# Patent

## Title
Therapeutic peptides

## Abstract

The present disclosure provides, in part, compositions comprising an antibody or antibody fragment that immunospecifically binds to MCH class I polypeptide-related sequence A (MICA), or an epitope thereof.

## Background
CLAIM OF PRIORITY
This application is a continuation of International Application No. PCT/US2012/057839, filed Sep. 28, 2012, which claims the benefit of U.S. Provisional Patent Application Ser. No. 61/541,921, filed on Sep. 30, 2011, the entire contents of which are hereby incorporated by reference.


GOVERNMENT SUPPORT
This invention was made with Government support under Grant No. P01 AI045757, awarded by the National Institutes of Health. The Government has certain rights in the invention.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Sep. 27, 2012, is named 53293WO1.txt and is 90,411 bytes in size.
TECHNICAL FIELD
This invention relates to therapeutic compositions (e.g., peptides) related to human subjects.
BACKGROUND
Human subjects exposed to a condition or disease offer a source of antibodies with therapeutic potential and general methods for obtaining such antibodies are known in the art. However, methods for specifically obtaining antibodies with therapeutic potential are generally limited by the low frequency, slow proliferation rate, and low antibody secretion levels of B cells that express such antibodies. For example, memory B cells with defined specificity typically account for only one cell per million peripheral blood mononuclear cells or approximately one milliliter of blood (Lanzavecchia et al., Curr. Opin. Immunol., 21:298-304 (2009): Yoshida et al., Immunol. Rev., 237:117-139 (2010)). The frequency of antibodies with therapeutic potential is likely to be even lower in cancer patients, necessitating the development of novel approaches that enable isolation of such cells with high sensitivity and efficiency.
Conventional methods generally rely on conversion of memory B cells into antibody secreting cells by in vitro culture and/or use of immunized animal models (e.g., mice) (Crotty et al., J. Immunol., 171:4969-4973 (2003): Fecteau et al., Immunology, 128:e353-e365 (2009): Buisman et al., Vaccine, 28:179-186 (2009): Corti et al., PLoS One, 5:e8805 (2010)). For example, following in vitro culture for up to one week, antibodies can be measured in culture supernatants and frequencies of antibody secreting cells assessing using enzyme-linked immunosorbent spot (ELISPOT) assay. Limitations of such methods are reported (Henn et al., J. Immunol., 183:31777-3187 (2009): Cao et al., J. Immunol., Methods, 358:56-65 (2010)). For instances, in vitro culture of memory B cells alters the memory B cell phenotype to resemble plasma cells with distinct functional properties (Jiang et al., Eur. J. Immunol., 37:2205-2213 (2007): Huggins et al., Blood, 109:1611-1619 (2007): Jourdan et al., Blood, 114:5173-5181 (2009)). Limitations for fluorescent antigen-based methods are also reported (Hofer et al., Immunol. Rev., 211:295-302 (2006): Odendahl et al., Blood, 105:1614-1621 (2005); Kunkel et al., Nat. Rev. Immunol., 3:822-829 (2003): Scheid et al., Nature, 458:636-640 (2009): Wu et al., Science, 329:856-861 (2010)).
Improved methods for specifically obtaining or targeting antibodies with therapeutic potential are required.
MICA is a ligand for NKG2D, a C-type lectin-like, type II transmembrane receptor expressed on most human NK cells, γδ T cells, and CD8+ T cells. Upon ligation, NKG2D signals through the adaptor protein DAP10 to evoke perforin dependent cytolysis and to provide co-stimulation. In humans, the NKG2D ligands include MHC class I chain-related protein A (MICA), the closely related MICB, UL-16 binding proteins (ULBP) 1-4, and RAE-1G. While NKG2D ligands are not usually found on healthy tissues, various forms of cellular stress, including DNA damage, may upregulate ligand expression, resulting in their frequent detection in multiple solid and hematologic malignancies, including melanoma. NKG2D activation through ligand positive transformed cells contributes to extrinsic tumor suppression, since NKG2D deficient and wild type mice treated with anti-NKG2D blocking antibodies manifest enhanced tumor susceptibility. Immune escape may be achieved in patients, however, by the shedding of NKG2D ligands from tumor cells, which triggers internalization of surface NKG2D and impaired function of cytotoxic lymphocytes. Soluble NKG2D ligands may also stimulate the expansion of regulatory NKG2D+CD4+Foxp3− T cells that may antagonize anti-tumor cytotoxicity through Fas ligand, IL-10, and TGF-β. MICA is a NKG2D ligand shed from tumor cells, i.e., released from the cell surface into the surrounding medium, and sera from cancer patients typically contain elevated levels of the soluble form (sMICA). MICA shedding is accomplished in part through interactions with the protein disulfide isomerase ERp5, which forms a disulfide bond with a critical cysteine that results in unfolding of the α3 domain, rendering it susceptible to proteolysis by ADAM-10/17 and MMP14.
Angiogenesis is the process of forming new capillaries from preexisting blood vessels and has been implicated as a critical part of tumor growth and dissemination. Tumors stimulate angiogenesis to meet increasing oxygen and nutrient requirements that exceed those that can be met by diffusion alone. Consequently, tumors recruit, remodel and expand existing vascular to meet their metabolic demand. The dependence of growing tumors on new blood vessel formation has made angiogenesis an appealing target for anti-cancer therapies. Many cytokines have been are believed to play a role in the regulation of angiogenesis, including vascular endothelial growth factor (VEGF) family members and the angiopoietins. The angiopioetins were discovered as ligands for the Ties, a family of tyrosine kinases that is selectively expressed in the vascular endothelium. There are four know angiopoietins: angiopoietin-1 (“Ang-1”) through angiopoietin-4 (“Ang-4”). Studies have suggested that angiopoietins (e.g., Ang-1 and Ang-2) may be involved and tumor angiogenesis. With this information, angiopoietins have been identified as potential targets of immune-based cancer therapy.
There is a need to identify new agents that specifically recognize and bind targets of immune-based cancer therapy, such as MICA and angiopoietins. Such agents would be useful for diagnostic screening and therapeutic intervention in disease states that are associated with tumor development.
SUMMARY
The present disclosure provides compositions and methods related to antibodies with therapeutic potential.
In some embodiments, the disclosure provides compositions comprising peptides that immunospecifically bind to MHC class I polypeptide-related sequence A (MICA), or an epitope thereon. In some aspects, peptides of the compositions include complementarity determining region (CDR) 3 of the VH of antibody ID 1, 6, 7, 8 or 9 shown in Table 1 having 5 or fewer conservative amino acid substitutions, and CDR3 of the VL of antibody ID 1, 6, 7, 8 or 9 shown in Table 1 having 5 or fewer conservative amino acid substitutions. In some aspects, such peptides include complementarity determining region (CDR) 3 of the VH of antibody ID 1, 6, 7, 8 or 9 shown in Table 1, and CDR3 of the VL of antibody ID 1, 6, 7, 8 or 9 shown in Table 1. In some aspects, peptides further include CDR2 of the VH of antibody ID 1, 6, 7, 8 or 9 shown in Table 1 having 5 or fewer conservative amino acid substitutions, or CDR2 of the VL of antibody ID 1, 6, 7, 8 or 9 shown in Table 1 having 5 or fewer conservative amino acid substitutions, or both. In some aspects, such peptides include complementarity determining region CDR2 of the VH of antibody ID 1, 6, 7, 8 or 9 shown in Table 1, or CDR2 of the VL of antibody ID 1, 6, 7, 8 or 9 shown in Table 1, or both. In some aspects, peptides further include CDR1 of the VH of antibody ID 1, 6, 7, 8 or 9 shown in Table 1 having 5 or fewer conservative amino acid substitutions, or CDR1 of the VL of antibody ID 1, 6, 7, 8 or 9 shown in Table 1 having 5 or fewer conservative amino acid substitutions, or both. In some aspects, such peptides include complementarity determining region CDR1 of the VH of antibody ID 1, 6, 7, 8 or 9 shown in Table 1, or CDR1 of the VL of antibody ID 1, 6, 7, 8 or 9 shown in Table 1, or both.
In some aspects, peptides are antibody or antibody fragment that include: a VH chain with identity to SEQ ID NO:2, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 1 shown in table 1 having 5 or fewer conservative amino acid substitutions, and regions within SEQ ID NO:2 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 1 shown in table 1; and a VL chain with identity to SEQ ID NO:11, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 1 shown in table 1 having 5 or fewer conservative amino acid substitutions, and regions within SEQ ID NO:11 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 1 shown in table 1. In some aspects, peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:2 and a VL chain comprising SEQ ID NO:11. In some aspects, in addition the peptides, compositions further include one or more (e.g., 1 2, 3, 4, 5, 6, 7, 8, 9, 10, or less than 20) anti-cancer therapeutics. In some aspects, compositions are formulated as pharmaceutical compositions (e.g., for administration to a subject).
In some aspects, peptides are antibody or antibody fragment that include: a VH chain with identity to SEQ ID NO:149, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 6 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:149 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 6 shown in table 1; and a VL chain with identity to SEQ ID NO:151, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 6 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:151 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 6 shown in table 1. In some aspects, peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:149 and a VL chain comprising SEQ ID NO:151. In some aspects, in addition the peptides, compositions further include one or more (e.g., 1 2, 3, 4, 5, 6, 7, 8, 9, 10, or less than 20) anti-cancer therapeutics. In some aspects, compositions are formulated as pharmaceutical compositions (e.g., for administration to a subject).
In some aspects, peptides are antibody or antibody fragment that include: a VH chain with identity to SEQ ID NO:168, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 7 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:168 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 7 shown in table 1; and a VL chain with identity to SEQ ID NO:170, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 7 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:170 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 7 shown in table 1. In some aspects, peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:168 and a VL chain comprising SEQ ID NO:170. In some aspects, in addition the peptides, compositions further include one or more (e.g., 1 2, 3, 4, 5, 6, 7, 8, 9, 10, or less than 20) anti-cancer therapeutics. In some aspects, compositions are formulated as pharmaceutical compositions (e.g., for administration to a subject).
In some aspects, peptides are antibody or antibody fragment that include: a VH chain with identity to SEQ ID NO:186, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 8 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:186 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 8 shown in table 1; and a VL chain with identity to SEQ ID NO:188, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 8 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:188 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 8 shown in table 1. In some aspects, peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:186 and a VL chain comprising SEQ ID NO:188. In some aspects, in addition the peptides, compositions further include one or more (e.g., 1 2, 3, 4, 5, 6, 7, 8, 9, 10, or less than 20) anti-cancer therapeutics. In some aspects, compositions are formulated as pharmaceutical compositions (e.g., for administration to a subject).
In some aspects, peptides are antibody or antibody fragment that include: a VH chain with identity to SEQ ID NO:204, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 9 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:204 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 9 shown in table 1; and a VL chain with identity to SEQ ID NO:206, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 9 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:206 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 9 shown in table 1. In some aspects, peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:204 and a VL chain comprising SEQ ID NO:206. In some aspects, in addition the peptides, compositions further include one or more (e.g., 1 2, 3, 4, 5, 6, 7, 8, 9, 10, or less than 20) anti-cancer therapeutics. In some aspects, compositions are formulated as pharmaceutical compositions (e.g., for administration to a subject).
In some embodiments, the disclosure provides compositions that include one or more peptides that bind to angiopoietin or an epitope thereon. In some aspects, peptides of the compositions include complementarity determining region (CDR) 3 of the VH of antibody ID 2, 3, 4, 5 or 10 shown in Table 1 having 5 or fewer conservative amino acid substitutions, and CDR3 of the VL of antibody ID 2, 3, 4 5 or 10 shown in Table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions. In some aspects, peptides can include complementarity determining region (CDR) 3 of the VH of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1, and CDR3 of the VL of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1. In some aspects, peptides can further include CDR2 of the VH of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1 having 5 or fewer conservative amino acid substitutions, or CDR2 of the VL of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1 having 5 or fewer conservative amino acid substitutions, or both. In some aspects, such peptides can include complementarity determining region CDR2 of the VH of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1, or CDR2 of the VL of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1, or both. In some aspects, peptides can further include CDR1 of the VH of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1 having 5 or fewer conservative amino acid substitutions, or CDR1 of the VL of antibody ID 2, 3, 4, or 5 shown in Table 1 having 5 or fewer conservative amino acid substitutions, or both. In some aspects, such peptides can include complementarity determining region CDR1 of the VH of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1, or CDR1 of the VL of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1, or both.
In some aspects, peptides include an antibody or antibody fragment comprising: a VH chain with identity to SEQ ID NO:20, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 2 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:20 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 2 shown in table 1; and a VL chain with identity to SEQ ID NO:29, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 2 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:29 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 2 shown in table 1. In some aspects, the peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:20 and a VL chain comprising SEQ ID NO:29.
In some aspects, the peptides an antibody or antibody fragment comprising: a VH chain with identity to SEQ ID NO:38, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 3 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:38 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 3 shown in table 1; and a VL chain with identity to SEQ ID NO:47, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 3 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:47 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 3 shown in table 1. In some aspects, peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:38 and a VL chain comprising SEQ ID NO:47.
In some aspects, peptides include an antibody or antibody fragment comprising: a VH chain with identity to SEQ ID NO:56, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 4 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:56 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 4 shown in table 1; and a VL chain with identity to SEQ ID NO:65, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 4 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:65 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 4 shown in table 1. In some aspects, peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:56 and a VL chain comprising SEQ ID NO:65.
In some aspects, peptides include an antibody or antibody fragment comprising: a VH chain with identity to SEQ ID NO:74, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 5 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:74 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 5 shown in table 1; and a VL chain with identity to SEQ ID NO:83, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 5 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:83 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 5 shown in table 1. In some aspects, the peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:74 and a VL chain comprising SEQ ID NO:83. In some aspects, the peptides immunospecifically bind to at least angiopoietin-2. In some aspects, the compositions further include one or more anti-cancer therapeutics. In some aspects, the compositions are formulated as a pharmaceutical composition.
In some aspects, peptides include an antibody or antibody fragment comprising: a VH chain with identity to SEQ ID NO:222, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VH of antibody ID 10 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:222 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VH of antibody ID 10 shown in table 1; and a VL chain with identity to SEQ ID NO:224, wherein regions corresponding to CDR1, CDR2, and CDR3 comprise CDR1, CDR2, and CDR3 of the VL of antibody ID 10 shown in table 1 having 5 or fewer conservative amino acid substitutions within the CDR1, CDR2, and CDR3 regions, and regions within SEQ ID NO:224 corresponding to FR1, FR2, FR3, FR4, comprise amino acid sequences with at least 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, or 100% identity to FR1, FR2, FR3, FR4 of the VL of antibody ID 10 shown in table 1. In some aspects, the peptides include an antibody or antibody fragment comprising a VH chain comprising SEQ ID NO:222 and a VL chain comprising SEQ ID NO:224. In some aspects, the peptides immunospecifically bind to at least angiopoietin-2. In some aspects, the compositions further include one or more anti-cancer therapeutics. In some aspects, the compositions are formulated as a pharmaceutical composition.
In some embodiments, the disclosure includes methods of treating cancer in a subject. In some aspects, methods include administering to a subject a composition comprising an antibody or antigen binding fragment as described herein.
The present disclosure also provides methods of isolating human antibodies from cancer patients following immunotherapy.
In some embodiments, the disclosure includes method of obtaining immune cells directed against a self antigen from a subject, the method comprising identifying a subject exhibiting a positive immune response towards the self antigen, providing a multimeric form of the self antigen, contacting the multimeric form of the self antigen with a sample from the subject exhibiting a positive immune response towards the self antigen, and obtaining immune cells bound to the multimeric form of the self antigen.
In some embodiments, the disclosure includes method of obtaining immune cells from a cancer patient directed against a self antigen, the method comprising identifying a subject exhibiting a positive immune response towards the self antigen; providing a multimeric form of the self antigen; contacting the multimeric form of the self antigen with a sample from the subject exhibiting a positive immune response towards the self antigen; and obtaining immune cells bound to the multimeric form of the self antigen.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.
Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims.



