, GI:5730095) or fragments thereof. In one embodiment, a CAR can have a co-stimulatory domain comprising the intracellular domain of 4-1BB corresponding to amino acids 214 to 255, or a fragment thereof. In another embodiment, a CAR can have a transmembrane domain of 4-1BB corresponding to amino acids 187 to 213, or a fragment thereof. An exemplary CAR is MBBz, which has an intracellular domain comprising a 4-1BB polypeptide (for example, amino acids 214 to 255 of NP_001552, SEQ ID NO:5) (see FIG. 1B). See GenBank NP_001552 for reference to domains within 4-1BB, for example, signal peptide, amino acids 1 to 17; extracellular domain, amino acids 18 to 186; transmembrane domain, amino acids 187 to 213; intracellular domain, amino acids 214 to 255. It is understood that sequences of 4-1BB that are shorter or longer than a specific delineated domain can be included in a CAR, if desired. It is also understood that a “4-1BB nucleic acid molecule” refers to a polynucleotide encoding a 4-1BB polypeptide.









1
MGNSCYNIVA TLLLVLNFER TRSLQDPCSN CPAGTFCDNN RNQICSPCPP NSFSSAGGQR



 


61
TCDICRQCKG VFRTRKECSS TSNAECDCTP GFHCLGAGCS MCEQDCKQGQ ELTKKGCKDC


 


121
CFGTFNDQKR GICRPWTNCS LDGKSVLVNG TKERDVVCGP SPADLSPGAS SVTPPAPARE


 


181
PGHSPQIISF FLALTSTALL FLLFFLTLRF SVVKRGRKKL LYIFKQPFMR PVQTTQEEDG


 


241
CSCRFPEEEE GGCEL (NP_001552; SEQ ID NO:5)






OX40. OX40, also referred to as tumor necrosis factor receptor superfamily member 4 precursor or CD134, is a member of the TNFR-superfamily of receptors. In one embodiment, a CAR can comprise a co-stimulatory signaling domain derived from OX40. An OX40 polypeptide can have an amino acid sequence corresponding to the sequence having GenBank No. P43489 (P43489.1, GI:1171933) or NP_003318 (NP_003318.1, GI:4507579), provided below, or fragments thereof. In one embodiment, a CAR can have a co-stimulatory domain comprising the intracellular domain of OX40 corresponding to amino acids 236 to 277, or a fragment thereof. In another embodiment, a CAR can have an amino acid sequence comprising the transmembrane domain of OX40 corresponding to amino acids 215 to 235 of OX40, or a fragment thereof. See GenBank NP_003318 for reference to domains within OX40, for example, signal peptide, amino acids 1 to 28; extracellular domain, amino acids 29 to 214; transmembrane domain, amino acids 215 to 235; intracellular domain, amino acids 236 to 277. It is understood that sequences of OX40 that are shorter or longer than a specific delineated domain can be included in a CAR, if desired. It is also understood that an “OX40 nucleic acid molecule” refers to a polynucleotide encoding an OX40 polypeptide.









1
MCVGARRLGR GPCAALLLLG LGLSTVTGLH CVGDTYPSND RCCHECRPGN GMVSRCSRSQ



 


61
NTVCRPCGPG FYNDVVSSKP CKPCTWCNLR SGSERKQLCT ATQDTVCRCR AGTQPLDSYK


 


121
PGVDCAPCPP GHFSPGDNQA CKPWTNCTLA GKHTLQPASN SSDAICEDRD PPATQPQETQ


 


181
GPPARPITVQ PTEAWPRTSQ GPSTRPVEVP GGRAVAAILG LGLVLGLLGP LAILLALYLL


 


241
RRDQRLPPDA HKPPGGGSFR TPIQEEQADA HSTLAKI (NP_003318; SEQ ID NO:6)






ICOS. Inducible T-cell costimulator precursor (ICOS), also referred to as CD278, is a CD28-superfamily costimulatory molecule that is expressed on activated T cells. In one embodiment, a CAR can comprise a co-stimulatory signaling domain derived from ICOS. An ICOS polypeptide can have an amino acid sequence corresponding to the sequence having GenBank No. NP_036224 (NP_036224.1, GI:15029518), provided below, or fragments thereof. In one embodiment, a CAR can have a co-stimulatory domain comprising the intracellular domain of ICOS corresponding to amino acids 162 to 199 of ICOS. In another embodiment, a CAR can have an amino acid sequence comprising the transmembrane domain of ICOS corresponding to amino acids 141 to 161 of ICOS, or a fragment thereof. See GenBank NP_036224 for reference to domains within ICOS, for example, signal peptide, amino acids 1 to 20; extracellular domain, amino acids 21 to 140; transmembrane domain, amino acids 141 to 161; intracellular domain, amino acids 162 to 199. It is understood that sequences of ICOS that are shorter or longer than a specific delineated domain can be included in a CAR, if desired. It is also understood that an “ICOS nucleic acid molecule” refers to a polynucleotide encoding an ICOS polypeptide.









1
MKSGLWYFFL FCLRIKVLTG EINGSANYEM FIFHNGGVQI LCKYPDIVQQ FKMQLLKGGQ



 


61
ILCDLTKTKG SGNTVSIKSL KFCHSQLSNN SVSFFLYNLD HSHANYYFCN LSIFDPPPFK


 


121
VTLTGGYLHI YESQLCCQLK FWLPIGCAAF VVVCILGCIL ICWLTKKKYS SSVHDPNGEY


 


181
MFMRAVNTAK KSRLTDVTL (NP_036224; SEQ ID NO:7)






DAP10. DAP10, also referred to as hematopoietic cell signal transducer, is a signaling subunit that associates with a large family of receptors in hematopoietic cells. In one embodiment, a CAR can comprise a co-stimulatory domain derived from DAP10. A DAP10 polypeptide can have an amino acid sequence corresponding to the sequence having GenBank No. NP_055081.1 (GI:15826850), provided below, or fragments thereof. In one embodiment, a CAR can have a co-stimulatory domain comprising the intracellular domain of DAP10 corresponding to amino acids 70 to 93, or a fragment thereof. In another embodiment, a CAR can have a transmembrane domain of DAP10 corresponding to amino acids 49 to 69, or a fragment thereof. See GenBank NP_055081.1 for reference to domains within DAP10, for example, signal peptide, amino acids 1 to 19; extracellular domain, amino acids 20 to 48; transmembrane domain, amino acids 49 to 69; intracellular domain, amino acids 70 to 93. It is understood that sequences of DAP10 that are shorter or longer than a specific delineated domain can be included in a CAR, if desired. It is also understood that a “DAP10 nucleic acid molecule” refers to a polynucleotide encoding an DAP10 polypeptide.









1
MIHLGHILFL LLLPVAAAQT TPGERSSLPA FYPGTSGSCS GCGSLSLPLL AGLVAADAVA



 


61
SLLIVGAVFL CARPRRSPAQ EDGKVYINMP GRG (NP_055081.1; SEQ ID NO:8)






The extracellular domain of a CAR can be fused to a leader or a signal peptide that directs the nascent protein into the endoplasmic reticulum and subsequent translocation to the cell surface. It is understood that, once a polypeptide containing a signal peptide is expressed at the cell surface, the signal peptide has generally been proteolytically removed during processing of the polypeptide in the endoplasmic reticulum and translocation to the cell surface. Thus, a polypeptide such as a CAR is generally expressed at the cell surface as a mature protein lacking the signal peptide, whereas the precursor form of the polypeptide includes the signal peptide. A signal peptide or leader can be essential if a CAR is to be glycosylated and/or anchored in the cell membrane. The signal sequence or leader is a peptide sequence generally present at the N-terminus of newly synthesized proteins that directs their entry into the secretory pathway. The signal peptide is covalently joined to the N-terminus of the extracellular antigen-binding domain of a CAR as a fusion protein. In one embodiment, the signal peptide comprises a CD8 polypeptide comprising amino acids MALPVTALLLPLALLLHAARP (SEQ ID NO:9). It is understood that use of a CD8 signal peptide is exemplary. Any suitable signal peptide, as are well known in the art, can be applied to a CAR to provide cell surface expression in an immune cell (see Gierasch Biochem. 28:923-930 (1989); von Heijne, J. Mol. Biol. 184 (1):99-105 (1985)). Particularly useful signal peptides can be derived from cell surface proteins naturally expressed in the immune cell, or precursor cell thereof, including any of the signal peptides of the polypeptides disclosed herein. Thus, any suitable signal peptide can be utilized to direct a CAR to be expressed at the cell surface of an immune cell, or precursor cell thereof.
In certain non-limiting embodiments, an extracellular antigen-binding domain of a CAR can comprise a linker sequence or peptide linker connecting the heavy chain variable region and light chain variable region of the extracellular antigen-binding domain. In one non-limiting example, the linker comprises amino acids having the sequence set forth in









(SEQ ID NO:10)



GGGGSGGGGSGGGGS.






In certain non-limiting embodiments, a CAR can also comprise a spacer region or sequence that links the domains of the CAR to each other. For example, a spacer can be included between a signal peptide and an antigen binding domain, between the antigen binding domain and the transmembrane domain, between the transmembrane domain and the intracellular domain, and/or between domains within the intracellular domain, for example, between a stimulatory domain and a co-stimulatory domain. The spacer region can be flexible enough to allow interactions of various domains with other polypeptides, for example, to allow the antigen binding domain to have flexibility in orientation in order to facilitate antigen recognition. The spacer region can be, for example, the hinge region from an IgG, the CH2CH3 (constant) region of an immunoglobulin, and/or portions of CD3 (cluster of differentiation 3) or some other sequence suitable as a spacer.
The transmembrane domain of a CAR generally comprises a hydrophobic alpha helix that spans at least a portion of the membrane. Different transmembrane domains result in different receptor stability. After antigen recognition, receptors cluster and a signal is transmitted to the cell. In an embodiment, the transmembrane domain of a CAR can be derived from another polypeptide that is naturally expressed in the immune cell, or precursor cell thereof. In one embodiment, a CAR can have a transmembrane domain derived from CD8, CD28, CD3ζ, CD4, 4-1BB, OX40, ICOS, CTLA-4, PD-1, LAG-3, 2B4, BTLA, or other polypeptides expressed in the immune cell, or precursor cell thereof, having a transmembrane domain, including others as disclosed herein. Optionally, the transmembrane domain can be derived from a polypeptide that is not naturally expressed in the immune cell, or precursor cell thereof, so long as the transmembrane domain can function in transducing signal from antigen bound to the CAR to the intracellular signaling and/or co-stimulatory domains. It is understood that the portion of the polypeptide that comprises a transmembrane domain of the polypeptide can include additional sequences from the polypeptide, for example, additional sequences adjacent on the N-terminal or C-terminal end of the transmembrane domain, or other regions of the polypeptide, as desired.
CD8. Cluster of differentiation 8 (CD8) is a transmembrane glycoprotein that serves as a co-receptor for the T cell receptor (TCR). CD8 binds to a major histocompatibility complex (MHC) molecule and is specific for the class I MHC protein. In one embodiment, a CAR can comprise a transmembrane domain derived from CD8. A CD8 polypeptide can have an amino acid sequence corresponding to the sequence having GenBank No. NP_001139345.1 (GI:225007536), as provided below, or fragments thereof. In one embodiment, a CAR can have an amino acid sequence comprising the transmembrane domain of CD8 corresponding to amino acids 183 to 203, or fragments thereof. In one embodiment, an exemplary CAR is Mz, which has a transmembrane domain derived from a CD8 polypeptide (see FIG. 1B). In another embodiment, an exemplary CAR is MBBz, which has a transmembrane domain derived from a CD8 polypeptide (see FIG. 1B). In one non-limiting embodiment, a CAR can comprise a transmembrane domain derived from a CD8 polypeptide comprising amino acids 183 to 203. In addition, a CAR can comprise a hinge domain comprising amino acids 137-182 of the CD8 polypeptide provided below. In another embodiment, a CAR can comprise amino acids 137-203 of the CD8 polypeptide provided below. In yet another embodiment, a CAR can comprise amino acids 137 to 209 of the CD8 polypeptide provided below. See GenBank NP_001139345.1 for reference to domains within CD8, for example, signal peptide, amino acids 1 to 21; extracellular domain, amino acids 22 to 182; transmembrane domain amino acids, 183 to 203; intracellular domain, amino acids 204 to 235. It is understood that additional sequence of CD8 beyond the transmembrane domain of amino acids 183 to 203 can be included in a CAR, if desired. It is further understood that sequences of CD8 that are shorter or longer than a specific delineated domain can be included in a CAR, if desired. It also is understood that a “CD8 nucleic acid molecule” refers to a polynucleotide encoding a CD8 polypeptide.









1
MALPVTALLL PLALLLHAAR PSQFRVSPLD RTWNLGETVE LKCQVLLSNP TSGCSWLFQP



 


61
RGAAASPTFL LYLSQNKPKA AEGLDTQRFS GKRLGDTFVL TLSDFRRENE GYYFCSALSN


 


121
SIMYFSHFVP VFLPAKPTTT PAPRPPTPAP TIASQPLSLR PEACRPAAGG AVHTRGLDFA


 


181
CDIYIWAPLA GTCGVLLLSL VITLYCNHRN RRRVCKCPRP VVKSGDKPSL SARYV


 








(NP_001139345.1; SEQ ID NO:11)







CD4. Cluster of differentiation 4 (CD4), also referred to as T-cell surface glycoprotein CD4, is a glycoprotein found on the surface of immune cells such as T helper cells, monocytes, macrophages, and dendritic cells. In one embodiment, a CAR can comprise a transmembrane domain derived from CD4. CD4 exists in various isoforms. It is understood that any isoform can be selected to achieve a desired function. Exemplary isoforms include isoform 1 (NP_000607.1, GI:10835167), isoform 2 (NP_001181943.1, GI:303522479), isoform 3 (NP_001181944.1, GI:303522485; or NP_001181945.1, GI:303522491; or NP_001181946.1, GI:303522569), and the like. One exemplary isoform sequence, isoform 1, is provided below. In one embodiment, a CAR can have an amino acid sequence comprising the transmembrane domain of CD4 corresponding to amino acids 397 to 418, or fragments thereof. See GenBank NP_000607.1 for reference to domains within CD4, for example, signal peptide, amino acids 1 to 25; extracellular domain, amino acids 26 to 396; transmembrane domain amino acids, 397 to 418; intracellular domain, amino acids 419 to 458. It is understood that additional sequence of CD4 beyond the transmembrane domain of amino acids 397 to 418 can be included in a CAR, if desired. It is further understood that sequences of CD4 that are shorter or longer than a specific delineated domain can be included in a CAR, if desired. It also is understood that a “CD4 nucleic acid molecule” refers to a polynucleotide encoding a CD4 polypeptide.









1
MNRGVPFRHL LLVLQLALLP AATQGKKVVL GKKGDTVELT CTASQKKSIQ FHWKNSNQIK



 


61
ILGNQGSFLT KGPSKLNDRA DSRRSLWDQG NFPLIIKNLK IEDSDTYICE VEDQKEEVQL


 


121
LVFGLTANSD THLLQGQSLT LTLESPPGSS PSVQCRSPRG KNIQGGKTLS VSQLELQDSG


 


181
TWTCTVLQNQ KKVEFKIDIV VLAFQKASSI VYKKEGEQVE FSFPLAFTVE KLTGSGELWW


 


241
QAERASSSKS WITFDLKNKE VSVKRVTQDP KLQMGKKLPL HLTLPQALPQ YAGSGNLTLA


 


301
LEAKTGKLHQ EVNLVVMRAT QLQKNLTCEV WGPTSPKLML SLKLENKEAK VSKREKAVWV


 


361
LNPEAGMWQC LLSDSGQVLL ESNIKVLPTW STPVQPMALI VLGGVAGLLL FIGLGIFFCV


 


421
RCRHRRRQAE RMSQIKRLLS EKKTCQCPHR FQKTCSPI 


 








(NP_000607.1; SEQ ID NO:12)







