# Patent

## Title
Domain-swap T cell receptors

## Abstract

Disclosed herein are genetically engineered T cell receptors, and methods, vectors, and genetically engineered T cells related to genetically engineered T cell receptors.

## Background
RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional application 61/928,142, filed on Jan. 16, 2014 which is hereby incorporated by reference in its entirety.


STATEMENT REGARDING FEDERALLY SPONSORED R&D
This invention was made with government support under CA132681 awarded by the National Institute of Health. The government has certain rights in the invention.


SEQUENCE LISTING IN ELECTRONIC FORMAT
The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled CALTE_104A_SEQLIST.TXT which is 202,964 bytes in size, created on Jan. 14, 2015 and last modified on Jan. 15, 2015, and updated by a file entitled CALTE_104A_SEQLIST_REPLACEMENT.TXT which is 203,050 bytes in size, created on Feb. 19, 2015 and last modified on Feb. 25, 2015.
FIELD
Some embodiments herein relate to genetically modified T cells, for example T cells comprising modified T cell receptors.
BACKGROUND
T cells are cells of the immune system. T cells express T cell receptors (TCRs) on their surface. The TCRs can recognize antigens and induce the T cell to generate an immune response against the recognized antigens. There are two main kinds of T cells namely, CD4 and CD8 T cells that typically generate an immune response. A small fraction of T cells, called regulatory T cells (Tregs), are typically involved in regulating the CD4 and CD8 T cell immune responses. Typically, CD4 T cells recognize antigens that are presented on antigen presenting cells in the context of an MHC Class II molecule. In contrast, CD8 T cells typically recognize antigens that are presented on antigen presenting cells in the context of an MHC Class I molecule.
Adaptive immunity to cancers and pathogens can be mediated by T cells, lymphocytes that are capable of identifying and killing cellular targets with exquisite specificity. This specificity is typically determined by the TCR, which is a heterodimer of two polypeptide chains. A typical wild-type (WT) TCR can be expressed on the surface of a T cell either as an alpha chain-beta chain heterodimer or as a gamma chain-delta chain heterodimer. During typical T cell development, the gene that encodes each polypeptide chain is uniquely rearranged by genetic recombination such that the sequence of each encoded polypeptide is unique for a given T cell. Each T cell typically expresses only one alpha and one beta, or one gamma and one delta chain.
Each TCR polypeptide chain comprises a variable domain, which confers specificity on the T cell, and several invariant domains including a constant domain, a connecting peptide, a transmembrane domain, and a short cytoplasmic tail. To achieve functional form, the TCR heterodimer typically recruits six additional chains which comprise the CD3 dimers gamma-epsilon, delta-epsilon and zeta-zeta. These additional chains can facilitate assembly and export of the TCR heterodimer to the T cell surface, as well as enable signal transduction upon engagement of a TCR heterodimer by its target antigen (Call et al., Ann. Rev. Immunol. 23: 101-125 (2005)).
Most T cells ( ̃90%) express TCRs that comprise an alpha chain and a beta chain. A smaller fraction ( ̃5-10%) of T cells express TCRs that comprise a gamma chain and a delta chain. Typically, a TCR heterodimer is assembled following recruitment of six additional polypeptide chains that form three CD3 dimers. The CD3 dimers are involved in expression of the heterodimeric TCR on the T cell surface. The CD3 dimers are also involved in signaling by TCRs following antigen recognition.
It has been observed that TCR heterodimers that are not properly assembled with the CD3 dimers prior to export are degraded (Bonifacino et al., J. Cell Biol. 109: 73-83 (1989)). Without being limited by any theory, the amino acid residues that are identified as involved in recruiting the CD3 dimers are present within the invariant domains of both chains of a TCR heterodimer (Call et al., Ann. Rev. Immunol. 23: 101-125 (2005); Kuhns et al., Immunity 26: 357-369 (2007); Xu et al., J. Biol. Chem. 281: 36977-36984 (2006)).
SUMMARY
In some embodiments, a method of making a T cell that expresses a domain-swap T cell receptor (DS-TCR) is provided. The method can comprise contacting a T cell with a first nucleic acid that encodes a first domain-swap chain in which the first domain-swap chain comprises a first chain transmembrane domain, a second chain variable domain and a second chain constant domain, but does not comprise a first chain variable domain and does not comprise a first chain constant domain. The method can comprise contacting the T cell with a second nucleic acid that encodes a second domain-swap chain, in which the second domain-swap chain comprises a second chain transmembrane domain, a first chain variable domain and a first chain constant domain, but does not comprise a second chain variable domain and does not comprise a second chain constant domain. The first chain variable domain can comprise an alpha or a gamma chain variable domain and the first chain constant domain can comprise an alpha or a gamma chain constant domain and the first chain transmembrane domain can comprise an alpha or a gamma chain transmembrane domain and the second chain variable domain can comprise a beta or a delta chain variable domain and the second chain constant domain can comprise a beta or a delta chain constant domain and the second chain transmembrane domain can comprises a beta or a delta chain transmembrane domain; or the first chain variable domain can comprise an alpha or a delta chain variable domain and the first chain constant domain can comprise an alpha or a delta chain constant domain and the first chain transmembrane domain can comprise an alpha or a delta chain transmembrane domain and the second chain variable domain can comprise a beta or a gamma chain variable domain and the second chain constant domain can comprise a beta or a gamma chain constant domain and the second chain transmembrane domain can comprise a beta or a gamma chain transmembrane domain. As such, the method can comprise configuring the T cell to express a DS-TCR comprising the first domain-swap chain and the second domain-swap chain. In some embodiments, the first domain-swap chain further comprises a second chain connecting peptide and the second domain-swap chain can further comprises a first chain connecting peptide, in which the first chain connecting peptide comprises an alpha or gamma chain connecting peptide and the second chain connecting peptide comprises a beta or delta chain connecting peptide, or in which the first chain connecting peptide comprises an alpha or delta chain connecting peptide and the second chain connecting peptide comprises a beta or gamma chain connecting peptide. In some embodiments, the first chain variable domain comprises an alpha chain variable domain and the first chain constant domain comprises an alpha chain constant domain and the first chain transmembrane domain comprises a beta chain transmembrane domain and the second chain variable domain comprises a beta chain variable domain and the second chain constant domain can comprise a beta chain constant domain and the second chain transmembrane domain comprises an alpha chain transmembrane domain. In some embodiments, the first chain variable domain comprises a gamma chain variable domain and the first chain constant domain comprises a gamma chain constant domain and the first chain transmembrane domain comprises a gamma chain transmembrane domain and the second chain variable domain comprises a delta chain variable domain and the second chain constant domain comprises a delta chain constant domain and the second chain transmembrane domain comprises a delta chain transmembrane domain. In some embodiments, the first chain variable domain comprises an alpha chain variable domain and the first chain constant domain comprises an alpha chain constant domain and the first chain transmembrane domain comprises a gamma chain transmembrane domain and the second chain variable domain comprises a beta chain variable domain and the second chain constant domain comprises a beta chain constant domain and the second chain transmembrane domain comprises a delta chain transmembrane domain. In some embodiments, the first chain variable domain comprises an alpha chain variable domain and the first chain constant domain comprises an alpha chain constant domain and the first chain transmembrane domain comprises a delta chain transmembrane domain and the second chain variable domain comprises a beta chain variable domain and the second chain constant domain comprises a beta chain constant domain and the second chain transmembrane domain comprises a gamma chain transmembrane domain.
In some embodiments, an expression vector is provided. The expression vector can comprise a first nucleic acid that encodes a first domain-swap chain comprising a first chain transmembrane domain, a second chain variable domain and a second chain constant domain. The expression vector can comprise a second nucleic acid that encodes a second domain-swap chain comprising a second chain transmembrane domain, a first chain variable domain and a first chain constant domain. The first chain variable domain can comprise an alpha or a gamma chain variable domain and the first chain constant domain can comprise an alpha or a gamma chain constant domain and the first chain transmembrane domain can comprise an alpha or a gamma chain transmembrane domain and the second chain variable domain can comprise a beta or a delta chain variable domain and the second chain constant domain can comprise a beta or a delta chain constant domain and the second chain transmembrane domain can comprise a beta or a delta chain transmembrane domain; or the first chain variable domain can comprise an alpha or a delta chain variable domain and the first chain constant domain can comprise an alpha or a delta chain constant domain and the first chain transmembrane domain can comprise an alpha or a delta chain transmembrane domain and the second chain variable domain can comprise a beta or a gamma chain variable domain and the second chain constant domain can comprise a beta or a gamma chain constant domain and the second chain transmembrane domain can comprise a beta or a gamma chain transmembrane domain. In some embodiments, the first domain-swap chain further comprises a second chain connecting peptide but not a first chain connecting peptide, and the second domain-swap chain further comprises a first chain connecting peptide but not a second chain connecting peptide, in which the first chain connecting peptide comprises an alpha or gamma chain connecting peptide and the second chain connecting peptide comprises a beta or delta chain connecting peptide; or the first chain connecting peptide comprises an alpha or delta chain connecting peptide and the second chain connecting peptide comprises a beta or gamma chain connecting peptide. In some embodiments, the first nucleic acid and the second nucleic acid are part of the same expression vector and the expression vector further comprises a 2A peptide-encoding sequence flanked by the first nucleic acid and the second nucleic acid in which the first nucleic acid and the second nucleic acid are driven by a single promoter. In some embodiments, the first nucleic acid and the second nucleic acid are part of separate expression vectors. Optionally, the first nucleic acid and the second nucleic acid can be driven by their own separate promoters. Optionally, the first nucleic acid and the second nucleic acid can be part of a single expression vector and driven by their own separate promoters. In some embodiments, the expression vector comprises a lentiviral vector, retroviral vector, adenoviral vector, or adeno-associated viral vector.
In some embodiments, a genetically engineered T cell is provided. The genetically engineered T cell can comprise a first nucleic acid that encodes a first domain-swap chain comprising a first chain transmembrane domain, a second chain variable domain and a second chain constant domain. The genetically engineered T cell can comprise a second nucleic acid that encodes a second domain-swap chain comprising a second chain transmembrane domain, a first chain variable domain and a first chain constant domain. The first chain variable domain can comprise an alpha or a gamma chain variable domain and the first chain constant domain can comprise an alpha or a gamma chain constant domain and the first chain transmembrane domain can comprise an alpha or a gamma chain transmembrane domain and the second chain variable domain can comprise a beta or a delta chain variable domain and the second chain constant domain can comprise a beta or a delta chain constant domain and the second chain transmembrane domain can comprise a beta or a delta chain transmembrane domain; or the first chain variable domain can comprise an alpha or a delta chain variable domain and the first chain constant domain can comprise an alpha or a delta chain constant domain and the first chain transmembrane domain can comprise an alpha or a delta chain transmembrane domain and the second chain variable domain can comprise a beta or a gamma chain variable domain and the second chain constant domain can comprise a beta or a gamma chain constant domain and the second chain transmembrane domain can comprise a beta or a gamma chain transmembrane domain. As such, the T cell can be configured to express a DS_TCR comprising the first domain-swap chain and the second domain-swap chain. In some embodiments, the first domain-swap chain further comprises a second chain connecting peptide and the second domain-swap chain further comprises a first chain connecting peptide, in which the first chain connecting peptide comprises an alpha or gamma chain connecting peptide and the second chain connecting peptide comprises a beta or delta chain connecting peptide; or in which the first chain connecting peptide comprises an alpha or delta chain connecting peptide and the second chain connecting peptide comprises a beta or gamma chain connecting peptide. In some embodiments, the genetically engineered T cell is configured to express the first domain-swap chain as a first polypeptide and the second domain-swap chain as a second polypeptide, in which the first domain-swap chain and second domain-swap chain are separate molecules. In some embodiments, expression of an endogenous TCR is repressed or eliminated in the genetically engineered T cell.
In some embodiments, a method of inducing an immune response in a subject is provided. The method can comprise configuring an isolated T cell to express a first domain-swap chain that comprises a first chain transmembrane domain, a second chain variable domain, and a second chain constant domain, but does not comprise a first chain variable domain and does not comprise a first chain constant domain. The method can comprise configuring the isolated T cell to express a second domain-swap chain that comprises a second chain transmembrane domain, a first chain variable domain, and a first chain constant domain, but does not comprise a second chain variable domain and does not comprise a second chain constant domain. The first chain variable domain can comprise an alpha or a gamma chain variable domain and the first chain constant domain can comprise an alpha or a gamma chain constant domain and the first chain transmembrane domain can comprise an alpha or a gamma chain transmembrane domain and the second chain variable domain can comprise a beta or a delta chain variable domain and the second chain constant domain can comprise a beta or a delta chain constant domain and the second chain transmembrane domain can comprise a beta or a delta chain transmembrane domain; or the first chain variable domain can comprise an alpha or a delta chain variable domain and the first chain constant domain can comprise an alpha or a delta chain constant domain and the first chain transmembrane domain can comprise an alpha or a delta chain transmembrane domain and the second chain variable domain can comprise a beta or a gamma chain variable domain and the second chain constant domain can comprise a beta or a gamma chain constant domain and the second chain transmembrane domain can comprise a beta or a gamma chain transmembrane domain. As such, the genetically engineered T cell configured to express a domain-swap T cell receptor (DS-TCR) comprising the first domain-swap chain and the second domain-swap chain can be administered to the subject. In some embodiments, the first domain-swap chain further comprises a second chain connecting peptide and the second domain-swap chain can further comprise a first chain connecting peptide, in which the first chain connecting peptide comprises an alpha or gamma chain connecting peptide and the second chain connecting peptide comprises a beta or delta chain connecting peptide; or in which the first chain connecting peptide comprises an alpha or delta chain connecting peptide and the second chain connecting peptide comprises a beta or gamma chain connecting peptide. In some embodiments, the isolated T cell is autologous to the subject. In some embodiments, the isolated T cell is allogeneic to the subject. In some embodiments, the T cell comprises a CD4 T cell. In some embodiments, the T cell comprises a CD8 T cell. In some embodiments, the T cell comprises a regulatory T cell (Treg). In some embodiments, the T cell is co-administered with a second genetically-engineered T cell population. In some embodiments, the T cell is administered in a single dose. In some embodiments, the T cell is administered in in multiple doses. In some embodiments, the subject has at least one of a tumor, a cancer, an infectious disease, an autoimmune disease and is in need of treatment therefor. In some embodiments, the subject has diminished or ineffective or exhausted T cells and is in need of treatment therefor. In some embodiments, the T cell is induced to express a plurality of DS-TCR against an array of antigens. In some embodiments, the T cell can be administered to the subject via at least one of intramuscular injection, intravaginal injection, intravenous injection, intraperitoneal injection, subcutaneous injection, epicutaneous administration, intradermal administration, or nasal administration. In some embodiments, the administered T cell is further be monitored over time. In some embodiments, the method can be repeated as desired.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A is a schematic diagram showing a T Cell Receptor (TCR) complex which comprises a TCR heterodimer and additional CD3 dimers in accordance with some embodiments herein. The TCR in this schematic comprises an alpha chain and a beta chain.
FIG. 1B is a schematic showing an endogenous (WT) TCR, TCRs resulting from mispairing between a domain-swap chain and a WT chain, and a DS-TCR with correctly paired domain-swap chains in accordance with some embodiments herein.
FIG. 2A is a schematic diagram showing an endogenous TCR and three different DS-TCR configurations comprising either a variable domain swap configuration, or a variable domain and constant domain swap configuration, or a variable domain, constant domain and connecting peptide swap configuration in accordance with some embodiments herein. To achieve the three domain swap configurations, domain swap was performed on both the alpha chain and the beta chain of the TCR.
FIG. 2B is a graph showing expression of WT and various DS-TCR configurations of FIG. 2A on the surface of CD3+ 293T cells as determined by binding of a cognate peptide-WIC tetramer in accordance with some embodiments herein. Plot shows mean+/−standard deviation (std. dev.) from triplicate measurements in one representative experiment of at least three independent experiments.
FIG. 2C top panel is a graph showing expression of TCR configurations on the surface of CD3+ 293T cells as determined by binding of a cognate peptide-WIC tetramer in accordance with some embodiments herein. Beneath the graph, each TCR configuration is shown schematically, including WT TCR, a mispaired TCR configuration, and a correctly paired DS-TCR. It is noted that the indicated mispaired TCRs in this schematic comprise a domain swap performed on either the alpha chain or the beta chain, but not both chains.
FIG. 3A is a graph comparing the intensity of expression of WT TCR and two domain swap TCR configurations on the surface of Jurkat T cells in accordance with some embodiments herein. The TCR configurations shown comprise variable domain and constant domain swap configuration, and variable domain, constant domain and connecting peptide domain swap configuration as detected by binding of a cognate peptide-WIC tetramer.
FIG. 3B is a graph comparing the amount of the cytokine IL-2 produced by Jurkat T cells expressing various TCR configurations in accordance with some embodiments herein. Plot shows mean+/−std. dev. from triplicate measurements in one representative experiment of at least three independent experiments.
FIG. 3C is a graph showing lack of expression of mispaired TCR configurations in contrast to WT TCR configuration on the surface of Jurkat T cells as determined by binding of a cognate peptide-WIC tetramer. Similar to FIG. 2C, the mispaired TCRs in this schematic herein result from domain swap performed on either the alpha chain or the beta chain but not both in accordance with some embodiments.
FIG. 4A is a graph showing expression on the surface of CD3+ 293T cells as determined by binding of a cognate peptide-WIC tetramer of TCR configurations in accordance with some embodiments herein. Data are shown for domain swap configurations of two human TCRs in addition to those of FIG. 2C, namely, M1 human TCR and 1G4 human TCR as determined by binding of the cognate peptide-WIC tetramer for each TCR. Plot shows mean+/−std. dev. from triplicate measurements in one representative experiment of at least three independent experiments.
FIG. 4B is a graph showing expression on the surface of CD3+ 293T cells as determined by binding of a cognate peptide-WIC tetramer of TCR configurations in accordance with some embodiments herein. Data are shown for cell surface expression for the domain swap configurations of the ovalbumin-specific OT1 mouse TCR as determined by binding of the cognate peptide-WIC tetramer. Plot shows mean+/−std. dev. from triplicate measurements in one representative experiment of at least two independent experiments.
FIG. 5A is a graph showing recruitment of CD3 chains in the same orientation as WT TCRs by domain-swap TCRs as determined by proliferation of BaF3 cells expressing CD3epsilon-EpoR and domain-swapped versions of the human F5 TCR. Plot shows mean+/−std. dev. from triplicate measurements in one representative experiment of three independent experiments.
FIG. 5B is a graph showing recruitment of CD3 chains in the same orientation as WT TCRs by domain-swap TCRs as determined by proliferation of BaF3 cells expressing with CD3epsilon-EpoR and domain-swapped versions of the mouse OTI TCR. Plot shows mean+/−std. dev. from triplicate measurements in one representative experiment of three independent experiments.
FIG. 6A is a graph showing comparable surface expression of DS-TCRs and WT TCRs, and absence of misparing between DS-TCRs and WT TCRs, as determined by flow cytometry-based detection of A2/Mart1 dextramer staining of Jurkat T cells expressing either WT or DS-TCRs derived from A2-restricted, Mart1(ELAGIGILTV)-specific F5 TCR.
FIG. 6B is a graph showing the percent dextramer positive events quantified from FIG. 6A. Plot shows mean+/−std. dev. from triplicate measurements in one representative experiment of three independent experiments.
FIG. 6C is a graph showing comparable function of DS-TCRs and WT TCRs as determined by antigen-specific IL-2 release following coincubation of Jurkat T cells expressing either WT or DS-TCR with K562 cells engineered to present cognate A2/Mart1 or control A2/NY-ESO-1. Plot shows mean+/−std. dev. from triplicate measurements in one representative experiment of three independent experiments.
FIG. 6D is a graph showing lack of detection of A2/Mart1 dextramer staining of TCRs by flow cytometry on the surface of Jurkat T cells expressing simulated mispaired F5 TCRs comprising one domain-swap chain and one WT chain.
FIG. 7A is a graph showing lack of surface expression of surface-expressed OTI alpha chain following expression of domain-swapped alpha chain only but not WT alpha chain only due to mispairing of introduced domain-swap alpha chain with endogenous TCR beta chain.
FIG. 7B is a graph showing lack of surface expression of surface-expressed OTI beta chain following expression of domain-swapped beta chain only but not WT beta chain only due to mispairing of introduced domain-swap beta chain with endogenous TCR alpha chain.
FIG. 7C is a Kaplan-Meier survival curve showing frequency and rate of deaths of mice due to TCR gene transfer-induced graft-vs-host disease. Data are from one experiment with five mice in each group. Repeat experiments are underway and results will be aggregated.
FIG. 8A is a graph showing flow cytometry analysis of A2/Mart1 dextramer staining of Jurkat T cells expressing either WT F5 TCR or chimeric F5-derived TCRs. Incorporation of only connecting peptide and transmembrane domain from gamma/delta chain into alpha/beta chain retains (perhaps improves) function of DS-TCR. Incorporation of constant domain along with connecting peptide and transmembrane domain from delta chain into alpha chain and constant domain along with connecting peptide and transmembrane domain from gamma chain into beta chain renders DS-TCR non-functional.
FIG. 8B is a graph showing detection by flow cytometry of A2/Mart1 dextramer staining of F5 DS-TCR on the surface of Jurkat T cells expressing both alpha-delta and beta-gamma or but not on the surface of T cells expressing one domain-swap chain and one WT chain.
FIG. 8C is a graph showing detection by flow cytometry of A2/Mart1 dextramer staining of F5 DS-TCR on the surface of Jurkat T cells expressing both alpha-gamma and beta-delta or but not on the surface of T cells expressing one domain-swap chain and one WT chain.
FIG. 9A is the sequence and annotation of the DS-TCR configuration with SEQ ID NO: 56.
FIG. 9B is the sequence and annotation of the DS-TCR configuration with SEQ ID NO: 57.
FIG. 9C is the sequence and annotation of the DS-TCR configuration with SEQ ID NO: 59.
FIG. 9D is the sequence and annotation of the DS-TCR configuration with SEQ ID NO: 61.
FIG. 9E is the sequence and annotation of the DS-TCR configuration with SEQ ID NO: 62.



