HLA-restricted VGLL1 peptides and use thereof in promoting an immune response in a subject

#This application is a national phase application under 35 U.S.C. § 371 of International Application No. PCT/US2017/055414, filed Oct. 5, 2017, which claims the benefit of U.S. Provisional Patent Application No. 62/405,779, filed Oct. 7, 2016, the entirety of each of which is incorporated herein by reference.

#The sequence listing that is contained in the file named “UTFCP1307WO_ST25.txt”, which is 1 KB (as measured in Microsoft Windows) and was created on Oct. 5, 2017, is filed herewith by electronic submission and is incorporated by reference herein.

#The present invention relates generally to the fields of immunology and medicine. More particularly, it concerns tumor antigen-specific peptides and uses thereof for the treatment of cancer.

#The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

#FIGS. 1A-1D: Mass spectrometry-based identification of a pancreatic tumor-associated antigen derived from VGLL1. (A) Tandem mass spectrometry (MS) analysis of an HLA class I-bound VGLL1 peptide, LSELETPGKY (SEQ ID NO:1), isolated from a pancreatic tumor organoid cell line (hMIA-2D) derived from PDAC patient MP015. The top panel shows the spectra of the original eluted peptide from discovery phase tandem MS. The middle and bottom spectra show a targeted MS experiment in which the isotope-labeled synthetic peptide LSELETPGKY (SEQ ID NO:1) (with heavy lysine residue underlined) was spiked into the tumor sample and co-eluted with the native peptide, demonstrating gold standard confirmation of peptide identity. (B) Same mass spectra as in (A), but with ‘y’ ions circled to highlight the expected mass shift of 8 atomic mass units for the isotope-labeled peptide, corresponding to the heavy lysine residue. (C) Same mass spectra as in (A), but with ‘b’ ions circled to highlight the expected mass shift of 8 atomic mass units for only the b9+ ion, but no other ‘b’ ions. (D) Analysis of expected tandem MS fragment ion masses for the native and isotope-labeled VGLL1 peptide LSELETPGKY (SEQ ID NO: 1) and LSELETPGKY (SEQ ID NO: 1).

#FIGS. 2A-2B: VGLL1 mRNA transcripts are overexpressed in several tumor types compared with normal tissues. (A) RNAseq analysis derived from the GTex Portal normal tissue (gtexportal.org) and TCGA (cancergenome.nih.gov) tumor tissue databases show VGLL1 transcript expression in normal tissues and various cancers, respectively. Each dot represents the results of one analyzed human sample. The left star and arrow indicates the highest mean normal tissue level of VGLL1 transcript, found in bladder. The right star and arrow indicates the level of VGLL1 transcript in the MP015 patient-derived organoid cell line hMIA2D, from which the VGLL1 peptide was detected. Boxes indicate the 5 cancer types that overexpress VGLL1 transcripts: pancreatic, ovarian, bladder, breast, and stomach cancers. TPM, transcripts per million. (B) VGLL1 expression prevalence in five cancer types derived from TCGA data. Tumor-associated expression was considered positive if VGLL1 mRNA expression was >3 TPM, as determined by RNAseq expression.

#For patients with many different cancer types, T cell based immunotherapies represent a promising approach with proven efficacy. However, antigen-specific T cell therapy for most cancer types is not feasible due to the lack of tumor-associated antigens currently known, which has stalled their clinical development. Studies in the present disclosure profiled the immunopeptidome of pancreatic cell lines and tumor specimens through mass spectrophotometry and identified peptide epitopes derived from a novel tumor-associated antigen VGLL1 that is expressed at substantially higher levels in pancreatic, ovarian, gastric, bladder, and breast cancer compared with normal tissues. Using these peptide epitopes, antigen-specific cytotoxic T lymphocytes (CTLs) were generated from pancreatic patient peripheral blood mononuclear cells (PBMCs) that recognized the endogenously-presented antigen on HLA-matched allogeneic tumor cell lines, leading to tumor cell killing. Thus, these antigen-specific CTLs provided herein may be used to target solid cancers (e.g., pancreatic, ovarian, gastric, and breast cancer).

#Accordingly, the present disclosure provides tumor antigen-specific peptides, such as to tumor antigen VGLL1, for use as immunotherapy for the treatment of a cancer. The present studies identified VGLL1 as a tumor-associated antigen from a pancreatic elution. The VGLL1 peptide had a predicted HLA-A*0101 affinity of 51 nM which has a world prevalence of 10-20%. Thus, in some embodiments, VGLL1 peptides (e.g. comprising SEQ ID NO:1) are provided herein. For example, a VGLL1-specific peptide may be contacted with or used to stimulate a population of T cells to induce proliferation of the T cells that recognize or bind the VGLL1-specific peptide. In other embodiments, a VGLL1-specific peptide of the present disclosure may be administered to a subject, such as a human patient, to enhance the immune response of the subject against a cancer.

#A VGLL1-specific peptide may be included in an active immunotherapy (e.g., a cancer vaccine) or a passive immunotherapy (e.g., an adoptive immunotherapy). Active immunotherapies include immunizing a subject with a purified tumor antigen or an immunodominant VGLL1-specific peptide (native or modified). Alternately, antigen presenting cells (APCs) pulsed with a VGLL1-specific peptide (or transfected with genes encoding the tumor antigen) may be administered to a subject. The VGLL1-specific peptide may be modified or contain one or more mutations, such as a substitution mutation. Passive immunotherapies include adoptive immunotherapies. Adoptive immunotherapies generally involve administering cells to a subject, wherein the cells (e.g., CTLs) have been sensitized in vitro to the VGLL1-specific peptide (see, e.g., U.S. Pat. No. 7,910,109), such as by using APCs to present the VGLL1 epitope to the CTLs in vitro.