DESCRIPTION OF DRAWINGS
FIG. 1|Nucleic acid sequence of the variable heavy (VH) chain of antibody ID 1 (anti-MHC class I polypeptide-related sequence A (MICA) antibody) (SEQ ID NO:1).
FIG. 2|Amino acid sequence of VH chain of antibody ID 1 (anti-MICA antibody) (SEQ ID NO:2).
FIG. 3|Nucleic acid sequence of the variable light (VL) chain of antibody ID 1 (anti-MICA antibody) (SEQ ID NO:10).
FIG. 4|Amino acid sequence of VL chain of antibody ID 1 (anti-MICA antibody) (SEQ ID NO:11).
FIG. 5|Nucleic acid sequence of the VH chain of antibody ID 2 (anti-angiopoietin-2 antibody) (SEQ ID NO:19).
FIG. 6|Amino acid sequence of VH chain of antibody ID 2 (anti-angiopoietin-2 antibody) (SEQ ID NO:20).
FIG. 7|Nucleic acid sequence of the VL chain of antibody ID 2 (anti-angiopoietin-2 antibody) (SEQ ID NO:28).
FIG. 8|Amino acid sequence of VL chain of antibody ID 2 (anti-angiopoietin-2 antibody) (SEQ ID NO:29).
FIG. 9|Nucleic acid sequence of the VH chain of antibody ID 3 (anti-angiopoietin-2 antibody) (SEQ ID NO:37).
FIG. 10|Amino acid sequence of VH chain of antibody ID 3 (anti-angiopoietin-2 antibody) (SEQ ID NO:38).
FIG. 11|Nucleic acid sequence of the VL chain of antibody ID 3 (anti-angiopoietin-2 antibody) (SEQ ID NO:46).
FIG. 12|Amino acid sequence of VL chain of antibody ID 3 (anti-angiopoietin-2 antibody) (SEQ ID NO:47).
FIG. 13|Nucleic acid sequence of the VH chain of antibody ID 4 (anti-angiopoietin-2 antibody) (SEQ ID NO:55).
FIG. 14|Amino acid sequence of VH chain of antibody ID 4 (anti-angiopoietin-2 antibody) (SEQ ID NO:56).
FIG. 15|Nucleic acid sequence of the VL chain of antibody ID 4 (anti-angiopoietin-2 antibody) (SEQ ID NO:64).
FIG. 16|Amino acid sequence of VL chain of antibody ID 4 (anti-angiopoietin-2 antibody) (SEQ ID NO:65).
FIG. 17|Nucleic acid sequence of the VH chain of antibody ID 5 (anti-angiopoietin-2 antibody) (SEQ ID NO:73).
FIG. 18|Amino acid sequence of VH chain of antibody ID 5 (anti-angiopoietin-2 antibody) (SEQ ID NO:74).
FIG. 19|Nucleic acid sequence of the VL chain of antibody ID 5 (anti-angiopoietin-2 antibody) (SEQ ID NO:82).
FIG. 20|Amino acid sequence of VL chain of antibody ID 5 (anti-angiopoietin-2 antibody) (SEQ ID NO:83).
FIG. 21A-21F|Illustrates exemplary methods for making antibodies from B-cells. (A) Antigen is expressed with a BirA tag for site-specific biotinylation and tetramerization with fluorescently-labeled streptavidin. (B) B cells are stained with tetramer and a panel of monoclonal antibodies. Tetramer+, class-switched memory B cells are single-cell sorted into PCR strips. (C) mRNA amplification is performed with T7 RNA polymerase. (D) Sequencing of PCR products is carried out using 300-400 bp PCR products. (E) Overlap PCR is used for construction of full-length IgG1 heavy chain and kappa/lambda light sequences which are cloned into separate vectors. Vectors are transiently transfected into CHO-S cells for expression of fully human recombinant antibodies. (F) Antibodies are tested for antigen binding and assessed for potential therapeutic properties.
FIGS. 22A-22B|Graphs showing comparison of monomeric and tetrameric antigen for identification of memory B cells. (A) Mono-biotinylated TTCF or CD80 antigens were directly labeled with Alexa-488 fluorophore; tetramers were generated with unlabeled streptavidin. Enriched B cells from each donor were split into three fractions and stained with control CD80 tetramer, TTCF monomer, or TTCF tetramer at the same total antigen concentration of 0.125 μg/mL. FACS plots depict CD19+ CD27+ IgM− class-switched memory B cells; numbers adjacent to the gate represent the percentage of the parental gate. (B) Frequencies of tetramer+ memory B cells detected in three different donors. Numbers are calculated as tetramer+ cells per 1×106 CD19+ memory B cells.
FIGS. 23A-23B|Line graphs showing high affinity binding of TTCF by antibodies generated from plasmablasts and memory B cells. Saturation binding experiments were carried out to determine the affinities of recombinant antibodies. TTCF antigen was labeled with europium, which emits a strong fluorescent signal at 615 nm upon incubation with a chelating reagent. Antibodies were immobilized in a 96-well plate and incubated with TTCF-europium (100 nM to 4 pM) for two hours at 37° C. Fluorescent counts at 615 nm were recorded and KD calculated using non-linear regression analysis. Control antibody (clone 8.18.C5) that was also produced in CHO-S cells was included in all experiments. (A) Recombinant TTCF Abs 1 and 2 were generated from TTCF tetramer+ plasmablasts (donor 1). (B) TTCF antibodies 3, 4, and 5 originated from TTCF tetramer+ memory B cells of three different donors.
FIG. 24|Bar chart showing binding of anti-MICA antibodies to MICA-coated luminex beads.
FIGS. 25A-25O|Line graphs showing binding of anti-MICA antibodies to MICA-coated beads.
FIGS. 26A-26D|Bar graphs showing binding of four human angiopoietin 2 specific antibodies as well as a control antibody to three human angiopoietins (angiopoietin-1, 2 and 4) and ang-like-3. Recombinant angiopoietins were immobilized in an ELISA plate and binding of human recombinant antibodies was detected with europium-labeled streptavidin.
FIGS. 27A-27C|Show graphs and a gel relating to isolation of angiopoietin-specific antibodies from a lung cancer patient. (A) Angiopoietin-2 reactivity of lung cancer patient (L19) serum (diluted 1:1000) determined by ELISA. (B) FACS plot showing PBMC sample (timepoint-10/98) gated on CD19+, CD27+ IgM-B cells with CD19 on the X-axis and fluorescently-tagged angiopoietin-2 on the Y-axis. (C) Heavy, light chain, and hinge region PCR products from 10 angiopoietin-2 reactive memory B-cells isolated from patient L19. The 500 base pair marker is indicated on the left.
FIG. 28|Nucleic acid sequence of the variable heavy (VH) chain of antibody ID 6 (anti-MHC class I polypeptide-related sequence A (MICA) antibody) (SEQ ID NO:148).
FIG. 29|Amino acid sequence of VH chain of antibody 6 (anti-MICA antibody) (SEQ ID NO:149).
FIG. 30|Nucleic acid sequence of the variable light (VL) chain of antibody ID 6 (anti-MICA antibody) (SEQ ID NO:150).
FIG. 31|Amino acid sequence of VL chain of antibody ID 6 (anti-MICA antibody) (SEQ ID NO: 151).
FIG. 32|Nucleic acid sequence of the variable heavy (VH) chain of antibody ID 7 (anti-MHC class I polypeptide-related sequence A (MICA) antibody) (SEQ ID NO:167).
FIG. 33|Amino acid sequence of VH chain of antibody ID 7 (anti-MICA antibody) (SEQ ID NO:168).
FIG. 34|Nucleic acid sequence of the variable light (VL) chain of antibody ID 7 (anti-MICA antibody) (SEQ ID NO:169).
FIG. 35|Amino acid sequence of VL chain of antibody ID 7 (anti-MICA antibody) (SEQ ID NO: 170).
FIG. 36|Nucleic acid sequence of the variable heavy (VH) chain of antibody ID 8 (anti-MHC class I polypeptide-related sequence A (MICA) antibody) (SEQ ID NO:185).
FIG. 37|Amino acid sequence of VH chain of antibody ID 8 (anti-MICA antibody) (SEQ ID NO:186).
FIG. 38|Nucleic acid sequence of the variable light (VL) chain of antibody ID 8 (anti-MICA antibody) (SEQ ID NO:187).
FIG. 39|Amino acid sequence of VL chain of antibody ID 8 (anti-MICA antibody) (SEQ ID NO: 188).
FIG. 40|Nucleic acid sequence of the variable heavy (VH) chain of antibody ID 9 (anti-MHC class I polypeptide-related sequence A (MICA) antibody) (SEQ ID NO:203).
FIG. 41|Amino acid sequence of VH chain of antibody ID 9 (anti-MICA antibody) (SEQ ID NO:204).
FIG. 42|Nucleic acid sequence of the variable light (VL) chain of antibody ID 9 (anti-MICA antibody) (SEQ ID NO:205).
FIG. 43|Amino acid sequence of VL chain of antibody ID 9 (anti-MICA antibody) (SEQ ID NO: 206).
FIG. 44|Nucleic acid sequence of the VH chain of antibody ID 10 (anti-angiopoietin-2 antibody) (SEQ ID NO:221).
FIG. 45|Amino acid sequence of VH chain of antibody ID 10 (anti-angiopoietin-2 antibody) (SEQ ID NO:222).
FIG. 46|Nucleic acid sequence of the VL chain of antibody ID 10 (anti-angiopoietin-2 antibody) (SEQ ID NO:223).
FIG. 47|Amino acid sequence of VL chain of antibody ID 10 (anti-angiopoietin-2 antibody) (SEQ ID NO:224).
FIGS. 48A-G|Line graphs showing assessment of MICA allele-specific binding by recombinant anti-MICA antibodies.
FIG. 49|Line graph showing labeling of autologous tumor cells by anti-MICA antibody CM24002 Ab2.
FIG. 50|A series of FACS plot showing regulation of NKG2D by serum MICA. Human NK cells were incubated with control serum from patient CM24002 and a 1:10 dilution for 48 hours. Indicated antibodies were added at the start of the incubation at a concentration of 10 μg/ml. NKG2D expression was assessed on CD56+ NK cells by flow cytometry.
FIG. 51|A series of FACS plot showing regulation of NKG2D by recombinant MICA. Human NK cells were incubated with recombinant MICA at a concentration of 2 ng/ml for 48 hours. Indicated antibodies were added at the start of the incubation at a concentration of 10 μg/ml. After 48 hours, NKG2D expression was assessed on CD56+ NK cells by flow cytometry.
FIG. 52|Line graph demonstrating enhancement of cell-mediated toxicity by anti-MICA antibody CM24002 Ab2. Human NK cells were incubated with recombinant MICA (2 ng/ml) for 48 hours in the presence of indicated antibodies at 10 μg/ml. The ability of NK cells (effectors) to kill K562 target cells was assessed by measuring LDH release following 4 hour incubation at the indicated ratios.
FIG. 53|Bar graph demonstration cell-mediated toxicity by anti-MICA antibodies CM24002 Ab2 and CM33322 Ab29. Human NK cells were incubated with recombinant MICA (2 ng/ml) for 48 hours in the presence of indicated antibodies at 10 μg/ml. The ability of NK cells (effectors) to kill K562 target cells was assessed by measuring LDH release following 4 hour incubation. NKG2D blocking antibody or Fc blocking antibody was added during the 4 hr incubation of effector and target cells to assess the contribution of Fc receptor and NKG2D to cell-mediated toxicity.
FIG. 54|A series of line graphs showing binding of MICA alpha 3 domain by recombinant anti-MICA antibodies. Recombinant MICA alpha 3 domains were biotinylated and captured on the surface of streptavidin-coated beads. Indicated antibodies were incubated at 10 μg/ml with the beads coated with the individual recombinant protein for 1 hr. Beads were subsequently washed and incubated with FITC-conjugated anti-human IgG secondary antibody. FITC fluorescence was quantified by flow cytometry.
FIG. 55|Line graphs demonstrating labeling of tumor cells by anti-MICA antibodies CM24002 Ab2 and CM33322 Ab29. Fluorescence was determined by flow cytometry.
FIG. 56|Bar graph demonstrating MICA allelic specificity of anti-MICA antibodies CM33322 Ab29 as determined by Luminex assay.
FIG. 57|Bar graphs showing binding of anti-angiopoietin 2 specific antibody anti-Ang6 Ab2 as well as a control antibody to three human angiopoietins (angiopoietin-1, 2 and 4) and ang-like-3. Recombinant angiopoietins were immobilized in an ELISA plate and binding of human recombinant antibodies was detected with europium-labeled streptavidin.



DETAILED DESCRIPTION
The present disclosure is based, in part, on the observation that antibodies directed against therapeutic targets important in a disease can be obtained from human subjects exposed to the disease by labeling of B cells with a tetrameric form of the antigen of interest. As described in the background section above, prior methods are limited at least in that they are inefficient at identifying appropriate B cells in human subjects and/or because they induce any captured B cells to undergo phenotypic changes, thus reducing their value. In contrast, methods are described herein that allow capture of rare memory B cells directed against specific disease-related antigens. As described below, the methods require tetramerization of the disease-related antigen, which process, as demonstrated in the Examples below, enhances the identification of appropriate memory B cells. Specifically, methods herein permit more efficient capture of appropriate memory B cells for increased periods of time following initial exposure of a subject to the antigen. Methods herein also include antibodies (and peptides generated from the sequences of such antibodies) generated using genetic material obtained from memory B cells captured using the methods disclosed herein.
Described herein are human antibodies against MHC class I polypeptide-related sequence A (MICA) and human antibodies targeted against angiopoietin-2. Both types of human antibodies were identified from patients who had received a cell-based cancer vaccine (GM-CSF transduced autologous tumor cells) by methods that entail the use of tetrameric antigens.
In some instances, the disclosure provides methods for specifically obtaining or targeting antibodies with therapeutic potential from select human subjects and therapeutic compositions resulting therefrom. These methods can include: obtaining or targeting immune cells in a human subject, wherein immune cells include but are not limited to, for example, B cells and/or memory B cells, isolating or purifying genetic material (e.g., DNA and/or mRNA) from the obtained or targeted immune cells, and using the isolated or purified genetic material to produce therapeutic compositions, e.g., therapeutic compositions disclosed herein. Further description of the methods is provided under the section entitled “Methods,” below.
In some instances, the disclosure provides therapeutic compositions (e.g., including therapeutic peptides, including antibodies, antibody fragments, antibody derivatives, and/or antibody conjugates) related to antibodies present in subjects that have or had a condition or disease and that exhibited a positive immune response towards the condition or disease.
Therapeutic Compositions
In some instances, therapeutic compositions herein can interact with (e.g., bind, bind specifically and/or bind immunospecifically) binding partners (e.g., an immunogen(s), antigen(s), and/or epitope(s)) related to a disease or condition, wherein interaction between the therapeutic composition and the binding partners results in a positive immune response towards the condition or disease (e.g., a decrease in the level of disease or symptoms thereof in a subject).
In some instances, therapeutic compositions can include peptides that include (e.g., comprise, consist essentially of, or consist of) at least one (e.g., one, two, three, four, five, and/or six) complementarity determining region (CDR) of the variable heavy chain (VH) and/or variable light chain (VL) of antibody ID 1, 2, 3, 4, or 5, 6, 7, 8, 9 or 10, shown in Table 1.
In some instances, therapeutic compositions can include peptides that include (e.g., comprise, consist essentially of, or consist of) at least one (e.g., one, two, three, four, five, and/or six) complementarity determining region (CDR) of the variable heavy chain (VH) and/or variable light chain (VL) of antibody ID 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10, shown in Table 1, and that interact with (e.g., bind, bind specifically and/or bind immunospecifically) to MHC class I polypeptide-related sequence A (MICA (e.g., UniGene Hs.130838)) (e.g., soluble MICA (sMICA)) and/or angiopoietin-2 (e.g., UniGene Hs.583870), including epitopes thereof.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 1, 6, 7, 8 and/or 9 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, peptides can include at least two CDRs, wherein the at least two CDRs are CDRs shown in Table 1 for different antibodies. In other words, CDRs (and FRs and/or AA sequences) shown in Table 1 for antibodies IDs 1, 6, 7, 8 and 9 are interchangeable and can be combined to generate peptides, so long as the peptides bind (e.g., bind specifically and/or bind immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 1, 6, 7, 8 and/or 9 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 1, 6, 7, 8 and/or 9 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 1, 6, 7, 8 and/or 9 shown in Table 1. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 1, 6, 7, 8 and/or 9. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 1, 6, 7, 8 and/or 9 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 1, 6, 7, 8 and/or 9, shown in Table 1. In some instances, such peptides include one of SEQ ID NO:2, 149, 168, 186 or 204 and/or one of SEQ ID NO:11, 151, 170, 188, or 206. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, the affinity of binding between the peptides and MICA can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 6 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 6 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 6 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 6 shown in Table 1. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 6. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 6 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 6, shown in Table 1. In some instances, such peptides include SEQ ID NO:149 and/or SEQ ID NO:151. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, the affinity of binding between the peptides and MICA can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 7 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 7 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 7 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 7 shown in Table 1. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 7. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 7 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 7, shown in Table 1. In some instances, such peptides include SEQ ID NO:168 and/or SEQ ID NO:170. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, the affinity of binding between the peptides and MICA can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 8 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 8 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 8 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 8 shown in Table 1. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 8. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 8 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 8, shown in Table 1. In some instances, such peptides include SEQ ID NO:186 and/or SEQ ID NO:188. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, the affinity of binding between the peptides and MICA can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 9 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 9 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 9 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 9 shown in Table 1. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 9. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 9 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 9, shown in Table 1. In some instances, such peptides include SEQ ID NO:204 and/or SEQ ID NO:206. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to MICA (e.g., human MICA (e.g., soluble MICA (sMICA))). In some instances, the affinity of binding between the peptides and MICA can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 2, 3, 4, 5, and/or 10 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, peptides can include at least two CDRs, wherein the at least two CDRs are CDRs shown in Table 1 for different antibodies. In other words, CDRs (and FRs and/or AA sequences) shown in Table 1 for antibodies IDs 2, 3 4, 5, and 10 are interchangeable and can be combined to generate peptides, so long as the peptides bind (e.g., bind specifically and/or bind immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 2, 3, 4, 5, and/or 10 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 2, 3, 4, 5, and/or 10 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 2, 3, 4, 5, and/or 10 shown in Table 1. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 2, 3, 4, 5, and/or 10. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 2, 3, 4, 5, and/or 10 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 2, 3, 4, 5, and/or 10 5, shown in Table 1. In some instances, such peptides include one of SEQ ID NO:20, 38, 56, 74, or 222 and/or one of SEQ ID NO:29, 47, 65, 83 or 224. In some instances, peptides include one of SEQ ID NO:20, 38, 56, 74, or 222 and one of SEQ ID NO:29, 47, 65, 83 or 224. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2 (e.g, UniGene Hs.583870)).
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 2 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 2 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 2 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 2 shown in Table 1. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 2. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 2 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 2, shown in Table 1. In some instances, such peptides include SEQ ID NO:20 and/or SEQ ID NO:29. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, the affinity of binding between the peptides and angiopoietin-2 can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 3 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 3 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 3 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 3 shown in Table 1. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 3. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 3 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 3, shown in Table 1. In some instances, such peptides include SEQ ID NO:38 and/or SEQ ID NO:47. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, the affinity of binding between the peptides and angiopoietin-2 can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 4 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 4 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 4 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 4 shown in Table 1. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 4. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 4 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 4, shown in Table 1. In some instances, such peptides include SEQ ID NO:56 and/or SEQ ID NO:65. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, the affinity of binding between the peptide and angiopoietin-2 can be between X-Y, for example, X-Y, X-Y. In some instances, the affinity of binding between the peptides and angiopoietin-2 can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 5 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 5 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 5 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 5 shown in Table 1. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 5. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 5 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 5, shown in Table 1. In some instances, such peptides include SEQ ID NO:74 and/or SEQ ID NO:83. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, the affinity of binding between the peptides and angiopoietin-2 can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, therapeutic compositions can include peptides that include at least one CDR of the VH and/or VL of antibody ID 10 shown in Table 1, wherein the peptide binds (e.g., binds specifically and/or binds immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, such peptides include CDR3 of the VH and/or VL of antibody ID 10 shown in Table 1. In some instances, such peptides include CDR3 of the VH and VL of antibody ID 10 and CDR1 and/or CDR2 of the VH and/or VL of antibody ID 10 shown in Table 1. In some instances, such peptides include CDR1, CDR2, and CDR3 of the VH and/or VL of antibody ID 10. In some instances, such peptides include CDR1 CDR2, and CDR3 of the VH and/or VL of antibody ID 10 and at least one of FR1 FR2 FR3, and/or FR4 of the VH and/or VL of antibody ID 10, shown in Table 1. In some instances, such peptides include SEQ ID NO:222 and/or SEQ ID NO:224. In each instance, the peptide can bind (e.g., bind specifically and/or bind immunospecifically) to angiopoietin-2 (e.g., human angiopoietin-2). In some instances, the affinity of binding between the peptides and angiopoietin-2 can be between about 0.1 nM to 1 μM, for example, about 10 nM.
In some instances, peptides that bind to angiopoietin-2 can also bind to angiopoietin-1 (e.g., Unigene Hs.369675) and/or angiopoietin-4 (e.g., Unigene Hs.278973). For example, in some instances, peptides that bind to angiopoietin-2 can also bind specifically and/or immunospecifically relative to other antigens (other than angiopoietin-1) to angiopoietin-1. In some instances, peptides that bind to angiopoietin-2 can also bind specifically and/or immunospecifically relative to other antigens (other than angiopoietin-4) to angiopoietin-4.
In some instances, therapeutic compositions can include peptides that include: SEQ ID NO: 2 and/or SEQ ID NO:11; SEQ ID NO: 149 and/or SEQ ID NO:151; SEQ ID NO: 168 and/or SEQ ID NO:170; SEQ ID NO: 186 and/or SEQ ID NO:188; SEQ ID NO: 204 and/or SEQ ID NO:206; SEQ ID NO:20 and/or SEQ ID NO:29; SEQ ID NO:38 and/or SEQ ID NO:47; SEQ ID NO:56 and/or SEQ ID NO:65; SEQ ID NO:74 and/or SEQ ID NO:83; and SEQ ID NO: 222 and/or SEQ ID NO:224.


