DETAILED DESCRIPTION
Various embodiments herein relate generally to domain-swap T cell receptors (DS-TCRs).
T cell receptors (TCRs) are expressed on the surface of T cells and are involved in the recognition of antigens. Each TCR comprises a heterodimer of two polypeptide chains. Some endogenous TCRs comprise a pairing of an alpha chain and a beta chain. Some endogenous TCRs comprise a pairing of a gamma chain and a delta chain. Each polypeptide chain of a typical TCR comprises a variant region comprising a variable domain, and an invariant region comprising a constant domain, a connecting peptide, a transmembrane domain and a short cytoplasmic tail.
In accordance with some embodiments herein, the DS-TCR comprises a first polypeptide chain and a second polypeptide chain whose variant and invariant regions comprise domains from a repertoire of sequences homologous to the domain sequences of the endogenous alpha, beta, gamma and/or delta chains. In some embodiments, reference is made to the nucleic acid sequences that encode the first and second polypeptide chains of a DS-TCR. In some embodiments, reference is made to the first and second polypeptide chains of a DS-TCR. Depending on the context, it will be evident to the skilled artisan whether reference is made to nucleic acids encoding the polypeptide chains of a DS-TCR or to the polypeptide chains of a DS-TCR. In some embodiments, DS-TCRs minimize or avoid mispairing with other T cell receptor chains such as endogenous (WT) T cell receptor chains. In some embodiments, a T cell is isolated from a subject (e.g., a cancer patient) and genetically engineered to express a DS-TCR. In some embodiments, the endogenous TCR expression is reduced or eliminated such that the DS-TCR is the predominant TCR or the only TCR expressed on the surface of T cell. In some embodiments, the DS-TCR-expressing T cell is administered to a subject as a treatment (e.g., preventive, prophylactic, or therapeutic). In some embodiments, the DS-TCR expressing T cell stimulates immunity in a subject (e.g., a cancer patient).
Domain-Swap T cell Receptors (DS-TCRs)
Some embodiments herein provide a strategy for preventing TCR mispairing that exploits our understanding of TCR biogenesis. Without being limited by any theory, functional surface expression of the TCR complex typically involves the recruitment of accessory CD3 proteins by invariant domains of the two polypeptide chains of the TCR. Disruption of the TCR-CD3 interactions can ablate both surface expression and signaling of the TCR complex. Accordingly, it can be useful to prevent mispairing of introduced and endogenous chains entirely, thereby eliminating the risk of autoimmunity and maximizing surface expression of the therapeutic TCR heterodimer. Additionally, it can be useful for modifications made to the introduced TCR chains to minimize or avoid foreign sequences, at least in that it is contemplated that the absence of foreign sequences can minimize immunogenicity and avoid development of antibodies against the introduced TCRs. It is noted that DS-TCR's in accordance with some embodiments herein can minimize or prevent mispairing, while also comprising host organism sequences (e.g. fully human TCR's for a human host) so as to minimize immunogenicity against the DS-TCR.
A number of suitable DS-TCR configurations are provided in accordance with some embodiments herein. Without being limited by any theory, DS-TCR's can be useful for minimizing mispairing, while maintaining TCR function, for example to minimize mispairing between an endogenous TCR chain and a chain of a genetically modified TCR, and/or to minimize mispairing between chains of two different genetically modified TCR's.
DS-TCR chains can comprise various domains, including the variable domain (V), constant domain (C), connecting peptide (CP), transmembrane domain (TM), and cytoplasmic tail (CT) (see, e.g. FIG. 1 for a schematic diagram of a WT TCR). A number of configurations for the chains of a DS-TCR in accordance with some embodiments herein are set forth in Alternatives 1-32 in Table 1, herein. It is contemplated that synthetic versions and variants of any or all of the indicated domains can be useful in DS-TCR's in accordance with some embodiments herein. As such, unless stated otherwise, V, C, CP, TM, and CT domains are contemplated to encompass naturally-occurring and synthetic versions of the indicated domains. In some embodiments, the DS-TCR comprises synthetic variants of naturally occurring human domains. In some embodiments, the DS-TCR comprises synthetic variants of naturally occurring murine domains. In some embodiments, the DS-TCR is a chimera of synthetic variants of naturally occurring human domains and murine domains.
In accordance with some embodiments herein, DS-TCR can be entirely of one organism. Optionally, the DS-TCR can be chimeric, comprising a combination of domains from two different organisms (for example, human and murine). For example, chimeric TCRs are described in U.S. Pat. No. 7,446,190, which is hereby incorporated by reference in its entirety. Without being limited by any theory, it is contemplated that fully human and/or chimeric DS-TCRs are less likely to be immunogenic in a human host than murine DS-TCRs. In some embodiments, a chimeric DS-TCR is provided. In some embodiments, the domains of the DS-TCR are fully human. In some embodiments, the domains of the DS-TCR are fully murine. In some embodiments, the DS-TCR is a chimera of human domains and murine domains.







