FIELD OF THE INVENTION

This invention relates to monoclonal anti-HLA-C antibodies, nucleic acids and expression vectors encoding the antibodies, recombinant cells containing the vectors, and compositions comprising the antibodies. Methods of making the antibodies, and methods of using the antibodies to treat diseases including psoriasis, are also provided.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

This application contains a sequence listing, which is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file name “JBI6065USNPSEQLIST.TXT” and a creation date of Mar. 28, 2019 and having a size of 126 kb. The sequence listing submitted via EFS-Web is part of the specification and is herein incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

It is estimated that autoimmune diseases afflict 1 in 20 persons (Hayter and Cook, Autoimmune Rev. 11(10):754-65 (2012)). The root cause of autoimmunity is emergence of dysregulated T cell clones reactive to self-antigens. Auto-reactive T cells initiate cytokine-driven feed-forward loops resulting in inflammation (e.g., leukocyte recruitment and edema), which when chronic, leads to tissue destruction and loss of function.

Antibodies that neutralize specific cytokines (e.g., anti-TNFα, IL-12, IL-23, IL-17) are useful to interrupt the feed-forward loops and minimize inflammation (Wolf and Ang, Immunol. Allergy Clin. North Am. 37(2):283-99 (2017); Her and Kavanaugh, J. Allergy Clin. Immunol. 137(1):19-27 (2016)). However, these agents require chronic treatment, as they do not address the initial root cause of the disease. Therefore, therapies that target the development and activation of auto-reactive T cells and not the cytokines are needed to address the root cause of disease versus targeting the downstream inflammation.

An improved selective approach that would address the root cause would be to develop antibodies that block the development and activation of auto-reactive T cells that recognize self-antigens. T cells recognize antigens by a heterodimeric surface receptor consisting of an β and a β chain and known as the T cell receptor (TCR). The α and β chain genes are subject to extensive somatic recombination in the thymus. Recombination during thymic T cell development gives rise to tremendous diversity in TCR genes expressed within an individual (Laydon et al., Philos. Trans. R. Soc. Long. B Biol. Sci. 370(1675):20140291 (2015)). Each TCR has distinct antigen recognition capability. The antigens are short peptides bound and displayed by one of six major histocompatibility complex (MHC) proteins of the host. Specifically, humans express three class I MHC genes (i.e., HLA-A, HLA-B, or HLA-C) and three class II MHC genes (i.e., HLA-DR, HLA-DP, or HLA-DQ) (Trowsdale, Immunol. Lett. 137(1-2):1-8 (2011)). MHC genes are among the most polymorphic genes in the genome and there are >1000 alleles of each MHC gene in the human population encoding hundreds of allomorphs (protein isoforms). Each MHC allomorph has a unique peptide binding surface and binds a unique repertoire of self and foreign peptides. TCRs expressed by mature T cells are “restricted” to one of the self MHC allomorphs, meaning that a T cell can only be activated by a specific peptide-MHC complex.

Much research effort has been made to determine the exact self-peptide-MHC complexes recognized by auto-reactive T cells. Although it is possible to detect T cells cognate for specific self-peptide-MHC complexes, it has been more difficult to identify self-peptide-MHC complexes recognized in a majority of patients or that are proven to drive disease. Further, autoimmune diseases may be driven by many T cell clones recognizing multiple self-peptide MHC complexes.

Although the identity of the self-peptide-MHC complexes remain obscure, genetics offer important clues as to the identity of the offending MHC, as many autoimmune diseases show a strong association with specific MHC alleles (Matzaraki et al., Genome Biology 18(1):76 (2017)). It is meaningful that specific alleles may be highly enriched in individuals with specific autoimmune diseases because each allomorph binds a unique repertoire of self-peptides. Thus, the genetic risk of an autoimmune disease is believed to reflect the ability of the allomorph to display tissue specific self-peptides. This is best exemplified by Goodpasture's disease where T cells recognize collagen IV peptide bound by HLA-DQ15 (Cairns et al., J. Am. Soc. Nephrol. 14(11):2801-12 (2003)).