TABLE 1
















Nuc.




VH|








Acid


ID
Target
VL
FR1*
CDR1**
FR2*
CDR2**
FR3*
CDR3**
FR4*
A.A.#
##







 1
Human MICA
VH
QVQLQQ
GGSFTDH
WSWIR
INHSGVT
NYNPS
AKTG
WGQGT
SEQ
SEQ





W
Y
QAPGK
(SEQ ID
LKSRLT
LYYD
LVTVSS
ID
ID





GAGLLKP
(SEQ ID
GLEWIGE
NO: 6)
ISVDTS
DVW
(SEQ ID
NO:
NO:





SETLALT
NO: 4)
(SEQ ID

KSQFSL
GTFR
NO: 9)
2
1





CAVS

NO: 5)

RLTSVT
PRGG

(see
(see





(SEQ ID



AADTA
FDS

FIG.
FIG.





NO: 3)



LYYC
(SEQ ID

2)
1)









(SEQ ID
NO: 8)












NO: 7)






 




VL
DIVMTQS
QSILYSSD
LAWYQ
WAS
IRESG
QQYYSP
FGQGTK
SEQ
SEQ





PD
NKNY
HKPGQPP
(SEQ ID
VPDRF
PCS
LEIQ
ID
ID





SLAVSLG
(SEQ ID
KLLFY
NO: 15)
SGGGSGT
(SEQ ID
(SEQ ID
NO:
NO:





ERATINC
NO: 13)
(SEQ ID

DFTLT
NO: 17)
NO: 18)
11
10





KSS

NO: 14)

ISSLQA


(see
(see





(SEQ ID



EDVAV


FIG.
FIG.





NO: 12)



YYC


4)
3)









(SEQ ID













NO: 16)






 


 6
Human MICA
VH
QVQLQES
GGSISRS
WSWVRQ
IHHIGRS
SYNPSLK
CAKNGYY
GQGTTVT
SEQ
SEQ





GPGLVEP
NW
PPGEGLE
(SEQ ID
SRVTMS
AMDVW
VSS
ID
ID





SGTLSLT
(SEQ ID
WIGE
NO: 
VDKSQN
(SEQ ID
(SEQ ID
NO:
NO:





CTVS
NO: 
(SEQ ID
156)
QFSLRLT
NO: 
NO: 
149
148





(SEQ ID
153)
NO: 

SVTAAD
158)
155)
(see
(see





NO: 

154)

TAVYY


FIG.
FIG.





152)



(SEQ ID


28)
29)









NO: 157)






 




VL
EIVLTQS
QSVSSDF
LAWYQQ
ATS
FRATGIS
CQHYRSS
AQGTKL
SEQ
SEQ





PGTLSLS
(SEQ ID
KPGQAPR
(SEQ ID
DRFSGSG
PPWYTF
DMRRTV
ID
ID





PGERATL
NO: 
LLIY
NO: 
SGTDFSL
(SEQ ID
AAPSV
NO:
NO:





SCRAS
160)
(SEQ ID
162)
TINRLEP
NO: 
(SEQ ID
151
150





(SEQ ID

NO: 

EDFAVYY
164)
NO: 
(see
(see





NO: 

161)

(SEQ ID

165)
FIG.
FIG.





159)



NO: 163)


31)
30)


 


 7
Human MICA
VH
QVQLQES
GASITNG
WSWVRQ
IYLNGNT
NSNPSLK
CAKNAAY
GQGALVT
SEQ
SEQ





GPGLVKP
AW
PPGKGLE
(SEQ ID
SRVIISVD
NLEFW
VSS
ID
ID





SGTLSLT
(SEQ ID
WIGE
NO: 
KSKNHFS
(SEQ ID
(SEQ ID
NO:
NO:





CAVS
NO: 
(SEQ ID
174)
LTLNSVT
NO: 
NO: 
168
167





(SEQ ID
172)
NO: 

AADTAV
176)
177)
(see
(see





NO: 

173)

YY


FIG.
FIG.





171)



(SEQ ID


33)
32)









NO: 166)






 




VL
EIVLTQS
QTVSSPY
VAWYQQ
GAS
TRATGIP
CQQYDRS
GQGTKLE
SEQ
SEQ





PGTLSLS
(SEQ ID
KRGQAP
(SEQ ID
DRFSGSG
YYYTF
IK
ID
ID





PGERATL
NO: 
RLLIY
NO: 
SGTDFTL
(SEQ ID
(SEQ ID
NO:
NO:





SCRAS
179)
(SEQ ID
181)
TISRLEP
NO: 
NO: 
170
169





(SEQ ID

NO: 

EDFAVYY
183)
184)
(see
(see





NO: 

180)

(SEQ ID


FIG.
FIG.





178)



NO: 182)


35)
34)


 


 8
Human MICA
VH
QVQLQES
DASMSD
WSWIRQ
MYSTGSP
YYKPSLK
CASGQHI
GQGTLVT
SEQ
SEQ





GPGLVKP
YH
AAGKGLE
(SEQ ID
GRVTMSI
GGWVPP
VSS
ID
ID





SENLSLT
(SEQ ID
WIGR
NO: 
DTSKNQ
DFW
(SEQ ID
NO:
NO:





CTVS
NO: 
(SEQ ID
192)
FSLKLAS
(SEQ ID
NO: 
186
185





(SEQ ID
190)
NO: 

V
NO: 
195)
(see
(see





NO: 

191)

TAADTAI
194)

FIG.
FIG.





189)



YY


37)
36)









(SEQ ID













NO: 193)






 




VL
DIVMTQT
EGLVYSD
LSWFHQ
KIS
NRFSGVP
CMQATH
GQGTKVE
SEQ
SEQ





PLSSPVT
GDTY
RPGQPPR
(SEQ ID
DRFSGSG
FPWTF
VKR
ID
ID





LGQPASI
(SEQ ID
LLIY
NO: 
AGTDFTL
(SEQ ID
(SEQ ID
NO:
NO:





SCRSS
NO: 
(SEQ ID
199)
KISRVEA
NO: 
NO: 
188
187





(SEQ ID
197)
NO: 

EDVGVY
201)
202)
(see
(see





NO: 

198)

Y


FIG.
FIG.





196)



(SEQ ID


39)
38)









NO: 200)






 


 9
Human MICA
VH
EVQLLES
GFTFSSY
LTWIRQA
ISGSGNN
YYADSVK
CLGVGQ
GHGIPVI
SEQ
SEQ





GGGLVQP
G
PGKGLE
T
GRFTISR
(SEQ ID
VSS
ID
ID





GGSLRLS
(SEQ ID
WVSS
(SEQ ID
DKVKKT
NO: 
(SEQ ID
NO:
NO:





CAAS
NO: 
(SEQ ID
NO: 
LYLQMD
212)
NO: 
204
203





(SEQ ID
208)
NO: 
210)
SLTVGDT

213)
(see
(see





NO: 

209)

AVYY


FIG.
FIG.





207)



(SEQ ID


41)
40)









NO: 211)






 




VL
DIVMTQT
QSLVHRD
LSWFLQ
RIS
NRFSGVP
CMQATQI
GQGTKLE
SEQ
SEQ





PLSSPVT
GNTY
RPGQAPR
(SEQ ID
DRFSGSG
PNTF
IK
ID
ID





LGQPASI
(SEQ ID
LLIY
NO: 
AGTDFTL
(SEQ ID
(SEQ ID
NO:
NO:





SCRSS
NO: 
(SEQ ID
217)
KISRVEA
NO: 
NO: 
206
205





(SEQ ID
215)
NO: 

EDVGVY
219)
220)
(see
(see





NO: 

216)

Y


FIG.
FIG.





214)



(SEQ ID


43)
42)









NO: 218)






 


 2
Angiopoietin-
VH
EVQLVES
GFTFSSY
MSWVRQ
IYWSGGS
YYADSVK
ARGDYYG
WGQGTL
SEQ
SEQ



2

GGGLVQP
A
APGKGLE
T
GRFTI
SGAHFDY
VTVSS
ID
ID





GGSLRLS
(SEQ ID
WVSG
(SEQ ID
SRDISKN
(SEQ ID
(SEQ ID
NO:
NO:





CAAS
NO: 22)
(SEQ ID
NO: 24)
TLYLQM
NO: 26)
NO: 27)
20
19





(SEQ ID

NO: 23)

NSLRAD


(see
(see





NO: 21)



D


FIG.
FIG.









TAVYYC


6)
5)









(SEQ ID













NO: 25)






 




VL
DIVMTQT
QSLVHSD
LSWLQQ
QIS
NRFSGVP
MQGTQF
FGQGTKV
SEQ
SEQ





PLSSPVT
GNTY
RPGQPPR
(SEQ ID
DRFSGS
PRT
EIK
ID
ID





LGQPASI
(SEQ ID
LLIY
NO: 33)
GAGTDF
(SEQ ID
(SEQ ID
NO:
NO:





SCRSS
NO: 31)
(SEQ ID

TLKISRV
NO: 35)
NO: 36)
29
28





(SEQ ID

NO: 32)

EAEDVG


(see
(see





NO: 30)



V YYC


FIG.
FIG.









(SEQ ID


8)
7)









NO: 34)






 


 3
Angiopoietin-
VH
EVQLVES
GFTFSNN
MHWVR
IRSDGNF
RYADSM
ARDYPYS
WGQGTL
SEQ
SEQ



2

GGGLVQP
W
QAPGKGL
T
KGRFTI
IDY
VTVSS
ID
ID





GGSLRLS
(SEQ ID
EWISE
(SEQ ID
SRDNAK
(SEQ ID
(SEQ ID
NO:
NO:





CAAS
NO: 40)
(SEQ ID
NO: 42)
STLYLQ
NO: 44)
NO: 45)
38
37





(SEQ ID

NO: 41)

MNSLRV


(see
(see





NO: 39)



ED


FIG.
FIG.









TGLYYC


10)
9)









(SEQ ID













NO: 43)






 




VL
DIVMTQT
QSLVHSN
LSWLQQ
EIS
KRVSGVP
MQGKQL
FGQGTKL
SEQ
SEQ





PLSSPVT
GNTY
RPGQPPR
(SEQ ID
DRFSGSG
RT
EIK
ID
ID





LGQPASI
(SEQ ID
LLIY
NO: 51)
AGTDFTL
(SEQ ID
(SEQ ID
NO:
NO:





SCTSS
NO: 49)
(SEQ ID

KISRVEA
NO: 53)
NO: 54)
47
46





(SEQ ID

NO: 50)

EDVGVY


(see
(see





NO: 48)



YC


FIG.
FIG.









(SEQ ID


12)
11)









NO: 52)






 


 4
Angiopoietin-
VH
EVQLVES
GFILSNF
MSWVRQ
NFGGRE
YY
ARGD
WGQGILV
SEQ
SEQ



2

GGGLVQP
A
A
NT
ADSVKG
YHGSGAH
TVSS
ID
ID





GGSVRLS
(SEQ ID
PGKGLD
(SEQ ID
RFTI
FDY
(SEQ ID
NO:
NO:





CAAS
NO: 58)
WVSG
NO: 60)
SRDSSKS
(SEQ ID
NO: 63)
56
55





(SEQ ID

(SEQ ID

TLYLQM
NO: 62)

(see
(see





NO: 57)

NO: 59)

NNLRAE


FIG.
FIG.









D


14)
13)









TAVYYC













(SEQ ID













NO: 61)






 




VL
DIVMTQS
QSLL
LSWLHQ
QIS
NRF
MQGTEFP
FGQGTKV
SEQ
SEQ





PLS
HSDGNT
RPGQPPR
(SEQ ID
SGVPDRF
RT
E IK
ID
ID





SPVILGQ
Y
LLIY
NO: 69)
SGS
(SEQ ID
(SEQ ID
NO:
NO:





PASISCRS
(SEQ ID
(SEQ ID

GTGTDF
NO: 71)
NO: 72)
65
64





S
NO: 67)
NO: 68)

TLKISRV


(see
(see





(SEQ ID



EAEDAGI


FIG.
FIG.





NO: 66)



YYC


16)
15)









(SEQ ID













NO: 70)






 


 5
Angiopoietin-
VH
EVQLVES
GFTFR
MSWVRR
IGAESHD
HY
AHHYYYG
WGQ
SEQ
SEQ



2

GGG
TSS
A
T
TDSAEG
SRQKPKD
GTMVSVS
ID
ID





LIQPGGS
(SEQ ID
PGKGLE
(SEQ ID
RFTI
WGDAFD
S
NO:
NO:





LRLSCAT
NO: 76)
WVSA
NO: 78)
SKDYSK
M
(SEQ ID
74
73





S

(SEQ ID

NTVYLQ
(SEQ ID
NO: 81)
(see
(see





(SEQ ID

NO: 77)

MNGLRV
NO: 80)

FIG.
FIG.





NO: 75)



DD


18)
17)









TAIYYC













(SEQ ID













NO: 79)






 




VL
DIQMTQS
QDIS TW
LTWYQQ
GAS
TLEDGVP
QQ
FGQ
SEQ
SEQ





PSS
(SEQ ID
RAGKAP
(SEQ ID
S
SHSFPYT
GTQLGIS
ID
ID





VSASVGD
NO: 85)
NLLIY
NO: 87)
RFSGSGS
(SEQ ID
(SEQ ID
NO:
NO:





RVTITCR

(SEQ ID

GTD
NO: 89)
NO: 90)
83
82





AS

NO: 86)

FTLTIDS


(see
(see





(SEQ ID



LQPDDF


FIG.
FIG.





NO: 84)



ATYYC


20)
19)









(SEQ ID













NO: 88)






 


10
Angiopoietin-
VH
EVQLVES
GFLISSYF
MSWVRQ
IYSDGST
YYVDSVK
CATRHLN
GQGTLVT
SEQ
SEQ



2

GGGLIQP
(SEQ ID
APGKGPE
(SEQ ID
GRFTIST
YDGDHW
VSSASTK
ID
ID





GGSLRLS
NO: 
WVSV
NO: 
DNSKNT
(SEQ ID
(SEQ ID
NO:
NO:





CAAS
226)
(SEQ ID
228)
LYLQMN
NO: 
NO: 
222
221





(SEQ ID

NO: 

SLRAEDT
230)
175)
(see
(see





NO: 

227)

ARYY


FIG.
FIG.





225)



(SEQ ID


45)
44)









NO: 229)






 




VL
DVVMTQ
QSLVHSD
LNWFHQ
KVS
KRDSGV
CMQGTH
GQGTKVE
SEQ
SEQ





SPLSLPV
GNTY
RPGQSPR
(SEQ ID
PDRFSGS
WPTF
IKRTVAA
ID
ID





TLGQPAS
(SEQ ID
RLIY
NO: 
GSGSDFT
(SEQ ID
(SEQ ID
NO:
NO:





ISCRSS
NO: 
(SEQ ID
234)
LKISRVE
NO: 
NO: 
224
223





(SEQ ID
232)
NO: 

AEDVGIY
236)
237)
(see
(see





NO: 

233)

Y


FIG.
FIG.





231)



(SEQ ID


47)
46)









NO: 235)





*Sequences include sequences or variants with (e.g., with at least) 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, and/or 100% sequence identity to the sequences shown.


**Sequences can include one, two, three, four, five, less than five, or less than ten conservative amino acid modifications.