TABLE 1







DS-TCR alternatives









Alter-

Domain













native

Vari-
Con-
Connecting
Trans-
Cytoplas-


#
Chain
able
stant
peptide
membrane
mic tail
















1
1st
Alpha
Alpha
Beta
Beta
Beta



2nd
Beta
Beta
Alpha
Alpha
Alpha


2
1st
Alpha
Alpha
Alpha
Beta
Beta



2nd
Beta
Beta
Beta
Alpha
Alpha


3
1st
Gamma
Gamma
Delta
Delta
Delta



2nd
Delta
Delta
Gamma
Gamma
Gamma


4
1st
Gamma
Gamma
Gamma
Delta
Delta



2nd
Delta
Delta
Delta
Gamma
Gamma


5
1st
Alpha
Alpha
Gamma
Gamma
Gamma



2nd
Gamma
Gamma
Alpha
Alpha
Alpha


6
1st
Alpha
Alpha
Alpha
Gamma
Gamma



2nd
Gamma
Gamma
Gamma
Alpha
Alpha


7
1st
Alpha
Alpha
Delta
Delta
Delta



2nd
Delta
Delta
Alpha
Alpha
Alpha


8
1st
Alpha
Alpha
Alpha
Delta
Delta



2nd
Delta
Delta
Delta
Alpha
Alpha


9
1st
Beta
Beta
Gamma
Gamma
Gamma



2nd
Gamma
Gamma
Beta
Beta
Beta


10
1st
Beta
Beta
Beta
Gamma
Gamma



2nd
Gamma
Gamma
Gamma
Beta
Beta


11
1st
Beta
Beta
Delta
Delta
Delta



2nd
Delta
Delta
Beta
Beta
Beta


12
1st
Beta
Beta
Beta
Delta
Delta



2nd
Delta
Delta
Delta
Beta
Beta


13
1st
Alpha
Alpha
Gamma
Gamma
Alpha



2nd
Beta
Beta
Delta
Delta
Beta


14
1st
Alpha
Alpha
Delta
Delta
Alpha



2nd
Beta
Beta
Gamma
Gamma
Beta


15
1st
Gamma
Gamma
Alpha
Alpha
Gamma



2nd
Delta
Delta
Beta
Beta
Delta


16
1st
Gamma
Gamma
Beta
Beta
Gamma



2nd
Delta
Delta
Alpha
Alpha
Delta


17
1st
Alpha
Alpha
Alpha
Alpha
Beta



2nd
Beta
Beta
Beta
Beta
Alpha


18
1st
Gamma
Gamma
Gamma
Gamma
Delta



2nd
Delta
Delta
Delta
Delta
Gamma


19
1st
Alpha
Alpha
Alpha
Alpha
Gamma



2nd
Gamma
Gamma
Gamma
Gamma
Alpha


20
1st
Alpha
Alpha
Alpha
Alpha
Delta



2nd
Delta
Delta
Delta
Delta
Alpha


21
1st
Beta
Beta
Beta
Beta
Gamma



2nd
Gamma
Gamma
Gamma
Gamma
Beta


22
1st
Beta
Beta
Beta
Beta
Delta



2nd
Delta
Delta
Delta
Delta
Beta


23
1st
Alpha
Beta
Beta
Beta
Beta



2nd
Beta
Alpha
Alpha
Alpha
Alpha


24
1st
Gamma
Delta
Delta
Delta
Delta



2nd
Delta
Gamma
Gamma
Gamma
Gamma


25
1st
Alpha
Gamma
Gamma
Gamma
Gamma



2nd
Gamma
Alpha
Alpha
Alpha
Alpha


26
1st
Alpha
Delta
Delta
Delta
Delta



2nd
Delta
Alpha
Alpha
Alpha
Alpha


27
1st
Beta
Gamma
Gamma
Gamma
Gamma



2nd
Gamma
Beta
Beta
Beta
Beta


28
1st
Beta
Delta
Delta
Delta
Delta



2nd
Delta
Beta
Beta
Beta
Beta


29
1st
Alpha
Gamma
Gamma
Gamma
Alpha



2nd
Beta
Delta
Delta
Delta
Beta


30
1st
Alpha
Delta
Delta
Delta
Alpha



2nd
Beta
Gamma
Gamma
Gamma
Beta


31
1st
Gamma
Alpha
Alpha
Alpha
Gamma



2nd
Delta
Beta
Beta
Beta
Delta


32
1st
Gamma
Beta
Beta
Beta
Gamma



2nd
Delta
Alpha
Alpha
Alpha
Delta









In accordance with Alternative 1, the DS-TCR comprises two polypeptide chains: in the first chain, the variable domain and constant domain of the alpha chain, and the connecting peptide, transmembrane domain and cytoplasmic tail of the beta chain, and reciprocally, in the second chain, the variable domain and constant domain of the beta chain, and the connecting peptide, transmembrane domain and cytoplasmic tail of the alpha chain. Schematically, this can be diagrammed as: first chain: Valpha-Calpha-CPbeta-TMbeta-CTbeta; second chain: Vbeta-Cbeta-CPalpha-TMalpha-CTalpha.
In accordance with Alternative 2, the DS-TCR comprises two polypeptide chains: in the first chain, the variable domain, constant domain and connecting peptide of the alpha chain and the transmembrane domain and cytoplasmic tail of the beta chain, and reciprocally, in the second chain, the variable domain, constant domain and connecting peptide of the beta chain combined with the transmembrane domain and cytoplasmic tail of the alpha chain. Schematically, this can be diagrammed as: first chain: Valpha-Calpha-CPalpha-TMbeta-CTbeta; second chain: Vbeta-Cbeta-CPbeta-TMalpha-CTalpha.
In accordance with Alternative 3, the DS-TCR comprises two polypeptide chains: in the first chain, the variable domain and constant domain of the gamma chain and the connecting peptide, transmembrane domain and cytoplasmic tail of the delta chain, and reciprocally, in the second chain, the variable domain and constant domain of the delta chain and the connecting peptide, transmembrane domain and cytoplasmic tail of the gamma chain. Schematically, this can be diagrammed as: first chain: Vgamma-Cgamma-CPdelta-TMdelta-CTdelta; second chain: Vdelta-Cdelta-CPgamma-TMgamma-CTgamma.
In accordance with Alternative 4, the DS-TCR comprises two polypeptide chains: in the first chain, the variable domain, constant domain and connecting peptide of the gamma chain and the transmembrane domain and cytoplasmic tail of the delta chain, and reciprocally, in the second chain, the variable domain, constant domain and connecting peptide of the delta chain and the transmembrane domain and cytoplasmic tail of the gamma chain. Schematically, this can be diagrammed as: first chain: Vgamma-Cgama-CPgama-TMdelta-CTdelta; second chain: Vdelta-Cdelta-CPdelta-TMgamma-CTgamma.
A number of other suitable DS-TCR Alternatives in accordance with some embodiments herein are listed in Table 1.
In some embodiments, the DS-TCR is in accordance with any of Alternatives 1-32. In some embodiments, the DS-TCR is in accordance with any of Alternatives 1-4. In some embodiments, the DS-TCR is in accordance with any of Alternatives 1-16. In some embodiments, the DS-TCR is in accordance with any of Alternatives 5-16. In some embodiments, the DS-TCR is in accordance with any of Alternatives 1-22. In some embodiments, the DS-TCR is in accordance with any of Alternatives 17-22. In some embodiments, the DS-TCR is in accordance with any of Alternatives 17-32. In some embodiments, the DS-TCR is in accordance with any of Alternatives 23-32.
Nucleic Acids
A number of nucleic acid arrangements encoding the first and second domain swap chains are suitable in accordance with some embodiments herein
In some embodiments (and in accordance with Alternative 1), a first nucleic acid encodes the first domain-swap chain comprising the variable domain and constant domain of the alpha chain combined with the connecting peptide, transmembrane domain and cytoplasmic tail of the beta chain, and reciprocally, a second nucleic acid encodes the second domain-swap chain comprising the variable domain and constant domain of the beta chain combined with the connecting peptide, transmembrane domain and cytoplasmic tail of the alpha chain.
In some embodiments (and in accordance with Alternative 2), a first nucleic acid encodes the first domain-swap chain comprising the variable domain, constant domain and connecting peptide of the alpha chain combined with the transmembrane domain and cytoplasmic tail of the beta chain, and reciprocally, a second nucleic acid encodes the second domain-swap chain comprising the variable domain, constant domain and connecting peptide of the beta chain combined with the transmembrane domain and cytoplasmic tail of the alpha chain.
In some embodiments (and in accordance with Alternative 3), a first nucleic acid encodes the first domain-swap chain comprising the variable domain and constant domain of the gamma chain combined with the connecting peptide, transmembrane domain and cytoplasmic tail of the delta chain, and reciprocally, a second nucleic acid encodes the second domain-swap chain comprising the variable domain and constant domain of the delta chain combined with the connecting peptide, transmembrane domain and cytoplasmic tail of the gamma chain.
In some embodiments (and in accordance with Alternative 4), a first nucleic acid encodes the first domain-swap chain comprising the variable domain, constant domain and connecting peptide of the gamma chain combined with the transmembrane domain and cytoplasmic tail of the delta chain, and reciprocally, a second nucleic acid encodes the second domain-swap chain comprising the variable domain, constant domain and connecting peptide of the delta chain combined with the transmembrane domain and cytoplasmic tail of the gamma chain.
In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with Alternatives 5-16. In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with Alternatives 17-22. In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with Alternatives 23-32.
In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with any of Alternatives 1-32. In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with any of Alternatives 1-4. In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with any of Alternatives 1-16. In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with any of Alternatives 5-16. In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with any of Alternatives 1-22. In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with any of Alternatives 17-22. In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with any of Alternatives 17-32. In some embodiments, a first nucleic acid encodes the first domain-swap chain and a second nucleic acid encodes the second domain-swap chain in accordance with any of Alternatives 23-32.
In some embodiments, the first nucleic acid and second nucleic acid are part of the same construct (e.g. a vector). Optionally, the first and second nucleic acid can be under the control of different promoters. Optionally, the first and second nucleic acid can be under the control of the same promoter.
Optionally, the first and second nucleic acid can be separated by a 2A polypeptide-encoding polynucleotide sequence. Examples of 2A polypeptide-encoding polynucleotide sequences and their corresponding encoded polypeptide sequence are described in U.S. Pat. Application Publication US 2013/0316366 A1 which is hereby incorporated by reference in its entirety. In some embodiments, a 2A polynucleotide sequence encoding a 2A polypeptide can be selected from Table 2. The corresponding encoded polypeptide sequence for each polynucleotide sequence is listed in Table 3.







TABLE 2







2A polynucleotide sequences













Corresponding





Polypeptide


SEQ
2A

SEQ ID NO


ID NO:
Polypeptide
Polypeptide sequence
(TABLE 3):













1 
F2A
CAGCTGTTGAATTTTGACCTTCTTAAGCTTG
19




CGGGAGACGTCGAGTCCAACCCCGGGCCC



 


2 
F2A(−I)
CTGTTGAATTTTGACCTTCTTAAGCTTGCGG
20


 




GAGACGTCGAGTCCAACCCCGGGCCC



3 
F2A(−2)
TTGAATTTTGACCTTCTTAAGCTTGCGGGAG
21




ACGTCGAGTCCAACCCCGGGCCC



 


4 
F2A(−3)
AATTTTGACCTTCTTAAGCTTGCGGGAGACG
22




TCGAGTCCAACCCCGGGCCC



 


5 
F2A(−4)
TTTGACCTTCTTAAGCTTGCGGGAGAACGTC
23




GAGTCCAACCCCGGGCCC



 


6 
F2A(−5)
GACCTTCTTAAGCTTGCGGGAGACGTCGAGT
24




CCAACCCCGGGCCC



 


7 
F2A(−6)
CTTCTTAAGCTTGCGGGAGACGTCGAGTCCA
25




ACCCCGGGCCC



 


8 
F2A(−7)
CTTAAGCTTGCGGGAGACGTCGAGTCCAACC
26




CCGGGCCC



 


9 
F2A(3)
CAGCTGTTGAATTTTGACCTTCTTAAGCTTG
27




CGGGAGACGTCCAGTCCAACCCCGGGCCC



 


10
F2A(11)
CAGCTGTTGAATTTTGACCTTCTTAAGCTTG
28




CGGGAGACGTCGAGATTAACCCCGGGCCC



 


11
F2A(14)
CAGCTGTTGAATTTTGACCTTCTTAAGCTTG
29




CGGGAGACGTCGAGTCCGAGCCCGGGCCC



 


12
F2A(19)
CAGCTGTTGAATTTTGACCTTCTTAAGCTTG
30




CGGGAGACGTCGAGTCCAACCCCGCGCCC



 


13
I2A(0)
ACGAGGGCGGAGATTGAGGATGAATTGATTC
31




GTCGAGGAATTGAATCAAATCCTGGGCCC



 


14
I2A(I)
ACGAGGGCGGAGATTGAGGATGAATTGATTC
32




GTGCAGGAATTGAATCAAATCCTGGACCC



 


15
I2A(I)
ACGAGGGCGGAGATTGAGGATGAATTGATTC
33




GTCGAGGAATTGAATCAAATCCTGGACCC



 


16
I2A(3)
ACGAGGGCGGAGATTGAGGATGAATTGATTC
34




GTCGAGGAATTGAATCAAATCCTGCGCCC



 


17
Furin-
AGGGCAAAACGTTCGGGTTCGGGTGCGGCCA
35



GSG-F2A
GTAAAGCAGACATTAAACTTTGATTTGTCGA





AACTTGCAGGTGATGTAGAGTCAAATCCAGG





TCCA



 