Inheritance of the HLA-C*06:02 allele is the strongest genetic determinant of who will develop the autoimmune disease called psoriasis (Nair et al., Am. J. Hum. Genet. 78(5):827-51 (2006); Elder et al., J. Invest. Dermatol. 130(5):1213-26 (2010)). A large majority (˜80%) of individuals experiencing the guttate form of psoriasis carry the HLA-C*06:02 allele (Asumalahti et al., J. Invest. Dermatol. 120(4):627-32 (2003)), while about 50% of individuals with the more common plaque psoriasis carry this allele compared with about 10-15% of healthy control individuals. One copy of the HLA-C*06:02 allele carries a ˜10% lifetime risk, which is 2.5× higher in homozygotes (Gudjonsson et al., Br. J. Dermatol. 148(2):233-5 (2003)), and individuals that are HLA-C*06:02 positive develop psoriasis at an earlier age and with greater severity (Gudjonsson et al., J. Invest. Dermatol. 126(4):740-5 (2006)). Importantly the risk of psoriasis in HLA-C*06:02 individuals is epistatic with a catalytically more active variant of ERAP1 (Strange et al., N. Genet. 42(11):985-90 (2010)), the primary endopeptidase required to customize peptides for class I MHC loading.

While the literature does not provide a consensus on self-peptides driving psoriasis, several self-peptides/proteins have been shown to activate T cells isolated from patient blood or skin. To date, these include the skin associated proteins keratin-17, LL37, ADAMTSL5, Maspin, and peroxiredoxin-2 or peptide derivatives (Yunusbaeva et al., Scientific Reports vol. 8, article number 6098 (2018); Lande et al., Nat. Commun. 5:5621 (2014); Arakawa et al, J. Exp. Med. 212(13):2203-12 (2015); and Besgen et al., J. Immunol. 184(9):5392-402 (2010)). Peptides derived from keratin-17, LL37, and ADAMTSL5 have been shown to be part of the repertoire of peptides that HLA-Cw6 may bind, and LL37 peptide-bound HLA-Cw6 tetramers have been used to identify cognate T cells in psoriasis patients. Meanwhile keratin-17 and peroxiredoxin-2-peptides activate T cells to a significantly greater frequency in HLA-C*06:02 positive psoriasis patients versus those that are negative. Evidence of clonal T cell expansion has been reported in psoriasis lesions, and the α and β TCR genes expressed by a few clones have been sequenced and reported (Kim et al., PLoS One 7(5):e37338 (2012)). The cognate peptide-MHC of one of these TCRs was deconvoluted and determined (Arakawa et al, J. Exp. Med. 212(13):2203-12 (2015)). The TCR was HLA-Cw6 restricted and ADAMTSL5(57-65) presented by HLA-Cw6 on melanocytes appeared to be the cognate antigen. Collectively, the data point to a critical role of HLA-Cw6 in presenting autoantigens to autoreactive T cells in psoriasis.

Antibodies to HLA-C that block the development and activation of auto-reactive T cells could be efficacious in addressing the root problem of psoriasis.

BRIEF SUMMARY OF THE INVENTION

In one general aspect, the invention relates to isolated monoclonal antibodies or antigen-binding fragments thereof that bind HLA-C, optionally, HLA-Cw6.