As disclosed herein, mesothelin CARs exemplify CARs that can target an antigen, and CARs directed to other antigens can be generated using similar methods and others well known in the art, as described above. It is understood that domains of the polypeptides described herein can be used in a CAR, as useful to provide a desired function such as a signal peptide, antigen binding domain, transmembrane domain, intracellular signaling domain and/or co-stimulatory domain. For example, a domain can be selected such as a signal peptide, a transmembrane domain, an intracellular signaling domain, or other domain, as desired, to provide a particular function to a CAR of the invention. Possible desirable functions can include, but are not limited to, providing a signal peptide and/or transmembrane domain.
7.3. Dominant Negative Forms of an Inhibitor of a Cell-Mediated Immune Response
According to the invention, an immune cell that is an immunostimulatory cell, such as a T cell, or a precursor cell thereof, or an immune cell that is an immunoinhibitory cell, such as a regulatory T cell, is engineered to express a dominant negative form (DN form) of an inhibitor of a cell-mediated immune response.
An inhibitor of a cell-mediated immune response of the immune cell, or precursor cell thereof, refers to a molecule that acts to inhibit or suppress the immune response effected by the immune cell, or precursor cell thereof. In one embodiment, the inhibitor of a cell-mediated immune response is an immune checkpoint inhibitor, also referred to as a checkpoint blockade.
In one embodiment, the invention provides immune cells, such as T cells, or precursor cells thereof, or regulatory T cells that express a dominant negative form of an inhibitor of a cell-mediated immune response of the immune cell, or that co-express a CAR and a dominant negative form of an inhibitor of a cell-mediated immune response of the immune cell, for example, a receptor that functions in an immune checkpoint inhibitor pathway. Immune checkpoint pathways are inhibitory pathways that suppress the immune response of an immune cell. The pathways deliver negative signals to the immune cells, such as T cells, and attenuate TCR-mediated signals, leading to decreased cell proliferation, cytokine production and cell cycle progression (see Pardoll, Nat. Rev. 12:252-264 (2012); Wu et al., Int. J. Biol. Sci. 8:1420-1430 (2012)). The immune checkpoint inhibitor pathway generally involves a ligand-receptor pair. Exemplary immune checkpoint inhibitor pathway receptors include, for example, PD-1, CTLA-4, BTLA, TIM-3, LAG-3, CD160, TIGIT, LAIR1, 2B4, and the like (see Chen et al., Nat. Rev. Immunol. 13(4):227-242 (2013)). The corresponding ligands for these receptors include, for example, PD-L1 (for PD-1); PD-L2 (for PD-1); CD80, CD86 (for CTLA-4); HVEM (for BTLA); Galectin-9, HMGB1 (for TIM-3); MHC II (for LAG-3); HVEM (for CD160); CD155, CD 112, CD 113 (for TIGIT); C1q, collagen (for LAIR1); CD48 (for 2B4), and the like (Chen et al., supra, 2013). Expression of a DN form in the immune cell, such as a T cell, or precursor cell thereof, provides for inhibition of a checkpoint inhibitor pathway that is intrinsic to the cell.
A DN form of an inhibitor of a cell-mediated immune response that is a cell-surface receptor such as an immune checkpoint inhibitor pathway receptor can be generated by deleting some portion of the receptor to prevent intracellular signaling, thereby suppressing the immune checkpoint pathway and sustaining activation of the immune cell, such as a T cell. A DN form of the invention is a polypeptide comprising (a) at least a portion of an extracellular domain of an immune checkpoint inhibitor, where the portion comprises the ligand binding region, and (b) a transmembrane domain, where the polypeptide is a dominant negative form of the immune checkpoint inhibitor. Generally, a DN form of an inhibitor of an immune checkpoint inhibitor pathway receptor retains most or all of an extracellular domain of the receptor such that the extracellular domain retains sufficient protein interaction activity to bind to its respective ligand. Thus, in a specific embodiment, a polypeptide encoding a DN form comprises substantially all of an extracellular domain of an immune checkpoint inhibitor. It is understood that a polypeptide comprising “substantially all” of an extracellular domain includes a polypeptide that comprises the entire extracellular domain or a portion of the extracellular domain in which one to a few amino acids have been deleted from the N-terminus and/or C-terminus of the extracellular domain, for example deletion of 1, 2, 3, 4, or 5 amino acids from the N-terminus and/or C-terminus, so long as the remaining portion of the extracellular domain retains sufficient protein interaction activity to bind to its respective ligand. A DN form of the invention generally also lacks some portion or all of a signaling domain, such as the intracellular/cytoplasmic domain, such that the DN form has reduced activity or is inactive for signaling in the immune checkpoint pathway. Without being bound by a particular mechanism or theory, binding of the ligand to the DN form decreases binding of the ligand to the intact endogenous receptor, and/or the DN form complexes with signaling molecules, including the endogenous receptor, resulting in decreased signaling of an immune checkpoint pathway.
A DN form of the invention generally has certain functional characteristics including, but not limited to, the ability to be expressed at the cell surface of an immune cell such as a T cell, or precursor cell thereof, the ability to bind to its respective ligand, and the inability or reduced ability to propagate an intracellular signal of an immune checkpoint pathway. One skilled in the art can readily generate a DN form of an inhibitor of a cell-mediated immune response by engineering the inhibitor to have such functional characteristics. In one embodiment, a DN form is constructed to retain the extracellular domain of inhibitor of a cell-mediated immune response, or at least a sufficient portion of the extracellular domain to retain ligand binding activity. In an exemplary embodiment, a DN form can be constructed using the extracellular domain of an inhibitor of a cell-mediated immune response, including, but not limited to, the extracellular domains of PD-1, CTLA-4, BTLA, TIM-3, LAG-3, CD160, TIGIT, LAIR1, 2B4, as disclosed herein. One skilled in the art will readily understand that it is not required to retain the entire extracellular domain of an inhibitor of a cell-mediated immune response, and that deletions from the N-terminus and/or C-terminus of the extracellular domain can be introduced so long as ligand binding activity is retained. One skilled in the art can readily determine the appropriateness of such N-terminal and/or C-terminal deletions based on the analysis of the receptor sequence to identify protein motifs known to provide ligand binding activity (see, for example, ExPASy (expasy.org), in particular PROSITE (prosite.expasy.org)). In addition or alternatively, suitable N-terminal and/or C-terminal deletions can be determined empirically by introducing deletions in a polypeptide and measuring binding activity for the respective ligand. Thus, one skilled in the art can readily determine an appropriate sequence of an inhibitor of a cell-mediated immune response to provide ligand binding activity to a DN form of the invention.
It is understood that, whether an entire extracellular domain or a portion of the extracellular domain of a receptor is used in a DN form, additional sequences can optionally be included in the extracellular domain of the DN form. Such additional sequences can be derived from the parent polypeptide of the DN form, or the additional sequences can be derived from a different polypeptide. Such a polypeptide comprising sequences from a parent polypeptide and a different polypeptide is a non-naturally occurring, chimeric polypeptide. For example, a signal peptide or leader peptide is generally included so that the DN form will be expressed at the cell surface of the immune cell such as a T cell, or precursor cell thereof, or a regulatory T cell. It is understood that, once a polypeptide containing a signal peptide is expressed at the cell surface, the signal peptide has generally been proteolytically removed during processing of the polypeptide in the endoplasmic reticulum and translocation to the cell surface. Thus, a polypeptide such as a DN form is generally expressed at the cell surface as a mature protein lacking the signal peptide, whereas the precursor form of the polypeptide includes the signal peptide. The signal peptide can be the naturally occurring signal peptide of the receptor, or alternatively can be derived from a different protein. Exemplary signal peptides are described herein, including those described herein as being suitable for a CAR. To additionally provide expression at the cell surface, the DN form will generally include a transmembrane domain that provides for retention of the DN form at the cell surface. The transmembrane domain can be the naturally occurring transmembrane of the receptor, or alternatively can be derived from a different protein. In a particular embodiment, the transmembrane domain derived from another protein is derived from another receptor expressed on the cell surface of the immune cell such as a T cell, or precursor cell thereof, or a regulatory T cell. Exemplary transmembrane domains are described herein, including those described herein as being suitable for a CAR.
In the case of an immune checkpoint pathway receptor, generally the signaling domain resides within the intracellular/cytoplasmic domain. The signaling activity of an immune checkpoint pathway receptor is generally mediated by protein-protein interactions with cell surface receptor(s) and/or intracellular signaling molecules. In one embodiment, a DN form lacks the entire intracellular domain, or a portion thereof, that functions in propagating the signal of an immune checkpoint pathway. It is understood that it is not necessary to delete the entire intracellular domain of the receptor so long as a sufficient portion of the intracellular signaling domain is deleted to inhibit or reduce signaling from the DN form. In addition or alternatively, mutations can be introduced into the intracellular signaling domain to inhibit or reduce signaling from the DN form. In addition or alternatively, a heterologous sequence with no signaling activity can be substituted for the intracellular signaling domain of the receptor to generate a DN form. One skilled in the art will readily understand that these and other well known methods can be utilized to generate a DN form of the invention.
One exemplary embodiment of a dominant negative form of an immune checkpoint inhibitor is a dominant negative form of PD-1. A dominant negative form of PD-1 is exemplary of a DN form of an inhibitor of a cell-mediated immune response, including an immune checkpoint inhibitor. It is understood that a PD-1 DN form as disclosed herein is exemplary.
As described herein, a DN form of an inhibitor of a cell-mediated immune response is designed to have reduced or inhibited intracellular signaling. The DN forms of the invention are generally based on inhibiting a receptor of an immune checkpoint pathway, which function to inhibit activation of an immune cell, such as T cell, for example, cell proliferation, cytokine production and/or cell cycle progression. The DN forms of the invention are designed to remove the intracellular signaling domain, or a portion thereof, so that the signaling ability of the receptor is reduced or inhibited. The DN form also functions to inhibit signaling of the endogenous receptor. In a particular embodiment, the reduced or inhibited signaling overcomes the checkpoint blockade, resulting in sustained signaling and activation of the immune cell, such as a T cell, or precursor cell thereof. It is understood that the signaling activity of the DN form can be completely knocked out or partially knocked out, so long as the partial reduction in activity is sufficient for the effect of providing enhanced activation of the immune cell, or precursor cell thereof, in comparison to the absence of the DN form. Also, the DN form is not required to result in complete inactivation of signaling from the endogenous receptor but can reduce the activation of the endogenous receptor sufficient to overcome the checkpoint blockade and allow activation of the immune cell, such as a T cell, or precursor cell thereof. One skilled in the art can readily determine the effect of a DN form on the activity of a parent receptor using assay methods well known in the art, including assays using in vivo models, such as animal models, to assess the effect of the DN form on the activity of the immune cell in which the DN form is expressed, including assays such as those disclosed herein.
In the case of using regulatory T cells isolated from a subject having a chronic viral infection, expression of a DN form of an inhibitor of a cell-mediated immune response of the immune cell, such as PD-1, inhibits the suppressive activity of the regulatory T cells resulting from interactions between the regulatory T cells that express the inhibitor of a cell-mediated immune response of the immune cell, e.g., PD-1, and immunostimulatory T cells, such as CD8+ T cells, that express the corresponding ligand, e.g., PD-L1. In such a case, the suppressive activity of the regulatory T cells on the immune response mediated by ligand-expressing immunostimulatory cells is reduced, thereby promoting the immune response against the virus.
As with a CAR for use in the invention, optional linker or spacer sequences can be included in a DN form, for example, a linker or spacer between a signal peptide and the extracellular ligand binding domain, particularly when heterologous sequences are fused. A linker or spacer can also optionally be included between the extracellular ligand binding domain and the transmembrane domain. Similarly, a linker or spacer can optionally be included between the transmembrane domain and any remaining intracellular domain. Such optional linkers or spacers are described herein. In addition, such linkers or spacers can be derived from a heterologous sequence. For example, as described above, a transmembrane domain derived from a heterologous polypeptide can optionally include additional sequences at the N-terminus and/or C-terminus derived from the heterologous polypeptide. Such additional sequences can function as a linker or spacer.
In one embodiment, as described above, a DN form can lack any signaling domain carboxy-terminal to the transmembrane domain of the DN form (i.e., the DN form can lack an intracellular signaling domain).
In a different specific embodiment, a DN form of the invention can optionally further comprise a fusion to a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form. Such a DN form is also referred to herein as a “switch receptor.” Such a DN form, or switch receptor, comprises at least a ligand binding domain of the extracellular region of an inhibitor of a cell-mediated immune response of the cell, such as an immune checkpoint inhibitor, fused to a transmembrane domain, fused to a co-stimulatory domain (i.e., cytoplasmic signaling domain) of an immunostimulatory molecule, thereby switching the activity upon ligand binding from inhibitory of the cell immune activity to stimulatory of the cell immune activity (see e.g., Liu et al., Cancer Res. 76:1578-1590 (2016)). A DN form further comprising a fusion to a co-stimulatory domain (i.e., switch receptor) also functions as a dominant negative form in such a construct since the signaling domain of the immune checkpoint inhibitor has been deleted. In one embodiment, a DN form further comprising a fusion to a co-stimulatory signaling domain is expressed in an immunostimulatory cell. In one embodiment, a DN form further comprising a fusion to a co-stimulatory signaling domain is expressed in an immunoinhibitory cell. In another embodiment, a DN form further comprising a fusion to a co-stimulatory signaling domain is co-expressed with a CAR in an immunostimulatory cell. In another embodiment, a DN form further comprising a fusion to a co-stimulatory signaling domain is co-expressed with a CAR in an immunostimulatory cell.
A co-stimulatory signaling domain in a DN form fusion polypeptide can be derived, for example, from a cytoplasmic signaling domain of a receptor such as the co-stimulatory molecules described herein for use in a CAR, including but not limited to a 4-1BB polypeptide, a CD28 polypeptide, an OX40 polypeptide, an ICOS polypeptide, a DAP10 polypeptide, and a 2B4 polypeptide. In a DN form comprising a fusion to a co-stimulatory signaling domain, the transmembrane domain can be derived from the polypeptide from which the co-stimulatory domain is derived, from the polypeptide from which the extracellular ligand binding domain of DN form is derived, or it can be a transmembrane domain from another polypeptide, similar to the description herein of the transmembrane domains that can be utilized to generate a CAR or DN form.
In one embodiment, the invention provides an immune cell (which can be immunostimulatory or immunoinhibitory, as desired) that recombinantly expresses a DN form, wherein the DN form further comprises a fusion to a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is fused carboxy-terminal to the transmembrane domain of the DN form. In certain embodiments of the invention, the cell or population of the invention recombinantly expresses a dominant negative form of an inhibitor of a cell-mediated immune response of the cell, wherein the dominant negative form further comprises a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain is fused to the transmembrane domain of the dominant negative form (which in turn is fused to the at least a portion of the extracellular domain of an immune checkpoint inhibitor containing the ligand binding region of the dominant negative form). Such cells optionally can co-express a dominant negative form that lacks an intracellular signaling domain. Such cells can be used to treat a viral infection as disclosed herein. The invention provides for recombinant expression by an immune cell of a switch receptor (i.e., a DN form further comprising a co-stimulatory signaling domain), which switch receptor comprises (i) at least the extracellular ligand binding domain of an immune checkpoint inhibitor, (ii) a transmembrane domain, and (iii) a co-stimulatory signaling domain. Such recombinant cells optionally can co-express a DN form that lacks an intracellular signaling domain. The invention also provides for recombinant expression by an immune cell of both a CAR and a DN form, which DN form further comprises a fusion to a co-stimulatory signaling domain (switch receptor), which DN form comprises (i) at least the extracellular ligand binding domain of an immune checkpoint inhibitor, (ii) a transmembrane domain, and (iii) a co-stimulatory signaling domain. Such cells optionally can co-express a DN form that lacks an intracellular signaling domain. It is understood that, in such immune cells co-expressing a CAR, and a DN form further comprising a fusion to a co-stimulatory signaling domain (switch receptor), and optionally a DN form lacking an intracellular signaling domain, the CAR binds to an antigen of the viral infection as being treated, i.e., the same virus of the viral infection. In one embodiment of cells co-expressing a CAR and a DN form comprising a fusion to a co-stimulatory signaling domain, the co-stimulatory signaling domain of the DN form is different from the co-stimulatory signaling domain of the CAR. In a particular embodiment, the co-stimulatory signaling domain of the DN form is the intracellular signaling domain of 4-1BB. In another particular embodiment, in an immune cell co-expressing a CAR and a DN form that further comprises a fusion to a co-stimulatory signaling domain, the co-stimulatory signaling domain of the CAR is the intracellular signaling domain of CD28. In another particular embodiment, the invention provides an immune cell co-expressing a CAR and a DN form that further comprises a fusion to a co-stimulatory signaling domain, and optionally co-expresses a DN form that lacks an intracellular signaling domain, where the co-stimulatory signaling domain of the DN form is the intracellular signaling domain of 4-1BB and the co-stimulatory signaling domain of the CAR is the intracellular signaling domain of CD28.
Exemplary DN forms of immune checkpoint inhibitors are described below in more detail. DN forms consisting essentially of the described sequences are also envisioned.
PD-1. Programmed cell death protein 1 (PD-1) is a negative immune regulator of activated T cells upon engagement with its corresponding ligands, PD-L1 and PD-L2, expressed on endogenous macrophages and dendritic cells. PD-1 is a type I membrane protein of 268 amino acids. PD-1 has two ligands, PD-L1 and PD-L2, which are members of the B7 family. The protein's structure comprises an extracellular IgV domain followed by a transmembrane region and an intracellular tail. The intracellular tail contains two phosphorylation sites located in an immunoreceptor tyrosine-based inhibitory motif and an immunoreceptor tyrosine-based switch motif. PD-1 negatively regulates TCR signals. SUP-1 and SHP-2 phosphatases bind to the cytoplasmic tail of PD-1 upon ligand binding. Upregulation of PD-L1 is one mechanism tumor cells use to evade the host immune system. In pre-clinical and clinical trials, PD-1 blockade by antagonistic antibodies induced anti-tumor responses mediated through the host endogenous immune system.
A PD-1 polypeptide can have an amino acid corresponding to GenBank No. NP_005009.2 (GI:167857792), as provided below, or fragments thereof. See GenBank NP_005009.2 for reference to domains within PD-1, for example, signal peptide, amino acids 1 to 20; extracellular domain, amino acids 21 to 170; transmembrane domain, amino acids 171 to 191; intracellular domain, amino acids 192 to 288. It is understood that an “PD-1 nucleic acid molecule” refers to a polynucleotide encoding an PD-1 polypeptide.