18
Furin-
AGAGCCAAAAGAGGCTCCGGAGCCACTAACT
36



GSG-P2A
TCTCCCTGTTGAAACAGGCTGGCGATGTTGA





AGAAAACCCCGGTCCT

















TABLE 3







2A polypeptide sequences encoded by the 2A polynucleotide sequences of Table 2










SEQ





ID NO:
2A Polypeptide
Mutation Type
Amino Acid Sequence





19
F2A
None
QLLNFDLLKLAGDVESNPGP


 


20
F2A(−I)
1aa N-terminal
LLNFDLLKLAGDVESNPGP




deletion



 


21
F2A(−2)
2aa N-terminal
LNFDLLKLAGDVESNPGP




deletion



 


22
F2A(−3)
3 aa N-terminal
NFDLLKLAGDVESNPGP




deletion



 


23
F2A(−4)
4aa N-terminal
FDLLKLAGDVESNPGP




deletion



 


24
F2A(−5)
5 aa N-terminal
DLLKLAGDVESNPGP




deletion



 


25
F2A(−6)
6aa N-terminal
LLKLAGDVESNPGP




deletion



 


26
F2A(−7)
7aa N-terminal
LKLAGDVESNPGP




deletion



 


27
F2A(3)
Point mutation
QLLNFDLLKLAGDVQSNPGP


 


28
F2A(11)
Point mutation
QLLNFDLLKLAGDVEINPGP


 


29
F2A(14)
Point mutation
QLLNFDLLKLAGDVESEPGP


 


30
F2A(19)
Point mutation
QLLNFDLLKLAGDVESNPAP


 


31
I2A(0)
Wild-type
TRAEIEDELIRRGIESNPGP


 


32
I2A(I)
Point mutation
TRAEIEDELIRAGIESNPGP


 


33
I2A(2)
Alternative codon
TRAEIEDELIRRGIESNPGP


 


34
I2A(3)
Point mutation
TRAEIEDELIRRGIESNPAP


 


35
Furin-GSG-F2A
RAKR = furin cleavage
RAKRSGSGAPVKQTLNFDLL




sequence; GSG = GlySerGly
KLAGDVESNPGP




linker; APVK . . . NPGP =





F2A sequence



 


36
Furin-GSG-P2A
RAKR = furin cleavage
RAKRGSGATNFSLLKQAGDV




sequence; GSG = GlySerGly
EENPGP




linker; ATNF . . . NPGP =





P2A sequence









In some embodiments, the first and second nucleic acid can be separated by an internal ribosome entry site (IRES). In some embodiments, the first nucleic acid and second nucleic acid are part of different constructs. Optionally, the different constructs can both be administered to the same T cell, for example simultaneously, or separately.
Vectors
A number of vectors such as expression vectors are suitable for comprising nucleic acids encoding one or both chains of a DS-TCR in accordance with some embodiments herein.
Exemplary suitable vectors include, but are not limited to, lentiviral vectors, adenoviral vectors, adeno-associated viral (AAV) vectors, and/or retroviral vectors. A suitable vector can be selected depending on a number of factors, for example, the cell type to be genetically engineered, construct to be expressed, patient characteristics, disease indication. Optionally, the vector is further modified and/or optimized for a particular use or set of uses.
In some embodiments, the first nucleic acid and second nucleic acid are present on separate expression vectors. Each vector can comprise a promoter positioned to drive expression of the first or second nucleic acid. In some embodiments, the first nucleic acid and second nucleic acid are present on the same expression vector. The first and second nucleic acid can be under the control of separate promoters, for example a first promoter positioned to drive expression of the first nucleic acid, and a second promoter positioned to drive expression of the second nucleic acid. In some embodiments, the first nucleic acid and second nucleic acid are present on the same expression vector. Optionally, the two nucleic acids can flank a nucleotide sequence that can mediate separation and/or the separate expression of the polypeptides encoded by the two nucleic acids. As such, the expression of both nucleic acids can be driven by one promoter. In some embodiments, the nucleotide sequence that can mediate separation and/or the separate expression encodes a 2A peptide (e.g. a 2A polynucleotide sequence of Table 2 encoding a 2A peptide of Table 3). In some embodiments, the nucleotide sequence that can mediate separation and/or the separate expression encodes a protease target site such as a furin cleavage site. In some embodiments, the nucleotide sequence that can mediate separation and/or the separate expression encodes a 2A peptide with a protease target site furin cleavage site. In some embodiments, the nucleotide sequence encodes an internal ribosome entry site (IRES). In some embodiments, the nucleotide sequence encodes a protease target site.
Recombinant adeno-associated viruses (AAVs) are provided and may be capable of expressing one or more proteins of interest in an appropriate environment, for example, in a cell, a tissue, an organ, or a subject transfected with the recombinant AAVs. Also disclosed herein are the methods for making and using the recombinant AAVs. For example, the recombinant AAVs can be used to produce a protein of interest, for example one or more chains of a DS-TCR, in vivo, ex vivo, or in vitro. In some embodiments, the expression of the protein of interest can be used to diagnose, prevent, or treat one or more diseases or disorders, such as to reduce or inhibit the risk of viral infections.
In some embodiments, an AAV comprises a 5′ inverted terminal repeat (ITR) of AAV and a 3′ AAV ITR, a promoter, a restriction site downstream of the promoter to allow insertion of a polynucleotide encoding one or more chains of a DS-TCR, and a posttranscriptional regulatory element downstream of the restriction site, where the promoter, the restriction site and the posttranscription regulatory element are located downstream of the 5′ AAV ITR and upstream of the 3′ AAV ITR.
Various vectors encoding example DS-TCRs in accordance with some embodiments herein are shown in Table 4. In some embodiments, a vector comprises a vector backbone of any of the constructs shown in Table 4, and nucleic acids encoding a DS-TCR of interest (e.g. a DS-TCR in accordance with any one of Alternatives 1-32, Alternatives 1-4, Alternatives 1-16, Alternatives 5-16, Alternatives 1-22, Alternatives 17-22, Alternatives 17-32, or Alternatives 23-32). Various features of the constructs of Table 4 are noted in Tables 5-14.







TABLE 4







Example constructs encoding DS-TCRs











SEQ


ID
Description
ID NO:





pMTB1184
pMX_2A OT1 TCR
37


pMTB1185
pMX_2A OT1 TCR VCswapBAorientation
38


pMTB1186
pMX_2A OT1 TCR VCswapABorientation
39


pMTB1281
pCCLc_MND_F5TCR-Myc271
40


pMTB1282
pCCLc_MND_F5TCR VCswap(BA)-Myc271
41


pMTB1283
pCCLc_MND_F5TCR VCswap(AB)-Myc271
42


pMTB1284
pCCLc_MND_F5TCR VCcpswap(BA)-Myc271
43


pMTB1285
pCCLc_MND_F5TCR VCcpswap(AB)-Myc271
44


pMTB1301
pCCLc_MND_F5TCR_alpha_cpTMdel-
45



ta_beta_cpTMgamma-Myc271


pMTB1302
pCCLc_MND_F5TCR_alpha_cpTMgam-
46



ma_beta_cpTMdelta-Myc271
















TABLE 5







Annotation of features in pMTB1184 (SEQ ID NO: 37)









Feature
Location
Annotation





CDS
 844 . . . 1895
GagPol\polyprotein


LTR
 7 . . . 599
5′\LTR


LTR
complement
3′\LTR



(3780 . . . 4372)


misc_feature
1060 . . . 1069
approx\packaging\signal


misc_feature
2322 . . . 2693
Mouse\TCR\Cbeta


misc_feature
2694 . . . 2741
Mouse\TCR\connecting\peptide\beta


misc_feature
2742 . . . 2807
Mouse\TCR\transmembrane\domain\




beta


misc_feature
2808 . . . 2834
Mouse\TCR\cyto\beta


misc_feature
2835 . . . 2903
GlySer\linked\2A\sequence


misc_feature
3321 . . . 3587
Mouse\TCR\Calpha


misc_feature
3588 . . . 3647
Mouse\TCR\connecting\peptide\alpha


misc_feature
3648 . . . 3713
Mouse\TCR\transmembrane\domain\




alpha


misc_feature
3714 . . . 3728
Mouse\TCR\cyto\alpha


misc_feature
3729 . . . 3731
STOP


misc_feature
3749 . . . 3784
PPT


misc_feature
524 . . . 598
aprox\U5


primer_bind
601 . . . 618
PBS


repeat_region
456 . . . 523
aprox\R


sig_peptide
1896 . . . 1982
Leader\sequence\2


sig_peptide
2904 . . . 2987
Leader\sequence\1


V_region
1983 . . . 2321
OTI\Vbeta


V_segment
2967 . . . 3320
OTI\Valpha
















TABLE 6







Annotation of features in pMTB1185 (SEQ ID NO: 38)









Feature
Location
Annotation





LTR
complement
3′\LTR



(3780 . . . 4372)


LTR
 7 . . . 599
5′\LTR


primer_bind
601 . . . 618
PBS


misc_feature
3749 . . . 3784
PPT


misc_feature
1060 . . . 1069
approx\packaging\signal


misc_feature
524 . . . 598
aprox\U5


repeat_region
456 . . . 523
aprox\R


CDS
 844 . . . 1895
GagPol\polyprotein


misc_feature
3729 . . . 3731
STOP


misc_feature
2835 . . . 2903
GlySer\linked\2A\sequence


sig_peptide
2904 . . . 2987
Leader\sequence\1


V_segment
2967 . . . 3320
OTI\Valpha


misc_feature
3321 . . . 3587
Mouse\TCR\Calpha


V_region
1983 . . . 2321
OTI\Vbeta


misc_feature
2322 . . . 2693
Mouse\TCR\Cbeta


sig_peptide
1896 . . . 1982
Leader\sequence\2


misc_feature
3588 . . . 3635
Mouse\TCR\connecting\peptide\beta


misc_feature
3636 . . . 3701
Mouse\TCR\transmembrane\domain\




beta


misc_feature
3702 . . . 3728
Mouse\TCR\cyto\beta


misc_feature
2694 . . . 2753
Mouse\TCR\connecting\peptide\alpha


misc_feature
2754 . . . 2819
Mouse\TCR\transmembrane\domain\




alpha


misc_feature
2820 . . . 2834
Mouse\TCR\cyto\alpha
















TABLE 7







Annotation of features in pMTB1186 (SEQ ID NO: 39)









Feature
Location
Annotation





LTR
complement
3′\LTR



(3780 . . . 4372)


LTR
 7 . . . 599
5′\LTR


primer_bind
601 . . . 618
PBS


misc_feature
3749 . . . 3784
PPT


misc_feature
1060 . . . 1069
approx\packaging\signal


misc_feature
524 . . . 598
aprox\U5


repeat_region
456 . . . 523
aprox\R


CDS
 844 . . . 1895
GagPol\polyprotein


misc_feature
3729 . . . 3731
STOP


misc_feature
2721 . . . 2789
GlySer\linked\2A\sequence


misc_feature
3588 . . . 3647
Mouse\TCR\connecting\peptide\alpha


misc_feature
3648 . . . 3713
Mouse\TCR\transmembrane\domain\




alpha


misc_feature
3714 . . . 3728
Mouse\TCR\cyto\alpha


misc_feature
2580 . . . 2627
Mouse\TCR\connecting\peptide\beta


misc_feature
2628 . . . 2693
Mouse\TCR\transmembrane\domain\




beta


misc_feature
2694 . . . 2720
Mouse\TCR\cyto\beta


V_region
2877 . . . 3215
OTI\Vbeta


misc_feature
3216 . . . 3587
Mouse\TCR\Cbeta


sig_peptide
2790 . . . 2876
Leader\sequence\2


sig_peptide
1896 . . . 1979
Leader\sequence\1


V_segment
1959 . . . 2312
OTI\Valpha


misc_feature
2313 . . . 2579
Mouse\TCR\Calpha
















TABLE 8







Annotation of features in pMTB1281 (SEQ ID NO: 40)









