{"doi":"10.1101/2020.08.04.236331","title":"Proteogenomic analysis unveils the HLA Class I presented immunopeptidome in melanoma and EGFR mutant lung adenocarcinoma","abstract":"Abstract Immune checkpoint inhibitor and adoptive lymphocyte transfer-based therapies have shown great therapeutic potential for cancers with high tumor mutation burden (TMB). Here, we employed mass spectrometry (MS)-based proteogenomic large-scale profiling to identify potential immunogenic human leukocyte antigen (HLA) Class I-presented peptides in both melanoma, a “hot tumor” with high TMB, and EGFR mutant lung adenocarcinoma, a “cold tumor” with low TMB. We identified several classes of neopeptides, including mutated neoantigens and more than 1000 post-translationally modified peptides representing 58 different PTMs. We constructed a cancer germline (CG) antigen database with 285 antigens and identified 42 Class I-presented CG antigens. Finally, we developed a non-canonical peptide discovery pipeline to identify 44 lncRNA-derived peptides and validated Class I binding for select neopeptides. We provide direct evidence of HLA Class I presentation of a large number of neopeptides for potential vaccine or adoptive cell therapy in melanoma and mutant EGFR lung cancer.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":123928,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9476,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":250445,"name":"Tapan K. Maity","orcid":"0009-0003-0184-0239","position":1,"is_corresponding":false},{"id":250447,"name":"Constance M. Cultraro","orcid":"0009-0006-7616-6885","position":2,"is_corresponding":false},{"id":567570,"name":"Vikram Misra","orcid":"0000-0001-6818-7156","position":3,"is_corresponding":false},{"id":567571,"name":"Xu Zhang","orcid":"0000-0003-2406-9478","position":4,"is_corresponding":false},{"id":567572,"name":"Catherine M. Ade","orcid":"0000-0002-5585-6258","position":5,"is_corresponding":false},{"id":252917,"name":"Shaojian Gao","orcid":null,"position":6,"is_corresponding":false},{"id":347040,"name":"David Milewski","orcid":"0000-0002-9778-8548","position":7,"is_corresponding":false},{"id":567366,"name":"Khoa Dang P. Nguyen","orcid":"0000-0003-0888-304X","position":8,"is_corresponding":false},{"id":566298,"name":"Mohammad Haghir Ebrahimabadi","orcid":"0000-0001-6265-4251","position":9,"is_corresponding":false},{"id":454553,"name":"Ken‐ichi Hanada","orcid":"0000-0003-2959-1257","position":10,"is_corresponding":false},{"id":250453,"name":"Javed Khan","orcid":"0000-0002-5858-0488","position":11,"is_corresponding":false},{"id":14308,"name":"S. Cenk Şahinalp","orcid":"0000-0002-2170-2808","position":12,"is_corresponding":false},{"id":454554,"name":"James C. Yang","orcid":"0000-0001-8935-5008","position":13,"is_corresponding":false},{"id":250454,"name":"Udayan Guha","orcid":"0000-0003-1087-9218","position":14,"is_corresponding":false},{"id":567365,"name":"Yue Qi","orcid":"0000-0003-1914-8710","position":0,"is_corresponding":true}],"reference_count":77,"raw_metadata":null,"created_at":"2026-07-18T23:15:03.403566Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}