Provided are isolated monoclonal antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, the heavy chain variable region comprising a heavy chain complementarity determining region 1 (HCDR1), HCDR2, and a HCDR3, the light chain variable region comprising a light chain complementarity determining region 1 (LCDR1), LCDR2, and LCDR3, wherein the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2 and LCDR3 comprise the amino acid sequences of:a. SEQ ID NOs: 37, 38, 39, 64, 65, and 66, respectively;b. SEQ ID NOs: 40, 41, 42, 67, 68, and 69, respectively;c. SEQ ID NOs: 43, 44, 45, 70, 71, and 72, respectively;d. SEQ ID NOs: 46, 47, 48, 73, 74, and 75, respectively;e. SEQ ID NOs: 49, 50, 51, 76, 77, and 78, respectively;f. SEQ ID NOs: 52, 53, 54, 79, 80, and 81, respectively;g. SEQ ID NOs: 55, 56, 57, 82, 83, and 84, respectively;h. SEQ ID NOs: 58, 59, 60, 85, 86, and 87, respectively; ori. SEQ ID NOs: 61, 62, 63, 88, 89, and 90, respectively;
wherein the antibody or antigen-binding fragment thereof specifically binds HLA-C, preferably HLA-Cw6.

Also provided are isolated monoclonal antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, the heavy chain variable region comprising a heavy chain complementarity determining region 1 (HCDR1), HCDR2, and a HCDR3, the light chain variable region comprising a light chain complementarity determining region 1 (LCDR1), LCDR2, and LCDR3, wherein the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2 and LCDR3 comprise the amino acid sequences of:a. SEQ ID NOs: 91, 92, 93, 118, 119, and 120, respectively;b. SEQ ID NOs: 94, 95, 96, 121, 122, and 123, respectively;c. SEQ ID NOs: 97, 98, 99, 124, 125, and 126, respectively;d. SEQ ID NOs: 100, 101, 102, 127, 128, and 129, respectively;e. SEQ ID NOs: 103, 104, 105, 130, 131, and 132, respectively;f. SEQ ID NOs: 106, 107, 108, 133, 134, and 135, respectively;g. SEQ ID NOs: 109, 110, 111, 136, 137, and 138, respectively;h. SEQ ID NOs: 112, 113, 114, 139, 140, and 141, respectively; ori. SEQ ID NOs: 115, 116, 117, 142, 143, and 144, respectively;
wherein the antibody or antigen-binding fragment thereof specifically binds HLA-C, preferably HLA-Cw6.

Also provided are isolated monoclonal antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, the heavy chain variable region comprising a heavy chain complementarity determining region 1 (HCDR1), HCDR2, and a HCDR3, the light chain variable region comprising a light chain complementarity determining region 1 (LCDR1), LCDR2, and LCDR3, wherein the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2 and LCDR3 comprise the amino acid sequences of:a. SEQ ID NOs: 145, 146, 147, 172, 173, and 174, respectively;b. SEQ ID NOs: 148, 149, 150, 175, 176, and 177, respectively;c. SEQ ID NOs: 151, 152, 153, 178, 179, and 180, respectively;d. SEQ ID NOs: 154, 155, 156, 181, 182, and 183, respectively;e. SEQ ID NOs: 157, 158, 159, 184, 185, and 186, respectively;f. SEQ ID NOs: 160, 161, 162, 187, 188, and 189, respectively;g. SEQ ID NOs: 163, 164, 165, 190, 191, and 192, respectively;h. SEQ ID NOs: 166, 167, 168, 193, 194, and 195, respectively; ori. SEQ ID NOs: 169, 170, 171, 196, 197, and 198, respectively;
wherein the antibody or antigen-binding fragment thereof specifically binds HLA-C, preferably HLA-Cw6.

In certain embodiments, the isolated monoclonal antibody or antigen-binding fragment thereof comprises a heavy chain variable region having a polypeptide sequence at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, or 17, or a light chain variable region having a polypeptide sequence at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, or 18.