Feature
Location
Annotation





misc_feature
4469 . . . 4648
cPPT


misc_feature
3725 . . . 3924
RRE


misc_feature
4660 . . . 5194
MNDU3


misc_feature
3123 . . . 3260
Psi


misc_feature
7661 . . . 7713
U3


misc_feature
2987 . . . 3070
U5


misc_feature
7810 . . . 7893
U5(1)


misc_feature
2891 . . . 2986
R


misc_feature
7714 . . . 7809
R(1)


misc_feature
2362 . . . 2890
CMV


primer_bind
2175 . . . 2194
T3


misc_feature
6066 . . . 6161
F2Aopt


misc_feature
5925 . . . 5984
Alpha\connecting\peptide


misc_feature
5790 . . . 5819
Pep3a


CDS
5646 . . . 6065
TCR-Alpha-Constant


primer_bind
complement
M13-fwd



(8323 . . . 8340)


sig_peptide
6162 . . . 6239
HGH\SS\2


misc_feature
5985 . . . 6050
Alpha\Transmembrane\Domain


misc_feature
5877 . . . 5912
Pep4a


CDS
6576 . . . 7100
TCR-Beta\Constant


primer_bind
2137 . . . 2157
M13-rev


sig_peptide
5232 . . . 5309
HGH\SS


misc_feature
6051 . . . 6065
Alpha\Cytoplasmic\tail


misc_feature
6876 . . . 6917
Pep1b


primer_bind
complement
T7



(8294 . . . 8314)


mutation
6941 . . . 6941
G−>A


misc_feature
6515 . . . 6526
N\region\addition


misc_feature
6876 . . . 6917
FG-Loop


rep_origin
1087 . . . 1769
ColE1\origin


V_region
5310 . . . 5588
TRAV12-2*01


misc_feature
6960 . . . 7007
Beta\connecting\peptide


rep_origin
8501 . . . 8807
F1\ori


J_segment
5592 . . . 5645
TRAJ23*01


misc_feature
7008 . . . 7073
Beta\Transmembrane\Domain


rep_origin
8484 . . . 8939
M13\origin


V_region
6240 . . . 6514
TRBV6-4*01


misc_feature
7074 . . . 7100
Beta\Cytoplasmic\tail


CDS
8411 . . . 8479
LacZ\alpha


J_segment
6527 . . . 6575
TRBJ1-1*01


misc_feature
6240 . . . 6575
F5\TCR\Vb


misc_binding
2109 . . . 2131
LacO


misc_feature
5589 . . . 5594
N\region\addition(1)


misc_feature
5646 . . . 5675
Pep1a


misc_feature
6576 . . . 6959
F5\TCR\Cb


CDS
330 . . . 989
AmpR


misc_feature
5310 . . . 5645
F5\TCR\Va


misc_feature
5727 . . . 5768
Pep2a


misc_feature
5646 . . . 5924
F5\TCR\Ca


misc_feature
7551 . . . 7553
STOP


misc_feature
7113 . . . 7121
GSG\linker


misc_feature
7122 . . . 7178
P2A


CDS
7179 . . . 7550
delta\LNGFR(CD271)_tm-cMyc


misc_feature
7266 . . . 7295
cMyc\tag


misc_feature
7179 . . . 7265
Signal\sequence\for\CD271


misc_feature
7101 . . . 7112
Furin\cleavage\sequence
















TABLE 9







Annotation of features in pMTB1282 (SEQ ID NO: 41)









Feature
Location
Annotation





misc_feature
4469 . . . 4648
cPPT


misc_feature
3725 . . . 3924
RRE


misc_feature
4660 . . . 5194
MNDU3


misc_feature
3123 . . . 3260
Psi


misc_feature
7661 . . . 7713
U3


misc_feature
2987 . . . 3070
U5


misc_feature
7810 . . . 7893
U5(1)


misc_feature
2891 . . . 2986
R


misc_feature
7714 . . . 7809
R(1)


misc_feature
2362 . . . 2890
CMV


primer_bind
2175 . . . 2194
T3


primer_bind
complement
M13-fwd



(8323 . . . 8340)


primer_bind
2137 . . . 2157
M13-rev


primer_bind
complement
T7



(8294 . . . 8314)


rep_origin
1087 . . . 1769
ColE1\origin


rep_origin
8501 . . . 8807
F1\ori


rep_origin
8484 . . . 8939
M13\origin


CDS
8411 . . . 8479
LacZ\alpha


misc_binding
2109 . . . 2131
LacO


CDS
330 . . . 989
AmpR


misc_feature
7551 . . . 7553
STOP


misc_feature
7113 . . . 7121
GSG\linker


misc_feature
7122 . . . 7178
P2A


CDS
7179 . . . 7550
delta\LNGFR(CD271)_tm-cMyc


misc_feature
7266 . . . 7295
cMyc\tag


misc_feature
7179 . . . 7265
Signal\sequence\for\CD271


misc_feature
7101 . . . 7112
Furin\cleavage\sequence


misc_feature
6171 . . . 6266
F2Aopt


sig_peptide
6267 . . . 6344
HGH\SS\2


sig_peptide
5232 . . . 5309
HGH\SS


misc_feature
6030 . . . 6089
Alpha\connecting\peptide


misc_feature
6090 . . . 6155
Alpha\Transmembrane\Domain


misc_feature
6156 . . . 6170
Alpha\Cytoplasmic\tail


misc_feature
6960 . . . 7007
Beta\connecting\peptide


misc_feature
7008 . . . 7073
Beta\Transmembrane\Domain


misc_feature
7074 . . . 7100
Beta\Cytoplasmic\tail


V_region
6345 . . . 6623
TRAV12-2*01


J_segment
6627 . . . 6680
TRAJ23*01


misc_feature
6624 . . . 6629
N\region\addition


misc_feature
6345 . . . 6680
F5\TCR\Va


V_region
5310 . . . 5584
TRBV6-4*01


J_segment
5597 . . . 5645
TRBJ1-1*01


misc_feature
5585 . . . 5596
N\region\addition


misc_feature
5310 . . . 5645
F5\TCR\Vb


misc_feature
6681 . . . 6959
F5\TCR\Ca


mutation
6011 . . . 6011
G−>A


misc_feature
5646 . . . 6029
F5\TCR\Cb
















TABLE 10







Annotation of features in pMTB1283 (SEQ ID NO: 42)









Feature
Location
Annotation





misc_feature
4469 . . . 4648
cPPT


misc_feature
3725 . . . 3924
RRE


misc_feature
4660 . . . 5194
MNDU3


misc_feature
3123 . . . 3260
Psi


misc_feature
7661 . . . 7713
U3


misc_feature
2987 . . . 3070
U5


misc_feature
7810 . . . 7893
U5(1)


misc_feature
2891 . . . 2986
R


misc_feature
7714 . . . 7809
label = R(1)


misc_feature
2362 . . . 2890
CMV


primer_bind
2175 . . . 2194
T3


primer_bind
complement
M13-fwd



(8323 . . . 8340)


primer_bind
2137 . . . 2157
M13-rev


primer_bind
complement
T7



(8294 . . . 8314)


rep_origin
1087 . . . 1769
ColE1\origin


rep_origin
8501 . . . 8807
F1\ori


rep_origin
8484 . . . 8939
M13\origin


CDS
8411 . . . 8479
LacZ\alpha


misc_binding
2109 . . . 2131
LacO


CDS
330 . . . 989
AmpR


misc_feature
7551 . . . 7553
STOP


misc_feature
7113 . . . 7121
GSG\linker


misc_feature
7122 . . . 7178
P2A


CDS
7179 . . . 7550
delta\LNGFR(CD271)_tm-cMyc


misc_feature
7266 . . . 7295
cMyc\tag


misc_feature
7179 . . . 7265
Signal\sequence\for\CD271


misc_feature
7101 . . . 7112
Furin\cleavage\sequence


misc_feature
6066 . . . 6161
F2Aopt


sig_peptide
6162 . . . 6239
HGH\SS\2


sig_peptide
5232 . . . 5309
HGH\SS


misc_feature
6960 . . . 7019
Alpha\connecting\peptide


misc_feature
7020 . . . 7085
Alpha\Transmembrane\Domain


misc_feature
7086 . . . 7100
Alpha\Cytoplasmic\tail


V_region
6240 . . . 6514
TRBV6-4*01


J_segment
6527 . . . 6575
TRBJ1-1*01


misc_feature
6515 . . . 6526
N\region\addition


misc_feature
6240 . . . 6575
F5\TCR\Vb


misc_feature
6576 . . . 6959
F5\TCR\Cb


misc_feature
5925 . . . 5972
Beta\connecting\peptide


misc_feature
5973 . . . 6038
Beta\Transmembrane\Domain


misc_feature
6039 . . . 6065
Beta\Cytoplasmic\tail


V_region
5310 . . . 5588
TRAV12-2*01


J_segment
5592 . . . 5645
TRAJ23*01


misc_feature
5589 . . . 5594
N\region\addition


misc_feature
5310 . . . 5645
F5\TCR\Va


misc_feature
5646 . . . 5924
F5\TCR\Ca
















TABLE 11







Annotation of features in pMTB1284 (SEQ ID NO: 43)









Feature
Location
Annotation





misc_feature
4469 . . . 4648
cPPT


misc_feature
3725 . . . 3924
RRE


misc_feature
4660 . . . 5194
MNDU3


misc_feature
3123 . . . 3260
Psi


misc_feature
7661 . . . 7713
U3


misc_feature
2987 . . . 3070
U5


misc_feature
7810 . . . 7893
U5(1)


misc_feature
2891 . . . 2986
R


misc_feature
7714 . . . 7809
R(1)


misc_feature
2362 . . . 2890
CMV


primer_bind
2175 . . . 2194
T3


primer_bind
complement
M13-fwd



(8323 . . . 8340)


primer_bind
2137 . . . 2157
M13-rev


primer_bind
complement
T7



(8294 . . . 8314)


rep_origin
1087 . . . 1769
ColE1\origin


rep_origin
8501 . . . 8807
F1\ori


rep_origin
8484 . . . 8939
M13\origin


CDS
8411 . . . 8479
LacZ\alpha


misc_binding
2109 . . . 2131
LacO


CDS
330 . . . 989
AmpR


misc_feature
7551 . . . 7553
STOP


misc_feature
7113 . . . 7121
GSG\linker


misc_feature
7122 . . . 7178
P2A


CDS
7179 . . . 7550
delta\LNGFR(CD271)_tm-cMyc


misc_feature
7266 . . . 7295
cMyc\tag


misc_feature
7179 . . . 7265
Signal\sequence\for\CD271


misc_feature
7101 . . . 7112
Furin\cleavage\sequence


misc_feature
6162 . . . 6257
F2Aopt


sig_peptide
6258 . . . 6335
HGH\SS\2


sig_peptide
5232 . . . 5309
HGH\SS


misc_feature
6078 . . . 6146
Alpha\Transmembrane\Domain\(a1\




joint)


misc_feature
6147 . . . 6161
Alpha\Cytoplasmic\tail


misc_feature
7008 . . . 7073
Beta\Transmembrane\Domain\(b4\




joint)


misc_feature
7074 . . . 7100
Beta\Cytoplasmic\tail


V_region
6336 . . . 6614
TRAV12-2*01


J_segment
6618 . . . 6671
TRAJ23*01


misc_feature
6615 . . . 6620
N\region\addition


misc_feature
6336 . . . 6671
F5\TCR\Va


V_region
5310 . . . 5584
TRBV6-4*01


J_segment
5597 . . . 5645
TRBJ1-1*01


misc_feature
5585 . . . 5596
N\region\addition


misc_feature
5310 . . . 5645
F5\TCR\Vb


misc_feature
6672 . . . 6950
F5\TCR\Ca


mutation
6011 . . . 6011
G−>A


misc_feature
5646 . . . 6029
F5\TCR\Cb


misc_feature
6951 . . . 7007
Alpha\connecting\peptide\(a1\joint)


misc_feature
6030 . . . 6077
Beta\connecting\peptide\(b4\joint)
















TABLE 12







Annotation of features in pMTB1285 (SEQ ID NO: 44)









Feature
Location
Annotation





misc_feature
4469 . . . 4648
cPPT


misc_feature
3725 . . . 3924
RRE


misc_feature
4660 . . . 5194
MNDU3


misc_feature
3123 . . . 3260
Psi


misc_feature
7661 . . . 7713
U3


misc_feature
2987 . . . 3070
U5


misc_feature
7810 . . . 7893
U5(1)


misc_feature
2891 . . . 2986
R


misc_feature
7714 . . . 7809
R(1)


misc_feature
2362 . . . 2890
CMV


primer_bind
2175 . . . 2194
T3


primer_bind
complement
M13-fwd



(8323 . . . 8340)


primer_bind
2137 . . . 2157
M13-rev


primer_bind
complement
T7



(8294 . . . 8314)


rep_origin
1087 . . . 1769
ColE1\origin


rep_origin
8501 . . . 8807
F1\ori


rep_origin
8484 . . . 8939
M13\origin


CDS
8411 . . . 8479
LacZ\alpha


misc_binding
2109 . . . 2131
LacO


CDS
330 . . . 989
AmpR


misc_feature
7551 . . . 7553
STOP


misc_feature
7113 . . . 7121
GSG\linker


misc_feature
7122 . . . 7178
P2A


CDS
7179 . . . 7550
delta\LNGFR(CD271)_tm-cMyc


misc_feature
7266 . . . 7295
cMyc\tag


misc_feature
7179 . . . 7265
Signal\sequence\for\CD271


misc_feature
7101 . . . 7112
Furin\cleavage\sequence


misc_feature
6075 . . . 6170
F2Aopt


misc_feature
7017 . . . 7085
Alpha\Transmembrane\Domain\(a1\




joint)


misc_feature
7086 . . . 7100
Alpha\Cytoplasmic\tail


V_region
6249 . . . 6523
TRBV6-4*01


J_segment
6536 . . . 6584
TRBJ1-1*01


misc_feature
6524 . . . 6535
N\region\addition


misc_feature
6249 . . . 6584
F5\TCR\Vb


mutation
6950 . . . 6950
G−>A


misc_feature
6585 . . . 6968
F5\TCR\Cb


misc_feature
6969 . . . 7016
Beta\connecting\peptide\(b4\joint)


misc_feature
5982 . . . 6047
Beta\Transmembrane\Domain\(b4\




joint)


misc_feature
6048 . . . 6074
Beta\Cytoplasmic\tail


V_region
5310 . . . 5588
TRAV12-2*01


J_segment
5592 . . . 5645
TRAJ23*01


misc_feature
5589 . . . 5594
N\region\addition


misc_feature
5310 . . . 5645
F5\TCR\Va


misc_feature
5646 . . . 5924
F5\TCR\Ca


misc_feature
5925 . . . 5981
Alpha\connecting\peptide\(a1\joint)


sig_peptide
6171 . . . 6248
HGH\SS\2


sig_peptide
5232 . . . 5309
HGH\SS
















TABLE 13







Annotation of features in pMTB1301 (SEQ ID NO: 45)