1
MQIPQAPWPV VWAVLQLGWR PGWFLDSPDR PWNPPTFSPA LLVVTEGDNA TFTCSFSNTS



 


61
ESFVLNWYRM SPSNQTDKLA AFPEDRSQPG QDCRFRVTQL PNGRDFHMSV VRARRNDSGT


 


121
YLCGAISLAP KAQIKESLRA ELRVTERRAE VPTAHPSPSP RPAGQFQTLV VGWGGLLGS


 


181
LVLLVWVLAV ICSRAARGTI GARRTGQPLK EDPSAVPVFS VDYGELDFQW REKTPEPPVP


 


241
CVPEQTEYAT IVFPSGMGTS SPARRGSADG PRSAQPLRPE DGHCSWPL  


 








(NP_005009.2; SEQ ID NO:13)







In one embodiment, the invention provides an inhibitor of a cell-mediated immune response that is a PD-1 dominant negative form (DN form). In one embodiment, the PD-1 DN form comprises the extracellular ligand binding domain of PD-1. In one embodiment, the PD-1 DN form comprises the extracellular ligand binding domain of PD-1 and a transmembrane domain (e.g., mature form). In another embodiment, the PD-1 DN form comprises the extracellular ligand binding domain of PD-1, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the PD-1 DN forms of the invention. In a particular embodiment, the PD-1 extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the PD-1 DN form is a chimeric sequence. For example, the PD-1 extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a PD-1 DN form can comprise a transmembrane domain that is optionally a heterologous transmembrane domain, including any of various transmembrane domains described herein. Although the PD-1 DN form exemplified in the Example herein comprises heterologous sequences fused to the extracellular domain of PD-1, it is understood that a PD-1 DN form can comprise PD-1 sequence only.
In one embodiment, the invention provides a PD-1 DN form that comprises the extracellular domain, or a ligand binding portion thereof, of PD-1, for example, amino acids 21 to 170 corresponding to the extracellular domain of PD-1 (GenBank NP_005009.2; SEQ ID NO:13). A cell expressing such a PD-1 DN form should lack the ability or have reduced ability to signal in a PD-1 immune checkpoint pathway. In one embodiment, a PD-1 DN form is a deletion mutant having a deletion of the intracellular domain, for example, amino acids 192 to 288 of PD-1 (GenBank NP_005009.2; SEQ ID NO:13), or a portion thereof, such that intracellular signaling of the immune checkpoint pathway mediated by PD-1 is reduced or inhibited. Additional embodiments of a DN form of PD-1 are described below.
In one embodiment, a PD-1 DN form comprises an amino acid sequence comprising the extracellular domain of PD-1 fused to the transmembrane and hinge domains of CD8. In one embodiment, a PD-1 DN form comprises amino acids 21 to 165 of a PD-1 sequence (NP_005009.2; SEQ ID NO:13). Such a PD-1 DN form comprises the extracellular domain of PD-1. In another embodiment, the invention provides a PD-1 DN form comprising amino acids 1 to 165 (precursor form) or amino acids 21 to 165 (mature form) of a PD-1 sequence (NP_005009.2; SEQ ID NO:13). Such a DN form comprises the signal peptide of PD-1, amino acids 1 to 20, and extracellular domain amino acids 21 to 165, whereas the mature form lacks the signal peptide. In one embodiment, a PD-1 DN form comprises amino acids 21 to 151 of a PD-1 sequence (NP_005009.2; SEQ ID NO:13). In another embodiment, the invention provides a PD-1 DN form comprising amino acids 1 to 151 (precursor form) or amino acids 21 to 151 (mature form) of a PD-1 sequence (NP_005009.2; SEQ ID NO:13). Optionally, a PD-1 DN form comprises an extracellular ligand binding domain starting at amino acid 21 through an amino acid between amino acids 151 to 165 of a PD-1 sequence (NP_005009.2; SEQ ID NO:13). In another embodiment, a PD-1 DN form comprises the transmembrane domain of CD8, amino acids 183 to 203 of a CD8 sequence (NP_001139345.1; SEQ ID NO:11). Such an embodiment is representative of a chimeric DN form comprising a transmembrane domain from a different (heterologous) polypeptide. As described above, a DN form comprising a heterologous domain such as a transmembrane domain can optionally include additional sequence from the heterologous polypeptide. In one such embodiment, a DN form is provided that comprises additional sequence from the heterologous polypeptide N-terminal of the transmembrane domain. In one embodiment, the DN form comprises the hinge domain of CD8. In a particular embodiment, the heterologous sequence comprises additional N-terminal sequence of amino acids 137 to 182, or optionally starting at amino acids 138 or 139, of a CD8 sequence (NP_001139345.1; SEQ ID NO:11). In another embodiment, a DN form is provided that comprises additional sequence from the heterologous polypeptide C-terminal of the transmembrane domain. In a particular embodiment, the heterologous sequence comprises additional C-terminal sequence from amino acids 204 to 209 of a CD8 sequence (NP_001139345.1; SEQ ID NO:11). In one embodiment, the PD-1 DN form comprises the transmembrane domain of CD8, amino acids 183 to 203, optionally a hinge domain comprising amino acids 137 to 182 (or optionally starting at amino acids 138 or 139), and/or additional C-terminal sequence comprising amino acids 204 to 209. In a particular embodiment of the invention, a PD-1 DN form is provided that comprises amino acids 1 to 165 of a PD-1 sequence (NP_005009.2; SEQ ID NO:13), and amino acids 137 to 209, optionally starting at amino acids 138 or 139, of a CD8 sequence (NP_001139345.1; SEQ ID NO:11).
In a further particular embodiment, the invention provides a PD-1 DN form comprising the sequence provided below, where the underlined sequence is derived from PD-1 and the italicized sequence is derived from CD8.







(SEQ ID NO:14)


MQIPQAPWPVVWAVLQLGWRPGWFLDSPDRPWNPPTFSPALLVVTEGDN


 


ATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVT


 


QLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTER


 


RAEVPTAHPSPSPRPAGQAAAPTTTPAPRPPTPAPTIASQPLSLRPEAC


 


RPAAGGAVHTRGLDFACDIYIWAPLAGTCGVLLLSLVITLYCNHRRIQ






In an additional embodiment, a DN form of the invention optionally comprises a P2A sequence, which provides for optional co-expression of a reporter molecule. P2A is a self-cleaving peptide sequence, which can be used for bicistronic or multicistronic expression of protein sequences (see Szymczak et al., Expert Opin. Biol. Therapy 5(5):627-638 (2005)). An exemplary P2A sequence is GSGATNFSLLKQAGDVEENPGPM (SEQ ID NO:15). In a further embodiment, a DN form of the invention is co-expressed with a reporter protein. In a particular embodiment, the reporter protein is mCherry fluorescent protein. In a particular embodiment, the mCherry polypeptide sequence is as provided below. It is understood that mCherry is merely exemplary and that any desired reporter molecule, such as a fluorescent protein can be included as a reporter, as described herein.







(SEQ ID NO:16)


MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTA


 


KLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKW


 


ERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMG


 


WEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPG


 


AYNVNIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK 






In a further particular embodiment, a PD-1 DN form is expressed as a polypeptide construct as provided below, where the underlined sequence is derived from PD-1, the italicized sequence is derived from CD8, the P2A sequence is double underlined, and the mCherry sequence is underlined and italicized.







(SEQ ID NO:17)


MQIPQAPWPVVWAVLQLGWRPGWFLDSPDRPWNPPTFSPALLVVTEGDN


 


ATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVT


 


QLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTER


 


RAEVPTAHPSPSPRPAGQAAAPTTTPAPRPPTPAPTIASQPLSLRPEAC


 


RPAAGGAVHTRGLDFACDIYIWAPLAGTCGVLLLSLVITLYCNHRRIQG


 


SGATNFSLLKQAGDVEENPGPMVSKGEEDNMAIIKEFMRFKVHMEGSVN


 


GHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAY


 


VKHPADIPDYLKLSFPEGFKWERVMNFEDGGWTVTQDSSLQDGEFIYKV


 


KLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGG


 


HYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGR 


 


HSTGGMDELYK






In a particular embodiment, a nucleic acid encoding a PD-1 DNR form construct is provided below, where the underlined sequence encodes amino acids derived from PD-1 DN, the italicized sequence encodes amino acids derived from CD8, the P2A encoding sequence is double underlined, the mCherry encoding sequence is underlined and italicized, a Kozak sequence is bolded with a dashed underline, and restriction sites Age I and Xho I are underlined with a dotted line at the 5′ and 3′ ends, respectively.








(SEQ ID NO: 18)



 GGTACCTCACCCTTACCGAGTCGGCGACACAGTGTGGGTCCGCCGACACC



 


AGACTAAGAACCTAGAACCTCGCTGGAAAGGACCTTACACAGTCCTGCTGACCACC


 


CCCACCGCCCTCAAAGTAGACGGCATCGCAGCTTGGATACACGCCGCCCACGTGAA


 


GGCTGCCGACCCCGGGGGTGGACCATCCTCTAGACTG ATGCAGATCCCAC


 


AGGCGCCCTGGCCAGTCGTCTGGGCGGTGCTACAACTGGGCTGGCGGCCAGGATGG


 


TTCTTAGACTCCCCAGACAGGCCCTGGAACCCCCCCACCTTCTCCCCAGCCCTGCTC


 


GTGGTGACCGAAGGGGACAACGCCACCTTCACCTGCAGCTTCTCCAACACATCGGA


 


GAGCTTCGTGCTAAACTGGTACCGCATGAGCCCCAGCAACCAGACGGACAAGCTGG


 


CCGCTTTCCCCGAGGACCGCAGCCAGCCCGGCCAGGACTGCCGCTTCCGTGTCACAC


 


AACTGCCCAACGGGCGTGACTTCCACATGAGCGTGGTCAGGGCCCGGCGCAATGAC


 


AGCGGCACCTACCTCTGTGGGGCCATCTCCCTGGCCCCCAAGGCGCAGATCAAAGA


 


GAGCCTGCGGGCAGAGCTCAGGGTGACAGAGAGAAGGGCAGAAGTGCCCACAGCC


 


CACCCCAGCCCCTCACCCAGGCCAGCCGGCCAGGCGGCCGCACCCACCACGACGCCA


 


GCGCCGCGACCACCAACCCCGGCGCCCACGATCGCGTCGCAGCCCCTGTCCCTGCGCC


 


CAGAGGCGTGCCGGCCAGCGGCGGGGGGCGCAGTGCACACGAGGGGGCTGGACTTCG


 


CCTGTGATATCTACATCTGGGCGCCCCTGGCCGGGACTTGTGGGGTCCTTCTCCTGTCAC


 


TGGTTATCACCCTTTACTGCAACCACAGGCGGATCCAAGGATCTGGAGCAACAAACTT


 


CTCACTACTCAAACAAGCAGGTGACGTGGAGGAGAATCCCGGCCCCATGGTGAGCAA


 


GGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGA


 


GGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTAC


 


GAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCT


 


GGGACATCCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCC


 


GACATCCCCGACTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATG


 


AACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCG


 


AGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGC


 


AGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGC


 


CCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCT


 


GAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGT


 


CAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGA


 


ACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAGTAA 






CTLA-4. Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) is an inhibitory receptor expressed by activated T cells, which when engaged by its corresponding ligands (CD80 and CD86; B7-1 and B7-2, respectively), mediates activated T cell inhibition or anergy. In both preclinical and clinical studies, CTLA-4 blockade by systemic antibody infusion enhanced the endogenous anti-tumor response albeit, in the clinical setting, with significant unforeseen toxicities. CTLA-4 contains an extracellular V domain, a transmembrane domain, and a cytoplasmic tail. Alternate splice variants, encoding different isoforms, have been characterized. The membrane-bound isoform functions as a homodimer interconnected by a disulfide bond, while the soluble isoform functions as a monomer. The intracellular domain is similar to that of CD28, in that it has no intrinsic catalytic activity and contains one YVKM (SEQ ID NO:29) motif able to bind PI3K, PP2A and SHP-2 and one proline-rich motif able to bind SH3 containing proteins. One role of CTLA-4 in inhibiting T cell responses seems to be directly via SHP-2 and PP2A dephosphorylation of TCR-proximal signaling proteins such as CD3 and LAT. CTLA-4 can also affect signaling indirectly via competing with CD28 for CD80/86 binding. CTLA-4 has also been shown to bind and/or interact with PI3K, CD80, AP2M1, and PPP2R5A.
A CTLA-4 polypeptide can have an amino acid sequence corresponding to GenBank No. AAH69566.1 (GI:46854814) or NP_005205.2 (GI:21361212), sequence as provided below, or fragments thereof. See GenBank NP_005205.2 for reference to domains within CTLA-4, for example, signal peptide, amino acids 1 to 35; extracellular domain, amino acids 36 to 161; transmembrane domain, amino acids 162 to 182; intracellular domain, amino acids 183 to 223. It is understood that a “CTLA-4 nucleic acid molecule” refers to a polynucleotide encoding a CTLA-4 polypeptide.









1
MACLGFQRHK AQLNLATRTW PCTLLFFLLF IPVFCKAMHV AQPAVVLASS RGIASFVCEY



 


61
ASPGKATEVR VTVLRQADSQ VTEVCAATYM MGNELTFLDD SICTGTSSGN QVNLTIQGLR


 


121
AMDTGLYICK VELMYPPPYY LGIGNGTQIY VIDPEPCPDS DFLLWILAAV SSGLFFYSFL


 


181
LTAVSLSKML KKRSPLTTGV YVKMPPTEPE CEKQFQPYFI PIN  


 








(NP_005205.2; SEQ ID NO:19)







In one embodiment, the invention provides a CTLA-4 DN form. In one embodiment, the CTLA-4 DN form comprises the extracellular ligand binding domain of CTLA-4. In one embodiment, the CTLA-4 DN form comprises the extracellular ligand binding domain of CTLA-4 and a transmembrane domain (e.g., mature form). In another embodiment, the CTLA-4 DN form comprises the extracellular ligand binding domain of CTLA-4, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the CTLA-4 DN forms of the invention. In a particular embodiment, the CTLA-4 extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the CTLA-4 DN form is chimeric. For example, the CTLA-4 extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a CTLA-4 DN form can comprise a transmembrane domain that is optionally a heterologous transmembrane domain, including any of various transmembrane domains described herein.
In an embodiment of the invention, the CTLA-4 DN form can comprise the extracellular domain, or a ligand binding portion thereof, of CTLA-4, for example, amino acids 36 to 161 corresponding to the extracellular domain of CTLA-4 (GenBank NP_005205.2; SEQ ID NO:19). A cell expressing such a CTLA-4 DN form should lack the ability or have reduced ability to signal in a CTLA-4 immune checkpoint pathway. In one embodiment, a CTLA-4 DN form is a deletion mutant having a deletion of the intracellular domain, for example, amino acids 183 to 223 of CTLA-4 (GenBank NP_005205.2; SEQ ID NO:19), or a portion thereof, such that intracellular signaling of the immune checkpoint pathway mediated by CTLA-4 is reduced or inhibited.
BTLA. B- and T-lymphocyte attenuator (BTLA) expression is induced during activation of T cells, and BTLA remains expressed on Th1 cells but not Th2 cells. BTLA interacts with a B7 homolog, B7H4. BTLA displays T-Cell inhibition via interaction with tumor necrosis family receptors (TNF-R), not just the B7 family of cell surface receptors. BTLA is a ligand for tumor necrosis factor (receptor) superfamily, member 14 (TNFRSF14), also known as herpes virus entry mediator (HVEM). BTLA-HVEM complexes negatively regulate T-cell immune responses. BTLA activation has been shown to inhibit the function of human CD8+ cancer-specific T cells. BTLA has also been designated as CD272 (cluster of differentiation 272).
A BTLA polypeptide can have an amino acid sequence corresponding to GenBank No. AAP44003.1 (GI:31880027) or NP_861445.3 (GI:145580621), sequence provided below, or fragments thereof. See GenBank NP_861445.3 for reference to domains within BTLA, for example, signal peptide, amino acids 1 to 30; extracellular domain, amino acids 31 to 157; transmembrane domain, amino acids 158 to 178; intracellular domain, amino acids 179 to 289. It is understood that a “BTLA nucleic acid molecule” refers to a polynucleotide encoding a BTLA polypeptide.









1
MKTLPAMLGT GKLFWVFFLI PYLDIWNIHG KESCDVQLYI KRQSEHSILA GDPFELECPV



 


61
KYCANRPHVT WCKLNGTTCV KLEDRQTSWK EEKNISFFIL HFEPVLPNDN GSYRCSANFQ


 


121
SNLIESHSTT LYVTDVKSAS ERPSKDEMAS RPWLLYSLLP LGGLPLLITT CFCLFCCLRR


 


181
HQGKQNELSD TAGREINLVD AHLKSEQTEA STRQNSQVLL SETGIYDNDP DLCFRMQEGS


 


241
EVYSNPCLEE NKPGIVYASL NHSVIGPNSR LARNVKEAPT EYASICVRS 


 








(NP_861445.3; SEQ ID NO:20)







In one embodiment, the invention provides a BTLA DN form. In one embodiment, the BTLA DN form comprises the extracellular ligand binding domain of BTLA. In one embodiment, the BTLA DN form comprises the extracellular ligand binding domain of BTLA and a transmembrane domain (e.g., mature form). In another embodiment, the BTLA DN form comprises the extracellular ligand binding domain of BTLA, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the BTLA DN forms of the invention. In a particular embodiment, the BTLA extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the BTLA DN form is chimeric. For example, the BTLA extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a BTLA DN form can comprise a transmembrane domain that is optionally a heterologous transmembrane domain, including any of various transmembrane domains described herein.
In an embodiment of the invention, the BTLA DN form can comprise the extracellular domain, or a ligand binding portion thereof, of BTLA, for example, amino acids 31 to 157 corresponding to the extracellular domain of BTLA (GenBank NP_861445.3; SEQ ID NO:20). A cell expressing such a BTLA DN form should lack the ability or have reduced ability to signal in a BTLA immune checkpoint pathway. In one embodiment, a BTLA DN form is a deletion mutant having a deletion of the intracellular domain, for example, amino acids 179 to 289 of BTLA (GenBank NP_861445.3; SEQ ID NO:20), or a portion thereof, such that intracellular signaling of the immune checkpoint pathway mediated by BTLA is reduced or inhibited.
TIM-3. T cell immunoglobulin mucin-3 (TIM-3), also referred to as hepatitis A virus cellular receptor 2 precursor, is a Th1-specific cell surface protein that regulates macrophage activation. Tim-3 was first identified as a molecule selectively expressed on IFN-γ-producing CD4+ T helper 1 (Th1) and CD8+ T cytotoxic 1 (Tc1) T cells. TIM-3 possess an N-terminal Ig domain of the V type, followed by a mucin domain.
A TIM-3 polypeptide can have an amino acid sequence corresponding to GenBank No. NP_116171.3 (GI:49574534), sequence provided below, or fragments thereof. See GenBank NP_116171.3 for reference to domains within TIM-3, for example, signal peptide, amino acids 1 to 21; extracellular domain, amino acids 22 to 202; transmembrane domain, amino acids 203 to 223; intracellular domain, amino acids 224 to 301. It is understood that a “TIM-3 nucleic acid molecule” refers to a polynucleotide encoding a TIM-3 polypeptide.