#Sequences include sequences or variants with (e.g., with at least) 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, and/or 100% sequence identity to the sequences shown, e.g., within regions corresponding to FR1, FR2, FR3, and/or FR4, and/or one, two, three, four, five, less than 5, or less than ten conservative amino acid modifications within regions corresponding to CDRs 1, 2, and/or 3.


##Sequences include sequences or variants with (e.g., with at least) 80%, 85%, 90%, 95%, 96%, 97%, 98, 99%, and/or 100% sequence identity to the sequences shown, wherein the sequences encode the corresponding AA.


A.A.# shows the VH or VL amino acid sequence.


Nuc. Acid## shows the VH or VL nucleic acid sequence.


While CDR and FR regions are shown above, such regions can also be defined according to Kabat (Sequences of Proteins of Immunological Interest (National Institutes of Health, Bethesda, Md., 1987 and 1991)). Amino acid numbering of antibodies or antigen binding fragments is also according to that of Kabat.






In some instances, therapeutic compositions can include peptides, including for example, antibodies, including full length and/or intact antibodies, or antibody fragments. An “antibody” is an immunoglobulin molecule capable of specific binding to a target, such as a carbohydrate, polynucleotide, lipid, polypeptide, etc., through at least one antigen recognition site, located in the variable region of the immunoglobulin molecule. As used herein, the term “antibody” encompasses not only intact polyclonal or monoclonal antibodies, but also any antigen binding fragment (i.e., “antigen-binding portion”) or single chain thereof, fusion proteins comprising an antibody, and any other modified configuration of the immunoglobulin molecule that comprises an antigen recognition site including. An antibody includes an antibody of any class, such as IgG, IgA, or IgM (or sub-class thereof), and the antibody need not be of any particular class. Depending on the antibody amino acid sequence of the constant region of its heavy chains, immunoglobulins can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2. The heavy-chain constant regions that correspond to the different classes of immunoglobulins are called alpha, delta, epsilon, gamma, and mu, respectively. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known. Exemplary antibodies and antibody fragments include, but are not limited to, monoclonal antibodies (including full-length monoclonal antibodies), polyclonal antibodies, multispecific antibodies formed from at least two different epitope binding fragments (e.g., bispecific antibodies), camelised antibodies, chimeric antibodies, single-chain Fvs (scFv), single-chain antibodies, single domain antibodies, domain antibodies, Fab fragments, F(ab′)2 fragments, antibody fragments that exhibit the desired biological activity (e.g. the antigen binding portion), disulfide-linked Fvs (dsFv), and anti-idiotypic (anti-Id) antibodies (including, e.g., anti-Id antibodies to antibodies of the invention), intrabodies, and epitope-binding fragments of any of the above. Antibodies or antibody fragments can be human or humanized.
Fragments of antibodies are suitable for use in the methods provided so long as they retain the desired affinity and specificity of the full-length antibody. Thus, a fragment of an anti-MICA antibody or the anti-Angiopoietin antibody will retain an ability to bind to MICA or angiopoietin, respectively, in the Fv portion and the ability to bind the Fc receptor on dendritic cells in the FC portion. Such fragments are characterized by properties similar to the corresponding full-length anti-MICA antibody or the anti-Angiopoietin antibody, that is, the fragments will specifically bind a human MICA antigen or the angiopoietin antigen, respectively, expressed on the surface of a human cell or the corresponding sMICA antigen that has been shed into the media.
An Fv fragment is an antibody fragment which contains a complete antigen recognition and binding site. This region consists of a dimer of one heavy and one light chain variable domain in tight association, which can be covalent in nature, for example in scFv. It is in this configuration that the three CDRs of each variable domain interact to define an antigen binding site on the surface of the VH-VL dimer. Collectively, the six CDRs or a subset thereof confer antigen binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) can have the ability to recognize and bind antigen, although usually at a lower affinity than the entire binding site.
Single-chain Fv or (scFv) antibody fragments comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain. Generally the Fv polypeptide further comprises a polypeptide linker between the VH and VL domains, which enables the scFv to form the desired structure for antigen binding.
The Fab fragment contains a variable and constant domain of the light chain and a variable domain and the first constant domain (CH1) of the heavy chain. F(ab′)2 antibody fragments comprise a pair of Fab fragments which are generally covalently linked near their carboxy termini by hinge cysteines between them. Other chemical couplings of antibody fragments are also known in the art.
Diabodies are small antibody fragments with two antigen-binding sites, which fragments comprise a VH connected to a VL in the same polypeptide chain (VH and VL). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites.
Linear antibodies comprise a pair of tandem Fd segments (VH-CH1-VH-CH1) which, together with complementary light chain polypeptides, form a pair of antigen binding regions. Linear antibodies can be bispecific or monospecific.
Antibodies and antibody fragments of the present disclosure can be modified in the Fc region to provide desired effector functions or serum half-life. In some instances, the Fc region can be conjugated to PEG or albumin to increase the serum half-life, or some other conjugation that results in the desired effect. Alternatively, where it is desirable to eliminate or reduce effector function, so as to minimize side effects or therapeutic complications, certain other Fc regions may be used.
Human and humanized antibodies include antibodies having variable and constant regions derived from (or having the same amino acid sequence as those derived from) human germline immunoglobulin sequences. Human antibodies may include amino acid residues not encoded by human germline immunoglobulin sequences (e.g., mutations introduced by random or site-specific mutagenesis in vitro or by somatic mutation in vivo), for example in the CDRs and in particular CDR3.
A “CDR” of a variable domain are amino acid residues within the hypervariable region that are identified in accordance with the definitions of the Kabat, Chothia, the cumulation of both Kabat and Chothia, AbM, contact, and/or conformational definitions or any method of CDR determination well known in the art. Antibody CDRs may be identified as the hypervariable regions originally defined by Kabat et al. See, e.g., Kabat et al., 1992, Sequences of Proteins of Immunological Interest, 5th ed., Public Health Service, NIH, Washington D.C. The positions of the CDRs may also be identified as the structural loop structures originally described by Chothia and others. See, e.g., Chothia et al., 1989, Nature 342:877-883. Other approaches to CDR identification include the “AbM definition,” which is a compromise between Kabat and Chothia and is derived using Oxford Molecular's AbM antibody modeling software (now Accelrys®), or the “contact definition” of CDRs based on observed antigen contacts, set forth in MacCallum et al., 1996, J. Mol. Biol., 262:732-745. In another approach, referred to herein as the “conformational definition” of CDRs, the positions of the CDRs may be identified as the residues that make enthalpic contributions to antigen binding. See, e.g., Makabe et al., 2008, Journal of Biological Chemistry, 283:1156-1166. Still other CDR boundary definitions may not strictly follow one of the above approaches, but will nonetheless overlap with at least a portion of the Kabat CDRs, although they may be shortened or lengthened in light of prediction or experimental findings that particular residues or groups of residues or even entire CDRs do not significantly impact antigen binding. As used herein, a CDR may refer to CDRs defined by any approach known in the art, including combinations of approaches. The methods used herein may utilize CDRs defined according to any of these approaches. For any given embodiment containing more than one CDR, the CDRs may be defined in accordance with any of Kabat, Chothia, extended, AbM, contact, and/or conformational definitions.
In some instances, amino acid sequences of the peptides disclosed herein can be modified and varied to create peptide variants (e.g., peptides with a defined sequence homology to the peptides disclosed herein), for example, so long as the antigen binding property of the peptide variant is maintained or improved relative to the unmodified peptide (antigen binding properties of any modified peptide can be assessed using the in vitro and/or in vivo assays described herein and/or techniques known in the art).
While peptide variants are generally observed and discussed at the amino acid level, the actual modifications are typically introduced or performed at the nucleic acid level. For example, variants with 80%, 85%, 90%, 95%, 96%, 97%, 98, or 99% amino acid sequence identity to the peptides shown in Table 1 can be generated by modifying the nucleic acids encoding SEQ ID NOs:1, 10, 19, 28, 37, 46, 55, 64, 73, and/or 82 or portions/fragments thereof, using techniques (e.g., cloning techniques) known in the art and/or that are disclosed herein.
Amino acid sequence modifications typically fall into one or more of three classes: substitutional, insertional, or deletional modifications. Insertions include amino and/or terminal fusions as well as intra-sequence insertions of single or multiple amino acid residues. Insertions ordinarily will be smaller insertions than those of amino or carboxyl terminal fusions, for example, on the order of one to four residues. Deletions are characterized by the removal of one or more amino acid residues from the protein sequence. Typically, no more than about from 2 to 6 residues are deleted at any one site within the protein molecule. Amino acid substitutions are typically of single residues, but can occur at a number of different locations at once; insertions usually will be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues. Deletions or insertions can be made in adjacent pairs, i.e., a deletion of 2 residues or insertion of 2 residues. Substitutions, deletions, insertions or any combination thereof may be combined to arrive at a final construct. The mutations must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure. Substitutional modifications are those in which at least one residue has been removed and a different residue inserted in its place. In some instances, substitutions can be conservative amino acid substitutions. In some instances, peptides herein can include one or more conservative amino acid substitutions relative to a peptide shown in Table 1. For example, variants can include 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-30, 30-40, or 40-50 conservative amino acid substitutions relative to a peptide shown in Table 1. Alternatively, variants can include 50 or fewer, 40 or fewer, 30 or fewer, 20 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer conservative amino acid substitutions relative to a peptide shown in Table 1. Such substitutions generally are made in accordance with the following Table 2 and are referred to as conservative substitutions. Methods for predicting tolerance to protein modification are known in the art (see, e.g., Guo et al., Proc. Natl. Acad. Sci., USA, 101(25):9205-9210 (2004)).







TABLE 2







Conservative Amino Acid Substitutions










Amino Acid
Substitutions (others are known in the art)