Feature
Location
Annotation





misc_feature
4469 . . . 4648
cPPT


misc_feature
3725 . . . 3924
RRE


misc_feature
4660 . . . 5194
MNDU3


misc_feature
3123 . . . 3260
Psi


misc_feature
7751 . . . 7803
U3


misc_feature
2987 . . . 3070
U5


misc_feature
7900 . . . 7983
U5(1)


misc_feature
2891 . . . 2986
R


misc_feature
7804 . . . 7899
R(1)


misc_feature
2362 . . . 2890
CMV


primer_bind
2175 . . . 2194
T3


primer_bind
complement
M13-fwd



(8413 . . . 8430)


primer_bind
2137 . . . 2157
M13-rev


primer_bind
complement
T7



(8384 . . . 8404)


rep_origin
1087 . . . 1769
ColE1\origin


rep_origin
8591 . . . 8897
F1\ori


rep_origin
8574 . . . 9029
M13\origin


CDS
8501 . . . 8569
LacZ\alpha


misc_binding
2109 . . . 2131
LacO


CDS
330 . . . 989
AmpR


misc_feature
7641 . . . 7643
STOP


misc_feature
7203 . . . 7211
GSG\linker


misc_feature
7212 . . . 7268
P2A


CDS
7269 . . . 7640
delta\LNGFR(CD271)_tm-cMyc


misc_feature
7356 . . . 7385
cMyc\tag


misc_feature
7269 . . . 7355
Signal\sequence\for\CD271


misc_feature
7191 . . . 7202
Furin\cleavage\sequence


misc_feature
6117 . . . 6212
F2Aopt


sig_peptide
6213 . . . 6290
HGH\SS\2


sig_peptide
5232 . . . 5309
HGH\SS


mutation
6992 . . . 6992
G−>A


V_region
5310 . . . 5588
TRAV12-2*01


J_segment
5592 . . . 5645
TRAJ23*01


V_region
6291 . . . 6565
TRBV6-4*01


J_segment
6578 . . . 6623
TRBJ1-1*01


misc_feature
5589 . . . 5594
N\region\addition


misc_feature
5310 . . . 5645
F5\TCR\Va


misc_feature
6102 . . . 6116
Alpha\Cytoplasmic\tail


misc_feature
6566 . . . 6577
N\region\addition


misc_feature
7164 . . . 7190
Beta\Cytoplasmic\tail


misc_feature
6291 . . . 6626
F5\TCR\Vb


misc_feature
5646 . . . 5924
F5\TCR\Ca


misc_feature
6627 . . . 7010
F5\TCR\Cb


misc_feature
5925 . . . 6035
Delta\connecting\peptide


misc_feature
7011 . . . 7100
GammaC1a\connecting\peptide


misc_feature
6036 . . . 6101
Delta\transmembrane\domain


misc_feature
7101 . . . 7163
GammaC1a\transmembrane\domain
















TABLE 14







Annotation of features in pMTB1302 (SEQ ID NO: 46)









Feature
Location
Annotation





misc_feature
4469 . . . 4648
cPPT


misc_feature
3725 . . . 3924
RRE


misc_feature
4660 . . . 5194
MNDU3


misc_feature
3123 . . . 3260
Psi


misc_feature
7751 . . . 7803
U3


misc_feature
2987 . . . 3070
U5


misc_feature
7900 . . . 7983
U5(1)


misc_feature
2891 . . . 2986
R


misc_feature
7804 . . . 7899
R(1)


misc_feature
2362 . . . 2890
CMV


primer_bind
2175 . . . 2194
T3


primer_bind
complement
M13-fwd



(8413 . . . 8430)


primer_bind
2137 . . . 2157
M13-rev


primer_bind
complement
T7



(8384 . . . 8404)