1
MFSHLPFDCV LLLLLLLLTR SSEVEYRAEV GQNAYLPCFY TPAAPGNLVP VCWGKGACPV



 


61
FECGNVVLRT DERDVNYWTS RYWLNGDFRK GDVSLTIENV TLADSGIYCC RIQIPGIMND


 


121
EKFNLKLVIK PAKVTPAPTR QRDFTAAFPR MLTTRGHGPA ETQTLGSLPD INLTQISTLA


 


181
NELRDSRLAN DLRDSGATIR IGIYIGAGIC AGLALALIFG ALIFKWYSHS KEKIQNLSLI


 


241
SLANLPPSGL ANAVAEGIRS EENIYTIEEN VYEVEEPNEY YCYVSSRQQP SQPLGCRFAM


 


301
P (NP_116171.3; SEQ ID NO:21)






In one embodiment, the invention provides a TIM-3 DN form. In one embodiment, the TIM-3 DN form comprises the extracellular ligand binding domain of TIM-3. In one embodiment, the TIM-3 DN form comprises the extracellular ligand binding domain of TIM-3 and a transmembrane domain (e.g., mature form). In another embodiment, the TIM-3 DN form comprises the extracellular ligand binding domain of TIM-3, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the TIM-3 DN forms of the invention. In a particular embodiment, the TIM-3 extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the TIM-3 DN form is chimeric. For example, the TIM-3 extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a TIM-3 DN form can comprise a transmembrane domain that is optionally a heterologous transmembrane domain, including any of various transmembrane domains described herein.
In an embodiment of the invention, the TIM-3 DN form can comprise the extracellular domain, or a ligand binding portion thereof, of TIM-3, for example, amino acids 22 to 202 corresponding to the extracellular domain of TIM-3 (GenBank NP_116171.3; SEQ ID NO:21). A cell expressing such a TIM-3 DN form should lack the ability or have reduced ability to signal in a TIM-3 immune checkpoint pathway. In one embodiment, a TIM-3 DN form is a deletion mutant having a deletion of the intracellular domain, for example, amino acids 224 to 301 of TIM-3 (GenBank NP_116171.3; SEQ ID NO:21), or a portion thereof, such that intracellular signaling of the immune checkpoint pathway mediated by TIM-3 is reduced or inhibited.
LAG-3. Lymphocyte-activation protein 3 (LAG-3) is a negative immune regulator of immune cells. LAG-3 belongs to the immunoglobulin (Ig) superfamily and contains 4 extracellular Ig-like domains. The LAG3 gene contains 8 exons. The sequence data, exon/intron organization, and chromosomal localization all indicate a close relationship of LAG-3 to CD4. LAG-3 has also been designated CD223 (cluster of differentiation 223).
A LAG-3 polypeptide can have an amino acid sequence corresponding to GenBank No. CAA36243.3 (GI:15617341) or NP_002277.4 (GI:167614500), sequence provided below, or fragments thereof. See GenBank NP_002277.4 for reference to domains within LAG-3, for example, signal peptide, amino acids 1 to 22; extracellular domain, amino acids 23 to 450; transmembrane domain, amino acids 451 to 471; intracellular domain, amino acids 472 to 525. It is understood that a “LAG-3 nucleic acid molecule” refers to a polynucleotide encoding a LAG-3 polypeptide.









1
MWEAQFLGLL FLQPLWVAPV KPLQPGAEVP VVWAQEGAPA QLPCSPTIPL QDLSLLRRAG



 


61
VTWQHQPDSG PPAAAPGHPL APGPHPAAPS SWGPRPRRYT VLSVGPGGLR SGRLPLQPRV


 


121
QLDERGRQRG DFSLWLRPAR RADAGEYRAA VHLRDRALSC RLRLRLGQAS MTASPPGSLR


 


181
ASDWVILNCS FSRPDRPASV HWFRNRGQGR VPVRESPHHH LAESFLFLPQ VSPMDSGPWG


 


241
CILTYRDGFN VSIMYNLTVL GLEPPTPLTV YAGAGSRVGL PCRLPAGVGT RSFLTAKWTP


 


301
PGGGPDLLVT GDNGDFTLRL EDVSQAQAGT YTCHIHLQEQ QLNATVTLAI ITVTPKSFGS


 


361
PGSLGKLLCE VTPVSGQERF VWSSLDTPSQ RSFSGPWLEA QEAQLLSQPW QCQLYQGERL


 


421
LGAAVYFTEL SSPGAQRSGR APGALPAGHL LLFLILGVLS LLLLVTGAFG FHLWRRQWRP


 


481
RRFSALEQGI HPPQAQSKIE ELEQEPEPEP EPEPEPEPEP EPEQL  


 








(NP_302277.4; SEQ ID NO: 22)







In one embodiment, the invention provides a LAG-3 DN form. In one embodiment, the LAG-3 DN form comprises the extracellular ligand binding domain of LAG-3. In one embodiment, the LAG-3 DN form comprises the extracellular ligand binding domain of LAG-3 and a transmembrane domain (e.g., mature form). In another embodiment, the LAG-3 DN form comprises the extracellular ligand binding domain of LAG-3, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the LAG-3 DN forms of the invention. In a particular embodiment, the LAG-3 extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the LAG-3 DN form is chimeric. For example, the LAG-3 extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a LAG-3 DN form can comprise a transmembrane domain that is optionally a heterologous transmembrane domain, including any of various transmembrane domains described herein.
In an embodiment of the invention, the LAG-3 DN form can comprise the extracellular domain, or a ligand binding portion thereof, of LAG-3, for example, amino acids 23 to 450 corresponding to the extracellular domain of LAG-3 (GenBank NP_002277.4; SEQ ID NO:22). A cell expressing such a LAG-3 DN form should lack the ability or have reduced ability to signal in a LAG-3 immune checkpoint pathway. In one embodiment, a LAG-3 DN form is a deletion mutant having a deletion of the intracellular domain, for example, amino acids 472 to 525 of LAG-3 (GenBank NP_002277.4; SEQ ID NO:22), or a portion thereof, such that intracellular signaling of the immune checkpoint pathway mediated by LAG-3 is reduced or inhibited.
TIGIT. T-cell immunoreceptor with Ig and ITIM domains (TIGIT) is a cell surface protein that suppresses T-cell activation. It belongs to the poliovirus receptor (PVR) family of immunoglobulin (Ig) proteins that share 3 conserved sequence motifs in their N-terminal Ig domains. A TIGIT polypeptide can have an amino acid sequence corresponding to GenBank No. NP_776160.2 (GI:256600228), sequence provided below, or fragments thereof. See GenBank NP_776160.2 for reference to domains within TIGIT, for example, signal peptide, amino acids 1 to 21; extracellular domain, amino acids 22 to 141; transmembrane domain, amino acids 142 to 162; intracellular domain, amino acids 163 to 244. It is understood that a “TIGIT nucleic acid molecule” refers to a polynucleotide encoding a TIGIT polypeptide.









1
MRWCLLLIWA QGLRQAPLAS GMMTGTIETT GNISAEKGGS IILQCHLSST TAQVTQVNWE



 


61
QQDQLLAICN ADLGWHISPS FKDRVAPGPG LGLTLQSLTV NDTGEYFGIY HTYPDGTYTG


 


121
RIFLEVLESS VAEHGARFQI PLLGAMAATL VVICTAVIVV VALTRKKKAL RIHSVEGDLR


 


181
RKSAGQEEWS PSAPSPPGSC VQAEAAPAGL CGEQRGEDCA ELHDYFNVLS YRSLGNCSFF


 


241
TETG (NP_776160.2; SEQ ID NO:23)






In one embodiment, the invention provides a TIGIT DN form. In one embodiment, the TIGIT DN form comprises the extracellular ligand binding domain of TIGIT. In one embodiment, the TIGIT DN form comprises the extracellular ligand binding domain of TIGIT and a transmembrane domain (e.g., mature form). In another embodiment, the TIGIT DN form comprises the extracellular ligand binding domain of TIGIT, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the TIGIT DN forms of the invention. In a particular embodiment, the TIGIT extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the TIGIT DN form is chimeric. For example, the TIGIT extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a TIGIT DN form can comprise a transmembrane domain that is optionally a heterologous transmembrane domain, including any of various transmembrane domains described herein.
In an embodiment of the invention, the TIGIT DN form can comprise the extracellular domain, or a ligand binding portion thereof, of TIGIT, for example, amino acids 22 to 141 corresponding to the extracellular domain of TIGIT (GenBank NP_776160.2; SEQ ID NO:23). A cell expressing such a TIGIT DN form should lack the ability or have reduced ability to signal in a TIGIT immune checkpoint pathway. In one embodiment, a TIGIT DN form is a deletion mutant having a deletion of the intracellular domain, for example, amino acids 163 to 244 of TIGIT (GenBank NP_776160.2; SEQ ID NO:23), or a portion thereof, such that intracellular signaling of the immune checkpoint pathway mediated by TIGIT is reduced or inhibited.
LAIR1. Leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is an inhibitory receptor that plays a constitutive negative regulatory role on cytolytic function of natural killer (NK) cells, B-cells and T-cells. LAIR exists in various isoforms. It is understood that any isoform can be selected to achieve a desired function. Exemplary isoforms include isoform a (NP_002278.2, GI:612407859), isoform b (NP_068352.2, GI:612407861), isoform c (NP_001275952.2, GI:612407867), isoform e (NP_001275954.2, GI:612407869), isoform f (NP_001275955.2, GI:612407863), isoform g (NP_001275956.2, GI:612407865), and the like. One exemplary isoform sequence, isoform a, is provided below. In one embodiment, a LAIR1 polypeptide can have an amino acid sequence corresponding to NP_002278.2, sequence provided below, or fragments thereof. See GenBank NP_002278.2 for reference to domains within LAIR1, for example, signal peptide, amino acids 1 to 21; extracellular domain, amino acids 22 to 165; transmembrane domain, amino acids 166 to 186; intracellular domain, amino acids 187 to 287. It is understood that a “LAIR1 nucleic acid molecule” refers to a polynucleotide encoding a LAIR1 polypeptide.









1
MSPHPTALLG LVLCLAQTIH TQEEDLPRPS ISAEPGTVIP LGSHVTFVCR GPVGVQTFRL



 


61
ERDSRSTYND TEDVSQASPS ESEARFRIDS VREGNAGLYR CIYYKPPKWS EQSDYLELLV


 


121
KESSGGPDSP DTEPGSSAGP TQRPSDNSHN EHAPASQGLK AEHLYILIGV SVVFLFCLLL


 


181
LVLFCLHRQN QIKQGPPRSK DEEQKPQQRP DLAVDVLERT ADKATVNGLP EKDRETDTSA


 


241
LAAGSSQEVT YAQLDHWALT QRTARAVSPQ STKPMAESIT YAAVARH (NP_002278.2; 


 








SEQ ID NO:24)







In one embodiment, the invention provides a LAIR1 DN form. In one embodiment, the LAIR1 DN form comprises the extracellular ligand binding domain of LAIR1. In one embodiment, the LAIR1 DN form comprises the extracellular ligand binding domain of LAIR1 and a transmembrane domain (e.g., mature form). In another embodiment, the LAIR1 DN form comprises the extracellular ligand binding domain of LAIR1, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the LAIR1 DN forms of the invention. In a particular embodiment, the LAIR1 extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the LAIR1 DN form is chimeric. For example, the LAIR1 extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a LAIR1 DN form can comprise a transmembrane domain that is optionally a heterologous transmembrane domain, including any of various transmembrane domains described herein.
In an embodiment of the invention, the LAIR1 DN form can comprise the extracellular domain, or a ligand binding portion thereof, of LAIR1, for example, amino acids 22 to 165 corresponding to the extracellular domain of LAIR1 (GenBank NP_002278.2; SEQ ID NO:24). A cell expressing such a LAIR1 DN form should lack the ability or have reduced ability to signal in a LAIR1 immune checkpoint pathway. In one embodiment, a LAIR1 DN form is a deletion mutant having a deletion of the intracellular domain, for example, amino acids 187 to 287 of LAIR1 (GenBank NP_002278.2; SEQ ID NO:24), or a portion thereof, such that intracellular signaling of the immune checkpoint pathway mediated by LAIR1 is reduced or inhibited.
2B4. Natural Killer Cell Receptor 2B4 (2B4) mediates non-MHC restricted cell killing on NK cells and subsets of T cells. The 2B4-S isoform is believed to be an activating receptor, and the 2B4-L isoform is believed to be a negative immune regulator of immune cells. 2B4 becomes engaged upon binding its high-affinity ligand, CD48. 2B4 contains a tyrosine-based switch motif, a molecular switch that allows the protein to associate with various phosphatases. 2B4 has also been designated CD244 (cluster of differentiation 244).
A 2B4 polypeptide can have an amino acid sequence corresponding to GenBank No. NP_001160135.1 (GI:262263435), sequence provided below, or fragments thereof. See GenBank NP_001160135.1 for reference to domains within 2B4, for example, signal peptide, amino acids 1 to 18; extracellular domain, amino acids 19 to 229; transmembrane domain, amino acids 230 to 250; intracellular domain, amino acids 251 to 370. It is understood that a “2B4 nucleic acid molecule” refers to a polynucleotide encoding a 2B4 polypeptide.









1
MLGQVVTLIL LLLLKVYQGK GCQGSADHVV SISGVPLQLQ PNSIQTKVDS IAWKKLLPSQ



 


61
NGFHHILKWE NGSLPSNTSN DRFSFIVKNL SLLIKAAQQQ DSGLYCLEVT SISGKVQTAT


 


121
FQVFVFESLL PDKVEKPRLQ GQGKILDRGR CQVALSCLVS RDGNVSYAWY RGSKLIQTAG


 


181
NLTYLDEEVD INGTHTYTCN VSNPVSWESH TLNLTQDCQN AHQEFRFWPF LVIIVILSAL


 


241
FLGTLACFCV WRRKRKEKQS ETSPKEFLTI YEDVKDLKTR RNHEQEQTFP GGGSTIYSMI


 


301
QSQSSAPTSQ EPAYTLYSLI QPSRKSGSRK RNHSPSFNST IYEVIGKSQP KAQNPARLSR


 


361
KELENFDVYS (NP_001160135.1; SEQ ID NO:25) 






In one embodiment, the invention provides a 2B4 DN form. In one embodiment, the 2B4 DN form comprises the extracellular ligand binding domain of 2B4. In one embodiment, the 2B4 DN form comprises the extracellular ligand binding domain of 2B4 and a transmembrane domain (e.g., mature form). In another embodiment, the 2B4 DN form comprises the extracellular ligand binding domain of 2B4, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the 2B4 DN forms of the invention. In a particular embodiment, the 2B4 extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the 2B4 DN form is chimeric. For example, the 2B4 extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a 2B4 DN form can comprise a transmembrane domain that is optionally a heterologous transmembrane domain, including any of various transmembrane domains described herein.
In an embodiment of the invention, the 2B4 DN form can comprise the extracellular domain, or a ligand binding portion thereof, of 2B4, for example, amino acids 19 to 229 corresponding to the extracellular domain of 2B4 (GenBank NP_001160135.1; SEQ ID NO:25). A cell expressing such a 2B4 DN form should lack the ability or have reduced ability to signal in a 2B4 immune checkpoint pathway. In one embodiment, a 2B4 DN form is a deletion mutant having a deletion of the intracellular domain, for example, amino acids 251 to 370 of 2B4 (GenBank NP_001160135.1; SEQ ID NO:25), or a portion thereof, such that intracellular signaling of the immune checkpoint pathway mediated by 2B4 is reduced or inhibited.
CD160. CD160 is a glycosylphosphatidylinositol-anchored molecule containing a single IgV-like domain that binds to HVEM and functions as a co-inhibitory receptor on T cells. A CD160 polypeptide can have an amino acid sequence corresponding to GenBank NP_008984.1 (GI:5901910), sequence provided below, or fragments thereof. See GenBank NP_008984.1 for reference to domains within CD160, for example, signal peptide, amino acids 1 to 26; extracellular domain, amino acids 27 to 159. It is understood that a “CD160 nucleic acid molecule” refers to a polynucleotide encoding a CD160 polypeptide.









