{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T00:22:00Z","timestamp":1793146920981,"version":"4.5.0"},"reference-count":55,"publisher":"National Academy of Sciences","issue":"47","license":[{"start":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T00:00:00Z","timestamp":1763596800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"HHS | NIH","doi-asserted-by":"publisher","award":["DP2AI158126"],"award-info":[{"award-number":["DP2AI158126"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | NIH","doi-asserted-by":"publisher","award":["R21-AI156664"],"award-info":[{"award-number":["R21-AI156664"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | NIH","doi-asserted-by":"publisher","award":["R01-AI022553"],"award-info":[{"award-number":["R01-AI022553"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | NIH","doi-asserted-by":"publisher","award":["R35-GM142900"],"award-info":[{"award-number":["R35-GM142900"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | NIH","doi-asserted-by":"publisher","award":["P30-CA14051"],"award-info":[{"award-number":["P30-CA14051"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000008","name":"David and Lucile Packard Foundation","doi-asserted-by":"publisher","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}],"id":[{"id":"10.13039\/100000008","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100027426","name":"Schmidt Futures","doi-asserted-by":"publisher","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}],"id":[{"id":"10.13039\/100027426","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100023581","name":"NSF | NSF Graduate Research Fellowship Program","doi-asserted-by":"publisher","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}],"id":[{"id":"10.13039\/100023581","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2025,11,25]]},"abstract":"<jats:p>\n                    T cells rely on short peptides presented by highly polymorphic major histocompatibility complexes (MHCs) to selectively initiate adaptive immune responses. Despite its importance, few techniques can systematically evaluate stable peptide presentation across diverse MHC alleles. Here, we describe a yeast display pipeline that can be deployed to rapidly screen peptides to identify class I pMHC binders across many alleles. Through this, we isolate unique biological phenomena such as alteration of the peptide presentation of HLA-B57 via interaction with the antiviral small molecule abacavir. We apply this approach to multiple pathogen proteomes (\n                    <jats:italic toggle=\"yes\">\n                      <jats:italic toggle=\"yes\">Mycobacterium tuberculosis<\/jats:italic>\n                    <\/jats:italic>\n                    Type VII secretion substrates, SARS-CoV-2, Dengue, and Zika) to create a comprehensive list of potential T cell antigens. Altogether, this platform acts as a flexible tool to generate large unbiased datasets for class I peptide binding at a speed and scale competitive with the biological systems they represent.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2514741122","type":"journal-article","created":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T16:21:33Z","timestamp":1763655693000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":5,"title":["High-throughput screening for class I peptide MHC binding via yeast surface display"],"prefix":"10.1073","volume":"122","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2342-7616","authenticated-orcid":false,"given":"Patrick V.","family":"Holec","sequence":"first","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology","place":["Cambridge"]},{"name":"Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology","place":["Cambridge"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5784-9876","authenticated-orcid":false,"given":"Kathryn C.","family":"Breuckman","sequence":"additional","affiliation":[{"name":"Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology","place":["Cambridge"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Owen","family":"Leddy","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology","place":["Cambridge"]},{"name":"Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology","place":["Cambridge"]},{"name":"Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard","place":["Cambridge"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1545-1651","authenticated-orcid":false,"given":"Forest M.","family":"White","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology","place":["Cambridge"]},{"name":"Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology","place":["Cambridge"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1716-6712","authenticated-orcid":false,"given":"Bryan D.","family":"Bryson","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology","place":["Cambridge"]},{"name":"Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard","place":["Cambridge"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2281-3518","authenticated-orcid":false,"given":"Michael E.","family":"Birnbaum","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology","place":["Cambridge"]},{"name":"Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology","place":["Cambridge"]},{"name":"Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard","place":["Cambridge"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2025,11,20]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0952-7915(01)00298-9"},{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/sj.jid.5700001"},{"key":"e_1_3_4_3_2","volume-title":"The HLA FactsBook","author":"Marsh S. G. E.","year":"1999","unstructured":"S. G. E. Marsh, P. Parham, L. D. Barber, The HLA FactsBook (Academic Press, San Diego, CA, 1999)."},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.166.5.3345"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-2776(02)80012-8"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.09.015"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.85126"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-022-00707-2"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.8.3429"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/368215a0"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/329506a0"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature24627"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jim.2016.02.016"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-1759(94)00327-S"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molimm.2015.06.010"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2017.02.007"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2111173118"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-024-01076-x"},{"key":"e_1_3_4_19_2","first-page":"1","article-title":"High-throughput, targeted MHC class I immunopeptidomics using a functional genetics screening platform","volume":"2","author":"Bruno P. M.","year":"2023","unstructured":"P. M. Bruno , High-throughput, targeted MHC class I immunopeptidomics using a functional genetics screening platform. Nat. Biotechnol. 2, 1\u201313 (2023).","journal-title":"Nat. Biotechnol."},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn202"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa379"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2018.05.014"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-023-04867-2"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1158\/2326-6066.CIR-19-0464"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.2174\/1574893615999200429122801"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac965"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.78589"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.2c02198"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1021\/acssynbio.2c00101"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11147"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.03.047"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-2285-8_15"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.11.043"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M604343200"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-1759(02)00439-8"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2011.09.013"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18204-2"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2023.102913"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2007.07.010"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M303716200"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1042\/BST20210410"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.849004"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku938"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2022.1034810"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1007\/s002510050240"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05501-7"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.873"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1207-1"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2007.08.012"},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.25040"},{"key":"e_1_3_4_51_2","first-page":"211","volume-title":"Visualizing Data with Pandas and Matplotlib. Hands-on Matplotlib","author":"Pajankar A.","year":"2022","unstructured":"A. Pajankar, Visualizing Data with Pandas and Matplotlib. Hands-on Matplotlib (Apress, Berkeley, CA, 2022), pp. 211\u2013241."},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1088\/1742-6596\/1833\/1\/012002"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","unstructured":"P. Holec Supplemental Data for \u201cHigh-throughput screening for class I peptide\u2013MHC binding via yeast surface display\u201d (Holec et al. 2025). Zenodo. https:\/\/zenodo.org\/uploads\/17093099. Deposited 10 September 2025.","DOI":"10.1101\/2025.05.24.655874"},{"key":"e_1_3_4_54_2","unstructured":"P. Holec PRJNA1257316. Sequence Read Archive (SRA). https:\/\/www.ncbi.nlm.nih.gov\/bioproject\/PRJNA1257316. Deposited 23 April 2025."},{"key":"e_1_3_4_55_2","unstructured":"P. Holec birnbaumlab\/Holec-et-al-2025. Github. https:\/\/github.com\/birnbaumlab\/Holec-et-al-2025. Deposited 7 October 2025."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.2514741122","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T00:56:09Z","timestamp":1763686569000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/10.1073\/pnas.2514741122"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,20]]},"references-count":55,"journal-issue":{"issue":"47","published-print":{"date-parts":[[2025,11,25]]}},"alternative-id":["10.1073\/pnas.2514741122"],"URL":"https:\/\/doi.org\/10.1073\/pnas.2514741122","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,20]]},"assertion":[{"value":"2025-06-10","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-10-17","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-11-20","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e2514741122"}}