rep_origin
1087 . . . 1769
ColE1\origin


rep_origin
8591 . . . 8897
F1\ori


rep_origin
8574 . . . 9029
M13\origin


CDS
8501 . . . 8569
LacZ\alpha


misc_binding
2109 . . . 2131
LacO


CDS
330 . . . 989
AmpR


misc_feature
7641 . . . 7643
STOP


misc_feature
7203 . . . 7211
GSG\linker


misc_feature
7212 . . . 7268
P2A


CDS
7269 . . . 7640
delta\LNGFR(CD271)_tm-cMyc


misc_feature
7356 . . . 7385
cMyc\tag


misc_feature
7269 . . . 7355
Signal\sequence\for\CD271


misc_feature
7191 . . . 7202
Furin\cleavage\sequence


misc_feature
6093 . . . 6188
F2Aopt


sig_peptide
6189 . . . 6266
HGH\SS\2


sig_peptide
5232 . . . 5309
HGH\SS


CDS
6603 . . . 7190
TCR-Beta\Constant


mutation
6968 . . . 6968
G−>A


CDS
5646 . . . 6092
TCR-Alpha-Constant


V_region
5310 . . . 5588
TRAV12-2*01


J_segment
5592 . . . 5645
TRAJ23*01


V_region
6267 . . . 6541
TRBV6-4*01


J_segment
6554 . . . 6602
TRBJ1-1*01


misc_feature
5589 . . . 5594
N\region\addition


misc_feature
5310 . . . 5645
F5\TCR\Va


misc_feature
6078 . . . 6092
Alpha\Cytoplasmic\tail


misc_feature
6542 . . . 6553
N\region\addition


misc_feature
7164 . . . 7190
Beta\Cytoplasmic\tail


misc_feature
6267 . . . 6602
F5\TCR\Vb


misc_feature
5925 . . . 6014
GammaC1a\connecting\peptide


misc_feature
6987 . . . 7097
Delta\connecting\peptide


misc_feature
6015 . . . 6077
GammaC1a\transmembrane\domain


misc_feature
7098 . . . 7163
Delta\transmembrane\domain









Promoters

A number of promoters are suitable for driving expression of the first and/or second nucleic acid in accordance with some embodiments herein. The promoter can be naturally-occurring or non-naturally occurring. Examples of promoters, include, but are not limited to, viral promoters, plant promoters and mammalian promoters. In some embodiments, the promoter drives expression in a particular cell type or combination of cell types. In some embodiments, the promoter drives expression in a particular cell lineage, for example a T cell lineage. In some embodiments, the promoter drives expression in a particular tissue type or combination of tissue types. In some embodiments, the promoter is inducible. In some embodiments, the promoter is inducible via a hormone, drug, small molecule, or stimulus, such as heat or electromagnetic radiation.
Examples of viral promoters include, but are not limited to cytomegalovirus (CMV) immediate early promoter, CAG promoter (which is a combination of the CMV early enhancer element and chicken beta-actin promoter, described in Alexopoulou et al. BMC Cell Biology 9:2, (2008)), simian virus 40 (SV40) promoter, the 35S RNA and 19S RNA promoters of cauliflower mosaic virus (CaMV) described in Brisson et al., Nature 1984, 310:511-514, the coat protein promoter to tobacco mosaic virus (TMV), and any variants thereof. Examples of plant promoters include, but are not limited to, heat shock promoters, such as soybean hsp17.5-E or hsp17.3-B described in Gurley et al., Mol. Cell. Biol. 1986, 6:559-565, and any variants thereof. Examples of mammalian promoters include, but are not limited to, human elongation factor 1alpha-subunit (EF1-1alpha) promoter, human ubiquitin C (UCB) promoter, murine phosphoglycerate kinase-1 (PGK) promoter, and any variants thereof.
In some embodiments, a cell-type specific promoter can be used (e.g., CD4 vs CD8 vs Treg), depending on the type of cell to be genetically engineered. In some embodiments, a promiscuous promoter can be used.
Markers
In some embodiments, a vector provided herein includes a gene for a selectable marker that is effective in a eukaryotic cell. This selectable marker gene can encode a factor necessary for the survival or growth of a T cell contacted with the vector in a selective culture medium. T cells not contacted with the vector containing the selectable marker will not survive in the selective culture medium. Typical selectable marker genes encode proteins that confer resistance to an antibiotic or toxin (e.g., neomycin, methotrexate, gentamycin, zeocin) or complement auxotrophic deficiencies.
T Cells
In some embodiments, the DS-TCR is expressed in a CD4 T cell. In some embodiments, the DS-TCR is expressed in a CD8 T cell. In some embodiments, the DS-TCR is expressed in a Treg T cell. In some embodiments the DS-TCR is expressed in two or more types of T cell, for example CD4 and CD8, CD4 and Treg, CD8 and Treg, or CD4 and CD8 and Treg. In some embodiments, the DS-TCR is expressed in a T cell of a cell line, for example Jurkat T cells. In some embodiments, the DS-TCR is expressed in an autologous T cell of a subject. In some embodiments, the DS-TCR is expressed in an allogeneic T cell of a donor who is different from the subject.
Methods of Making T Cells Expressing DS-TCRs
In accordance with some embodiments herein, methods of making T cells expressing DS-TCRs are provided. T cells can be isolated from a subject or a donor. Optionally, T cells can be provided from a cell line. T cells can be genetically engineered to express a DS-TCR. T cells can be genetically modified using any of a number of approaches known to the skilled artisan. The T cells can be contacted with/transfected with an expression vector or collection of expression vectors encoding a DS-TCR as described herein. In some embodiments, two expression vectors, one vector encoding a first chain of a DS-TCR and one vector encoding a second chain of a DS-TCR, are contacted with the isolated T cells. In some embodiments, the expression vector carries both the first and second nucleic acids and therefore only one expression vector is contacted with the isolated T cells. The vectors express DS-TCR in accordance with any of the DS-TCR configurations described herein (Table 1).
Optionally, following contact with a single vector or two vectors, a T cell is placed in a selective culture medium. In some embodiments, the vector comprises a selectable marker gene which encodes a protein that confers resistance to an antibiotic or toxin present in the selective culture medium. Optionally, the selectable marker gene encodes a protein that complements an auxotrophic deficiency and enables the T cell to survive in a selective culture medium. Optionally, a selection step can be performed wherein T cells contacted with/transfected with a DS-TCR expression vector are sorted by flow cytometry to select for T cells that express the DS-TCR and separate them from the T cells that do not express the DS-TCR. Optionally, sorting by flow cytometry is used to select for T cells expressing relatively high levels of DS-TCR. Optionally, the expression of endogenous TCR is knocked down or eliminated in the transfected T cell. Optionally, the effect of knockdown or elimination of endogenous TCR is measured, for example, by determining messenger RNA levels and/or polypeptide levels of endogenous TCR. Suitable approaches for preparing nucleic acid expression vectors and transforming mammalian cells such as T cells are described in Green and Sambrook, Molecular Cloning: A Laboratory Manual (Fourth ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 2012), which is hereby incorporated by reference in its entirety.
In some embodiments, the expression of an endogenous TCR is repressed or eliminated prior to sorting by flow cytometry of DS-TCR-expressing T cell and prior to administering a DS-TCR-expressing T cell to a subject. In some embodiments the method of repressing or eliminating an endogenous TCR comprises RNA interference (RNAi), using siRNA or antisense RNA, blocking translation using miRNA, or generating a TCR knockout by gene deletion using homologous recombination, zinc finger nucleases, CRISPR, or TALEN.
Optionally, the genetically modified T cells are subsequently used, for example, to induce an immune response in a subject with a cancer or an infectious disease. Optionally, genetically modified T cells are preserved for later use, for example cryogenically preserved. For example, allogeneic T cells may be preserved in a bank for later use is a suitable subject.
In some embodiments, the genetically modified T cell comprises a first nucleic acid encoding the first domain swap chain and a second nucleic acid encoding the second domain swap chain of any of the DS-TCRs of any of Alternatives 1-32. In some embodiments, the first nucleic acid and the second nucleic acid encode the first domain swap chain and the second domain swap chain of any of a DS-TCR of any of Alternatives 1-4. In some embodiments, the first nucleic acid and the second nucleic acid encode the first domain swap chain and the second domain swap chain of any of Alternatives 5-16. In some embodiments, the first nucleic acid and the second nucleic acid encode the first domain swap chain and the second domain swap chain of any of Alternatives 1-16. In some embodiments, the first nucleic acid and the second nucleic acid encode the first domain swap chain and the second domain swap chain of any of Alternatives 17-22. In some embodiments, the first nucleic acid and the second nucleic acid encode the first domain swap chain and the second domain swap chain of any of Alternatives 1-22. In some embodiments, the first nucleic acid and the second nucleic acid encode the first domain swap chain and the second domain swap chain of any of Alternatives 23-32.
In some embodiments, a CD4 T cell comprises any of the DS-TCR configurations of Alternatives 1-4. In some embodiments, a CD4 T cell comprises any of the DS-TCR configurations of Alternatives 5-16. In some embodiments, a CD4 T cell comprises any of the DS-TCR configurations of Alternatives 17-22. Optionally, the CD4 T cell comprises nucleic acid encoding the DS-TCR, for example a first nucleic acid encoding the first chain of the DS-TCR, and a second nucleic acid encoding the second chain. Optionally, the nucleic acids can be integrated into the genome of the CD4 T cell. Optionally, the nucleic acids can be on a stably-replicated extragenomic construct of the CD4 T cell.
In some embodiments, a CD8 T cell comprises any of the DS-TCR configurations of Alternatives 1-4. In some embodiments, a CD8 T cell comprises any of the DS-TCR configurations of Alternatives 5-16. In some embodiments, a CD8 T cell comprises any of the DS-TCR configurations of Alternatives 17-22. Optionally, the CD8 T cell comprises nucleic acid encoding the DS-TCR, for example a first nucleic acid encoding the first chain of the DS-TCR, and a second nucleic acid encoding the second chain. Optionally, the nucleic acids can be integrated into the genome of the CD8 T cell. Optionally, the nucleic acids can be on a stably-replicated extragenomic construct of the CD8 T cell.
In some embodiments, a Treg T cell comprises any of the DS-TCR configurations of Alternatives 1-4. In some embodiments, a Treg T cell comprises any of the DS-TCR configurations of Alternatives 5-16. In some embodiments, a Treg T cell comprises any of the DS-TCR configurations of Alternatives 17-22. Optionally, the Treg T cell comprises nucleic acid encoding the DS-TCR, for example a first nucleic acid encoding the first chain of the DS-TCR, and a second nucleic acid encoding the second chain. Optionally, the nucleic acids can be integrated into the genome of the Treg T cell. Optionally, the nucleic acids can be on a stably-replicated extragenomic construct of the Treg T cell.
Methods of Inducing an Immune Response
In accordance with some embodiments herein, methods of inducing an immune response in a subject in need thereof are provided. A T cell comprising nucleic acids encoding any of the DS-TCR configurations discussed herein, for example, any of Alternatives 1-4, 5-16, 17-22, and/or 23-32 can be administered to the subject. Optionally, the T cell expresses any of the DS-TCR configurations described herein, for example, any of Alternatives 1-4, 5-16, 17-22, and/or 23-32. Optionally, the T cell encodes any of the DS-TCR configurations described herein, for example, any of Alternatives 1-4, 5-16, 17-22, and/or 23-32, and can be subsequently induced to express them.
The DS-TCR expressing T cell can be administered to a subject. Optionally, the subject is in need of inducing an immune response. For example, the subject can be either susceptible to or have a tumor or cancer, infectious disease, parasitic disease or autoimmune disease. The subject is in need of a preventive treatment, prophylactic treatment, or therapeutic treatment.
In some embodiments, the T cell is isolated and administered to the same subject such that the administered DS-TCR-expressing T cell is autologous. In some embodiments, the T cell is isolated from one subject and administered to a different subject such that the administered DS-TCR-expressing T cell is allogeneic.
It has been observed that co-administration of two or more types of T cells can induce a more robust immune response than administration of a single type of T cell. As such, in some embodiments, two or more populations of different types of T cells, each encoding a DS-TCR are administered to the subject, for example, two, three, four, five, six, seven, eight, nine, or ten, different populations of T cell, each encoding a DS-TCR. In some embodiments, a first genetically engineered CD4 T cell encoding a DS-TCR is co-administered with a second genetically engineered CD8 T cell encoding a DS-TCR. In some embodiments, a first genetically engineered CD4 T cell encoding a DS-TCR is co-administered with a second genetically engineered Treg cell encoding a DS-TCR. In some embodiments, a first genetically engineered CD8 T cell encoding a DS-TCR is co-administered with a second genetically engineered Treg T cell encoding a DS-TCR. In some embodiments, a first genetically engineered T cell encoding a DS-TCR is co-administered with a second T cell encoding an endogenous TCR. Optionally, two or more of the populations of co-administered T cells are administered simultaneously. Optionally, two or more of the populations of co-administered T cells are administered at different times.
Without being limited by any theory, it is contemplated that co-administration of the two genetically engineered T cells can boost the immune response.
In some embodiments, the T cells are isolated once, configured to express DS-TCR and administered in a single administration. A therapeutically effective amount can be administered.
In some embodiments, the T cells are isolated once, configured to express DS-TCR and administered in multiple administrations. For example, the T cells can be isolated multiple times and administered in multiple administrations. The DS-TCR expressing T cell can be a CD4, CD8, or regulatory T cell. Optionally, at least 2 administrations are performed, for example 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50, including ranges between any two of the listed values.
In some embodiments a vector encoding a DS-TCR is administered directly to a subject. The vector can provide nucleic acids encoding the chains of a DS-TCR to a T cell in the subject, so as to provide a DS-TCR in vivo.
The effective amount T cells administered in accordance with some embodiments herein can depend on a variety of factors, for example characteristics of the subject, the type of disease state being treated, characteristics of the DS-TCR, activity levels of the DS-TCR-expressing T cell, and/or the level of immune response desired. Optionally, the amount of T cells administered is determined by the skilled artisan. In some embodiments, at least about 10 DS-TCR-expressing T cells are administered to the subject, for example, at least about 10, 102, 103, 104, 105, 106, 107, 108, 109, or 1010 T cells, including ranges between any two of the listed values.
In some embodiments, the DS-TCR-expressing T cell is administered via intramuscular injection, intravaginal injection, intravenous injection, intraperitoneal injection, subcutaneous injection, epicutaneous administration, intradermal administration, or nasal administration.
In some embodiments, The DS-TCR is generated against a multitude of antigens (e.g., two or more tumor antigens).
In some embodiments, the subject is monitored for the induction of immune responses by the administered DS-TCR-expressing T cells against the clinical condition for which the therapeutic DS-TCR-expressing T cells are administered. Optionally, the administered DS-TCR-expressing T cell is monitored by determining levels over time, rate of attrition, surface expression of DS-TCR, cytokine secretion. Optionally, the condition of the subject is monitored over time for remission of tumor or cancer, clearance or suppression of an infectious disease agent, alleviation of an autoimmune condition, or the lack of development of a tumor or cancer, the prevention of infection by an infectious agent or the prevention of development of autoimmune symptoms.
Inducing an immune response can be useful for a clinical intervention made in response to a disease, disorder or physiological condition manifested by a patient or to which a patient may be susceptible. The aim of treatment can include, but is not limited to, the alleviation or prevention of symptoms, slowing or stopping the progression or worsening of a disease, disorder, or condition and/or the remission of the disease, disorder or condition. “Treatments” refer to one or both of therapeutic treatment and prophylactic or preventative measures. Subjects in need of treatment include those already affected by a disease or disorder or undesired physiological condition as well as those in which the disease or disorder or undesired physiological condition is to be prevented.
Additional Embodiments
Given that the TCR is typically the sole determinant of T cell specificity, transfer into a T cell of genes encoding the two polypeptide chains of a TCR that is specific for a particular antigen (e.g., a tumor antigen) can redirect the T cell to target that tumor antigen. Upon adoptive transfer into patients such engineered T cells have been shown to mediate potent anti-tumor cytotoxicity without the significant bystander toxicity observed with anti-tumor chemotherapy (Park et al., Trends Biotechnol. 29: 550-557 (2011)). This therapeutic approach, termed TCR gene therapy, can be useful for treatment of cancers, for example, blood cancers (Johnson et al., Blood 114: 535-546 (2009)), and has demonstrated up to a 30% objective response rate in clinical trials targeting melanoma (Morgan et al., Science 314: 126-129 (2006)).
However, in conventional T cell therapy, there is a potential for the introduced TCR polypeptide chains to mispair with the endogenous chains. For example, the introduced alpha chain can mispair with the endogenous beta chain and, reciprocally, the introduced beta chain can mispair with the endogenous alpha chain. Mispairing between TCR chains reduces the level of correctly paired, tumor-reactive TCR heterodimers expressed on the T cell surface, a key determinant of therapeutic efficacy (Jorritsma, A. et al., Blood 110: 3564-3572 (2007)). Moreover, mispairing can give rise to self-reactive TCR heterodimers that mediate autoimmunity (van Loenen et al., Proc. Natl. Acad. Sci. 107: 10972-10977 (2010)). Indeed, TCR chain mispairing causes a lethal graft-versus-host disease in up to 90% of mice when a protocol closely mimicking human clinical trials is followed (Bendle et al., Nat. Med. 16: 565-570 (2010)).
It can also be useful for modifications to be restricted to the invariant TCR domains, such that they can be generalized to any TCR of therapeutic interest without further optimization. It is noted that DS-TCR's in accordance with some embodiments herein involve modification to invariant TCR domains, while providing a platform that can be generalized to a plurality of TCR's of interest.
It is contemplated that DS-TCRs in accordance with some embodiments herein will improve the safety and efficacy of TCR gene therapies under clinical investigation for a broad array of cancers as well as pathogens. As the approach can be readily extended to any TCR of interest, it is contemplated that DS-TCR's in accordance with some embodiments herein can have broad application to human health and commercial potential.
Example 1
To prevent mispairing between the first and second chains of the TCR, the invariant domains between the TCR first and second chains were swapped in a complementary manner. Guided by the crystal structure of human TCR comprising an alpha chain and a beta chain, three DS-TCRs were designed in which the alpha and beta sequences were swapped at various inter-domain junctions as illustrated in FIG. 2A. It is noted that some embodiments herein, for example the DCS-TCR of Alternatives 1-3 correspond to the DS-TCRs that were constructed. Correctly paired DS-TCRs retain all domains necessary to recruit CD3 and express on the cell surface, whereas mispaired TCRs comprising one DS-TCR chain and one endogenous (WT) TCR chain did not recruit CD3, and are apparently degraded. Vectors encoding either the indicated DS-TCRs or endogenous WT TCR (human F5 TCR15) were contacted with/transfected into CD3+ 293T cells, and surface expression of the TCR was assessed by flow cytometry by staining with a fluorescent cognate peptide-MHC tetramer. Expression of TCR from vector encoding Alternative 23 (schematically diagrammed as: first chain: Valpha-Cbeta-CPbeta-TMbeta-CTbeta; second chain: Vbeta-Calpha-CPalpha-TMalpha-CTalpha) (Table 1) was not detectable on the cell surface, but expression of TCR from vectors encoding Alternative 1 (schematically diagrammed as: first chain: Valpha-Calpha-CPbeta-TMbeta-CTbeta; second chain: Vbeta-Cbeta-CPalpha-TMalpha-CTalpha) (Table 1) and Alternative 2 (schematically diagrammed as: first chain: Valpha-Calpha-CPalpha-TMbeta-CTbeta; second chain: Vbeta-Cbeta-CPbeta-TMalpha-CTalpha) (Table 1) was comparable to expression of TCR from vector encoding WT TCR (FIG. 2B). Thus, in accordance with some of the embodiments described herein, correctly paired DS-TCRs are expressed on the T cell surface.
Example 2
To simulate mispairing with WT TCR chains, expression constructs were made in which only the alpha or beta chain was domain-swapped, but not both. These constructs were then tested for surface expression in CD3+ 293T by flow cytometry as described in Example 1. Compared to fully WT or DS-TCRs, surface expression of mispaired TCRs was significantly reduced (FIG. 2C). This significantly reduced expression was not due to lower transfection efficiency. Thus, preliminary results with some of the embodiments described herein suggest that domain-swapping significantly mitigates mispairing. It is contemplated in accordance with some embodiments herein that the residual level of mispaired TCR expression observed on the surface could be due to very high, non-physiological levels of expression of TCR and CD3 chains in light of the observation that some TCR is exported to the surface even when one CD3 chain is omitted. Without being limited by any theory, it is further contemplated that domain swap TCRs in accordance with some of the embodiments herein can to prevent mispairing through at least three mechanisms: 1) DS-TCR chains will mispair with WT TCR chains inefficiently due to juxtaposition of non-pairing domains (i.e. neither alpha nor beta self-associate); 2) Mispaired TCRs will lack domains necessary to recruit CD3 and will be degraded; and 3) Mispaired TCR complexes that express on the surface without recruiting CD3 will have impaired signaling capacity. Thus, in accordance with some embodiments herein, significantly higher expression levels of DS-TCRs were achieved as compared to TCRs with mispaired chains (FIG. 2C).
Example 3
To determine whether DS-TCRs are expressed on the surface of T cells, we produced retroviral vectors encoding the DS-TCR and used these to infect Jurkat T cells, again using flow cytometry to assess surface expression. At levels similar to the parental WT TCR, DS-TCRs compete for endogenous CD3, express on the cell surface, and retain specificity for cognate peptide-WIC ligand (FIG. 3A).
Example 4
To determine whether DS-TCRs are functional, DS-TCR-transduced Jurkat cells were coincubated with K562 cells that express cognate peptide-WIC. After two days, supernatant was collected and tested by ELISA for IL-2 secretion as an indicator of antigen-specific activation. DS-TCR-transduced Jurkat cells produced IL-2 in an antigen-specific, WIC-restricted manner, indicating these constructs are indeed functional (FIG. 3B).
Example 5
In contrast to Example 2, mispaired constructs comprising one DS-TCR chain and one WT TCR chain were not detectable on the surface of transduced Jurkats and did not produce IL-2 when stimulated (FIG. 3C and data not shown). Together these results demonstrate the feasibility of domain swapping: DS-TCR alpha and beta chains pair together to form antigen-specific, functional heterodimers but do not mispair with WT TCR chains.
Example 6
The DS-TCR configurations and techniques in accordance with some embodiments herein may be applied to any new TCR of clinical interest with minimal additional optimization. We constructed DS-TCR variants of two additional human TCRs and for the ovalbumin-specific OT1 mouse TCR. Using the transfection assay from Example 1 using CD+ 293T cells, we confirmed for all of these TCRs that the domain-swap derivatives do indeed express on the cell surface and mitigate mispairing (FIG. 4). These data demonstrate generality of the domain-swapping approach, suggesting application of this approach to other human TCRs of clinical interest is feasible. Moreover, the OT1 mouse DS-TCR we constructed enables preclinical characterization of the function and safety of this approach in the context of a fully functional immune system.
Example 7
Recruitment of CD3 chains is typically mediated by the constant domains of the TCR heterodimer, predominantly the transmembrane domains. In light of the swap in the orientation of the constant domains, a BaF3 cell-based assay was used to determine whether the domain-swapped TCRs recruit CD3 chains in a similar or different orientation as the WT TCR. The assay is described in detail in Kuhns et al. accessible on the world wide web at www.ncbi.nlm.nih.gov/pubmed/20202921 (Kuhns et al., Proc. Natl. Acad. Sci. 107: 5094-5099 (2010)). BaF3 cells do not grow in the absence of IL3 unless provided a surrogate input. EpoR expressed on the BaF3 surface can provide this input only if its cytoplasmic domains are dimerized. An expression vector, generated previously, was used which encodes all CD3 chains, including a CD3epsilon chain fused to the cytoplasmic domain of EpoR (Kuhns et al., Proc. Natl. Acad. Sci. 107: 5094-5099 (2010)). This expression vector, when introduced into BaF3 by itself, does not rescue growth (FIG. 5A). However, when a TCR alpha/beta (or gamma/delta) heterodimer is co-delivered with the CD3epsilon-EpoR fusion, the TCR assembles CD3 chains, bringing the two CD3-epsilon chains in the complex into proximity and inducing BaF3 cells to grow (FIG. 5A). The results suggest that CD3 chains are recruited by domain-swap human TCRs in a similar orientation and to a similar extent as by WT F5 human TCRs (FIG. 5A). As with human DS-TCR, CD3 chains are also recruited by murine DS-TCRs in a similar orientation and to a similar extent as by WT OTI murine TCRs (FIG. 5B)
Example 8
To assess whether or not DS-TCRs precipitate TCR gene transfer-induced graft-vs-host disease, mice, for example, C57BL/6J mice from Jackson Laboratories, were gamma-irradiated on day −1 with a sub-lethal dose of 500 Rad. On Day 0, mice were retro-orbitally injected with 1×10e6 T cells that were transduced with LNGFR only or LNGFR plus either WT or domain-swapped OTI TCR. On Days 10, 11, and 12, mice were injected twice daily with 7.2×10e5 U IL-2. Cachexia was the primary indicator used to assess graft-vs-host disease. Mice were weighed once daily starting on Day 10 and were euthanized when weight loss exceeded 15% of initial weight. Results (FIG. 7C) suggest that the DS-TCRs do not cause gene transfer-induced graft-vs-host disease in mice. The assay is described in detail in Bendle et al. accessible on the world wide web at www.ncbi.nlm.nih.gov/pubmed/20400962. (Bendle et al., Nat. Med. 16: 565-570 (2010)).
Example 9
A number of expression constructs were used to express DS-TCRs in accordance with some embodiments herein. Example constructs, which were used in Examples 1-8 are shown in Table 4.
Example 10
In accordance with some embodiments herein, a human subject is selected. The subject has prostate cancer, and has an elevated level of a biomarker, for example, the prostate-specific antigen (PSA) in the subject's serum. The endogenous CD8 T cell TCR repertoire does not target a dominant antigen of this cancer. CD8 T cells are isolated from the subject. A DS-TCR specific for a dominant antigen of the cancer is selected. The DS-TCR is designed with a first domain swap chain configuration Valpha-Calpha-CPbeta-TMbeta-CTbeta and a second domain swap chain configuration Vbeta-Cbeta-CPalpha-TMalpha-CTalpha. The isolated CD8 T cell is transfected with a lentivirus comprising two nucleic acid sequences which encode the two domain swap chains of the DS-TCR. The two nucleic acid sequences flank a 2A nucleotide sequence. The nucleotide sequence encodes a 2A peptide that mediates separation of the two chains of the DS-TCR encoded by the two nucleic acid sequences. The two separate polypeptides are expressed in the CD8 T cell, and assemble, along with the endogenous CD3 chains, into a DS-TCR which is expressed on the surface of the T cell. Additionally, miRNA sequences against the endogenous TCR are included in the lentivirus. The miRNAs generated from the lentivirus suppress the expression of endogenous TCR in the transfected CD8 T cells. Flow cytometry-based cell sorting is used to enrich for T cells based on their suppressed or lack of expression of endogenous TCR and enhanced expression of DS-TCR against the dominant cancer antigen. The selected DS-TCR-expressing T cell is then administered to the subject via the intravenous route. Follow-up testing is performed on the subject to assess the status of the administered T cells and their effect on the cancer. For example, blood is drawn from the subject at various times following administration of the T cells. Testing is performed to determine whether the administered T cells are activated, for example, by assessing their secretion of the cytokine IL-2. Testing is also performed to determine the half-life of the administered cells, and whether they are able to induce a T cell memory response. Follow-up testing is also performed to assess whether there is a decrease in level of PSA in the serum of the subject suggesting a decrease in cancer load. Additional scans, for example, ultrasound and MRI, are performed to determine whether there is a decrease in cancer prevalence in the subject.