1
MLLEPGRGCC ALAILLAIVD IQSGGCINIT SSASQEGTRL NLICTVWHKK EEAEGFVVFL



 


61
CKDRSGDCSP ETSLKQLRLK RDPGIDGVGE ISSQLMFTIS QVTPLHSGTY QCCARSQKSG


 


121
IRLQGHFFSI LFTETGNYTV TGLKQRQHLE FSHNEGTLSS GFLQEKVWVM LVTSLVALQA


 


181
L (NP_008984.1; SEQ ID NO:26)






In one embodiment, the invention provides a CD160 DN form. In one embodiment, the CD160 DN form comprises the extracellular ligand binding domain of CD160. In one embodiment, the CD160 DN form comprises the extracellular ligand binding domain of CD160 and a transmembrane domain (e.g., mature form). In another embodiment, the CD160 DN form comprises the extracellular ligand binding domain of CD160, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the CD160 DN forms of the invention. In a particular embodiment, the CD160 extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the CD160 DN form is chimeric. For example, the CD160 extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a CD160 DN form can comprise a transmembrane domain that is a heterologous transmembrane domain, including any of various transmembrane domains described herein.
In an embodiment of the invention, the CD160 DN form can comprise the extracellular domain, or a ligand binding portion thereof, of CD160, for example, amino acids 27 to 159 corresponding to the extracellular domain of CD160 (GenBank NP_008984.1; SEQ ID NO:26). A cell expressing such a CD160 DN form should lack the ability or have reduced ability to signal in an immune checkpoint pathway. In one embodiment, the CD160 DN form comprises the extracellular domain of CD160, or a ligand binding portion thereof, and a transmembrane domain derived from a heterologous polypeptide, including but not limited to one of the transmembrane domains described herein. In one non-limiting embodiment, the CD160 DN form comprises the transmembrane domain of CD8. In a cell expressing the CD160 DN form, intracellular signaling of the immune checkpoint pathway mediated by CD160 should be reduced or inhibited.
TGF-β Receptor Type 2. TGF-β receptor type 2 binds to TGF-β and a type I receptor dimer forming a heterotetrameric complex with the ligand. A TGF-β receptor type 2 polypeptide can have an amino acid sequence corresponding to GenBank No. NP_001020018.1 (GI:67782326), sequence provided below, or fragments thereof. See GenBank NP_001020018.1 for reference to domains within TGF-β receptor type 2, for example, signal peptide, amino acids 1 to 22; extracellular domain, amino acids 23 to 191; transmembrane domain, amino acids 192 to 212; intracellular domain, amino acids 213 to 592 (see also annotation in UniProtKB—P37173). It is understood that a “TGF-0 receptor type 2 nucleic acid molecule” refers to a polynucleotide encoding a TGF-β receptor type 2 polypeptide.









1
MGRGLLRGLW PLHIVLWTRI ASTIPPHVQK SDVEMEAQKD EIICPSCNRT AHPLRHINND



 


61
MIVTDNNGAV KFPQLCKFCD VRFSTCDNQK SCMSNCSITS ICEKPQEVCV AVWRKNDENI


 


121
TLETVCHDPK LPYHDFILED AASPKCIMKE KKKPGETFFM CSCSSDECND NIIFSEEYNT


 


181
SNPDLLLVIF QVTGISLLPP LGVAISVIII FYCYRVNRQQ KLSSTWETGK TRKLMEFSEH


 


241
CAIILEDDRS DISSTCANNI NHNTELLPIE LDTLVGKGRF AEVYKAKLKQ NTSEQFETVA


 


301
VKIFPYEEYA SWKTEKDIFS DINLKHENIL QFLTAEERKT ELGKQYWLIT AFHAKGNLQE


 


361
YLTRHVISWE DLRKLGSSLA RGIAHLHSDH TPCGRPKMPI VHRDLKSSNI LVKNDLTCCL


 


421
CDFGLSLRLD PTLSVDDLAN SGQVGTARYM APEVLESRMN LENVESFKQT DVYSMALVLW


 


481
EMTSRCNAVG EVKDYEPPFG SKVREHPCVE SMKDNVLRDR GRPEIPSFWL NHQGIQMVCE


 


541
TLTECWDHDP EARLTAQCVA ERFSELEHLD RLSGRSCSEE KIPEDGSLNT TK


 








(NP_001020018.1 SEQ ID NO:27)







