title: Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction.
abstract: 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.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors.forename: Jennifer G
authors.initials: JG
authors.lastname: Abelin
authors.affiliation: 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.
authors.forename: Derin B
authors.initials: DB
authors.lastname: Keskin
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02142, USA.
authors.forename: Siranush
authors.initials: S
authors.lastname: Sarkizova
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors.forename: Christina R
authors.initials: CR
authors.lastname: Hartigan
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
authors.forename: Wandi
authors.initials: W
authors.lastname: Zhang
authors.affiliation: La Jolla Institute for Allergy and Immunology, 92037, La Jolla, CA.
authors.forename: John
authors.initials: J
authors.lastname: Sidney
authors.affiliation: Tissue Typing Laboratory, Brigham and Women's Hospital, Boston, MA, 02115, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Stevens
authors.affiliation: Tissue Typing Laboratory, Brigham and Women's Hospital, Boston, MA, 02115, USA.
authors.forename: William
authors.initials: W
authors.lastname: Lane
authors.affiliation: 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.
authors.forename: Guang Lan
authors.initials: GL
authors.lastname: Zhang
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Eisenhaure
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors.forename: Karl R
authors.initials: KR
authors.lastname: Clauser
authors.affiliation: 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.
authors.forename: Nir
authors.initials: N
authors.lastname: Hacohen
authors.affiliation: 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.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Rooney
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: scarr@broad.mit.edu.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Carr
authors.affiliation: 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.
authors.forename: Catherine J
authors.initials: CJ
authors.lastname: Wu
mesh_terms: D000465:Algorithms; D000483:Alleles; D017951:Antigen Presentation / Q000276:immunology*; D002460:Cell Line; D002853:Chromatography, Liquid / Q000379:methods; D000939:Epitopes; D020869:Gene Expression Profiling / Q000379:methods*; D015395:Histocompatibility Antigens Class I / Q000235:genetics / Q000276:immunology*; D006801:Humans; D016571:Neural Networks, Computer; D010455:Peptides / Q000276:immunology; D054730:Protein Interaction Domains and Motifs / Q000276:immunology; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D000939:Epitopes; D015395:Histocompatibility Antigens Class I; D010455:Peptides