## Claims

1. A method of making a T cell that expresses a domain-swap T cell receptor (DS-TCR), the method comprising contacting a T cell with:
a first nucleic acid that encodes a first domain-swap chain, wherein the first domain-swap chain comprises a first chain transmembrane domain, a second chain variable domain and a second chain constant domain, but does not comprise a first chain variable domain and does not comprise a first chain constant domain; and
a second nucleic acid that encodes a second domain-swap chain, wherein the second domain-swap chain comprises a second chain transmembrane domain, a first chain variable domain and a first chain constant domain, but does not comprise a second chain variable domain and does not comprise a second chain constant domain,
wherein, the first chain variable domain comprises an alpha chain variable domain, the first chain constant domain comprises an alpha chain constant domain, the first chain transmembrane domain comprises an alpha chain transmembrane domain, the second chain variable domain comprises a beta chain variable domain, the second chain constant domain comprises a beta chain constant domain, and the second chain transmembrane domain comprises a beta chain transmembrane domain,
so as to configure the T cell to express a DS-TCR comprising the first domain-swap chain and the second domain-swap chain.

2. The method of claim 1, wherein the first domain-swap chain further comprises a second chain connecting peptide, but does not comprise a first chain connecting peptide, and wherein the second domain-swap chain further comprises a first chain connecting peptide, but does not comprise a second chain connecting peptide,
wherein the first chain connecting peptide comprises an alpha chain connecting peptide and the second chain connecting peptide comprises a beta chain connecting peptide.

3. An expression vector or a set of expression vectors comprising:
a first nucleic acid that encodes a first domain-swap chain, wherein the first domain-swap chain comprises a first chain transmembrane domain, a second chain variable domain and a second chain constant domain, but does not comprise a first chain variable domain and does not comprise a first chain constant domain; and
a second nucleic acid that encodes a second domain-swap chain, wherein the second domain-swap chain comprises a second chain transmembrane domain, a first chain variable domain and a first chain constant domain, but does not comprise a second chain variable domain and does not comprise a second chain constant domain,
wherein, the first chain variable domain comprises an alpha chain variable domain, the first chain constant domain comprises an alpha chain constant domain, the first chain transmembrane domain comprises an alpha chain transmembrane domain, the second chain variable domain comprises a beta chain variable domain, the second chain constant domain comprises a beta chain constant domain, and the second chain transmembrane domain comprises a beta chain transmembrane domain.

4. The expression vector or the set of expression vectors of claim 3, wherein the first domain-swap chain further comprises a second chain connecting peptide, but does not comprise a first chain connecting peptide, and wherein the second domain-swap chain further comprises a first chain connecting peptide, but does not comprise a second chain connecting peptide, and
wherein:
the first chain connecting peptide comprises an alpha chain connecting peptide and the second chain connecting peptide comprises a beta chain connecting peptide.

5. The expression vector or the set of expression vectors of claim 3, wherein the first nucleic acid and the second nucleic acid are part of a same polypeptide expression vector, the vector further comprising a 2A peptide-encoding sequence flanked by the first nucleic acid and the second nucleic acid.

6. The expression vector or the set of expression vectors of claim 3, further comprising a promoter configured to drive expression of the first nucleic acid and the second nucleic acid.

7. The expression vector or the set of expression vectors of claim 3, wherein the first nucleic acid and the second nucleic acid are part of separate expression vectors.

8. The expression vector or the set of expression vectors of claim 3, wherein the expression vector or the set of expression vectors comprises a lentiviral vector, retroviral vector, adenoviral vector, or adeno-associated viral vector.

9. A genetically engineered T cell, comprising:
a first nucleic acid that encodes a first domain-swap chain, wherein the first domain-swap chain comprises a first chain transmembrane domain, a second chain variable domain and a second chain constant domain, but does not comprise a first chain variable domain and does not comprise a first chain constant domain; and
a second nucleic acid that encodes a second domain-swap chain, wherein the second domain-swap chain comprises a second chain transmembrane domain, a first chain variable domain and a first chain constant domain, but does not comprise a second chain variable domain and does not comprise a second chain constant domain,
wherein, the first chain variable domain comprises an alpha chain variable domain, the first chain constant domain comprises an alpha chain constant domain, the first chain transmembrane domain comprises an alpha chain transmembrane domain, the second chain variable domain comprises a beta chain variable domain, the second chain constant domain comprises a beta chain constant domain, and the second chain transmembrane domain comprises a beta chain transmembrane domain,
wherein the T cell is configured to express a DS-TCR comprising the first domain-swap chain and the second domain-swap chain.

10. The genetically engineered T cell of claim 9,
wherein the first domain-swap chain further comprises a second chain connecting peptide, but does not comprise a first chain connecting peptide, and wherein the second domain-swap chain further comprises a first chain connecting peptide, but does not comprise a second chain connecting peptide,
wherein:
the first chain connecting peptide comprises an alpha chain connecting peptide and the second chain connecting peptide comprises a beta chain connecting peptide.

11. The genetically engineered T cell of claim 9, wherein the T genetically engineered T cell is configured to express the first domain-swap chain as a first polypeptide and the second domain-swap chain as second polypeptide, and
wherein the first domain-swap chain and second domain-swap chain are separate molecules.

12. The genetically engineered T cell of claim 9, wherein expression of an endogenous TCR is repressed or eliminated.

13. A method of inducing an immune response in a subject, the method comprising:
configuring an isolated T cell to express:
a first domain-swap chain, wherein the first domain-swap chain comprises a first chain transmembrane domain, a second chain variable domain and a second chain constant domain, but does not comprise a first chain variable domain and does not comprise a first chain constant domain; and
a second domain-swap chain, wherein the second domain-swap chain comprises a second chain transmembrane domain, a first chain variable domain and a first chain constant domain, but does not comprise a second chain variable domain and does not comprise a second chain constant domain,
wherein, the first chain variable domain comprises an alpha chain variable domain, the first chain constant domain comprises an alpha chain constant domain, the first chain transmembrane domain comprises an alpha chain transmembrane domain, the second chain variable domain comprises a beta chain variable domain, the second chain constant domain comprises a beta chain constant domain, and the second chain transmembrane domain comprises a beta chain transmembrane domain,
thereby producing a genetically engineered T cell configured to express a domain-swap T cell receptor (DS-TCR) comprising the first domain-swap chain and the second domain-swap chain; and
administering the genetically engineered T cell to the subject.

14. The method of claim 13, wherein the first domain-swap chain further comprises a second chain connecting peptide, but does not comprise a first chain connecting peptide, and wherein the second domain-swap chain further comprises a first chain connecting peptide, but does not comprise a second chain connecting peptide,
wherein:
the first chain connecting peptide comprises an alpha chain connecting peptide and the second chain connecting peptide comprises a beta chain connecting peptide.

15. The method of claim 13, wherein the T cell comprises an autologous cell of the subject.

16. The method of claim 13, wherein the T cell comprises a donor cell that is allogeneic to the subject.

17. The method of claim 13, wherein the T cell comprises a CD4 T cell, or a CD8 T cell or a regulatory T cell.

18. The method of claim 13, wherein the genetically engineered T cell is co-administered with a second genetically engineered T cell population.

19. The method of claim 13, wherein the subject has at least one of: a tumor or a cancer, an infectious disease, an autoimmune disease, or diminished or ineffective or exhausted T cells, and is in need of treatment therefor.

20. The method of claim 13, wherein the T cell is induced to express a plurality of DS-TCR against an array of antigens.

21. The method of claim 13, wherein administering to the subject comprises at least one of intravenous injection, or intraperitoneal injection.

22. The method of claim 13, further comprising monitoring the administered T cell over time.

23. The method of claim 13, wherein the method is repeated.

24. A domain-swap T cell receptor (DS-TCR) comprising: a first domain-swap chain, wherein the first domain-swap chain comprises a first chain transmembrane domain, a second chain variable domain and a second chain constant domain, but does not comprise a first chain variable domain and does not comprise a first chain constant domain; and
a second domain-swap chain, wherein the second domain-swap chain comprises a second chain transmembrane domain, a first chain variable domain and a first chain constant domain, but does not comprise a second chain variable domain and does not comprise a second chain constant domain,
wherein, the first chain variable domain comprises an alpha chain variable domain, the first chain constant domain comprises an alpha chain constant domain, the first chain transmembrane domain comprises an alpha chain transmembrane domain, the second chain variable domain comprises a beta chain variable domain, the second chain constant domain comprises a beta chain constant domain, and the second chain transmembrane domain comprises a beta chain transmembrane domain.

25. The domain-swap T cell receptor of claim 24, wherein the first domain-swap chain further comprises a second chain connecting peptide, but does not comprise a first chain connecting peptide, and wherein the second domain-swap chain further comprises a first chain connecting peptide, but does not comprise a second chain connecting peptide, and
wherein the first chain connecting peptide comprises an alpha chain connecting peptide and the second chain connecting peptide comprises a beta chain connecting peptide.

26. The domain-swap T cell receptor of claim 24, wherein the first domain-swap chain and the second domain-swap chain are expressed by a single expression vector.

27. The domain-swap T cell receptor of claim 24, wherein the first domain-swap chain and the second domain-swap chain are expressed by separate expression vectors.