In one embodiment, the invention provides a TGFβ receptor DN form. In one embodiment, the TGFβ receptor DN form comprises the extracellular ligand binding domain of TGFβ receptor. In one embodiment, the TGFβ receptor DN form comprises the extracellular ligand binding domain of TGFβ receptor and a transmembrane domain (e.g., mature form). In another embodiment, the TGFβ receptor DN form comprises the extracellular ligand binding domain of TGFβ receptor, a transmembrane domain and a signal peptide (e.g., precursor form). The invention also provides encoding polypeptides and nucleic acids of the TGF-β receptor DN forms of the invention. In a particular embodiment, the TGFβ receptor extracellular ligand binding domain is fused to one or more heterologous polypeptide sequences, that is, the TGFβ receptor DN form is chimeric. For example, the TGFβ receptor extracellular ligand binding domain can be fused at its N-terminus to a signal peptide that is optionally a heterologous signal peptide, including various signal peptides described herein. In addition, a TGFβ receptor DN form can comprise a transmembrane domain that is a heterologous transmembrane domain, including any of various transmembrane domains described herein.
TGFβ receptor DN forms have been described previously (see, for example, Bottinger et al., EMBO J. 16:2621-2633 (1997), describing a DN form comprising TGFβ receptor extracellular and transmembrane domains; Foster et al., J. Immunother. 31:500-505 (2008); Bollard et al., Blood 99:3179-3187 (2002); Wieser et al., Mol. Cell. Biol. 13:7239-7247 (1993)). In an embodiment of the invention, the TGFβ receptor DN form can comprise the extracellular domain, or a ligand binding portion thereof, of TGFβ receptor, for example, amino acids 23 to 191 corresponding to the extracellular domain of TGFβ receptor (GenBank NP_001020018.1, SEQ ID NO:27). A cell expressing such a TGFβ receptor DN form lacks the ability or has reduced ability to signal in the cell. In one embodiment, a TGFβ receptor DN form is a deletion mutant having a deletion of the intracellular domain, for example, amino acids 213 to 592 of TGFβ receptor (GenBank NP_001020018.1, SEQ ID NO:27), or a portion thereof, such that intracellular signaling of mediated by TGFβ receptor is reduced or inhibited (see also Bottinger et al., EMBO J. 16:2621-2633 (1997); Foster et al., J. Immunother. 31:500-505 (2008); Bollard et al., Blood 99:3179-3187 (2002); Wieser et al., Mol. Cell. Biol. 13:7239-7247 (1993)).
It is understood that, optionally, a second DN form of an inhibitor of a cell-mediated immune response, such as an immune checkpoint inhibitor, can be expressed in a cell of the invention. In this case, it can be desirable to inhibit more than one cell-mediated immune response in the same cell. Thus, a cell can express two or more DN forms, each directed to a different inhibitor of a cell-mediated immune response, including those described above. For example, a DN form of PD-1 can be co-expressed in a cell with a DN form of TGF-β receptor, a DN form of PD-1 can be co-expressed with a DN form of CTLA-4, a CTLA-4 DN form can be co-expressed with a DN form of TGF-β, and so forth, as desired, including combinations of any of the DN forms described above.
In a specific embodiment, a nucleic acid encoding a DN form is used to transduce both CD4+ and CD8+ T cells. In such an embodiment, administration of the transduced T cells to a subject should generate both helper and cytotoxic T lymphocyte (CTL) responses in the subject, resulting in a sustained anti-viral response.
7.4. Methods of Treatment
The invention also relates to methods of treating a viral infection using the cells of the invention or pharmaceutical compositions comprising the cells and a pharmaceutically acceptable carrier. In one embodiment, the methods can include administering an immune cell that is an immunostimulatory cell, or precursor cell thereof, expressing a viral antigen-binding CAR and a DN form of an inhibitor of a cell-mediated immune response. The viral antigen is chosen to target a viral infection in the subject. In another embodiment, the methods can include administering a viral-antigen specific immune cell, such as a T cell that recognizes and is sensitized to a viral antigen, where the cell recombinantly expresses a DN form of an inhibitor of a cell-mediated immune response (and may, but need not, express a viral antigen-binding CAR). In another embodiment, the methods can include administering an immune cell that is an immunoinhibitory cell, such as a regulatory T cell, in particular a regulatory T cell isolated from a subject having a chronic viral infection, where the cell recombinantly expresses a DN form of an inhibitor of a cell-mediated immune response.
The methods of the invention can be used to treat a viral infection. In a particular embodiment, the viral infection can be, but is not limited to, infection with HIV (e.g., HIV-1 and/or HIV-2), HBV or HCV. The methods of the invention can be used to treat persistent viral infections, such as latent infections, chronic infections or slow infections, for example, persistent viral infections with HIV, HBV or HCV.
Sustaining Activation of Viral-Specific Immunostimulatory Cells. In one embodiment, the invention provides methods of treating a viral infection comprising administering to a patient immune cells of the invention, in particular immunostimulatory cells, or precursor cells thereof, that are virus specific and that express a DN form of an inhibitor of a cell-mediated immune response. In one particular embodiment, the immunostimulatory cells are made virus specific by expressing a CAR that binds to a viral antigen. In one particular embodiment, the immunostimulatory cells that are virus specific are isolated from a subject having a viral infection. In a particular embodiment, the virus specific immunostimulatory cell is a T cell that recognizes and is sensitized to a viral antigen. In a particular embodiment, the T cell is a CD4+ T cell and/or a CD8+ T cell. In a particular embodiment, the inhibitor of a cell-mediated immune response is PD-1.
The methods can be used to treat a viral infection. Such viral infections include, but are not limited to, infection with HIV, HBV or HCV. The methods of the invention can be used to reduce or eliminate viral load or a persistent viral infection, such as a chronic, latent or slow viral infection, or to prevent or reduce the severity of relapse or recurrent viral infection.
Promoting Virus-Specific Memory Cells. In one embodiment, the invention provides methods of treating a viral infection comprising administering to a patient immune cells of the invention, in particular immunostimulatory cells, or precursor cells thereof, that are virus specific and that express a DN form of an inhibitor of a cell-mediated immune response. In such an embodiment, expression of the DN form can promote production of virus-specific memory cells. In one particular embodiment, the immunostimulatory cells are made virus specific by expressing a CAR that binds to a viral antigen. In one particular embodiment, the immunostimulatory cells that are virus specific are isolated from a subject having a viral infection. In a particular embodiment, the virus specific immunostimulatory cell is a T cell that recognizes and is sensitized to a viral antigen. In a particular embodiment, the T cell is a CD4+ T cell and/or a CD8+ T cell. In a particular embodiment, the inhibitor of a cell-mediated immune response is PD-1.
The methods can be used to treat a viral infection. Such viral infections include, but are not limited to, infection with HBV, HCV or HIV. The methods of the invention can be used to reduce or eliminate viral load or a persistent viral infection, such as a chronic, latent or slow viral infection, or to prevent or reduce the severity of relapse or recurrent viral infection, by promoting the production of virus-specific memory cells.
Inhibiting Immune Suppression Activity of Immunoinhibitory Cells. In one embodiment, the invention provides methods of treating a viral infection comprising administering to a patient immune cells that are immunoinhibitory cells, in particular regulatory T cells, and that express a DN form of an inhibitor of a cell-mediated immune response. In such an embodiment, regulatory T cells can be isolated from a subject, in particular a subject having a chronic viral infection. Expression of the DN form in the regulatory T cell can be used to inhibit the suppressive effect of the regulatory T cell upon immunostimulatory cells, in particular a suppressive effect associated with the expression of the inhibitor of a cell-mediated immune response by the regulatory T cell. In an embodiment, the inhibition of the suppressive effect promotes an immune response mediated by T cells, in particular CD8+ T cells. In a particular embodiment, the inhibitor of a cell-mediated immune response is PD-1. In a particular embodiment, the inhibition of the suppressive effect promotes an immune response mediated by T cells, in particular CD8+ T cells, that express PD-L1 and which are suppressed by PD-1-expressing regulatory T cells.
The methods can be used to treat a viral infection. Such viral infections include, but are not limited to, infection with HCV, HBV or HIV (e.g., HIV-1 and/or HIV-2). The methods of the invention can be used to reduce or eliminate viral load or a persistent viral infection, such as a chronic, latent or slow viral infection, or to prevent or reduce the severity of relapse or recurring viral infection. Without intending to be limited by mechanism, the methods inhibit immunosuppression by the regulatory T cells, where the suppression is mediated by an inhibitor of a cell-mediated immune response, e.g., PD-1. In a particular embodiment, regulatory T cells are harvested from a subject having a chronic viral infection, such as with HCV, HBV or HIV, and then genetically engineered to express the DN form. For example, the cells can be harvested from a subject in remission and not exhibiting signs or symptoms of acute infection. In a specific embodiment, the method can be used to treat a chronic infection and to prevent relapse into an active infection.
Dosages and Administration. In the methods of the invention, the immune cells of the invention are administered to a subject or patient in need of treatment. The subject or patient can be a mammal, in particular a human. Preferably, the subject or patient is a human. The human can be a child or an adult.
For treatment, the amount administered is an amount effective for producing the desired effect. An effective amount or therapeutically effective amount is an amount sufficient to provide a beneficial or desired clinical result upon treatment. An effective amount can be provided in a single administration or a series of administrations (one or more doses). An effective amount can be provided in a bolus or by continuous perfusion. In terms of treatment, an effective amount is an amount that is sufficient to palliate, ameliorate, stabilize, reverse or slow the progression of the disease, or otherwise reduce the pathological consequences of the disease. The effective amount can be determined by the physician for a particular subject. Several factors are typically taken into account when determining an appropriate dosage to achieve an effective amount. These factors include age, sex and weight of the subject, the condition being treated, the severity of the condition and the form and effective concentration of the cells of the invention being administered.
The cells of the invention are generally administered as a dose based on cells per kilogram (cells/kg) of body weight of the subject to which the cells are administered. Generally the cell doses are in the range of about 104 to about 1010 cells/kg of body weight, for example, about 105 to about 109, about 105 to about 108, about 105 to about 107, or about 105 to 106 cells/kg, depending on the mode and location of administration. In general, in the case of systemic administration, a higher dose is used than in regional administration, where the immune cells of the invention are administered in the region of a viral infection or virally infected cells or tissue. Exemplary dose ranges include, but are not limited to, 1×104 to 1×108, 2×104 to 1×108, 3×104 to 1×108, 4×104 to 1×108, 5×104 to 1×108, 6×104, to 1×108, 7×104 to 1×108, 8×104 to 1×108, 9×104 to 1×108, 1×105 to 1×108, for example, 1×105 to 9×107, 1×105 to 8×107, 1×105 to 7×107, 1×105 to 6×107, 1×105 to 5×107, 1×105 to 4×107, 1×105 to 3×107, 1×105 to 2×107, 1×105 to 1×107, 1×105 to 9×106, 1×105 to 8×106, 1×105 to 7×106, 1×105 to 6×106, 1×105 to 5×106, 1×105 to 4×106, 1×105 to 3×106, 1×105 to 2×106, 1×105 to 1×106, 2×105 to 9×107, 2×105 to 8×107, 2×105 to 7×107, 2×105 to 6×107, 2×105 to 5×107, 2×105 to 4×107, 2×105 to 3×107, 2×105 to 2×107, 2×105 to 1×107, 2×105 to 9×106, 2×105 to 8×106, 2×105 to 7×106, 2×105 to 6×106, 2×105 to 5×106, 2×105 to 4×106, 3×105 to 3×106 cells/kg, and the like. Such dose ranges can be particularly useful for regional administration. In a particular embodiment, cells are provided in a dose of 1×105 to 1×108, for example 1×105 to 1×107, 1×105 to 1×106, 1×106 to 1×108, 1×106 to 1×107, 1×107 to 1×108, 1×105 to 5×106, 1×105 to 3×106 or 3×105 to 3×106 cells/kg for regional administration. Exemplary dose ranges also can include, but are not limited to, 5×105 to 1×108, for example, 6×105 to 1×108, 7×105 to 1×108, 8×105 to 1×108, 9×105 to 1×108, 1×106 to 1×108, 1×106 to 9×107, 1×106 to 8×107, 1×106 to 7×107, 1×106 to 6×107, 1×106 to 5×107, 1×106 to 4×107, 1×106 to 3×107 cells/kg, and the like. Such does can be particularly useful for systemic administration. In a particular embodiment, cells are provided in a dose of 1×106 to 3×107 cells/kg for systemic administration. Exemplary cell doses include, but are not limited to, a dose of 1×104, 2×104, 3×104, 4×104, 5×104, 6×104, 7×104, 8×104, 9×104, 1×105, 2×105, 3×105, 4×105, 5×105, 6×105, 7×105, 8×105, 9×105, 1×106, 2×106, 3×106, 4×106, 5×106, 6×106, 7×106, 8×106, 9×106, 1×107, 2×107, 3×107, 4×107, 5×107, 6×107, 7×107, 8×107, 9×107, 1×108, 2×108, 3×108, 4×108, 5×108, 6×108, 7×108, 8×108, 9×108, 1×109 and so forth in the range of about 104 to about 1010 cells/kg. In addition, the dose can also be adjusted to account for whether a single dose is being administered or whether multiple doses are being administered. The precise determination of what would be considered an effective dose can be based on factors individual to each subject, including their size, age, sex, weight, and condition of the particular subject, as described above. Dosages can be readily determined by those skilled in the art based on the disclosure herein and knowledge in the art.
In a specific embodiment, the dosage for human administration is in the range of 1×105 to 1×108 cells/kg body weight of the human.
The cells of the invention can be administered by any methods known in the art, including, but not limited to, pleural administration, intravenous administration, subcutaneous administration, intranodal administration, intrahepatic administration, intrathecal administration, intrapleural administration, intraperitoneal administration, intracranial administration, intratracheal administration, intraarticular administration, intrauterine administration, intraocular administration, intranasal administration, intraspinal administration, epidural administration, direct administration at a tendon insertion site, and direct administration to the thymus. In one embodiment, the cells of the invention can be delivered regionally to desired site using well known methods, including but not limited to, hepatic or aortic pump; limb, lung or liver perfusion; in the portal vein; through a venous shunt; in a cavity or in a vein that is nearby a desired site, and the like, such that the cells of the invention are delivered to a region of viral infection or where virally infected cells or tissue occur. For example, the cells can be delivered to a region or tissue in which a latent or chronic viral infection occurs. In another embodiment, the cells of the invention can be administered systemically. In a preferred embodiment, the cells are administered regionally at a desired site. One skilled in the art can select a suitable mode of administration based on the type of viral infection to be treated. The cells can be introduced by injection or catheter. In one embodiment, the cells are administered by intravenous infusion. Optionally, expansion and/or differentiation agents can be administered to the subject prior to, during or after administration of cells to increase production of the cells of the invention in vivo.
Proliferation of the cells of the invention is generally done ex vivo, prior to administration to a subject, and can be desirable in vivo after administration to a subject (see Kaiser et al., Cancer Gene Therapy 22:72-78 (2015)). Cell proliferation should be accompanied by cell survival to permit cell expansion and persistence. Cell isolation and/or expansion can be carried out using any method known in the art, e.g., as described in Lee et al., Cancer Res. 71:2871-2881 (2011).
The methods of the invention can further comprise adjuvant therapy in combination with, either prior to, during, or after treatment with the cells of the invention. Thus, the cell therapy methods of the invention can be used with other standard care and/or therapies for treating a particular viral infection that are compatible with administration of the cells of the invention.
Optionally, the methods of administering cells of the invention can additionally include combination therapy that comprises immunomodulation of the host to facilitate the effectiveness of the administered cells of the invention. In an embodiment of the invention, the methods of the invention can further comprise administering at least one immunomodulatory agent. Non-limiting examples of immunomodulatory agents include immunostimulatory agents when immunostimulatory cells are administered, or immunoinhibitory agents when immunoinhibitory cells are administered.
In one embodiment, the immune cells of the invention expressing a DN form lacking an intracellular signaling domain, as disclosed herein), or such a DN form and a CAR, can be co-administered with immune cells co-expressing a CAR and a switch receptor (i.e., a DN form that further comprises a co-stimulatory signaling domain, where the co-stimulatory signaling domain is carboxy-terminal to the transmembrane domain of the dominant negative form). In such immune cells co-expressing a CAR and a switch receptor that are to be co-administered with immune cells expressing a DN form that does not contain an intracellular signaling domain (and thus lacks the co-stimulatory domain) (i.e., is not a switch receptor), the CAR binds to an antigen of the same viral infection as being treated, i.e., the same virus of the viral infection. In another embodiment, the switch receptor can be transduced into the same cell in which a DN form lacking an intracellular signaling domain, and a CAR, are transduced, so that the cell recombinantly expresses all three constructs. Alternatively and preferably, the switch receptor is transduced into a cell in which the CAR, but not the DN form is transduced, so as to produce a cell expressing both the switch receptor and CAR, which can be used in combination therapy with cells that express the DN form, or both the CAR and DN form, but not the switch receptor. In this case, two types of cells, either cells expressing a DN form lacking an intracellular signaling domain and cells expressing a CAR and a switch receptor, or cells expressing a CAR and the DN form and cells expressing a CAR and a switch receptor, are administered to the subject. Generally, the two types of cells are administered concurrently, but can also be administered sequentially, for example, within 1 or 2 hours, or within 1 or 2 days, or on the same day, as each other, as desired. In a particular embodiment, the co-stimulatory signaling domain of the CAR is different than the co-stimulatory signaling domain of the switch receptor being expressed in the same cell. This should result in two co-stimulatory signaling domains in the same cell and enhanced efficacy of the cells for immune cell therapy. In the case where it is believed that the administered immune cells will proliferate sufficiently in the subject being treated such that additional doses of cells need not be administered, it may be suitable to administer the immune cells of the invention at the initiation of immune cell therapy. Optionally, the immune cells of the invention, including optionally immune cells that express a switch receptor, can be administered more than once, as needed.
Administering an immunomodulatory agent, or cells expressing a CAR and a switch receptor, in a combination therapy with an immune cell of the invention expressing a DN form lacking an intracellular signaling domain, can occur concurrently with administration of the immune cells of the invention, for example, when immune cell therapy is initiated, or can occur sequentially at any time during the course of immune cell therapy, as desired. A person skilled in the art can readily determine appropriate regimens for administering cells of the invention and an immunomodulatory agent, or cells expressing a CAR and a switch receptor, in a combination therapy, including the timing and dosing of an immunomodulatory agent to be used in a combination therapy, based on the needs of the subject being treated.
7.5. Pharmaceutical Compositions
The invention additionally provides pharmaceutical compositions comprising the cells of the invention. The pharmaceutical composition comprises an effective amount of a cell of the invention and a pharmaceutically acceptable carrier. The cells of the invention and compositions comprising the cells can be conveniently provided in sterile liquid preparations, for example, typically isotonic aqueous solutions with cell suspensions, or optionally as emulsions, dispersions, or the like, which are typically buffered to a selected pH. The compositions can comprise carriers, for example, water, saline, phosphate buffered saline, and the like, suitable for the integrity and viability of the cells, and for administration of a cell composition.
Sterile injectable solutions can be prepared by incorporating cells of the invention in a suitable amount of the appropriate solvent with various amounts of the other ingredients, as desired. Such compositions can include a pharmaceutically acceptable carrier, diluent, or excipient such as sterile water, physiological saline, glucose, dextrose, or the like, that are suitable for use with a cell composition and for administration to a subject such as a human. Suitable buffers for providing a cell composition are well known in the art. Any vehicle, diluent, or additive used is compatible with preserving the integrity and viability of the cells of the invention.
The compositions will generally be isotonic, that is, they have the same osmotic pressure as blood and lacrimal fluid. The desired isotonicity of the cell compositions of the invention can be accomplished using sodium chloride, or other pharmaceutically acceptable agents such as dextrose, boric acid, sodium tartrate, or other inorganic or organic solutes. Sodium chloride is preferred particularly for buffers containing sodium ions. One particularly useful buffer is saline, for example, normal saline. Those skilled in the art will recognize that the components of the compositions should be selected to be chemically inert and will not affect the viability or efficacy of the cells of the invention and will be compatible for administration to a subject, such as a human. The skilled artisan can readily determine the amount of cells and optional additives, vehicles, and/or carrier in compositions to be administered in methods of the invention.
The cells of the invention can be administered in any physiologically acceptable vehicle. Suitable doses for administration are described herein. A cell population comprising cells of the invention can comprise a purified population of cells. Those skilled in the art can readily determine the percentage of cells in a cell population using various well-known methods, as described herein. The ranges of purity in cell populations comprising genetically modified cells of the invention can be from about 50% to about 55%, from about 55% to about 60%, from about 65% to about 70%, from about 70% to about 75%, from about 75% to about 80%, from about 80% to about 85%; from about 85% to about 90%, from about 90% to about 95%, or from about 95 to about 100%. Dosages can be readily adjusted by those skilled in the art; for example, a decrease in purity may require an increase in dosage.
The invention also provides kits for preparation of cells of the invention. In one embodiment, the kit comprises one or more vectors for generating a genetically engineered immune cell, such as a T cell or regulatory T cell, that expresses a DN form or co-expresses a CAR and DN form of an inhibitor of a cell-mediated immune response. The kits can be used to generate genetically engineered immune cells from autologous cells derived from a subject or from non-autologous cells to be administered to a compatible subject. In another embodiment, the kits can comprise cells of the invention, for example, autologous or non-autologous cells, for administration to a subject. In specific embodiments, the kits comprise the immune cells of the invention in one or more containers.
It is understood that modifications which do not substantially affect the activity of the various embodiments of this invention are also provided within the definition of the invention provided herein. Accordingly, the following example is intended to illustrate but not limit the present invention.
8. EXAMPLE
This example describes the construction and use of T cells expressing CARs and a dominant negative PD-1 mutant. Although this example relates to the use of CD4+ T cells and CD8+ T cells that are directed to cancer antigens instead of viral antigens, it describes methodology that can be applied in the instant invention. Furthermore, the results described below, although with CD4+ T cells and CD8+ T cells, show that a dominant negative form of PD-1 can function as a dominant negative and can sustain the activity of a T cell expressing the dominant negative form of PD-1.
8.1. Methods and Procedures
The experimental procedures were approved by the Institutional Animal Care and Use Committee of Memorial Sloan Kettering Cancer Center (MSKCC). Each experiment was performed multiple times, using different donor T cells. To avoid confounding variables—such as differences due to transduction efficiencies, donor-related variability, and E:T ratios—data are presented using a representative experiment, with sample replicates of more than 3.
Cell lines. MSTO-211H human pleural mesothelioma cells (ATCC, Manassas, Va.) were retrovirally transduced to express GFP and firefly luciferase fusion protein (MSTO GFP-ffLuc+). These cells were then transduced with the human MSLN variant 1 subcloned into an SFG retroviral vector to generate MSTO MSLN+ GFP-ffLuc+. Similarly, A549 cells and 3T3 murine fibroblasts were transduced with human MSLN variant 1 alone to generate A549 MSLN+ and 3T3 MSLN+ cell lines. 3T3 cells were also cotransduced with PD-L1 to generate 3T3 MSLN+PDL1+ cells.
γ-Retroviral vector construction and viral production. To generate MSLN-specific CARs, a cDNA encoding for a fully human scFv m912 specific for MSLN (provided by D. Dimitrov, National Cancer Institute at Frederick) (Feng et al., Mol. Cancer Ther. 8(5):1113-1118 (2009)), linked to the human CD8 leader domain and the CD8/CD3ζ, CD28/CD3ζ, or CD8/4-1BB/CD3ζ domain was engineered, as previously described (Zhong et al., Mol. Ther. 18(2):413-420 (2010)). The control PSMA-specific CAR was generated similarly, using a previously characterized PSMA-targeting scFv (Gade et al., Cancer Res. 65(19):9080-9088 (2005)). For construction of the PD-1 DNR, commercial gene synthesis was used to encode the extracellular portion of the PD-1 receptor (amino acids 1-151) fused to the CD8 transmembrane and hinge domains. The CAR sequence was inserted into the SFG γ-retroviral vector (provided by I. Riviere, MSKCC) and linked to a P2A sequence to induce coexpression of the LNGFR reporter (truncated low-affinity nerve growth factor receptor) or, in the case of the PD-1 DNR, the mCherry fluorescent protein reporter (Markley et al., Blood 115(17):3508-3519 (2010); Papapetrou et al., Proc. Natl. Acad. Sci. USA 106(31):12759-12764 (2009)). The CAR and PD-1 DNR encoding plasmids were then transfected into 293T H29 packaging cell lines to produce the retrovirus, as previously described (Hollyman et al., J. Immunother. 32(2):169-180 (2009)).
T-cell isolation, gene transfer, and CD4/CD8 isolation. Peripheral blood leukocytes were isolated from the blood of healthy volunteer donors under an institutional review board-approved protocol. Peripheral blood mononuclear cells (PBMCs) were isolated by low-density centrifugation on Lymphoprep (Stem Cell Technology, Vancouver, Canada) and activated with phytohemagglutinin (2 μg/mL; Remel, Lenexa, Kans.). Two days after isolation, PBMCs were transduced with 293T RD114-produced retroviral particles encoding for CARs and PD-1 DNR and spinoculated for 1 h at 3000 rpm on plates coated with retronectin (15 μg/mL; r-Fibronectin, Takara, Tokyo, Japan). After 1 day, transduced PBMCs were maintained in IL-2 (20 UI/mL; Novartis, Basel, Switzerland). Transduction efficiencies were determined by flow cytometric analysis. Pure populations of CD4+ and CD8+ CAR+ T cells, or mCherry-positive PD-1 DNR-expressing and mCherry-positive EV-expressing CAR+ T cells, were obtained by flow cytometric-based sorting (BD Aria Sorter; BD Biosciences, San Jose, Calif.).
Flow cytometry. Human MSLN expression was detected using a phycoerythrin- or allophycocyanin-conjugated anti-human MSLN rat IgG2a (R&D Systems, Minneapolis, Minn.). Expression of costimulation or inhibitory proteins on tumor cells was analyzed using the following antibodies: 4-1BBL (PE, clone 5F4; BioLegend, San Diego, Calif.), MHC HLA-DR (PE, clone L203; R&D Systems), PD-L1 (APC, clone MI11; eBioscience, San Diego, Calif.), PD-L2 (APC, clone MIH18; eBioscience), and galectin-9 (APC, clone 9M13; BioLegend). T-cell phenotype and transduction efficiency were determined with monoclonal antibodies for CD3, CD4, CD8, and CD69m LNGFR. Expression of T-cell inhibitory receptors was analyzed using PD1 (APC, eBioJIU5; eBioscience), TIM-3 (PE, clone 344823; R&D Systems), and Lag-3 (PE, clone C9B7W; BioLegend). Cell staining was analyzed using a BD LSRII flow cytometer (BD, Franklin Lakes, N.J.) and FlowJo analysis software (FlowJo, Ashland, Oreg.).
T-cell functional assays. The cytotoxicity of T cells transduced with a CAR or vector control was determined by standard 51Cr-release assays, as previously described (McCoy et al., National Cancer Institute Monograph 37:59-67 (1973)). To perform the luciferase-activity assay, CAR+ T cells and MSTO-211H cells expressing MSLN and firefly luciferase were incubated for 18 h at different E:T ratios. Tumor-cell quantity was determined by BLI using IVIS 100/lumina II, after the addition of 100 μL of D-luciferin (15 mg/mL) per well, and was compared to the signal emitted by the tumor cells alone. CD107a and intracellular staining were performed after incubation of effector cells and irradiated MSTO-211H MSLN tumor cells for 18 h in 24-well plates at a ratio of 5:1. For the CD107a assay, 5 μL of CD107a-PeCy7 antibody (BD Biosciences, San Jose, Calif.) and Golgi STOP (4 μL/6 mL; BD Biosciences) were added at the time of stimulation. For intracellular staining, Golgi Plug (1 μL/1 mL; BD Biosciences) was added at the time of stimulation. After incubation, effector cells were stained for CD4, CD8, LNGFR, and CD3 marker, then fixed and permeabilized in accordance with the manufacturer's instructions (Cytofix/Cytoperm Kit; BD Biosciences). Staining for intracellular cytokines was performed using granzyme B-APC, perforin-PE, and IFN-γ-FITC antibodies (BD Biosciences).
Cytokine-release assays were performed by coculturing 3×104 to 5×103 T cells with target cells in a 1:1 to 5:1 ratio, in 200 μL of medium, in 96-well round-bottomed plates as triplicates. After 6 to 24 h of coculture, supernatants were collected. Cytokine levels were determined using a multiplex bead Human Cytokine Detection kit, in accordance with the manufacturer's instructions (Millipore, Darmstadt, Germany).
To analyze the proliferation capacity of T cells, 1×106 CAR+ T cells were stimulated over irradiated MSTO-211H or 3T3 cells with or without MSLN expression (and, in the case of 3T3, with or without PD-L1). Proliferation assays were performed in the absence of exogenous IL-2. Cells were counted every 7 days and then overlaid on irradiated target cells for repeated stimulations. The CAR+ T cell number versus time was plotted for each T-cell group.
