PMID- 28228285 OWN - NLM STAT- MEDLINE DCOM- 20170913 LR - 20191210 IS - 1097-4180 (Electronic) IS - 1074-7613 (Print) IS - 1074-7613 (Linking) VI - 46 IP - 2 DP - 2017 Feb 21 TI - Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. PG - 315-326 LID - S1074-7613(17)30042-0 [pii] LID - 10.1016/j.immuni.2017.02.007 [doi] AB - Identification of human leukocyte antigen (HLA)-bound peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules underlying antigen presentation. However, a key obstacle is the ambiguity that arises from the co-expression of multiple HLA alleles. Here, we have implemented a scalable mono-allelic strategy for profiling the HLA peptidome. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing an application-specific spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of subdominant binding motifs and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression. We trained neural-network prediction algorithms with our large dataset (>24,000 peptides) and outperformed algorithms trained on datasets of peptides with measured affinities. We thus demonstrate a strategy for systematically learning the rules of endogenous antigen presentation. CI - Copyright (c) 2017 Elsevier Inc. All rights reserved. FAU - Abelin, Jennifer G AU - Abelin JG AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. FAU - Keskin, Derin B AU - Keskin DB AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA; Harvard Medical School, Boston, MA, 02115, USA; Department of Computer Science, Metropolitan College, Boston University, Boston, MA, 02215, USA. FAU - Sarkizova, Siranush AU - Sarkizova S AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02142, USA. FAU - Hartigan, Christina R AU - Hartigan CR AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. FAU - Zhang, Wandi AU - Zhang W AD - Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. FAU - Sidney, John AU - Sidney J AD - La Jolla Institute for Allergy and Immunology, 92037, La Jolla, CA. FAU - Stevens, Jonathan AU - Stevens J AD - Tissue Typing Laboratory, Brigham and Women's Hospital, Boston, MA, 02115, USA. FAU - Lane, William AU - Lane W AD - Tissue Typing Laboratory, Brigham and Women's Hospital, Boston, MA, 02115, USA. FAU - Zhang, Guang Lan AU - Zhang GL AD - Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Harvard Medical School, Boston, MA, 02115, USA; Department of Computer Science, Metropolitan College, Boston University, Boston, MA, 02215, USA. FAU - Eisenhaure, Thomas M AU - Eisenhaure TM AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. FAU - Clauser, Karl R AU - Clauser KR AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. FAU - Hacohen, Nir AU - Hacohen N AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Center for Cancer Immunology, Massachusetts General Hospital, Boston, MA, 02114, USA. Electronic address: nhacohen@mgh.harvard.edu. FAU - Rooney, Michael S AU - Rooney MS AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard/MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, 02139 USA; Neon Therapeutics, Cambridge, MA, 02139, USA. Electronic address: mrooney@neontherapeutics.com. FAU - Carr, Steven A AU - Carr SA AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: scarr@broad.mit.edu. FAU - Wu, Catherine J AU - Wu CJ AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA; Harvard Medical School, Boston, MA, 02115, USA. Electronic address: cwu@partners.org. LA - eng GR - P50 CA101942/CA/NCI NIH HHS/United States GR - R01 CA155010/CA/NCI NIH HHS/United States GR - T32 HG002295/HG/NHGRI NIH HHS/United States GR - U24 CA160034/CA/NCI NIH HHS/United States PT - Journal Article PL - United States TA - Immunity JT - Immunity JID - 9432918 RN - 0 (Epitopes) RN - 0 (Histocompatibility Antigens Class I) RN - 0 (Peptides) SB - IM MH - *Algorithms MH - Alleles MH - Antigen Presentation/*immunology MH - Cell Line MH - Chromatography, Liquid/methods MH - Epitopes MH - Gene Expression Profiling/*methods MH - Histocompatibility Antigens Class I/genetics/*immunology MH - Humans MH - Neural Networks, Computer MH - Peptides/immunology MH - Protein Interaction Domains and Motifs/immunology MH - Tandem Mass Spectrometry/*methods PMC - PMC5405381 MID - NIHMS851841 EDAT- 2017/02/24 06:00 MHDA- 2017/09/14 06:00 PMCR- 2018/02/21 CRDT- 2017/02/24 06:00 PHST- 2016/07/08 00:00 [received] PHST- 2016/11/29 00:00 [revised] PHST- 2016/12/29 00:00 [accepted] PHST- 2017/02/24 06:00 [entrez] PHST- 2017/02/24 06:00 [pubmed] PHST- 2017/09/14 06:00 [medline] PHST- 2018/02/21 00:00 [pmc-release] AID - S1074-7613(17)30042-0 [pii] AID - 10.1016/j.immuni.2017.02.007 [doi] PST - ppublish SO - Immunity. 2017 Feb 21;46(2):315-326. doi: 10.1016/j.immuni.2017.02.007.