title: Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens.
abstract: The antigenicity of cells is demarcated by the peptides bound by their Human Leucocyte Antigen (HLA) molecules. Through this antigen presentation, T cell specificity response is controlled. As a fraction of the expressed mutated peptides is presented on the HLA, these neo-epitopes could be immunogenic. Such neo-antigens have recently been identified through screening for predicted mutated peptides, using synthetic peptides or ones expressed from minigenes, combined with screening of patient tumor-infiltrating lymphocytes (TILs). Here we present a time and cost-effective method that combines whole-exome sequencing analysis with HLA peptidome mass spectrometry, to identify neo-antigens in a melanoma patient. Of the 1,019 amino acid changes identified through exome sequencing, two were confirmed by mass spectrometry to be presented by the cells. We then synthesized peptides and evaluated the two mutated neo-antigens for reactivity with autologous bulk TILs, and found that one yielded mutant-specific T-cell response. Our results demonstrate that this method can be used for immune response prediction and promise to provide an alternative approach for identifying immunogenic neo-epitopes in cancer.
authors.affiliation: Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Shelly
authors.initials: S
authors.lastname: Kalaora
authors.affiliation: Department of Biology, Technion, Haifa, Israel.
authors.forename: Eilon
authors.initials: E
authors.lastname: Barnea
authors.affiliation: The Ella Lemelbaum Institute for Melanoma, Chaim Sheba Medical Center, Tel Hashomer, Israel.
authors.forename: Efrat
authors.initials: E
authors.lastname: Merhavi-Shoham
authors.affiliation: Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Nouar
authors.initials: N
authors.lastname: Qutob
authors.affiliation: Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
authors.forename: Jamie K
authors.initials: JK
authors.lastname: Teer
authors.affiliation: The Ella Lemelbaum Institute for Melanoma, Chaim Sheba Medical Center, Tel Hashomer, Israel.
authors.forename: Nilly
authors.initials: N
authors.lastname: Shimony
authors.affiliation: The Ella Lemelbaum Institute for Melanoma, Chaim Sheba Medical Center, Tel Hashomer, Israel.
authors.forename: Jacob
authors.initials: J
authors.lastname: Schachter
authors.affiliation: National Cancer Institute, NIH, MD, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Rosenberg
authors.affiliation: The Ella Lemelbaum Institute for Melanoma, Chaim Sheba Medical Center, Tel Hashomer, Israel.|Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Michal J
authors.initials: MJ
authors.lastname: Besser
authors.affiliation: Department of Biology, Technion, Haifa, Israel.
authors.forename: Arie
authors.initials: A
authors.lastname: Admon
authors.affiliation: Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Yardena
authors.initials: Y
authors.lastname: Samuels
mesh_terms: D017951:Antigen Presentation / Q000276:immunology*; D000951:Antigens, Neoplasm / Q000276:immunology*; D059472:Exome / Q000276:immunology*; D015395:Histocompatibility Antigens Class I / Q000276:immunology*; D006801:Humans; D057786:Peptidomimetics / Q000276:immunology*
chemical_list: D000951:Antigens, Neoplasm; D015395:Histocompatibility Antigens Class I; D057786:Peptidomimetics
keywords: HLA; TILs
references.citation: J Chromatogr A. 2002 Dec 6;979(1-2):233-9
references.pmid: 12498253
references.citation: Science. 2015 Apr 3;348(6230):62-8
references.pmid: 25838374
references.citation: J Immunol Methods. 1987 Aug 24;102(1):127-41
references.pmid: 3305708
references.citation: Tissue Antigens. 1998 Oct;52(4):368-73
references.pmid: 9820600
references.citation: Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):16013-8
references.pmid: 16247014
references.citation: PLoS One. 2007;2(8):e796
references.pmid: 17726526
references.citation: Nat Biotechnol. 2008 Dec;26(12):1367-72
references.pmid: 19029910
references.citation: Pigment Cell Melanoma Res. 2015 May;28(3):281-94
references.pmid: 25645385
references.citation: Cancer Immunol Res. 2015 Sep;3(9):992-8
references.pmid: 26048577
references.citation: J Clin Invest. 2015 Oct 1;125(10):3981-91
references.pmid: 26389673
references.citation: Science. 2015 Dec 11;350(6266):1387-90
references.pmid: 26516200
references.citation: Cell Cycle. 2009 Feb 1;8(3):505-6
references.pmid: 19176997
references.citation: Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18769-76
references.pmid: 20974924
references.citation: Nat Genet. 2011 May;43(5):442-6
references.pmid: 21499247
references.citation: Nat Med. 2013 Jun;19(6):747-52
references.pmid: 23644516
references.citation: J Immunol. 2013 Jun 15;190(12):6034-42
references.pmid: 23690473
references.citation: Mol Cell Proteomics. 2013 Jul;12(7):1853-64
references.pmid: 23538226
references.citation: Immunol Rev. 2014 Jan;257(1):56-71
references.pmid: 24329789
references.citation: Science. 2014 May 9;344(6184):641-5
references.pmid: 24812403
references.citation: Anal Chem. 2003 Feb 1;75(3):663-70
references.pmid: 12585499