Orthotopic pleural mesothelioma animal model and ex vivo experiments. To develop the orthotopic mouse model of pleural mesothelioma, female NOD/SCIDγ mice (The Jackson Laboratory, Bar Harbor, Me.) aged 4 to 6 weeks were used. All procedures were performed under approved Institutional Animal Care and Use Committee protocols. Mice were anesthetized using inhaled isoflurane and oxygen, with bupivacaine administered for analgesia. Direct intrapleural injection of 1×105 to 1×106 tumor cells in 200 μL of serum-free medium via a right thoracic incision was performed to establish orthotopic MPM tumors, as previously described (Adusumilli et al., Science Translational Medicine 6(261):261ra151 (2014); Servais et al., Clin. Cancer Res. 18(9):2478-2489 (2012); Servais et al., in Current Protocols in Pharmacology, Enna, ed., Chapter 14 (Unit14 21), John Wiley & Sons (2011)). In total, 3×104 to 1×105 transduced T cells (in 200 μL of serum-free medium) were adoptively transferred into tumor-bearing mice, either into the thoracic cavity by direct intrapleural injection or systemically by tail vein injection. Tumor growth was monitored and quantified in vivo by BLI performed 20 minutes after a single intraperitoneal dose of D-luciferin (150 mg/kg; Perkin Elmer, Waltham, Mass.). BLI data were analyzed using Living Image software (version 2.60; Perkin Elmer); BLI signal was reported as total flux (photons per second), which represents the average of ventral and dorsal flux. To analyze the functional capacity of CAR T cells ex vivo, tumor tissues and mouse spleen were processed as follows: Tissues were weighed and harvested into ice-cold RPMI 1640. The tissues were manually morselized with a scalpel and then mechanically disaggregated through 40- to 100-μm filters. Next, samples were analyzed by FACS (fluorescence activated cell sorting) for phenotyping, or CAR+ CD4+ or CD8+ T cells were sorted using a FACS Aria sorter then rested for 24 h in RPMI with IL-2 (60 UI/mL), and 51Cr-release and cytokine-release assays were performed as described above.
Histologic analysis and immunostaining. Histopathologic evaluation of tumors was performed after hematoxylin and eosin (H&E) staining of paraffin-embedded, 4% paraformaldehyde-fixed tissue samples. Immunohistochemical analysis for human MSLN was performed with mouse anti-human MSLN immunoglobulin G, as previously described (Kachala et al., Clin. Cancer Res. 20(4):1020-1028 (2014); Rizk et al., Cancer Epidemiol. Biomarkers Prev. 21(3):482-486 (2012); Tozbikian et al., PLoS One 9(12):e114900 (2014)).
Quantitative Real-time PCR. The mRNA from CD4+ LNGFR+ or CD8+ LNGFR+ sorted T cells were extracted and reverse transcribed into cDNA using MACS One-Step cDNA kit (MACS molecular, Miltenyi Biotech Inc, Auburn, USA). Quantitative Real Time PCR (RT-PCR) was performed with the Taqman® method using Applied Biosystems® 7500 systems (Foster, Calif., USA), Taqman® Universal PCR Mastermix and Taqman® probes labeled with 6-carboxyfluorescein (FAM-MBG) and designed by Life Technologies (Carlsbad, Calif.): Tbet (Hs00203436_m1); Eomes (Hs00172872_m1); Granzyme B (Hs01554355_m1); IFNγ (Hs00989291_m1); IL-2 (Hs00174114_m1); PD-1 (Hs01550088_m1). The comparative threshold cycle (CT) of the gene of interest was used and normalized to the β2m housekeeping gene using the following formula: ΔCt (sample)=Ct (gene of interest)−Ct (β2m). Then, the 2−ΔΔct method was used to analyze the relative fold change expression compared to control condition and calculated as follow: 2ΔΔCt=2{circumflex over ( )}−(ΔCt (sample)−ΔCt (control)).
Statistical methods. Data were analyzed using Prism (version 6.0; GraphPad Software, La Jolla, Calif.) software and are presented as mean±SEM, as stated in the figure legends. Results were analyzed using the unpaired Student's t test (two-tailed), with the Bonferroni correction used for multiple comparisons, when applicable. Survival curves were analyzed using the log-rank test. Statistical significance was defined as P<0.05. All statistical analyses were performed with Prism software.
8.2. CARs with CD28 or 4-1BB Costimulation Exhibit Equivalent Effector Cytokine Secretion and Proliferation In Vitro Upon Initial Antigen Stimulation
Three CARs were constructed that incorporated a human MSLN-specific scFv (Feng et al., Mol. Cancer Ther. 8(5):1113-1118 (2009)) and either CD3c, CD28/CD3ζ or 4-1BB/CD3ζ signaling domains (Mz, M28z, MBBz) (FIGS. 1A and 1B). The P28z CAR, which is specific for prostate-specific membrane antigen (PSMA), served as a negative effector to control for alloreactivity and xenoreactivity. Both CD4+ and CD8+ human peripheral blood T lymphocytes were effectively transduced using the SFG-retroviral vector (50%-70% transduction) (FIG. 2). MSLN-transduced MSTO-211H cells (MSLN+) and PSMA-transduced EL-4 mouse lymphoma cells (MSLN-) served as MSLN-positive and -negative targets in the in vitro experiments. Mz-, M28z-, and MBBz-transduced T cells demonstrated similar MSLN-specific lysis in vitro (FIG. 1C). P28z CAR T cells did not lyse MSTO MSLN+ cells, and MSLN-targeted CARs did not lyse EL4 PSMA+ cells, demonstrating that lysis is antigen specific. Validating the functionality of costimulatory signaling (Brentjens et al., Clin. Cancer Res. 13(18 Pt 1):5426-5435 (2007)), M28z and MBBz CAR T cells secreted 2- to 15-fold higher levels of Th1 cytokines (FIG. 1D) and achieved 14-fold greater T-cell accumulation upon repeated exposure to MSLN+ cells when compared to Mz in the absence of exogenous IL-2 (FIG. 1E). Having established antigen specificity and validated the functionality of costimulatory signaling domains, evaluation of the therapeutic potential of MSLN-targeted CAR T cells in mice bearing established pleural tumors was performed.
These results demonstrate that CARs with CD28 or 4-1BB costimulation exhibit equivalent effector cytokine secretion and proliferation in vitro upon initial antigen stimulation.
8.3. Mesothelin CAR T Cells Become Exhausted Following In Vivo Antigen Exposure
To assess whether there is ongoing immuno inhibition of CAR T cells and to compare the relative abilities of M28z and MBBz CAR T cells to overcome tumor-mediated immuno inhibition, 1×106 CAR T cells were injected into the pleural cavities of MSTO MSLN+ tumor-bearing mice, allowed sufficient time for repeated antigen encounter and T-cell activation (confirmed by forward- and side-scatter and upregulation of the activation marker CD69), and then performed ex vivo stimulation of harvested CD4 or CD8 CAR tumor-infiltrating or splenic T cells with MSLN+ targets (schematic shown in FIG. 3A). Uninjected in vitro resting T cells (“preinfusion cells”) were used to establish the baseline level of function (before antigen exposure). Compared with resting M28z CD8+ CAR T cells, T cells exposed to MSLN antigen in vivo had lower levels of cytolytic function (FIG. 3A) (preinfusion cell lysis, 20.5%; tumor-infiltrating T-cell lysis, 13.1%; splenic T-cell lysis, 8.7%). In contrast, MBBz CAR T cells retained cytolytic function (preinfusion cell lysis, 18.3%; tumor-infiltrating T-cell lysis, 37.2%; splenic T-cell lysis, 22.2%). Sorted CD4+ CAR T cells demonstrated a similar pattern of results.
Cytokine levels were also measured upon ex vivo stimulation of tumor-infiltrating and splenic CAR T cells, and a decrease in Th1 cytokine secretion was observed for CD4+ M28z CAR T cells exposed in vivo to MSLN+ antigen. CD4+ MBBz CAR T cells also demonstrated a decrease in Th1 cytokine secretion, although these cells were better able to retain cytokine secretion when compared with M28z CAR T cells (FIG. 3B). CD8+ T cell supernatants contained significantly lower levels of cytokines, compared with CD4+ T cell supernatants (a finding previously observed Adusumilli et al., Science Translational Medicine 6(261):261ra151 (2014)). CD8+ T cells also had a decreased ability to secrete cytokines upon in vivo antigen exposure; CD8+ MBBz CAR T cells preferentially retained their ability to secrete IFN-γ. The mRNA levels of T cells harvested from tumor and spleen on day 3 after administration were assessed, and it was found that the in vivo expression levels of GzB, IL-2, and IFN-γ were mostly greater for CD4+ and CD8+ MBBz CAR T cells than for M28z CAR T cells, with the exception of IL-2 expression in the CD8+ subset (FIG. 3C).
These results demonstrate that mesothelin CAR T cells become exhausted following in vivo antigen exposure.
8.4. MBBz CAR T Cells Show Delayed Exhaustion In Vivo
Having demonstrated inhibition of both the cytolytic function and effector cytokine secretion in costimulated CAR T cells exposed to antigen in vivo, it was reasoned that repeated antigen stimulation may, similar to models of chronic infection, play a role in T-cell inhibition and that differing abilities to retain function upon repeated antigen encounter might explain enhanced efficacy of MBBz CAR T cells. Therefore, Mz, M28z, and MBBz CAR T cells were tested for their ability to withstand repeated antigen encounter in an in vitro model system, wherein cells were assessed for proliferation, cytolytic function, and cytokine secretion upon MSLN+ antigen stimulation every 7 days. M28z and MBBz CAR T cells had similar abilities to expand upon serial MSLN+ stimulation, expanding to levels 14-fold greater than those of Mz CAR T cells; they lost the ability to expand following the third stimulation (FIG. 4A). Both MBBz and M28z CAR T cells lost cytolytic function upon repeated antigen stimulation, although MBBz CAR T cells were better able to retain lytic function. Whereas lysis was equal among the three T-cell groups at the first stimulation, by the third stimulation, M28z lytic function was inhibited to a more pronounced level, such that MBBz CAR T cells had enhanced tumor lysis at multiple E:T ratios (FIG. 4B, right). Lytic function (as assessed by a degranulation assay measuring CD107a expression) at the third stimulation correlated with the results of chromium-release assays (FIG. 4C).
Next, Th1 cytokine secretion was measured. Similar levels between M28z and MBBz CAR T cells were noted at the first stimulation, as well as a successive decrease with each stimulation. As with cytotoxicity, MBBz CAR T cells preferentially retained cytokine secretion; cytokine concentrations decreased >30-fold for M28z and only around 2-fold for MBBz CAR T cells, when levels at the first and second stimulations were compared (FIG. 4D). The differences in cytokine production were confirmed by measuring intracellular levels of cytokines at the second stimulation. Reverse-transcriptase PCR analysis of CAR T cells at the time of antigen stimulation revealed that MBBz CAR T cells expressed markers that correlate with lower levels of exhaustion and inhibition, compared with M28z CAR T cells; MBBz CAR T cells expressed higher levels of Tbet and Eomesodermin and lower levels of PD1 and FoxP3 (FIG. 5). The in vivo function of persisting CAR T cells that had already been exposed to tumor antigen was tested. Although quantitative persistence is equal between M28z and MBBz CAR T cells, it was thought that MBBz CAR T cells would demonstrate enhanced function upon tumor rechallenge. Mice with established MSLN+ pleural tumors were administered intrapleural M28z or MBBz CAR T cells (at a dose of 1×105, E:T ratio 1:3000) to eradicate pleural tumor (FIG. 4E). Twenty days after the initial T-cell injection, tumor rechallenge was performed by injecting MSLN+ tumor cells (1×106) into the pleural cavity of survivors; tumor burden was monitored using BLI. Persisting MBBz CAR T cells were better able to control tumor burden (4 of 4 MBBz-treated mice had a BLI signal at baseline levels vs. 2 of 4 M28z-treated mice) (FIG. 4E).
These results demonstrate that MBBz CAR T cells show delayed exhaustion in vivo.
8.5. Tumor Cell PD-L1 Inhibits Mesothelin CAR T-Cell Effector Functions
Having established that CAR T cells are inhibited by the in vivo tumor environment and that MBBz CAR T cells are better able to overcome this inhibition, at least in part because of their ability to retain function upon repeated antigen encounter (see above), it was next sought to assess the role that inhibitory receptor and ligand pathways play in the model. Tumor-infiltrating T cells, in M28z-treated mice with tumor progression, were stained for the expression of well-known pathways of inhibition. High levels of expression of PD-1, Tim-3, and LAG-3 were found (FIG. 6A). Tumor-infiltrating MBBz CAR T cells harvested 6 days after administration demonstrated upregulation of inhibitory receptors as well, although they expressed significantly lower levels of PD-1 receptor at both the protein and the mRNA level (FIG. 6B-D). CD4+ T cells expressed higher levels of PD-1, compared with CD8+ T cells. It was also observed that a significant fraction of both M28z and MBBz CAR T cells coexpressed PD-1 and LAG-3 or PD-1 and Tim-3, suggesting that multiple inhibitory pathways could be functioning simultaneously (FIG. 7). Next, tumor-expressed ligands were assessed: PD-L1 and PD-L2 (ligands for PD-1), galectin-9 (ligand for Tim-3), and MHC class II (ligand for LAG-3). Only PD-1 ligands were expressed on pleural tumor cells harvested after intrapleural administration of M28z CAR T cells (FIG. 6E). As reported elsewhere (McGray et al., Mol. Ther. 22(1):206-218 (2014); Spranger et al., Science Translational Medicine 5(200):200ra116 (2013)), coculture of tumor cells with IFN-γ and TNF-α (at concentrations similar to those secreted by T cells in FIGS. 1 and 4) resulted in a similar level of upregulation of PD-L1 and PD-L2 expression on tumor cells (FIG. 6F), reflecting an adaptation of tumor cells to resist immune attack (“adaptive immunoresistance”). The unique presence of expression of both PD-1 receptor and ligand in vivo suggests that this pathway may play a significant inhibitory role.
As some studies have suggested that costimulation may be sufficient to overcome inhibition by PD-1 (Carter et al., Eur. J. Immunol. 32(3):634-643 (2002); Freeman et al., J. Exp. Med. 192(7):1027-1034 (2000); Koehler et al., Cancer Res. 67(5):2265-2273 (2007)), it was next assessed whether overexpressed PD-L1 can inhibit CAR T-cell function in an in vitro model of PD-L1-mediated immuno inhibition (using 3T3 mouse fibroblasts transduced with either MSLN alone (MSLN+) or both MSLN and PD-L1 (MSLN+PD-L1+)) (FIG. 8A). In both M28z and MBBz CAR T cells, PD-L1 overexpression resulted in decreased accumulation upon successive stimulation (FIG. 8B) and Th1 effector cytokine secretion (FIG. 8D). Although tumor-cell lysis was not inhibited upon initial stimulation, chromium release assay performed with 3T3s as targets following two stimulations against MSTO MSLN+ tumor cells demonstrates decreased lytic function in both M28z and MBBz CAR T cells, a higher extent of decrease in M28z CAR T cells (FIG. 8C). This result may be due to the differential upregulation of PD-1 on M28z and MBBz CAR T cells following exposure to MSTO MSLN+ tumor cells.
These results demonstrate that tumor cell PD-L1 inhibits mesothelin CAR T-cell effector functions.
8.6. Cell Intrinsic PD-1 Resistance Rescues M28z CAR T-Cell Function In Vivo
The above results indicate that the PD-1 pathway is a functioning mechanism of tumor-mediated immuno inhibition and that PD-1 upregulation following repeated antigen stimulation decreases CAR T-cell efficacy. Therefore, checkpoint blockade was combined with CD28 costimulatory signaling. Since the goal was to provide CAR T-cell-specific checkpoint blockade that was not reliant on repeated dosing of systemically administered antibodies, the studies were focused on genetically engineered methods of overcoming immuno inhibition. A PD-1 dominant negative receptor (DNR) was constructed that contained the extracellular ligand binding domain of the receptor fused to a CD8 transmembrane domain. Since the PD-1 DNR lacks any signaling domain, it was thought that sufficiently overexpressed receptor would enhance T-cell efficacy by saturating PD-1 ligands and thereby blocking signaling through the endogenous PD-1 receptor. M28z CAR T cells were cotransduced with either the PD-1 DNR linked by a P2A element to an mCherry reporter (PD-1 DNR) or an empty vector containing only the reporter (EV) (FIG. 9A). M28z CAR T cells cotransduced with the PD-1 DNR had slight but statistically significant advantages in proliferative ability (FIG. 9B), enhanced cytotoxicity (FIG. 9C) at multiple E:T ratios, as well as augmented levels of IL-2 and IFN-γ secretion (FIG. 9D).
Next, it was assessed whether intrapleural administration of M28z CAR T cells cotransduced with a genetically engineered PD-1 resistance would provide an in vivo advantage. Mice with established pleural MSLN+-expressing tumors were administered a single intrapleural dose of 5×104 CAR+ M28z EV or M28z PD-1 DNR T cells, and treatment response was monitored by tumor burden measurements (using serial BLI) and median survival. Mice treated with M28z PD-1 DNR T cells had significantly enhanced tumor burden control and prolonged median survival (FIG. 9E); however, only some mice (7/16, 44%) had long-term tumor-free survival, suggesting that there are redundant mechanisms of immuno inhibition that must be overcome. A cohort of the mice (M28z PD-1 DNR) in this experiment survived beyond 450 days in spite of repeated tumor rechallenge, demonstrating the “functional persistence” of CAR T cells transduced with PD-1 DNR. These results demonstrate that, with an injection of 50,000 CAR T cells, not only was a large tumor burden eradicated but tumor relapse was prevented in spite of multiple tumor rechallenge over more than 15 months.
To investigate an alternative genetic strategy for overcoming PD-1-mediated immuno inhibition, M28z CAR T cells were cotransduced with vectors expressing PD-1-targeting shRNAs (FIG. 10A), which generated >60% PD-1 receptor knockdown at the protein level (FIG. 10B). In M28z CAR T cells, cotransduction with PD-1 shRNAs enhanced proliferative function upon MSLN+ antigen stimulation (FIG. 10C), augmented cytotoxicity (FIG. 10D), and enhanced cytokine secretion upon stimulation with either mesothelioma cells or MSLN+ PDL1+ 3T3 mouse fibroblasts (FIG. 10E), compared with cotransduction with an shRNA targeting a non-mammalian gene (M28z KanR). M28z PD-1 shRNA-transduced T cells did not achieve greater in vivo tumor rejection efficacy than M28z KanR T cells, but it is noteworthy that the level of knockdown was significantly lower in vivo than in vitro. Thus, the PD1 DNR proved to be the more effective strategy in vivo than the RNA interference approach.
These results demonstrate that cell intrinsic PD-1 resistance rescues M28z CAR T-cell function in vivo.
8.7 PD-1 DNR Binds Efficiently to Both PD-L1 and PD-L2
To test the binding of PD-1 DNR to the ligands PD-L1 and PD-L2, T cells labeled with mCherry and transduced with PD-1 DNR were exposed to plates coated with PD-L1 fused to an Fc (“PD-L1 Fc”), PD-L2 fused to an Fc (“PD-L2 Fc”), or control isotype Fc (“iso Fc”). Human T cells were transduced with an mCherry construct to label the T cells with mCherry essentially as described in section 7.6. The PD-L1 Fc fusion, PD-L2 Fc fusion and control Fc were purchased commercially.
Plates coated with PD-L1 Fc fusion protein, PD-L2 Fc protein, or control isotype Fc were exposed to mCherry labeled T cells alone, mCherry labeled T cells in the presence of a PD-1 antibody, mCherry labeled T cells transduced with PD-1 DNR, and mCherry labeled T cells transduced with PD-1 DNR in the presence of PD-1 antibody.
As shown in FIG. 11, compared to control T cells with mCherry and without PD-1 DNR transduction, T cells transduced with PD-1 DNR bound to both PD-L1 and PD-L2 efficiently. These results demonstrate that the PD-1 DNR binds to both PD-L1 and PD-L2. Since some tumor cells express either PD-L1 or PD-L2, and since some immune cells (T cells and non-T cells such as macrophages, etc.) express either PD-L1 or PD-L2, it is significant that the PD-1 DNR binds to both PD-L1 and PD-L2. Thus, the T cells transduced with PD-1 DNR can neutralize both PD-L1 and PD-L2.
8.8 Addition of Intracellular 4-1BB Signaling to PD-1 DNR Improves CAR T Cell Efficiency
A PD-1 DNR, which inhibits PD-L1- or PD-L2-mediated inhibition of T cell activation, can be converted into a positive co-stimulatory signal. Human T cells were transduced with a mesothelin-specific (MSLN-specific) CAR having CD28 and CD3zeta domains (M28z) (see also description of m28z above in section 7.2). To counteract PD-1/PD-L1 inhibition, cell-intrinsic genetic-engineering strategies were evaluated by cotranducing M28z CAR T cells with a PD-1 dominant negative receptor (PD-1 DNR) fused to a transmembrane domain fused to a 4-1BB intracellular signaling domain, also referred to as a switch receptor.
FIG. 12A shows a schematic diagram illustrating co-expression of a CAR and a PD-1 DNR. The lower portion of FIG. 12A represents a T cell expressing a CAR that binds to an antigen on a target cell, exemplified in FIG. 12A as a tumor cell expressing the tumor cell antigen mesothelin (MSLN). Binding of the T cell expressing a tumor cell antigen-specific CAR to a tumor cell expressing the tumor cell antigen results in activation of the T cell. Co-expression of the PD-1 DNR inhibits the immune checkpoint inhibitor pathway mediated by the binding of PD-L1 or PD-L2 to wild type PD-1. FIG. 12B shows a schematic diagram illustrating co-expression of a CAR and a PD-1 DNR, where the PD-1 DNR has been converted into a costimulatory construct by fusing a costimulatory molecule, exemplified as 4-1 BB, to a transmembrane domain fused to the ligand binding domain of PD-1. Such a construct is an example of a construct referred to herein as a switch receptor (see Liu et al., Cancer Res. 76:1578-1590 (2016)). The 4-1BB domain acts as a second costimulatory signal for T cell activation.
Human T cells were transduced with M28z CAR, both M28z CAR and PD-1 DNR, or both M28z CAR and a PD-1/4-1BB switch receptor construct. Transduced cells were antigen stimulated and analyzed for T cell accumulation in culture. As shown in FIG. 12C, M28z CAR T cell accumulation was increased at day 7, and the accumulation was enhanced when the T cells expressing M28z CAR were cotransduced with PD-1 DNR or a PD-1/4-1BB switch receptor construct.
FIG. 12D shows cytokine secretion of interferon gamma (IFN-γ), interleukin 2 (IL-2), tumor necrosis factor alpha (TNF-α) and granulocyte-macrophage colony-stimulating factor (GM-CSF) in human T cells transduced with M28z CAR, both M28z CAR and PD-1 DNR, or both M28z CAR and a PD-1/4-1BB switch receptor construct. Cytokine secretion assays were performed essentially as described above in section 7.1. As shown in FIG. 12D, secretion of IFN-γ, IL-2, TNF-α and GM-CSF was enhanced in cells expressing M28z CAR and a PD-1/4-1BB switch receptor construct relative to the cytokine secretion observed in cells expressing M28z CAR or cells coexpressing M28z CAR and PD-1 DNR. These results demonstrate that PD-L1 (or PD-L2) inhibition can be converted into a positive costimulatory signal by cotransducing in T cells a PD-1/4-1BB switch receptor construct with M28z CAR, resulting in enhanced cytokine secretion and T-cell accumulation.
8.9. Overview and Discussion of Experimental Results
As described above, CAR T-cell therapy and PD-1 checkpoint blockade have been demonstrated to be a rational combination in a solid tumor model. In vitro and ex vivo stimulation assays were performed to assess the impact of PD-1/PD-L1 inhibition on mesothelin CAR T-cell function. To directly counteract PD-1-mediated inhibition, retroviral vectors were used to combine CAR-mediated costimulation with a PD-1 DNR. Optimal signaling provided by this combinatorial strategy (costimulation and checkpoint blockade) enhanced T-cell function in the presence of tumor-encoded PD-L1 expression, resulting in long-term tumor-free survival following a single low dose of CAR T cells. These studies are relevant to the clinical practice of adoptive T-cell therapy and are immediately translational for the following reasons: (1) the costimulatory signaling domains tested—CD28 and 4-1BB—are the two costimulatory domains used in ongoing clinical trials (NCT02414269, NCT02159716, NCT01583686), (2) the models of pleural mesothelioma recapitulate human disease and uses large, clinically relevant tumor burdens that elucidate the relevance of T-cell exhaustion (Adusumilli et al., Science Translational Medicine 6(261):261ra151 (2014); Servais et al., Clin. Cancer Res. 18(9):2478-2489 (2012); Servais et al., in Current Protocols in Pharmacology, Enna, ed., Chapter 14 (Unit14 21), John Wiley & Sons (2011); Servais et al., PLoS One 6(10):e26722 (2011)), and (3) the strategy of potentiating CAR T cells by genetically encoded checkpoint blockade uses human sequences that can be readily applied in the clinic (Adusumilli et al., Science Translational Medicine 6(261):261ra151 (2014); Feng et al., Mol. Cancer Ther. 8(5):1113-1118 (2009)).
The relatively higher expression of PD-1 in M28z CAR T cells led to the focus on CD28-stimulated CAR T cells. On the basis of this analysis, genetic strategies were pursued for counteracting PD-1 inhibitory signaling, such as generating a PD-1 dominant negative receptor (PD-1 DNR) and shRNAs targeting PD-1. When expressed at sufficient levels, the PD-1 DNR competes with the endogenous PD-1 receptor for binding PD-1 ligands (PD-L1 and PD-L2). CD28-costimulated T cells cotransduced with PD-1 DNR demonstrated enhanced in vitro T-cell functions and in vivo T-cell efficacy, suggesting PD-1 signaling as a significant mechanism by which tumor cells evade CAR T cells in the tumor model. Although only in vitro efficacy was demonstrated for PD-1-targeting shRNAs, the absence of in vivo efficacy is likely related to saturation of shRNA machinery by the high volume of PD-1 transcripts induced following multiple in vivo antigen encounters, a conclusion supported by the finding that PD-1 knockdown was significantly lower in vivo than in vitro. The findings described above point to the therapeutic usefulness of adoptively transferred T cells that are genetically engineered to resist tumor-mediated immune inhibition. A DNR that targets TGF-β has been validated in preclinical models and is currently being tested in clinical trials (Foster et al., J. Immunother. 31(5):500-505 (2008); Bollard et al., Blood 99(9):3179-3187 (2002)).
Whereas others have combined T-cell therapy with PD-1-blocking antibodies either in vivo or in vitro, the addition of a genetic strategy for coinhibitory blockade described in the experiments above overcomes several major obstacles limiting antibody therapy, including (1) the reliance on repeated administrations of antibodies and (2) the incidence of immune-related adverse events. T-cell therapy, then, has advantages over antibody therapy because it can establish long-term engraftment of T cells programmed for resistance to inhibition after a single dose and because it provides blockade of inhibitory pathways that is limited to a tumor-targeted T-cell repertoire, which may limit the autoimmunity that results from a more broadly applied antibody checkpoint blockade. Furthermore, it is possible that perhaps PD-L1 blocking antibodies can further prolong the efficacy of M28z and M28z PD-1 DNR CAR T cells.
The studies described above have identified one of the inhibitory mechanisms responsible for CAR T-cell and highlighted differences in the ability of costimulatory strategies to withstand immuno inhibition. Other inhibitory pathways may also function to potentially limit T-cell function. That a proportion of mice treated with PD-1 DNR-cotransduced M28z CAR T cells died of tumor progression suggests the action of other inhibitory mechanisms. Furthermore, the literature on chronic infection suggests the existence of other mechanisms of inhibition, both cell intrinsic and cell extrinsic, which are being assessed in tumor-targeted T-cell therapies (Moon et al., Clin. Cancer Res. 20(16):4262-4273 (2014); Riese et al., Cancer Res. 73(12):3566-3577 (2013)). Additional studies on inhibitory signaling can use an immunocompetent model that includes elements such as myeloid-derived suppressor cells and endogenous T cells, which have been shown to play important roles in tumor immune evasion.
The results described above have established the importance of tumor-mediated inhibition of CAR T-cell effector functions. By performing a comprehensive analysis of T-cell effector functions, it has been established that even costimulated CAR T cells, although they demonstrate enhanced persistence, are subject to inhibition upon repeated antigen encounter, both in vitro and within the tumor microenvironment. The results described demonstrate that CAR T-cell therapy can be used to counteract inhibitory signaling and provides the flexibility to engineer signaling domains that provide optimal costimulation and directly counteract inhibitory signals such as PD-1. Furthermore, in ongoing CAR T-cell therapy clinical trials in patients who show T-cell infiltration but a limited clinical response, combining PD-1/PD-L1 blockade following CAR T-cell therapy can be utilized to improve the efficacy of CAR T-cell therapy. The knowledge acquired from the clinical trials and the strategies presented herein are highly valuable to improve immunotherapy methods using CAR T cells, which is particularly use for therapy of solid tumors. Thus, the results described above exemplify methods that can be applied in a clinical setting to improve the efficacy of CAR T-cell therapy.
As described above, low-level tumor infiltration was modeled, and it was found that CAR T cells can be susceptible to tumor cell-mediated immune-inhibition, resulting in impaired T-cell function and diminished tumor rejection. T cells engineered to resist PD-1 signaling displayed enhanced anti-tumor potency. Following a single low-dose CAR T-cell therapy of advanced tumors, it was observed that, in response to CAR T-cell secreted cytokines, tumor cells upregulate PD-L1 leading to CAR T-cell inhibition and tumor relapse. To directly overcome the PD-L1-mediated immunosuppression, a PD-1 dominant negative receptor (PD-1 DNR) lacking the intracellular inhibitory signaling domain was designed. The cotransduction of PD-1 DNR with a CAR enhanced CAR T-cell function, resulting in a long-term cancer free survival following a single low-dose of CAR T cells. The coexpression of an immune checkpoint pathway receptor DNR with a CAR is immediately translatable to the clinic since a DNR can be added to any CAR without inhibiting CAR function or adding toxicity. Without being bound by a particular theory, it is believed that the DNR simply binds (consumes) negative signal induced by its corresponding ligand (for example, PD-L1 in the case of PD-1) and avoids downstream signaling.
The effectiveness of an immune cell expressing a CAR and a dominant negative form of an immune checkpoint inhibitor can also be enhanced by expression of a switch receptor, in which an intracellular co-stimulatory signaling domain is fused to a transmembrane domain fused to the extracellular ligand binding domain of an immune checkpoint inhibitor, such as PD-1. The results described above show that expression of a PD-1 extracellular domain fused to a transmembrane domain fused to the cytoplasmic domain of 4-1BB increased cytokine production and increased accumulation of CAR T cells. Expression of a switch receptor in an immune cell expressing a CAR can improve the efficacy of the immune cell for immunotherapy. Alternatively, a switch receptor can be expressed in a cell without a CAR. In both cases, the switch receptor functions as a dominant negative. Immune cells expressing a CAR and a switch receptor can be administered, concurrently or sequentially, with immune cells expressing a dominant negative form of an immune checkpoint inhibitor (that does not contain the co-stimulatory signaling domain, and thus is not a switch receptor), or with cells co-expressing a CAR and a dominant negative form of an immune checkpoint inhibitor (that does not contain the co-stimulatory signaling domain, and thus is not a switch receptor), to enhance the effectiveness of immunotherapy using such immune cells.
9. REFERENCES CITED
All references cited herein are incorporated herein by reference in their entirety and for all purposes to the same extent as if each individual publication or patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety for all purposes.
Many modifications and variations of this invention can be made without departing from its spirit and scope, as will be apparent to those skilled in the art. The specific embodiments described herein are offered by way of example only, and the invention is to be limited only by the terms of the appended claims, along with the full scope of equivalents to which such claims are entitled.