Ala
Ser, Gly, Cys



Arg
Lys, Gln, His



Asn
Gln, His, Glu, Asp



Asp
Glu, Asn, Gln



Cys
Ser, Met, Thr



Gln
Asn, Lys, Glu, Asp, Arg



Glu
Asp, Asn, Gln



Gly
Pro, Ala, Ser



His
Asn, Gln, Lys



Ile
Leu, Val, Met, Ala



Leu
Ile, Val, Met, Ala



Lys
Arg, Gln, His



Met
Leu, Ile, Val, Ala, Phe



Phe
Met, Leu, Tyr, Trp, His



Ser
Thr, Cys, Ala



Thr
Ser, Val, Ala



Trp
Tyr, Phe



Tyr
Trp, Phe, His



Val
Ile, Leu, Met, Ala, Thr










In some instances, substitutions are not conservative. For example, an amino acid in a peptide shown in Table 1 can be replaced with an amino acid that can alter some property or aspect of the peptide. In some instances, non-conservative amino acid substitutions can be made, e.g., to change the structure of a peptide, to change the binding properties of a peptide (e.g., to increase or decrease the affinity of binding of the peptide to an antigen and/or to alter increase or decrease the binding specificity of the peptide to the antigen).
In some instances, peptides and/or peptide variants can include or can be fragments of the peptides shown in Table 1. Such fragments can include, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 50-100, 101-150, fewer amino acids than the CDRs, FRs, and/or AAs shown in Table 1, e.g., so long as the fragments retain at least at portion of the binding properties of the full-length peptide (e.g., at least 50%, 60%, 70%, 80%, 90%, or 100% of the binding properties of the full-length peptide). Truncations can be made at the amino-terminus, the carboxy-terminus, and/or within the peptides herein.
In some instances, the interacting face of a peptide variant can be the same (e.g., substantially the same) as an unmodified peptide, e.g., to alter (e.g., increase or decrease), preserve, or maintain the binding properties of the peptide variant relative to the unmodified peptide. Methods for identifying the interacting face of a peptide are known in the art (Gong et al., BMC: Bioinformatics, 6:1471-2105 (2007); Andrade and Wei et al., Pure and Appl. Chem., 64(11):1777-1781 (1992); Choi et al., Proteins: Structure, Function, and Bioinformatics, 77(1):14-25 (2009); Park et al., BMC: and Bioinformatics, 10:1471-2105 (2009).
Those of skill in the art readily understand how to determine the identity of two polypeptides (e.g., an unmodified peptide and a peptide variant). For example, identity can be calculated after aligning the two sequences so that the identity is at its highest level. Another way of calculating identity can be performed by published algorithms. Optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman, Adv. Appl. Math, 2:482 (1981), by the identity alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by inspection.
The same types of identity can be obtained for nucleic acids by, for example, the algorithms disclosed in Zuker, Science 244:48-52 (1989); Jaeger et al., Proc. Natl. Acad. Sci. USA 86:7706-10 (1989); Jaeger et al., Methods Enzymol. 183:281-306 (1989), which are herein incorporated by reference for at least material related to nucleic acid alignment. It is understood that any of the methods typically can be used and that in certain instances the results of these various methods may differ, but the skilled artisan understands if identity is found with at least one of these methods, the sequences would be said to have the stated identity and to be disclosed herein.
In some instances, as described in more detail under the methods section below, therapeutic compositions disclosed herein can be produced using genetic material (e.g., DNA and/or mRNA) isolated and/or purified from immune cells (e.g., B cells, including memory B cells) obtained using the methods disclosed herein. Once such genetic material has been obtained, methods for using it to produce the therapeutic compositions disclosed herein are known in the art and/or are summarized below.
In some instances, peptides can include a detectable label. As used herein, a “label” refers to a moiety that has at least one element, isotope, or functional group incorporated into the moiety which enables detection of the peptide to which the label is attached. Labels can be directly attached (ie, via a bond) or can be attached by a linker (e.g., such as, for example, a cyclic or acyclic, branched or unbranched, substituted or unsubstituted alkylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted alkenylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted alkynylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroalkylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroalkenylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroalkynylene; substituted or unsubstituted arylene; substituted or unsubstituted heteroarylene; or substituted or unsubstituted acylene, or any combination thereof, which can make up a linker). Labels can be attached to a peptide at any position that does not interfere with the biological activity or characteristic of the inventive polypeptide that is being detected.
Labels can include: labels that contain isotopic moieties, which may be radioactive or heavy isotopes, including, but not limited to 2H, 3H, 13C, 14C, 15N, 31P, 32P, 35S, 67Ga, 99mTc (Tc-99m), 111In, 123I, 125I, 169Yb, and 186Re; labels that include immune or immunoreactive moieties, which may be antibodies or antigens, which may be bound to enzymes {e.g., such as horseradish peroxidase); labels that are colored, luminescent, phosphorescent, or include fluorescent moieties (e.g., such as the fluorescent label FITC); labels that have one or more photoaffinity moieties; labels that have ligand moieties with one or more known binding partners (such as biotin-streptavidin, FK506-FKBP, etc.).
In some instances, labels can include one or more photoaffinity moieties for the direct elucidation of intermolecular interactions in biological systems. A variety of known photophores can be employed, most relying on photoconversion of diazo compounds, azides, or diazirines to nitrenes or carbenes (see, e.g., Bayley, H., Photogenerated Reagents in Biochemistry and Molecular Biology (1983), Elsevier, Amsterdam, the entire contents of which are incorporated herein by reference). In certain embodiments of the invention, the photoaffinity labels employed are o-, m- and p-azidobenzoyls, substituted with one or more halogen moieties, including, but not limited to 4-azido-2,3,5,6-tetrafluorobenzoic acid.
Labels can also be or can serve as imaging agents. Exemplary imaging agents include, but are not limited to, those used in positron emissions tomography (PET), computer assisted tomography (CAT), single photon emission computerized tomography, x-ray, fluoroscopy, and magnetic resonance imaging (MRI); anti-emetics; and contrast agents. Exemplary diagnostic agents include but are not limited to, fluorescent moieties, luminescent moieties, magnetic moieties; gadolinium chelates (e.g., gadolinium chelates with DTPA, DTPA-BMA, DOTA and HP-DO3A), iron chelates, magnesium chelates, manganese chelates, copper chelates, chromium chelates, iodine-based materials useful for CAT and x-ray imaging, and radionuclides. Suitable radionuclides include, but are not limited to, 123I, 125I, 130I, 131I, 133I, 135I, 47Sc, 72As, 72Se, 90Y, 88Y, 97Ru, 100Pd, 101mRh, 119Sb, 128Ba, 197Hg, 211At, 212Bi, 212Pb, 109Pd, 111In, 67Ga, 68Ga, 67Cu, 75Br, 77Br, 99mTc, 14C, 13N, 15O, 32P, 33P and 18F.
Fluorescent and luminescent moieties include, but are not limited to, a variety of different organic or inorganic small molecules commonly referred to as “dyes,” “labels,” or “indicators.” Examples include, but are not limited to, fluorescein, rhodamine, acridine dyes, Alexa dyes, cyanine dyes, etc. Fluorescent and luminescent moieties may include a variety of naturally occurring proteins and derivatives thereof, e.g., genetically engineered variants. For example, fluorescent proteins include green fluorescent protein (GFP), enhanced GFP, red, blue, yellow, cyan, and sapphire fluorescent proteins, reef coral fluorescent protein, etc. Luminescent proteins include luciferase, aequorin and derivatives thereof. Numerous fluorescent and luminescent dyes and proteins are known in the art (see, e.g., U.S. Patent Publication 2004/0067503; Valeur, B., “Molecular Fluorescence: Principles and Applications,” John Wiley and Sons, 2002; and Handbook of Fluorescent Probes and Research Products, Molecular Probes, 9th edition, 2002).
The term “purified” as used herein, refers to other molecules, e.g. polypeptide, nucleic acid molecule that have been identified and separated and/or recovered from a component of its natural environment. Thus, in one embodiment the antibodies of the invention are purified antibodies wherein they have been separated from one or more components of their natural environment.
The term “epitope” as used herein refers to a protein determinant capable of binding to an antibody. Epitopes usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics. Conformational and non-conformational epitopes are distinguished in that the binding to the former but not the latter is lost in the presence of denaturing solvents.
In some instances, the disclosure provides nucleotide sequences corresponding to (e.g., encoding) the disclosed peptides (e.g., disclosed in Table 1). These sequences include all degenerate sequences related to the disclosed peptides, i.e., all nucleic acids having a sequence that encodes one particular peptide and variants and derivatives thereof. Thus, while each particular nucleic acid sequence may not be written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed polypeptide sequences.
In some instances, nucleic acids of the disclosed can include expression vectors. Examples of suitable vectors include, but are not limited to, plasmids, artificial chromosomes, such as BACs, YACs, or PACs, and viral vectors.
The provided vectors also can include, for example, origins of replication and/or markers. A marker gene can confer a selectable phenotype, e.g., antibiotic resistance, on a cell. The marker product is used to determine if the vector has been delivered to the cell and once delivered is being expressed. Examples of selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hygromycin, puromycin, and blasticidin. When such selectable markers are successfully transferred into a mammalian host cell, the transformed mammalian host cell can survive if placed under selective pressure. Examples of other markers include, for example, the E. coli lacZ gene, green fluorescent protein (GFP), and luciferase. In addition, an expression vector can include a tag sequence designed to facilitate manipulation or detection (e.g., purification or localization) of the expressed polypeptide. Tag sequences, such as GFP, glutathione S-transferase (GST), polyhistidine, c-myc, hemagglutinin, or FLAGTM tag (Kodak; New Haven, Conn.) sequences typically are expressed as a fusion with the encoded polypeptide. Such tags can be inserted anywhere within the polypeptide including at either the carboxyl or amino terminus.
In some instances, the disclosure includes cells comprising the nucleic acids (e.g., vectors) and/or peptides disclosed herein. Cells can include, for example, eukaryotic and/or prokaryotic cells. In general, cells that can be used herein are commercially available from, for example, the American Type Culture Collection (ATCC), P.O. Box 1549, Manassas, Va. 20108. See also F. Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., (1998). Transformation and transfection methods useful in the generation of the cells disclosed herein are described, e.g., in F. Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., (1998).
Pharmaceutical Formulations
In some instances, therapeutic compositions disclosed herein can include other compounds, drugs, and/or agents used for the treatment of cancer. Such compounds, drugs, and/or agents can include, for example, chemotherapy drugs, small molecule drugs or antibodies that stimulate the immune response to a given cancer. In some instances, therapeutic compositions can include, for example, one or more peptides disclosed herein and one or more of an anti-CTLA-4 antibody or peptide, an anti-PD-1 antibody or peptide, and/or an anti-PDL-1 antibody or peptide. For example, in some instances, therapeutic compositions disclosed herein can be combined with one or more (e.g., one, two, three, four, five, or less than ten) compounds.
In some instances, therapeutic compositions disclosed herein can include other compounds including histone deacetylase inhibitors (“HDAC”) inhibitors. Examples of HDAC inhibitors include, for example, hydroxamic acids such as, vorinostat (Zolinza®), suberoylanilide hydroxamic acid (SAHA)(Merck), Trichostatin A (TSA), LAQ824 (Novartis), Panobinostat (LBH589) (Novartis), Belinostat (PXD101)(CuraGen), and ITF2357 (Italfarmaco SpA); Cyclic tetrapeptides such as the depsipeptide (romidepsin, FK228) (Gloucester Pharmaceuticals); benzamides such as Entinostat (SNDX-275/MS-275)(Syndax Pharmaceuticals), and MGCD0103 (Celgene); Short-chain aliphatic acids, such as, valproic acid, phenylbutyrate, and AN-9 (PivanexTM) (Titan Pharmaceutical); CHR-3996 (Chroma Therapeutics), and CHR-2845 (Chroma Therapeutics).
In some instances, therapeutic compositions disclosed herein can include other compounds including proteasome inhibitors, including, for example, Bortezomib, (Millennium Pharmaceuticals), NPI-0052 (Nereus Pharmaceuticals), Carfilzomib (PR-171)(Onyx Pharmaceuticals), CEP 18770, and MLN9708
In some instances, the therapeutic compositions disclosed herein can include alkylating agents such as mephalan and topoisomerase inhibitors such as Adriamycin (doxorubicin) have been shown to increase MICA expression, which could enhance efficacy of an anti-MICA monoclonal antibody.
In some instances, therapeutic compositions disclosed herein can be formulated for use as or in pharmaceutical compositions. Such compositions can be formulated or adapted for administration to a subject via any route, e.g., any route approved by the Food and Drug Administration (FDA). Exemplary methods are described in the FDA's CDER Data Standards Manual, version number 004 (which is available at fda.give/cder/dsm/DRG/drg00301.htm).
In some instances, pharmaceutical compositions can include an effective amount of one or more peptides. The terms “effective amount” and “effective to treat,” as used herein, refer to an amount or a concentration of one or more peptides for a period of time (including acute or chronic administration and periodic or continuous administration) that is effective within the context of its administration for causing an intended effect or physiological outcome.
In some instances, pharmaceutical compositions can include one or more peptides and any pharmaceutically acceptable carrier, adjuvant and/or vehicle. In some instances, pharmaceuticals can further include one or more additional therapeutic agents in amounts effective for achieving a modulation of disease or disease symptoms.
The term “pharmaceutically acceptable carrier or adjuvant” refers to a carrier or adjuvant that may be administered to a patient, together with a peptide of this invention, and which does not destroy the pharmacological activity thereof and is nontoxic when administered in doses sufficient to deliver a therapeutic amount of the compound.
Pharmaceutically acceptable carriers, adjuvants and vehicles that may be used in the pharmaceutical compositions of this invention include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, self-emulsifying drug delivery systems (SEDDS) such as d-α-tocopherol polyethyleneglycol 1000 succinate, surfactants used in pharmaceutical dosage forms such as Tweens or other similar polymeric delivery matrices, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, polyethylene glycol and wool fat. Cyclodextrins such as α-, β-, and γ-cyclodextrin, may also be advantageously used to enhance delivery of compounds of the formulae described herein.
The pharmaceutical compositions of this invention may contain any conventional non-toxic pharmaceutically-acceptable carriers, adjuvants or vehicles. In some cases, the pH of the formulation may be adjusted with pharmaceutically acceptable acids, bases or buffers to enhance the stability of the formulated compound or its delivery form. The term parenteral as used herein includes subcutaneous, intracutaneous, intravenous, intramuscular, intra-articular, intraarterial, intrasynovial, intrasternal, intrathecal, intralesional and intracranial injection or infusion techniques.
Pharmaceutical compositions can be in the form of a solution or powder for inhalation and/or nasal administration. Such compositions may be formulated according to techniques known in the art using suitable dispersing or wetting agents (such as, for example, Tween 80) and suspending agents. The sterile injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are mannitol, water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil may be employed including synthetic mono- or diglycerides. Fatty acids, such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated versions. These oil solutions or suspensions may also contain a long-chain alcohol diluent or dispersant, or carboxymethyl cellulose or similar dispersing agents which are commonly used in the formulation of pharmaceutically acceptable dosage forms such as emulsions and or suspensions. Other commonly used surfactants such as Tweens or Spans and/or other similar emulsifying agents or bioavailability enhancers which are commonly used in the manufacture of pharmaceutically acceptable solid, liquid, or other dosage forms may also be used for the purposes of formulation.
Pharmaceutical compositions can be orally administered in any orally acceptable dosage form including, but not limited to, capsules, tablets, emulsions and aqueous suspensions, dispersions and solutions. In the case of tablets for oral use, carriers which are commonly used include lactose and corn starch. Lubricating agents, such as magnesium stearate, are also typically added. For oral administration in a capsule form, useful diluents include lactose and dried corn starch. When aqueous suspensions and/or emulsions are administered orally, the active ingredient may be suspended or dissolved in an oily phase is combined with emulsifying and/or suspending agents. If desired, certain sweetening and/or flavoring and/or coloring agents may be added.
Alternatively or in addition, pharmaceutical compositions can be administered by nasal aerosol or inhalation. Such compositions are prepared according to techniques well-known in the art of pharmaceutical formulation and may be prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other solubilizing or dispersing agents known in the art.
In some embodiments, the present disclosure provides methods for using any one or more of the peptides or pharmaceutical compositions (indicated below as ‘X’) disclosed herein in the following methods:
Substance X for use as a medicament in the treatment of one or more diseases or conditions disclosed herein (e.g., cancer, referred to in the following examples as ‘Y’). Use of substance X for the manufacture of a medicament for the treatment of Y; and substance X for use in the treatment of Y.
In some instances, therapeutic compositions disclosed herein can be formulated for sale in the US, import into the US, and/or export from the US.
Methods
In some instances, methods can include selection of a human subject who has or had a condition or disease and who exhibits or exhibited a positive immune response towards the condition or disease. In some instances, suitable subjects include, for example, subjects who have or had a condition or disease but that resolved the disease or an aspect thereof, present reduced symptoms of disease (e.g., relative to other subjects (e.g., the majority of subjects) with the same condition or disease), and/or that survive for extended periods of time with the condition or disease (e.g., relative to other subjects (e.g., the majority of subjects) with the same condition or disease), e.g., in an asymptomatic state (e.g., relative to other subjects (e.g., the majority of subjects) with the same condition or disease). In some instances, subjects can be selected if they have been vaccinated (e.g., previously vaccinated and/or vaccinated and re-vaccinated (e.g., received a booster vaccine)) against a condition or disease.
The term “subject,” as used herein, refers to any animal. In some instances, the subject is a mammal. In some instances, the term “subject”, as used herein, refers to a human (e.g., a man, a woman, or a child). Samples for use in the methods can include serum samples, e.g., obtained from the selected subject.
In some instances, subject selection can include obtaining a sample from a subject (e.g., a candidate subject) and testing the sample for an indication that the subject is suitable for selection. In some instances, the subject can be confirmed or identified, e.g. by a health care professional, as having had or having a condition or disease. In some instances, exhibition of a positive immune response towards a condition or disease can be made from patient records, family history, and/or detecting an indication of a positive immune response. In some instances multiple parties can be included in subject selection. For example, a first party can obtain a sample from a candidate subject and a second party can test the sample. In some instances, subjects can be selected and/or referred by a medical practitioner (e.g., a general practitioner). In some instances, subject selection can include obtaining a sample from a selected subject and storing the sample and/or using the in the methods disclosed herein. Samples can include, for example, cells or populations of cells.
In some instances, obtaining or targeting immune cells can include one or more and/or combinations of, for example: obtaining or providing a tetrameric immunogen that can bind (e.g., bind specifically) to a target immune cell; contacting the tetrameric immunogen with a sample; detecting the tetrameric immunogen; determining whether the tetrameric immunogen is bound to a target immune cell; and, if the tetrameric immunogen is bound to a target immune cell, then obtaining the target immune cell.
Tetrameric immunogens can include immunogens related to a condition or disease and/or that bind (e.g., bind specifically) to a target immune cell, e.g., wherein the target immune cell is related to a selected condition or disease. Immunogens and target immune cells related to a condition or disease include, for example, immunogens or immune cells present in subjects with a certain condition or disease, but not subjects without the condition or disease; and/or immunogens or immune cells present at altered levels (e.g., increased) in subjects with a certain condition or disease relative to subjects without the condition or disease. In some instances, immunogens or immune cells can be cancer specific. Immunogens can be soluble. Tetrameric immunogen can include tetrameric (including, e.g., tetramerized monomeric, dimeric, and/or trimeric antigen immunogen (e.g., antigen and/or epitope). In some instances, a tetrameric immunogen has increased binding to a cell relative to the level of binding between a non-tetrameric form of the immunogen to the cell under similar conditions. In some instances, a tetrameric antigen includes a detectable moiety, e.g., a streptavidin moiety. Tetramerization methods are known in the art and are disclosed herein.
Detecting tetrameric immunogen and/or determining whether tetrameric immunogen is bound to a target cell can be performed using methods known in the art and/or disclosed herein. For example, methods can include flow cytometry. Optimization methods for flow cytometry, including sorting and gating methods, are known in the art and/or are disclosed herein. In some instances, methods can include analysis of the level of binding, binding affinity, and/or binding specificity between a tetrameric immunogen bound to a target immune cell. For example, a target immune cell can be obtained if (e.g., only if) a pre-determined level of binding between a tetrameric immunogen and a target immune cell is determined. Pre-determined levels of binding can be specific levels and/or can be relative levels. Obtaining target immune cells can include obtaining, providing, identifying, selecting, purifying, and/or isolating the target immune cells. Such methods can include, for example, cell sorting methods, cell enrichment, and/or background reduction.