In certain embodiments, the isolated monoclonal antibody or antigen-binding fragment thereof comprises:a. a heavy chain variable region having the polypeptide sequence of SEQ ID NO:1, and a light chain variable region having the polypeptide sequence of SEQ ID NO:2;b. a heavy chain variable region having the polypeptide sequence of SEQ ID NO:3, and a light chain variable region having the polypeptide sequence of SEQ ID NO:4;c. a heavy chain variable region having the polypeptide sequence of SEQ ID NO:5, and a light chain variable region having the polypeptide sequence of SEQ ID NO:6;d. a heavy chain variable region having the polypeptide sequence of SEQ ID NO:7, and a light chain variable region having the polypeptide sequence of SEQ ID NO:8;e. a heavy chain variable region having the polypeptide sequence of SEQ ID NO:9, and a light chain variable region having the polypeptide sequence of SEQ ID NO:10;f. a heavy chain variable region having the polypeptide sequence of SEQ ID NO:11, and a light chain variable region having the polypeptide sequence of SEQ ID NO:12;g. a heavy chain variable region having the polypeptide sequence of SEQ ID NO:13, and a light chain variable region having the polypeptide sequence of SEQ ID NO:14;h. a heavy chain variable region having the polypeptide sequence of SEQ ID NO:15, and a light chain variable region having the polypeptide sequence of SEQ ID NO:16; ori. a heavy chain variable region having the polypeptide sequence of SEQ ID NO:17, and a light chain variable region having the polypeptide sequence of SEQ ID NO:18.

In certain embodiments, the isolated monoclonal antibody or antigen-binding fragment thereof is chimeric.

In certain embodiments, the isolated monoclonal antibody or antigen-binding fragment thereof is human or humanized.

In certain embodiments, the isolated monoclonal antibody or antigen-binding blocks development and activation of T cells, through binding and inhibition of antigen presentation by HLA-Cw6.

Also provided are isolated nucleic acids encoding the monoclonal antibodies or antigen-binding fragments thereof of the invention.

Also provided are vectors comprising the isolated nucleic acids encoding the monoclonal antibodies or antigen-binding fragments thereof of the invention.

Also provided are host cells comprising the vectors comprising the isolated nucleic acids encoding the monoclonal antibodies or antigen-binding fragments thereof of the invention.

In certain embodiments, provided is a pharmaceutical composition comprising the isolated monoclonal antibody or antigen-binding fragment thereof of the invention and a pharmaceutically acceptable carrier.

Also provided are methods of treating or preventing an autoimmune disease in a subject in need thereof. The methods comprise administering to the subject the pharmaceutical compositions of the invention. The autoimmune disease can be selected from, but not limited to, psoriasis, plaque psoriasis, guttate psoriasis, and psoriatic arthritis.

Also provided are methods of inhibiting activation of auto-reactive T cells in a subject in need thereof. The methods comprise administering to the subject the pharmaceutical compositions of the invention, wherein administration of the pharmaceutical composition inhibits activation of the auto-reactive T cells in the subject.

Also provided are methods of inhibiting the functional binding of a T cell receptor (TCR) to a peptide-bound HLA-C (e.g., HLA-Cw6) in a HLA-C (e.g., HLA-Cw6) expressing cell. The methods comprise contacting the cell with an isolated monoclonal antibody or antigen-binding fragment thereof of the invention, wherein the monoclonal antibody or antigen-binding fragment thereof of the invention binds the peptide-bound HLA-C and inhibits the functional binding of the TCR. In certain embodiments, the cell is contacted in vitro. In certain embodiments, the cell is contacted in vivo.

Also provided are methods of producing the monoclonal antibody or antigen-binding fragment thereof of the invention. The methods comprise culturing a cell comprising a nucleic acid encoding the monoclonal antibody or antigen-binding fragment thereof under conditions to produce the monoclonal antibody or antigen-binding fragment thereof and recovering the antibody or antigen-binding fragment thereof from the cell or culture.

Also provided are methods of producing a pharmaceutical composition comprising the monoclonal antibody or antigen-binding fragment thereof of the invention. The methods comprise combining the monoclonal antibody or antigen-binding fragment thereof with a pharmaceutically acceptable carrier to obtain the pharmaceutical composition.