## Claims

1. A method of treating a viral infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a cell that is immunostimulatory cell or precursor cell thereof, which immunostimulatory cell or precursor cell recombinantly expresses:
(a) a chimeric antigen receptor (CAR), and
(b) a dominant negative form of programmed cell death protein 1 (PD-1), wherein the CAR binds to a viral antigen,
wherein the viral antigen is an antigen associated with the viral infection.

2. The method of claim 1, wherein the cell is derived from a human, and the subject is a human.

3. The method of claim 1, wherein the cell is a precursor cell of an immunostimulatory cell, and the precursor cell is a hematopoietic stem or hematopoietic progenitor cell.

4. The method of claim 1, wherein the cell is an immunostimulatory cell, and the immunostimulatory cell is a T cell.

5. The method of claim 1, wherein the cell is an immunostimulatory cell, and the immunostimulatory cell is a cytotoxic T lymphocyte (CTL).

6. The method of claim 1, wherein the cell is an immunostimulatory cell, and the immunostimulatory cell is a Natural Killer (NK) cell.

7. The method of claim 1, wherein the viral antigen is of a virus that is a human pathogen.

8. The method of claim 1, wherein the viral antigen is selected from the group consisting of a human immunodeficiency virus (HIV) antigen, a hepatitis B virus (HBV) antigen, a hepatitis C virus (HCV) antigen, a herpes simplex virus (HSV) antigen, a varicella zoster virus (VZV) antigen, an adenovirus antigen, a cytomegalovirus (CMV) antigen, and an Epstein-Barr virus (EBV) antigen.

9. The method of claim 1, wherein the cell further recombinantly expresses a suicide gene.

10. The method of claim 9, wherein the suicide gene comprises inducible Caspase 9.

11. The method of claim 1, wherein the dominant negative form of PD-1 comprises (a) at least a portion of an extracellular domain of PD-1, (b) a transmembrane domain from a heterologous polypeptide, and (c) lacks some portion or all of a signaling domain.

12. The method of claim 11, wherein the heterologous polypeptide is CD8.

13. A method of treating a viral infection in a subject in need thereof, comprising administering to the subject a pharmaceutical composition comprising
(a) a therapeutically effective amount of a cell that is an immunostimulatory cell or precursor cell thereof, which immunostimulatory cell or precursor cell recombinantly expresses:
(i) a chimeric antigen receptor (CAR), and
(ii) a dominant negative form of programmed cell death protein 1 (PD-1), wherein the CAR binds to a viral antigen; and

(b) a pharmaceutically acceptable carrier,
wherein the viral antigen is an antigen associated with the viral infection.

14. The method of claim 13, wherein the cell is derived from a human, and the subject is a human.

15. A method of treating a viral infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a T cell that recognizes and is sensitized to a viral antigen, which T cell recombinantly expresses a dominant negative form of programmed cell death protein 1 (PD-1),
wherein the viral antigen is an antigen associated with the viral infection.

16. The method of claim 15, wherein the cell is derived from a human and the subject is human.

17. The method of claim 15, wherein the therapeutically effective amount of the T cell is present in a pharmaceutical composition, which pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

18. The method of claim 15, wherein the T cell is immunostimulatory.

19. The method of claim 15, wherein the T cell is CD4+ or CD8+.

20. The method of claim 15, wherein the viral antigen is of a virus that is a human pathogen.

21. The method of claim 15, wherein the viral antigen is selected from the group consisting of a human immunodeficiency virus (HIV) antigen, a hepatitis B virus (HBV) antigen, a hepatitis C virus (HCV) antigen, a herpes simplex virus (HSV) antigen, a varicella zoster virus (VZV) antigen, an adenovirus antigen, a cytomegalovirus (CMV) antigen, and an Epstein-Barr virus (EBV) antigen.

22. The method of claim 15, wherein the dominant negative form of PD-1 comprises (a) at least a portion of an extracellular domain of PD-1, (b) a transmembrane domain from a heterologous polypeptide, and (c) lacks some portion or all of a signaling domain.

23. The method of claim 22, wherein the heterologous polypeptide is CD8.

24. A method of treating an infection caused by a pathogen in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a cell that is an immunostimulatory cell or precursor cell thereof, which immunostimulatory cell or precursor cell recombinantly expresses:
(a) a chimeric antigen receptor (CAR), and
(b) a dominant negative form of programmed cell death protein 1 (PD-1), wherein the CAR binds to an antigen of a pathogen,
wherein the antigen of the pathogen to which the CAR binds is an antigen of the pathogen causing the infection.

25. The method of claim 24, wherein the cell is derived from a human and the subject is human.

26. The method of claim 24, wherein the therapeutically effective amount of the cell is present in a pharmaceutical composition, which pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

27. The method of claim 24, wherein the cell is a precursor cell of an immunostimulatory cell, and the precursor cell is a hematopoietic stem or hematopoietic progenitor cell.

28. The method of claim 24, wherein the cell is an immunostimulatory cell, and the immunostimulatory cell is a T cell.

29. The method of claim 24, wherein the cell is an immunostimulatory cell, and the immunostimulatory cell is a cytotoxic T lymphocyte (CTL).

30. The method of claim 24, wherein the cell is an immunostimulatory cell, and the immunostimulatory cell is a Natural Killer (NK) cell.

31. The method of claim 24, wherein the pathogen is a human pathogen.

32. The method of claim 24, wherein the pathogen is selected from the group consisting of a bacterium, a fungus, and a protozoan.

33. The method of claim 24, wherein the dominant negative form of PD-1 comprises (a) at least a portion of an extracellular domain of PD-1, (b) a transmembrane domain from a heterologous polypeptide, and (c) lacks some portion or all of a signaling domain.

34. The method of claim 33, wherein the heterologous polypeptide is CD8.

35. A method of treating an infection caused by a pathogen in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a T cell that recognizes and is sensitized to an antigen of a pathogen, which T cell recombinantly expresses a dominant negative form of programmed cell death protein 1 (PD-1), wherein the antigen of the pathogen to which the T cell is sensitized is an antigen of the pathogen causing the infection.

36. The method of claim 35, wherein the cell is derived from a human and the subject is human.

37. The method of claim 35, wherein the therapeutically effective amount of the T cell is present in a pharmaceutical composition, which pharmaceutical composition further comprises a pharmaceutically acceptable carrier.

38. The method of claim 35, wherein the T cell is immunostimulatory.

39. The method of claim 35, wherein the T cell is CD4+ or CD8+.

40. The method of claim 35, wherein the pathogen is a human pathogen.

41. The method of claim 35, wherein the pathogen is selected from the group consisting of a bacterium, a fungus, and a protozoan.

42. The method of claim 35, wherein the dominant negative form of PD-1 comprises (a) at least a portion of an extracellular domain of PD-1, (b) a transmembrane domain from a heterologous polypeptide, and (c) lacks some portion or all of a signaling domain.

43. The method of claim 42, wherein the heterologous polypeptide is CD8.