In some instances, obtaining immune cells directed against a self antigen can include one or more and/or combinations of, for example, identifying a subject exhibiting a positive immune response towards the self antigen; obtaining or providing a multimeric form of the self antigen; contacting the multimeric form of the self antigen with a sample from the subject exhibiting a positive immune response towards the self antigen; obtaining immune cells bound to the multimeric form of the self antigen.
In some instances, methods can include obtaining immune cells directed against a self antigen from a cancer patient, can include one or more and/or combinations of, for example, identifying a subject exhibiting a positive immune response towards the self antigen; providing a multimeric form of the self antigen; contacting the multimeric form of the self antigen with a sample from the subject exhibiting a positive immune response towards the self antigen; and obtaining immune cells bound to the multimeric form of the self antigen.
Multimeric forms of a self antigen can include self antigens related to a condition or disease and/or that bind (e.g., bind specifically) to a target immune cell, e.g., wherein the target immune cell is related to a selected condition or disease. Self antigens and target immune cells related to a condition or disease include, for example, antigens or immune cells present in subjects with a certain condition or disease, but not subjects without the condition or disease; and/or immunogens or immune cells present at altered levels (e.g., increased) in subjects with a certain condition or disease relative to subjects without the condition or disease. In some instances, the condition or disease can be a cancer. In some embodiments, the cancer is melanoma, lung, breast, kidney, ovarian, prostate, pancreatic, gastric, and colon carcinoma, lymphoma or leukemia. In some instances, the self antigens or immune cells can be cancer specific. The self antigens can be soluble. Multimeric form of the self antigen can include a tetrameric form (including, e.g., tetramerized monomeric, dimeric, and/or trimeric antigen) of the self-antigen (e.g., antigen and/or epitope). In some instances, a multimeric form of the self antigen includes a detectable moiety, e.g., a streptavidin moiety. Multimerization methods are known in the art and are disclosed herein.
Methods for isolating or purifying genetic material (e.g., DNA and/or mRNA) from the obtained target immune cell are known in the art and are exemplified herein. Once such genetic material has been obtained, methods for using it to produce the therapeutic compositions disclosed herein are known in the art and/or are summarized below. As discussed above, genetic material can be varied, using techniques known in the art to create peptide variants disclosed herein.
Generating peptides from nucleic acids (e.g., cDNA) contained within or obtained from the target cell can include, for example, analysis, e.g., sequencing of heavy and light chain variable domains from target immune cells (e.g., single or isolated identified target immune cells). In some instances, methods can include generating fully human antibodies, or fragments thereof (e.g., as disclosed above), and humanization of non-human antibodies. DNA can be readily isolated and/or sequenced from the obtained immune cells using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies).
Once isolated, DNA can be placed into expression vectors, which are then transfected into host cells such as Escherichia coli cells, simian COS cells, Chinese Hamster Ovary (CHO) cells, or myeloma cells that do not otherwise produce antibody protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. Review articles on recombinant expression in bacteria of DNA encoding the antibody include Skerra et al., Curr. Opinion in Immunol., 5:256-262 (1993) and Pluckthun, Immunol. Revs., 130:151-188 (1992).
Recombinant expression of an antibody or variant thereof generally requires construction of an expression vector containing a polynucleotide that encodes the antibody. The invention, thus, provides replicable vectors comprising a nucleotide sequence encoding an antibody molecule, a heavy or light chain of an antibody, a heavy or light chain variable domain of an antibody or a portion thereof, or a heavy or light chain CDR, operably linked to a promoter. Such vectors may include the nucleotide sequence encoding the constant region of the antibody molecule (see, e.g., U.S. Pat. Nos. 5,981,216; 5,591,639; 5,658,759 and 5,122,464) and the variable domain of the antibody may be cloned into such a vector for expression of the entire heavy, the entire light chain, or both the entire heavy and light chains.
Once the expression vector is transferred to a host cell by conventional techniques, the transfected cells are then cultured by conventional techniques to produce an antibody. Thus, the invention includes host cells containing a polynucleotide encoding an antibody of the invention or fragments thereof, or a heavy or light chain thereof, or portion thereof, or a single-chain antibody of the invention, operably linked to a heterologous promoter. In certain embodiments for the expression of double-chained antibodies, vectors encoding both the heavy and light chains may be co-expressed in the host cell for expression of the entire immunoglobulin molecule, as detailed below.
Mammalian cell lines available as hosts for expression of recombinant antibodies are well known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC), including but not limited to Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), human epithelial kidney 293 cells, and a number of other cell lines. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the antibody or portion thereof expressed. To this end, eukaryotic host cells which possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product may be used. Such mammalian host cells include but are not limited to CHO, VERY, BHK, Hela, COS, MDCK, 293, 3T3, W138, BT483, Hs578T, HTB2, BT2O and T47D, NS0 (a murine myeloma cell line that does not endogenously produce any functional immunoglobulin chains), SP20, CRL7O3O and HsS78Bst cells. In one embodiment, human cell lines developed by immortalizing human lymphocytes can be used to recombinantly produce monoclonal antibodies. In one embodiment, the human cell line PER.C6. (Crucell, Netherlands) can be used to recombinantly produce monoclonal antibodies.
In some instances, peptides disclosed herein can be generated synthetically. Synthetic chemistry transformations and protecting group methodologies (protection and deprotection) useful in synthesizing peptides described herein are known in the art and include, for example, those such as described in R. Larock, Comprehensive Organic Transformations, VCH Publishers (1989); T. W. Greene and P. G. M. Wuts, Protective Groups in Organic Synthesis, 3d. Ed., John Wiley and Sons (1999); L. Fieser and M. Fieser, Fieser and Fieser's Reagents for Organic Synthesis, John Wiley and Sons (1994); and L. Paquette, ed., Encyclopedia of Reagents for Organic Synthesis, John Wiley and Sons (1995), and subsequent editions thereof.
Peptides can also be made by chemical synthesis methods, which are well known to the ordinarily skilled artisan. See, for example, Fields et al., Chapter 3 in Synthetic Peptides: A User's Guide, ed. Grant, W.H. Freeman & Co., New York, N.Y., 1992, p. 77. Hence, peptides can be synthesized using the automated Merrifield techniques of solid phase synthesis with the α-NH2 protected by either t-Boc or Fmoc chemistry using side chain protected amino acids on, for example, an Applied Biosystems Peptide Synthesizer Model 430A or 431.
One manner of making of the peptides described herein is using solid phase peptide synthesis (SPPS). The C-terminal amino acid is attached to a cross-linked polystyrene resin via an acid labile bond with a linker molecule. This resin is insoluble in the solvents used for synthesis, making it relatively simple and fast to wash away excess reagents and by-products. The N-terminus is protected with the Fmoc group, which is stable in acid, but removable by base. Any side chain functional groups are protected with base stable, acid labile groups.
Longer peptides could be made by conjoining individual synthetic peptides using native chemical ligation. Alternatively, the longer synthetic peptides can be synthesized by well-known recombinant DNA techniques. Such techniques are provided in well-known standard manuals with detailed protocols. To construct a gene encoding a peptide of this invention, the amino acid sequence is reverse translated to obtain a nucleic acid sequence encoding the amino acid sequence, preferably with codons that are optimum for the organism in which the gene is to be expressed. Next, a synthetic gene is made, typically by synthesizing oligonucleotides which encode the peptide and any regulatory elements, if necessary. The synthetic gene is inserted in a suitable cloning vector and transfected into a host cell. The peptide is then expressed under suitable conditions appropriate for the selected expression system and host. The peptide is purified and characterized by standard methods.
The peptides can be made in a high-throughput, combinatorial fashion, e.g., using a high-throughput multiple channel combinatorial synthesizer available from Advanced Chemtech.
Peptide bonds can be replaced, e.g., to increase physiological stability of the peptide, by: a retro-inverso bonds (C(O)—NH); a reduced amide bond (NH—CH2); a thiomethylene bond (S—CH2 or CH2—S); an oxomethylene bond (O—CH2 or CH2—O); an ethylene bond (CH2—CH2); a thioamide bond (C(S)—NH); a trans-olefin bond (CH═CH); a fluoro substituted trans-olefin bond (CF═CH); a ketomethylene bond (C(O)—CHR) or CHR—C(O) wherein R is H or CH3; and a fluoro-ketomethylene bond (C(O)—CFR or CFR—C(O) wherein R is H or F or CH3.
Peptides can be further modified by: acetylation, amidation, biotinylation, cinnamoylation, farnesylation, fluoresceination, formylation, myristoylation, palmitoylation, phosphorylation (Ser, Tyr or Thr), stearoylation, succinylation and sulfurylation. As indicated above, peptides can be conjugated to, for example, polyethylene glycol (PEG); alkyl groups (e.g., C1-C20 straight or branched alkyl groups); fatty acid radicals; and combinations thereof.
In some instances, peptides can be purified by any method known in the art for purification of an immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for the specific antigens Protein A or Protein G, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. Further, the antibodies of the present invention or fragments thereof may be fused to heterologous polypeptide sequences (referred to herein as “tags”) described above or otherwise known in the art to facilitate purification.
An exemplary, non-limiting, overview of the methods is shown in FIG. 21. Ordering is not implied.
Methods of Use
In some instances, the disclosure provides methods of treatment that include administering to a subject a composition disclosed herein.
Provided herein are methods for treating and/or preventing cancer or symptoms of cancer in a subject comprising administering to the subject a therapeutically effective amount of a composition comprising a peptide that immunospecifically binds to MHC class I polypeptide-related sequence A (MICA), wherein the peptide comprises complementarity determining region (CDR) 3 of the VH of antibody ID 1, 6, 7, 8 or 9 shown in Table 1 having 5 or fewer conservative amino acid substitutions, and CDR3 of the VL of antibody ID 1, 6, 7, 8 or 9 shown in Table 1 having 5 or fewer conservative amino acid substitutions. In some embodiments the cancer is a cancer associated with overexpression of MICA. In some embodiments, the cancer is melanoma, lung, breast, kidney, ovarian, prostate, pancreatic, gastric, and colon carcinoma, lymphoma or leukemia. In some embodiments, the cancer is melanoma. In some embodiments, the cancer is a plasma cell malignancy, for example, multiple myeloma (MM) or pre-malignant condition of plasma cells. In some embodiments the subject has been diagnosed as having a cancer or as being predisposed to cancer.
In some instances, the disclosure provides methods for treating and/or preventing cancer or symptoms of cancer in a subject comprising administering to the subject a therapeutically effective amount of a composition comprising an isolated antibody which specifically binds to MHC class I polypeptide-related sequence A (MICA), wherein the antibody comprises a heavy chain variable region (VH) comprising the VH CDR1, VH CDR2, and VH CDR3 as shown in the VH sequence of SEQ ID NO: 11, 149, 168, 186, or 204 and a light chain variable region (VL) sequence of SEQ ID No: 4, 151, 170, 189, or 206.
Also provided herein are methods for treating and/or preventing cancer or symptoms of cancer in a subject comprising administering to the subject a therapeutically effective amount of a peptide that immunospecifically binds to angiopoietin, wherein the peptide comprises complementarity determining region (CDR) 3 of the VH of antibody ID 2, 3, 4 or 5 or 10 shown in Table 1 having 5 or fewer conservative amino acid substitutions, and CDR3 of the VL of antibody ID 2, 3, 4 or 5 shown in Table 1 having 5 or fewer conservative amino acid substitutions. In some embodiments the cancer is a cancer associated with overexpression of MICA. In some embodiments, the cancer is melanoma, lung, breast, kidney, ovarian, prostate, pancreatic, gastric, and colon carcinoma, lymphoma or leukemia. In some embodiments, the cancer is melanoma. In some embodiments, the cancer is a plasma cell malignancy, for example, multiple myeloma (MM) or pre-malignant condition of plasma cells. In some embodiments the subject has been diagnosed as having a cancer or as being predisposed to cancer.
In some instances, the disclosure provides methods for treating and/or preventing cancer or symptoms of cancer in a subject comprising administering to the subject a therapeutically effective amount of a composition comprising an isolated antibody which specifically binds to angiopoietin (e.g., angiopoietin-2), wherein the antibody comprises a heavy chain variable region (VH) comprising the VH CDR1, VH CDR2, and VH CDR3 as shown in the VH sequence of SEQ ID NO: 20, 38, 56, 74, 222 and a light chain variable region (VL) sequence of SEQ ID No: 29, 47, 65, 83, or 224.
Symptoms of cancer are well-known to those of skill in the art and include, without limitation, unusual mole features, a change in the appearance of a mole, including asymmetry, border, color and/or diameter, a newly pigmented skin area, an abnormal mole, darkened area under nail, breast lumps, nipple changes, breast cysts, breast pain, death, weight loss, weakness, excessive fatigue, difficulty eating, loss of appetite, chronic cough, worsening breathlessness, coughing up blood, blood in the urine, blood in stool, nausea, vomiting, liver metastases, lung metastases, bone metastases, abdominal fullness, bloating, fluid in peritoneal cavity, vaginal bleeding, constipation, abdominal distension, perforation of colon, acute peritonitis (infection, fever, pain), pain, vomiting blood, heavy sweating, fever, high blood pressure, anemia, diarrhea, jaundice, dizziness, chills, muscle spasms, colon metastases, lung metastases, bladder metastases, liver metastases, bone metastases, kidney metastases, and pancreatic metastases, difficulty swallowing, and the like.
The methods disclosed herein can be applied to a wide range of species, e.g., humans, non-human primates (e.g., monkeys), horses, cattle, pigs, sheep, deer, elk, goats, dogs, cats, mustelids, rabbits, guinea pigs, hamsters, rats, and mice.
The terms “treat” or “treating,” as used herein, refers to partially or completely alleviating, inhibiting, ameliorating, and/or relieving the disease or condition from which the subject is suffering. In some instances, treatment can result in the continued absence of the disease or condition from which the subject is suffering.
In general, methods include selecting a subject at risk for or with a condition or disease. In some instances, the subject's condition or disease can be treated with a pharmaceutical composition disclosed herein. For example, in some instances, methods include selecting a subject with cancer, e.g., wherein the subject's cancer can be treated by targeting one or both of MICA and/or angiopoetin-2.
In some instances, treatments methods can include a single administration, multiple administrations, and repeating administration as required for the prophylaxis or treatment of the disease or condition from which the subject is suffering. In some instances treatment methods can include assessing a level of disease in the subject prior to treatment, during treatment, and/or after treatment. In some instances, treatment can continue until a decrease in the level of disease in the subject is detected.
The terms “administer,” “administering,” or “administration,” as used herein refers to implanting, absorbing, ingesting, injecting, or inhaling, the inventive peptide, regardless of form. In some instances, one or more of the peptides disclosed herein can be administered to a subject topically (e.g., nasally) and/or orally. For example, the methods herein include administration of an effective amount of compound or compound composition to achieve the desired or stated effect. Specific dosage and treatment regimens for any particular patient will depend upon a variety of factors, including the activity of the specific compound employed, the age, body weight, general health status, sex, diet, time of administration, rate of excretion, drug combination, the severity and course of the disease, condition or symptoms, the patient's disposition to the disease, condition or symptoms, and the judgment of the treating physician.
Following administration, the subject can be evaluated to detect, assess, or determine their level of disease. In some instances, treatment can continue until a change (e.g., reduction) in the level of disease in the subject is detected.
Upon improvement of a patient's condition (e.g., a change (e.g., decrease) in the level of disease in the subject), a maintenance dose of a compound, composition or combination of this invention may be administered, if necessary. Subsequently, the dosage or frequency of administration, or both, may be reduced, as a function of the symptoms, to a level at which the improved condition is retained. Patients may, however, require intermittent treatment on a long-term basis upon any recurrence of disease symptoms.
In some instances, the disclosure provides methods for detecting immune cells e.g., B cells and/or memory B cells, from a human subject. Such methods can be used, for example, to monitor the levels of immune cells e.g., B cells and/or memory B cells, in a human subject, e.g., following an event. Exemplary events can include, but are not limited to, detection of diseases, infection; administration of a therapeutic composition disclosed herein, administration of a therapeutic agent or treatment regimen, administration of a vaccine, induction of an immune response. Such methods can be used clinically and/or for research.
EXAMPLES
The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.
Methods are described herein that allow sensitive, specific, and reliable detection of rare memory B cells, with defined antigen specificity, from limited quantities of peripheral blood. Methods allowed visualization and isolation of memory B cells months to years after antigen had been cleared.
Proof of principle for the methods disclosed herein was established using tetramers of tetanus toxin C-fragment (TTCF), as reported in detail in Franz et al. (Blood, 118(2):348-357 (2011)), which reference is hereby incorporated by reference in its entirety.
TTCF (i.e., the 52 kDa, non-toxic, C-terminal fragment of TTCF) was selected as a model antigen because the majority of individuals have been vaccinated with tetanus toxoid and persistent IgG antibody titers are induced by the vaccine (Amanna et al., N. Engl. J. Med., 357:1903-1915, 2007). Accordingly, use of TTCF afforded a large pool of subjects in which the methods disclosed herein could be verified. One of skill in the art will appreciate, however, that the present methods can be adapted to include any disease-related antigen using routine skill. As demonstrated in the examples below, such adaption has been shown through the acquisition of antibodies directed against MICA and angiopoietin-2, which are cancer-related antigens.
Example 1
Antigen Expression and Tetramer Formation
As described in further detail below, TTCF was expressed in Eschericia coli and a BirA site was attached to the N-terminus for site-specific mono-biotinylation by BirA enzyme. A flexible linker was placed between the protein and the biotinylation site to prevent steric hindrance of antibody binding. TTCF was purified by anion-exchange chromatography, biotinylated with BirA, and separated from free biotin and BirA by gel filtration chromatography. TTCF tetramers were generated by incubating fluorescently tagged streptavidin with biotinylated TTCF antigen at a molar ratio of 1:4. These tetramers were then used along with a panel of mAbs for the identification of tetanus toxoid specific memory B cells.
TTCF was cloned in pET-15b (Novagen). Protein expression was induced in BL21(DE3) Eschericia coli with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) for 4 hours at 28° C. Cells were washed, lysed, and resulting supernatant was collected. TTCF was purified using a HIS-Select affinity column (Sigma). The His-tag was removed proteolytically. Murine CD80 membrane proximal domain was produced using similar methods. Proteins were mono-biotinylated. For certain experiments, Alexa-488 dye molecules (Molecular probes) were linked to primary amines on biotinylated TTCF or CD80.
Antigen tetramers were prepared by incubating biotinyated antigen with premium grade PE labeled streptavidin (Molecular Probes) for at least 20 minutes on ice at a molar ratio of 4:1. Prior to use, tetramer preparations were centrifuged to remove aggregates. In some experiments, tetramers were formed with Alexa-fluor-488 tagged antigens and non-fluorescent streptavidin at a 4:1 ratio.
Example 2
Identification Methods
Methods were performed as described in Franz et al., Blood, 118(2):348-357 (2011).
Cells were sorted on a BD FACS Aria II cell sorter. Cells were single-cell sorted. Samples were first gated on CD19+ cells that were negative for a panel of exclusion markers (CD3, CD14, CD16, 7AAD) then gated on plasmablasts, identified by high levels of CD27 and an immediate level of CD19 expression, and finally on tetramer+ CD19+ cells.
Due to the low frequency of memory B cells, it was necessary to carefully reduce background as much as possible. B cells were first enriched by negative selection (cocktail of antibodies to CD2, CD3, CD14, CD16, CD56 and glycophorin A) to remove most cells that could non-specifically bind the tetramer. Enriched cells were split evenly and stained with TTCF or a control tetramer followed by labeling with CD19, CD27 and IgM to specifically select class-switched memory B cells. The gating strategy considered expression of CD19, lack of labeling with a panel of exclusion markers (CD3, CD14, CD16, 7AAD), expression of the memory marker CD27 and lack of IgM expression as evidence of class switching. Tetramer staining was plotted versus CD27 staining for visualization of memory B cells with the antigen specificity of interest. Tetramer-positive B cells were directly sorted into PCR strips containing 3 μl mRNA extraction buffer.
Tubes were kept cold during sorting and sorted cells were frozen and stored at −80° C. CD19+ CD27+ IgM− B cells were used as positive controls.
A previously reported nest PCR protocol was used to amplify heavy and light chain variable segments (Wang et al., J. Immunol. Methods., 244:217-225, 2000). mRNA amplification was carried out under conditions suitable to minimize contamination. Primers used included:







(SEQ ID NO: 91)


TAATACGACTCACTATAGGTTCGGGGAAGTAGTCCTTGACCAGG;


 


(SEQ ID NO: 92)


TAATACGACTCACTATAGGGATAGAAGTTATTCAGCAGGCACAC;


 


(SEQ ID NO: 93)


TAATACGACTCACTATAGGCGTCAGGCTCAGRTAGCTGCTGGCCGC.


Nested RT-PCR was performed as described in


Franz et al., Blood, 118(2): 348-357 (2011).






Negative controls were included to monitor and guard against contamination. From a total of 35 single cells labeled with the TTCF tetramer, 32 heavy and 30 light chain segments were amplified and directly sequence from gel-purified PCR products, corresponding to an overall PCR efficiency of 89%. Sequence analysis revealed that TTCF tetramer+ cells employed a variety of different VHD-JH gene segments, without dominance of one particular gene segment. Sequences observed supported that clones represented cells diversified by somatic hypermutation.
Antibody production and purification included cloning heavy and light variable domain DNA into separate pcDNA3.3 expression vectors containing the bovine prolactin signal peptide sequence as well as full length IgG1 heavy or kappa light chain constant domains. Antibodies were expressed in CHO-S media (Invitrogen) supplemented with 8 mM Glutamax (Gibco) in 100 ml sinner flasks at 37° C. with 8% CO2. One day prior to transfection, cells were split to 6×105 cells/ml. On the day of transfection, cells were adjusted, were necessary, to 1×106 cells/ml. 25 μg of heavy and light chain plasmid DNA were co-transfected using MAX transfection reagent (Invitrogen) and transfected cells were cultured for 6-8 days. Protein was obtained using Protein G sepharose beads and antibody was eluted using 100 mM glycine pH2.5 and separated from beads using Spin-X centrifuge tubes. Purified antibody was exchanged into phosphate buffered saline (PBS) using Micro Bio-Spin columns (BioRad). Protein concentration was assessed by absorbance at 280 nm.
For saturation binding assay, non-biotinylated, MonoQ purified TTCF was labeled with europium and free europium was removed. 96-well flat bottom plates were coated overnight with 20 ng of antibody per well in 100 mM NaHCO3 buffer at pH 9.6. Blocking was performed with assay buffer supplemented with bovine serum albumin (BSA) and bovine gamma globulins. TTCF-europium was diluted in assay buffer (100 nM to 4 pM) and 200 μl was added per well in triplicate. Plates were incubated for 2 hours at 37° C. and washed three times with 200 μl wash buffer (50 mM Tris pH 8, 150 mM NaCl, 20 μM EDTA, 0.05% Tween). 100 μl enhancement solution was added to each well and fluorescence counts measured using a Victor3 plate reader at 615 nm.
Heavy and light chain variable domain sequences were analyzed using IMGT/V-Quest and JOINSOLVERTM software. Flow cytometry data were evaluated using FlowJo analysis software. Statistical analysis were carried out using GraphPad Prism 5 software using unpaired t-test. To determine KD values, saturation binding data were fitted using GraphPad Prism 5 software using non-linear regression analysis.
Example 3
Multimerization Enhances Identification of Memory B Cells
Tetrameric and monomeric TTCF were compared. TTCF was fluorescently labeled with Alexa-488 and then used in monomeric form or was converted to a tetramer using unlabeled streptavidin (see above). Enriched B cells were then incubated with tetrameric or monomeric TTCF-Alexa-488 at the same concentration. Control protein (CD80 membrane proximal domain) was labeled in the same way and also used as a tetramer.
As shown in FIGS. 22A and 22B, TTCF labeled some memory B cells, but frequencies identified with tetramer were substantially larger (1.6-7.3 fold) using cells from three donors. In one of the three donors TTCF specific memory B cells could be detected with the tetramer but not with the monomer.
These results demonstrate that antigen tetramers enable sensitive detection of memory B cells based on the antigen specificity of their BCR, despite such cells being very rare in peripheral blood. Class-switched memory B cells specific for TTCF were brightly labeled by the appropriate tetrameric TTCF antigen, while background labeling with control tetramer was consistently low.
Example 4
Method/Antibody Validation
Fully human antibodies were generated by joining constant regions of IgG heavy and kappa chains to isolated variable segments via overlap PCR. Antibodies were expressed in a transient, serum free mammalian expression system using CHO-S cells for a period of 6-8 days. Antibodies were purified using protein G and gel filtration chromatography.
As shown in FIG. 23, antibodies isolated from TTCF-specific plasmablasts showed high binding affinities to TTCF antigen, with a KD of 2.2 nM (TTCF Ab 1) and 323 pM (TTCF Ab 2)(FIG. 23B. Antibodies isolated from memory B cells also exhibited high binding affinities, with KD of 382 pM, 228 pM, and 1.4 nM, for other antibodies (TTCF Abs 3, 4, and 5)(FIG. 23B).
These data support the specificity of the methods disclosed herein. Moreover, the specificity of the methods herein was demonstrated by the construction of five anti-TTCF antibodies from three different donors, all of which bound to TTCF with high affinities.
Data herein also demonstrate that antigen tetramers enable sensitive detection of memory B cells long after clearance of the antigen from the host.
Example 5
Obtaining Anti-MICA Antibodies
Antibodies that immunospecifically bind to MICA were developed using the methods herein.
Briefly, MICA antigen (UniGene Hs.130838) was expressed with a C-terminal BirA tag (GLNDIFEAQKIEWHE (SEQ ID NO: 238)), which enables mono-biotinylation of the antigen. Antigen was tetramerized with streptavidin (SA) labeled with R-Phycoerythrin (PE) at a molar ration of 4 MICA: 1 SA. Peripheral blood mononuclear cells were obtained from advanced stage melanoma patients who had been vaccinated with autologous tumor cells transduced with a GM-CSF expression vector (GVAX) (PNAS 103: 9190, 2006), and subsequently treated with the anti-CTLA-4 monoclonal antibody ipilimumab (YERVOYTM (available from Bristol Myers Squib)) Peripheral blood mononuclear cells were quickly thawed, washed and resuspended at 5×106 in phosphate buffered saline (pH 7.2) supplemented with 2% fetal calf serum and stained with approximately 0.1 ug/mltetramer for 30 minutes on ice. Antibodies were added to identify class-switched, memory B-cells (CD19+, CD27+, and IgM−). A panel of exclusion antibodies labeling T-cells, natural killer-cells, marcrophages, and dead cells were included to reduce background tetramer staining (CD3, CD14, CD16, 7-AAD). Single B-cells that bound to the MICA tetramer were sorted into 8-tube-PCR strips using the BD FACS Aria II. The B-cell receptor (BCR) mRNA was amplified using a commercial kit from Epicentre Biotechnologies (catalog number: MBCL90310) using gene specific primers shown below:









mRNA Amplification



(SEQ ID NO: 94)



IgG-T7:



AATACGACTCACTATAGGTTCGGGGAAGTAGTCCTTGACCAGG



 



(SEQ ID NO: 95)



Kappa-T7:



TAATACGACTCACTATAGGGATAGAAGTTATTCAGCAGGCACAC



 



(SEQ ID NO: 96)



Lambda-T7:



TAATACGACTCACTATAGGCGTCAGGCTCAGRTAGCTGCTGGCCGC



 



PCR One



(SEQ ID NO: 97)



VHL-1:



TCACCATGGACTG(C/G)ACCTGGA



 



(SEQ ID NO: 98)



VHL-2:



CCATGGACACACTTTG(C/T)TCCAC



 



(SEQ ID NO: 99)



VHL-3:



TCACCATGGAGTTTGGGCTGAGC



 



(SEQ ID NO: 100)



VHL-4:



AGAACATGAAACA(C/T)CTGTGGTTCTT



 



(SEQ ID NO: 101)



VHL-5:



ATGGGGTCAACCGCCATCCT



 



(SEQ ID NO: 102)



VHL-6:



ACAATGTCTGTCTCCTTCCTCAT



 



(SEQ ID NO: 103)



VkL-1:



GCTCAGCTCCTGGGGCTCCTG



 



(SEQ ID NO: 104)



VkL-2:



CTGGGGCTGCTAATGCTCTGG



 



(SEQ ID NO: 105)



VkL-3:



TTCCTCCTGCTACTCTGGCTC



 



(SEQ ID NO: 106)



VkL-4:



CAGACCCAGGTCTTCATTTCT



 



(SEQ ID NO: 107)



VIL-1:



CCTCTCCTCCTCACCCTCCT



 



(SEQ ID NO: 108)



VIL-2:



CTCCTCACTCAGGGCACA



 



(SEQ ID NO: 109)



VIL-3:



ATGGCCTGGA(T/C)C(C/G)CTCTCC



 



(SEQ ID NO: 110)



CgII:



GCCAGGGGGAAGAC(C/G)GATG



 



(SEQ ID NO: 111)



CkII:



TTTCAACTGCTCATCAGATGGCGG



 



(SEQ ID NO: 112)



ClII:



AGCTCCTCAGAGGAGGG(C/T)GG



 



PCR Two



(SEQ ID NO: 113)



VH-1:



CAGGT(G/C)CAGCTGGT(G/A)CAGTC



 



(SEQ ID NO: 114)



VH-2:



CAG(A/G)TCACCTTGAAGGAGTC



 



(SEQ ID NO: 115)



VH-3:



(G/C)AGGTGCAGCTGGTGGAGTC



 



(SEQ ID NO: 116)



VH-4:



CAGGTGCAGCTGCAGGAGTC



 



(SEQ ID NO: 117)



VH-5:



GA(G/A)GTGCAGCTGGTGCAGTC



 



(SEQ ID NO: 118)



VH-6:



CAGGTACAGCTGCAGCAGTC



 



(SEQ ID NO: 119)



Vk-1:



CG(A/C)CATCC(A/G)G(A/T)TGACCCAGT



 



(SEQ ID NO: 120)



Vk-2:



CGAT(A/G)TTGTGATGAC(C/T)CAG



 



(SEQ ID NO: 121)



Vk-3:



CGAAAT(T/A)GTG(T/A)TGAC(G/A)CAGTCT



 



(SEQ ID NO: 122)



Vk-4:



CGACATCGTGATGACCCAGT



 



(SEQ ID NO: 123)



Vl-1:



CCAGTCTGTGCTGACTCAGC



 



(SEQ ID NO: 124)



Vl-2:



CCAGTCTGCCCTGACTCAGC



 



(SEQ ID NO: 125)



Vl-3:



CTCCTATGAGCTGAC(T/A)CAGC



 



(SEQ ID NO: 126)



CgIII:



GAC(C/G)GATGGGCCCTTGGTGGA



 



(SEQ ID NO: 127)



CkIII:



AAGATGAAGACAGATGGTGC



 



(SEQ ID NO: 128)



ClIII:



GGGAACAGAGTGACCG






The primers and PCR cycling conditions used in PCR one and PCR two are adapted from Wang and Stollar et al. (journal of immunological methods2000).
An alternate heavy chain variable region forward primer set was developed to cover heavy chain variable region sequences potentially not adequately covered by the above primer set. The following alternate primers were generated:









PCR One



(SEQ ID NO: 129)



VHL1-58:



TCACTATGGACTGGATTTGGA



 



(SEQ ID NO: 130)



VHL2-5:



CCATGGACA(C/T)ACTTTG(C/T)TCCAC



 



(SEQ ID NO: 131)



VHL3-7:



GTAGGAGACATGCAAATAGGGCC



 



(SEQ ID NO: 132)



VHL3-11:



AACAAAGCTATGACATATAGATC



 



(SEQ ID NO: 133)



VHL3-13.1:



ATGGAGTTGGGGCTGAGCTGGGTT



 



(SEQ ID NO: 134)



VHL3-13.2:



AGTTGTTAAATGTTTATCGCAGA



 



(SEQ ID NO: 135)



VHL3-23:



AGGTAATTCATGGAGAAATAGAA



 



(SEQ ID NO: 136)



VHL4-39:



AGAACATGAAGCA(C/T)CTGTGGTTCTT



 



(SEQ ID NO: 137)



VHL4-61:



ATGGACTGGACCTGGAGCATC



 



(SEQ ID NO: 138)



VHL-9:



CCTCTGCTGATGAAAACCAGCCC



PCR Two



 



(SEQ ID NO: 139)



VH1-3/18:



CAGGT(C/T)CAGCT(T/G)GTGCAGTC



 



(SEQ ID NO: 140)



VH1-45/58:



CA(A/G)ATGCAGCTGGTGCAGTC



 



(SEQ ID NO: 141)



VH2-5:



CAG(A/G)TCACCTTGA(A/G)GGAGTCTGGT



 



(SEQ ID NO: 142)



VH3-9/23/43:



GA(A/G)GTGCAGCTG(T/G)TGGAGTC



 



(SEQ ID NO: 143)



VH3-16:



GAGGTACAACTGGTGGAGTC



 



(SEQ ID NO: 144)



VH3-47:



GAGGATCAGCTGGTGGAGTC



 



(SEQ ID NO: 145)



V4-34:



CAGGTGCAGCTACAGCAGTG



 



(SEQ ID NO: 146)



V4-30-2/39:



CAGCTGCAGCTGCAGGAGTC



 



(SEQ ID NO: 147)



VH7-4-1:



CAGGTGCAGCTGGTGCAATC






Briefly, 2 ul cDNA generated via mRNA amplification was used as a template for first-round PCR, with the following cycling conditions: 3 cycles of preamplification (94° C./45 seconds, 45° C./45 seconds, 72° C./105 seconds); 30 cycles of amplification (94° C./45 seconds, 50° C./45 seconds, 72° C./105 seconds); 10 minutes of final extension at 72° C.
3 ul of first-round PCR product served as a template for the second round of nested PCR. The same cycling conditions were used for the first round of PCR, but the 3 cycles of preamplification were omitted. Both PCR steps were performed by the use of cloned Pfu polymerase AD (Agilent Technologies). PCR products were separated on 1% agarose gels and products of 300-400 nucleotides in size isolated with the use of Zymoclean DNA gel recovery kit (Zymo Research). Sequencing was performed by the use of forward and reverse primers used for the second-round nested PCR. A two-step nested PCR amplifies the BCR variable domains of heavy and light chains (see above). Peripheral blood mononuclear cells were obtained from advanced stage melanoma patients who had been vaccinated with autologous tumor cells transduced with a GM-CSF expression vector (GVAX) (PNAS 103: 9190, 2006). The antibodies were expressed as full-length IgG1 antibodies in a transient CHO-S expression system.
Validation of anti-MICA antibody binding to MICA was performed using two independent bead-based assays. The first assay used a commercially available solution-based bead assay kit designed for detection of anti-MICA antibodies reactive to a variety of MICA alleles (One Lambda, catalog number LSMICA001). Varying concentrations of the MICA antibody were incubated with beads, then washed, and incubated with an anti-human IgG antibody conjugated with phycoerythrin. Following a second wash step, beads were analyzed on a Luminex machine. A negative control consisted of incubation of beads with anti-human IgG antibody conjugated with phycoerythrin alone (no anti-MICA antibody). A positive control consisted of incubation of beads with a commercially available anti-MICA/MICB monoclonal antibody (clone 6D4) directly conjugated to phycoerythrin (BioLegend catalog #320906). The second assay was developed internally using polystyrene beads conjugated with streptavidin. Beads were coated with monobiotinylated MICA protein, and incubated with varying concentrations of anti-MICA antibody, anti-TTCF antibody (isotype negative control), or BioLegend anti-MICA/MICB antibody directly conjugated to phycoerythrin (positive control). Beads incubated with anti-MICA antibody or anti-TTCF antibody were washed and then incubated with anti-human IgG antibody conjugated with Alexa488. To determine background binding to the beads, the same incubation was performed using streptavidin-conjugated beads not coated with MICA protein for comparison. Beads were analyzed for binding to antibodies on a FACS Caliber flow cytometer.
As shown in FIGS. 24 and 25, anti-MICA antibodies (MICA-Ab12 and MICA-Ab20) bind with high affinity to MICA. MICA-Ab20 corresponds to the anti-MICA antibody ID-1 described in Table 1.
Example 6
Anti-MICA Antibodies
Additional anti-MICA antibodies with clinically relevant biological properties were developed using the methods herein. MICA-specific antibodies reactive to common alleles were identified in patients who had received a cellular cancer vaccine (GM-CSF transduced cancer cells, referred to as GVAX) and an antibody that blocks the inhibitory CTLA-4 receptor on T cells ipilimumab (YERVOYTM (available from Bristol Myers Squib)). MICA tetramers were then used to isolate B cells from peripheral blood mononuclear cells of patients with the highest serum MICA reactivity. Heavy and light chain sequences were determined from these B cells by single cell PCR, as outlined in the in Example 5. This effort led to the identification of antibodies that recognize alleles common in the North American population.
CM24002 Ab2 (anti-MICA antibody ID-6 described in Table 1) is an antibody isolated from a patient with acute myeloid leukemia (AML) who demonstrated a significant clinical response to the GVAX+Ipilimumab combination therapy and whose plasma reacted strongly with MICA. The CM24002 Ab2 light chain (FIGS. 30 and 31) and heavy chain (FIGS. 28 and 29) nucleotide and amino acid sequences are shown, with CDR1, CDR2 and CDR3 sequences underlined. An additional antibody with strong binding was obtained from the same patient and is labeled as CM24002 Ab4 (anti-MICA antibody ID-7 described in Table 1) The CM24002 Ab4 light chain (FIGS. 34 and 35) and heavy chain (FIGS. 23 and 32) nucleotide and amino acid sequences are shown, with CDR1, CDR2 and CDR3 sequences underlined.
CM33322 Ab11 (anti-MICA antibody ID-8 described in Table 1) and CM33322 Ab29 (anti-MICA antibody ID-9 described in Table 1) are antibodies isolated from a patient with metastatic melanoma who is a long-term responder (>15 years) to the GVAX+Ipilimumab combination therapy. The CM33322 Ab11 light chain ((FIGS. 38 and 39) and heavy chain (FIGS. 36 and 37) nucleotide and amino acid sequences are shown, with CDR1, CDR2 and CDR3 sequences underlined. The CM33322 Ab29 light chain ((FIGS. 42 and 43) and heavy chain (FIGS. 40 and 41) nucleotide and amino acid sequences are shown, with CDR1, CDR2 and CDR3 sequences underlined. Due to the long-term clinical response of this patient, these antibodies are of particular interest.
After initial identification, cloning, and expression of the antibodies of interest, the specificity of these antibodies for different MICA alleles was determined with a cytometric bead assay. Briefly, soluble, recombinant MICA alleles 002, 008, 009 and MICB with a single BirA biotinylation site were expressed, purified, and captured on streptavidin beads. Indicated anti-MICA antibodies were then incubated with the beads coated with recombinant MICA at different concentrations for one hour, then washed, and incubated with a FITC-labeled anti-human IgG secondary antibody. Following a second wash step, quantification of bead-bound FITC fluorescence was completed by flow cytometry. MICA alleles 002, 008, 009 as well as the related MICB protein were chosen based on their prevalence in the North American population (FIG. 48). MICA alleles 002, 008, 009 as well as the related MICB protein were also chosen based on their generally high prevalence worldwide. Importantly, CM24002 Ab2 and CM33322 Ab29 bound strongly to all MICA alleles as well as to MICB. The other two antibodies bound to a subset of alleles: CM24002 Ab4 bound highly to MICA*009 and MICB, and CM33322 Ab11 bound highly to MICA*002, MICA*008, and MICB. (FIGS. 48A-F) Specificity was documented by use of a negative human control antibody generated with the same technology (specific for tetanus toxoid C-terminal fragment, TTCF) and a positive control antibody to MICA (a commercial murine antibody from BioLegend directed against MICA). These studies identified CM24002 Ab2 and CM33322 Ab29 as potential candidates for clinical application.
Example 7
Binding of Anti-MICA Antibody to Autologous Tumor Cells
The ability of isolated anti-MICA antibody CM24002 Ab2 to bind to autologous tumor cells was examined by flow cytometry (FIG. 49). Bone marrow obtained from patient CM24002 and tested binding to tumor cells by CM24002 Ab2. Tumor cells were then identified from the bone marrow sample as CD33+ CD34+ cells. The tumor cells were then stained with 10 μg/ml with anti-MICA antibody CM24002 Ab2, positive control commercial MICA antibody (BioLegend) or a negative control antibody (TTCF specific). As shown in FIG. 49, CM24002 Ab2 strongly bound to these cells. CM24002 Ab2 did not display binding to non-tumor cells (CD16+ and CD3+ cells) and only background binding to CD14+ cells, demonstrating anti-tumor specificity (data not shown).
Example 8
Anti-MICA Antibody Inhibition of NKG2D Receptor on NK Cells
The ability of isolated anti-MICA antibody CM24002 Ab2 to prevent soluble MICA-mediated down-regulation of is cognate receptor, NKG2D was examined. Serum from patient CM24002 was used at a 1:10 dilution and incubated with human NK cells for a period of 48 hours. CM24002 Ab2 (concentration of 10 μg/ml), positive control commercial MICA antibody (BioLegend) or a negative control antibody (TTCF specific) were added to these cultures. NKG2D expression was assessed by flow cytometry at 48 hr (FIG. 50). Serum from patient CM24002 strongly down-regulated expression of NKG2D (thus disabling the function of this receptor). CM24002 Ab2 and the positive control MICA antibody partially restored NKG2D surface expression by NK cells. To demonstrate specificity, we repeated the above experiment by incubating cells with recombinant MICA at 2 ng/ml instead of patient serum (FIG. 51). CM24002 Ab2 completely prevented MICA-mediated down-regulation of NKG2D expression, while the negative control antibody (specific for TTCF) had no effect (FIG. 51). These data demonstrate that human MICA antibodies can prevent inhibition of the critical NKG2D receptor on human NK cells.
Example 9
Anti-MICA Antibody Cell-Mediated Cytotoxicity
To determine if CM24002 Ab2 enables cell-mediated cytotoxicity, human NK cells (effector cells) were incubated for 48 hours with recombinant MICA (2 ng/ml) in the presence of CM24002 Ab2, a negative control antibody (TTCF specific) or a positive control antibody (BioLegend), all at 10 μg/ml. After 48 hours, cells were washed and incubated with K562 tumor cells at 20:1, 10:1, and 5:1 effector:target ratios for 4 hours. Specific lysis of target cells by NK cells was determined by release of a cytosolic protein (LDH) from K562 tumor cells. In the absence of MICA antibodies, there was no killing of K562 tumor cells by NK cells. However, CM24002 Ab2 greatly enhanced NK cell mediated lysis of K562 tumor cells and was more effective than the positive control murine MICA antibody at all effector:target ratios (FIG. 52). It was further demonstrated that killing of K562 tumor cells was indeed mediated by the NKG2D pathway (rather than Fc receptors). The above experiment was repeated, with the addition two experimental groups: a blocking antibody for NKG2D and human Fc block. In addition, CM33322 Ab29 was also tested. The data show that addition of CM24002 Ab2 and CM33322 Ab29 enabled NK cell mediated cytotoxicity. Killing of K562 cells did not occur when a blocking NKG2D antibody was added, while the Fc blocking reagent had little effect (FIG. 53). These data show that CM24002 Ab2 and CM33322 Ab29 restore the anti-tumor function of the NKG2D pathway.
Example 10
Binding of Anti-MICA Antibody to Alpha 3 MICA Domain
The NKG2D receptor binds to the top alpha 1 and alpha 2 domains of MICA, and antibodies that bind to the same site may compete with the NKG2D receptor and thereby block killing of tumor cells by NK cells. Antibodies that bind to the alpha 3 domain are of particular interest because they cannot block NKG2D receptor binding. At the same time, such antibodies can interfere with proteolytic cleavage of MICA from the tumor cell surface. The ability of anti-MICA antibodies to the MICA alpha 3 domain was assessed using the previously described cytometric bead assay. The biotinylated recombinant protein was captured on streptavidin beads. Beads were then incubated with antibodies CM24002 Ab2, CM24002 Ab4, CM33322 Ab11, CM33322 AB29, a negative control antibody (TTCF specific) or a positive control antibody (BioLegend), at 10 μg/ml followed by a FITC-labeled anti-human IgG secondary antibody and quantification of bead-bound FITC fluorescence by flow cytometry (FIG. 54). As shown in FIG. 54, CM33322 Ab29 bound to the MICA alpha 3 domain and is therefore of great interest for therapeutic applications.
Example 11
Binding of Anti-MICA Antibody to Tumor Cells
The potential of CM24002 Ab2 and CM33322 Ab29 to be used to target a broad range of cancers was assessed. A panel of multiple myeloma (RPMI 8226 and Xg-1), ovarian cancer (OVCAR3), acute myeloid leukemia (U937), melanoma (K028), lung cancer (1792 and 827), and breast cancer (MCF7) cells were tested for labeling by CM24002 Ab2 and CM33322 Ab29. The tumor cells were resuspended at a concentration of 1×106 cells/ml in PBS with 1% BSA and stained with the CM24002 Ab2 and CM33322 Ab29, as well as positive and negative controls (murine MICA antibody and TTCF-specific antibody, respectively)(directly conjugated) at a concentration of 10 μg/ml for 1 hour at 4° C. Labeling was assessed by flow cytometry (FIG. 55). CM24002 Ab2 and CM33322 Ab29 both bound every tumor cell type tested, with labeling being greater than the commercial positive control for the majority of tested cell lines.
Example 12
MICA Allele Specificity of Anti-MICA Antibody
The allelic specificity of CM33322 Ab29 was assessed using a commercially available Luminex assay. The commercial test kit contains recombinant MICA alleles (MICA*001, *002, *007, *012, *017, *018, *027, *004, *009, and*015) directly conjugated to Luminex beads, each with intrinsic fluorescent properties enabling binding to be assessed in a single sample. Luminex beads coated with the indicated MICA alleles were incubated with CM33322 Ab29, BioLegend positive control, and the negative control (TTCF), at 10 μg/ml for 1 hr, with subsequent incubation with PE-conjugated anti-human IgG secondary antibody. Fluorescence was determined following incubation for 60 minutes with the indicated antibodies and subsequent incubation with anti-human PE-conjugated secondary antibody using a Luminex 200 instrument (FIG. 56). CM33322 Ab29 was able to bind to all alleles present in the commercial assay, indicating that it may be used in patients regardless of MICA genotype.
These data demonstrate the high biological activity of CM24002 Ab2 and CM33322 Ab29 and their ability to restore NK cell mediated lysis of tumor cells. These data demonstrate that cancer patients who responded to immunotherapies produced MICA antibodies that restored the anti-tumor activity of NK cells. Together, these results highlight the therapeutic potential of anti-MICA antibodies to overcome immune suppression and promote tumor destruction in cancer patients.
Example 13
Obtaining Anti-Angiopoietin-2 Antibodies
Antibodies that bind to angiopoietin-2 were developed using the methods herein. Briefly, biotinylated angiopoietin-2 (UniGene Hs.583870) was purchased from R&D Systems. Peripheral blood mononuclear cells were quickly thawed, washed and resuspended at 5×106 in phosphate buffered saline (pH 7.2) supplemented with 2% fetal calf serum and stained with approximately 0.5 ug/ml angiopoietin-2 for 30 minutes on ice. Cells were washed twice with 4 ml PBS/2% FCS. Then antibodies were added to identify class-switched, memory B-cells (CD19+, CD27+, and IgM−) as well as SA-PE to label B-cells with biotinylated angiopoietin on the surface. A panel of exclusion antibodies labeling T-cells, natural killer-cells, marcrophages, and dead cells were included to reduce background tetramer staining (CD3, CD14, CD16, 7-AAD). Single B-cells that bound to angiopoietin-2 were sorted into 8-tube-PCR strips using the BD FACS Aria II. The B-cell receptor (BCR) mRNA was amplified using a commercial kit from Epicentre Biotechnologies (catalog number: MBCL90310) using gene specific primers (see above). A two-step nested PCR amplifies the BCR variable domains of heavy and light chains (see above). Peripheral blood mononuclear cells were obtained from a patient with malignant non-small cell lung carcimonnoma who had been vaccinated with autologous tumor cells transduced with a GM-CSF expression vector (GVAX) (Cancer Res. 70: 10150, 2010). The antibodies were expressed as full-length IgG1 antibodies in a transient CHO-S expression system.
Validation of anti-angiopoietin-2 antibodies binding to angiopoietin-2 was performed using ELISA assays. Briefly, angiopoietin-2 was coated overnight at 4 μg/ml in 100 mM sodium bicarbonate buffer pH 9.6 in 96-well flat bottom plates (PerkinElmer) at 4° C. Plates were blocked with assay buffer containing bovine serum albumin and bovine gamma globulins (PerkinElmer) at room temperature for three hours. Antibodies were diluted in assay buffer at 20 ug/ml-0.16 ug/ml and incubated for 1 hour at 4° C. Plates were washed three times with 200 μl wash buffer (50 mM Tris pH8, 150 mM NaCl, 20 mM EDTA, 0.05% Tween). 100 μl enhancement solution (PerkinElmer) was added to each well and fluorescence counts measured using a Victor3 plate reader (PerkinElmer) at a wavelength of 615 nm. Human angiopoietin-1 and -4 was also tested for binding and showed similar reactivity.
Relevant data is shown in FIGS. 27A-27C, that provide graphs and a gel relating to isolation of angiopoietin-specific antibodies from a lung cancer patient. (A) Angiopoietin-2 reactivity of lung cancer patient (L19) serum (diluted 1:1000) determined by ELISA. Dates of serum collection are shown on the X-axis. The control protein bovine serum albumin (BSA) was included as a negative control. (B) FACS plot showing PBMC sample (timepoint-10/98) gated on CD19+, CD27+ IgM-B cells with CD19 on the X-axis and fluorescently-tagged angiopoietin-2 on the Y-axis. The gate indicates approximately where the sorting cut-off was made. Ten B-cells were sorted from this sample. (C) Heavy, light chain, and hinge region PCR products from 10 angiopoietin-2 reactive memory B-cells isolated from pateitn L19. Heavy (top) and light (bottom) chain PCR products after two rounds of nested PCR of approximately 350 base pairs.
Example 14
Binding of Anti-Angiopoietin-2 Antibodies Against Human Recombinant Angiopoietin Family Members
96 well plates were coated overnight with 4 μg/mL recombinant angiopoietin-1, -2, and -4 (R&D Systems) in sodium bicarbonate buffer at pH9.6. Plates were subsequently blocked for 3 hours at room temperature with assay buffer (Perkin Elmer) containing bovine serum albumin (BSA) and bovine gamma-globulins. Antibodies ID 2, 3, 4, and 5 (see Table 1), diluted between 20 μg/mL-0.16 μg/mL, were incubated on plates for 1 hour at 4° C. with rotation. Plates were subsequently washed before being incubated with anti-human IgG-Europium antibody (Perkin Elmer). Fluorescent counts at 615 nm were obtained via plate reader. A negative control antibody (clone 8.18.C5) was used to determine specificity. Data was determined in duplicate.
As shown in FIGS. 26A-26C, antibodies ID 2, 3, 4, and 5 (see Table 1) bind with high specificity to angiopoietin-1-2, and -4. Antibodies do not bind to Ang-like-3, a structurally-related protein (see FIG. 26D).
An additional anti-angiopoietin antibody, designated anti-Ang2 Ab6 (anti-MICA antibody ID-10 described in Table 1) with clinically relevant biological properties were developed using the methods herein. Binding of anti-Ang2 Ab6 to human recombinant angiopoietin family members was analyzed as described above. Briefly, ELISA plates were coated with 4 μg/ml of angiopoietins Ang-1, Ang-2, Ang4, and Ang-like-3 binding, and detection by anti-Ang2 Ab6 was tested at 20 μg/ml. 4 μg/ml, 0.8 μg/ml, and 0.16 μg/ml. Europium conjugated anti-human IgG secondary was used, with europium counts measured after 45 minutes. As shown in FIG. 57, anti-Ang2 Ab6 binds to all angiopoietins in a dose dependent manner.
Other Embodiments
It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

## Claims

1. A composition comprising an isolated antibody or antibody fragment that immunospecifically binds to human MHC class I polypeptide-related sequence A (MICA), wherein the antibody or antibody fragment comprises a heavy chain variable region (VH) and a light chain variable region (VL), wherein the VH complementarity determining region (CDR) 1 comprises the amino acid sequence set forth in SEQ ID NO: 153, the VH CDR2 comprises the amino acid sequence set forth in SEQ ID NO: 156, the VH CDR3 comprises the amino acid sequence set forth in SEQ ID NO:158, the VL CDR1 comprises the amino acid sequence set forth in SEQ ID NO: 160, the VL CDR2 comprises the amino acid sequence set forth in SEQ ID NO: 162 and the VL CDR3 comprises the amino acid sequence set forth in SEQ ID NO:164.

2. The composition of claim 1, further comprising an anti-cancer therapeutic.

3. The composition of claim 1, formulated as a pharmaceutical composition.

4. The composition of claim 1, further comprising an histone deacetylase inhibitor (HDAC) selected from the group consisting of suberoylanilide hydroxamic acid (SAHA), trichostatin A (TSA), LAQ824, panobinostat (LBH589), belinostat (PXD101), ITF2357, romidepsin (FK228), entinostat (SNDX-275/MS-275), MGCD0103, valproic acid, phenyl butyrate, AN-9, CHR-3996, and CHR-2845.

5. The composition of claim 1 further comprising a proteasome inhibitor selected from the group consisting of bortezomib, NPI-0052, carfilzomib (PR-171), CEP 18770, and MLN9708.

6. A composition comprising an isolated antibody or antibody fragment that immunospecifically binds to human MHC class I polypeptide-related sequence A (MICA), wherein the antibody or antibody fragment comprises:
(i) a VH comprising the amino acid sequence set forth in SEQ ID NO: 149, and a VL comprising the amino acid sequence set forth in SEQ ID NO: 151;
(ii) a VH comprising the amino acid sequence set forth in SEQ ID NO: 186, and a VL comprising the amino acid sequence set forth in SEQ ID NO: 188; or
(iii) a VH comprising the amino acid sequence set forth in SEQ ID NO: 204, and a VL comprising the amino acid sequence set forth in SEQ ID NO: 206.

7. The composition of claim 1, further comprising an antibody selected from the group consisting of an anti-CTLA-4 antibody, and anti-PD-1 antibody, an anti-PDL-1 antibody and a combination of one or more thereof.

8. A composition comprising an isolated antibody or antibody fragment that immunospecifically binds to human MHC class I polypeptide-related sequence A (MICA), wherein the antibody or antibody fragment comprises a heavy chain variable region (VH) and a light chain variable region (VL), wherein the VH CDR1 comprises the amino acid sequence set forth in SEQ ID NO: 190, the VH CDR2 comprises the amino acid sequence set forth in SEQ ID NO: 192, the VH CDR3 comprises the amino acid sequence set forth in SEQ ID NO:194, the VL CDR1 comprises the amino acid sequence set forth in SEQ ID NO: 197, the VL CDR2 comprises the amino acid sequence set forth in SEQ ID NO: 199, and the VL CDR3 comprises the amino acid sequence set forth in SEQ ID NO: 201.

9. The composition of claim 8, further comprising an anti-cancer therapeutic.

10. The composition of claim 8, formulated as a pharmaceutical composition.

11. The composition of claim 8, further comprising an histone deacetylase inhibitor (HDAC) selected from the group consisting of suberoylanilide hydroxamic acid (SAHA), trichostatin A (TSA), LAQ824, panobinostat (LBH589), belinostat (PXD101), ITF2357, romidepsin (FK228), entinostat (SNDX-275/MS-275), MGCD0103, valproic acid, phenyl butyrate, AN-9, CHR-3996, and CHR-2845.

12. The composition of claim 8, further comprising a proteasome inhibitor selected from the group consisting of bortezomib, NPI-0052, carfilzomib (PR-171), CEP 18770, and MLN9708.

13. A composition comprising an isolated antibody or antibody fragment that immunospecifically binds to human MHC class I polypeptide-related sequence A (MICA), wherein the antibody or antibody fragment comprises a heavy chain variable region (VH) and a light chain variable region (VL), wherein the VH CDR1 comprises the amino acid sequence set forth in SEQ ID NO: 208, the VH CDR2 comprises the amino acid sequence set forth in SEQ ID NO: 210, the VH CDR3 comprises the amino acid sequence set forth in SEQ ID NO:212, the VL CDR1 comprises the amino acid sequence set forth in SEQ ID NO: 215, the VL CDR2 comprises the amino acid sequence set forth in SEQ ID NO: 217, and the VL CDR3 comprises the amino acid sequence set forth in SEQ ID NO:219.

14. The composition of claim 13, further comprising an anti-cancer therapeutic.

15. The composition of claim 13, formulated as a pharmaceutical composition.

16. The composition of claim 13, further comprising an histone deacetylase inhibitor (HDAC) selected from the group consisting of suberoylanilide hydroxamic acid (SAHA), trichostatin A (TSA), LAQ824, panobinostat (LBH589), belinostat (PXD101), ITF2357, romidepsin (FK228), entinostat (SNDX-275/MS-275), MGCD0103, valproic acid, phenyl butyrate, AN-9, CHR-3996, and CHR-2845.

17. The composition of claim 13, further comprising a proteasome inhibitor selected from the group consisting of bortezomib, NPI-0052, carfilzomib (PR-171), CEP 18770, and MLN9708.

18. The composition of claim 6, further comprising an anti-cancer therapeutic.

19. The composition of claim 6, formulated as a pharmaceutical composition.

20. The composition of claim 6, further comprising an histone deacetylase inhibitor (HDAC) selected from the group consisting of suberoylanilide hydroxamic acid (SAHA), trichostatin A (TSA), LAQ824, panobinostat (LBH589), belinostat (PXD101), ITF2357, romidepsin (FK228), entinostat (SNDX-275/MS-275), MGCD0103, valproic acid, phenyl butyrate, AN-9, CHR-3996, and CHR-2845.

21. The composition of claim 6, further comprising a proteasome inhibitor selected from the group consisting of bortezomib, NPI-0052, carfilzomib (PR-171), CEP 18770, and MLN9708.

22. The composition of claim 6, further comprising an antibody selected from the group consisting of an anti-CTLA-4 antibody, and anti-PD-1 antibody, an anti-PDL-1 antibody and a combination of one or more thereof.

23. The composition of claim 8, further comprising an antibody selected from the group consisting of an anti-CTLA-4 antibody, and anti-PD-1 antibody, an anti-PDL-1 antibody and a combination of one or more thereof.

24. The composition of claim 13, further comprising an antibody selected from the group consisting of an anti-CTLA-4 antibody, and anti-PD-1 antibody, an anti-PDL-1 antibody and a combination of one or more thereof.