{"id":"https://openalex.org/W7214434286","doi":"https://doi.org/10.3390/ijms27188338","title":"HLA-II Expression Marks Activated and Clonally Expanded CD8+ T Cells and Improves Tumor-Reactivity Prediction Across Human Cancers","display_name":"HLA-II Expression Marks Activated and Clonally Expanded CD8+ T Cells and Improves Tumor-Reactivity Prediction Across Human Cancers","publication_year":2026,"publication_date":"2026-09-19","ids":{"openalex":"https://openalex.org/W7214434286","doi":"https://doi.org/10.3390/ijms27188338","pmid":"https://pubmed.ncbi.nlm.nih.gov/42794764","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13607992"},"language":"en","primary_location":{"id":"doi:10.3390/ijms27188338","doi":"https://doi.org/10.3390/ijms27188338","is_oa":true,"landing_page_url":"https://doi.org/10.3390/ijms27188338","pdf_url":null,"source":{"id":"https://openalex.org/S10623703","display_name":"International Journal of Molecular Sciences","issn_l":"1422-0067","issn":["1422-0067","1661-6596"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","medline","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Molecular Sciences","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3390/ijms27188338","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5153384904","display_name":"Xue Mi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xue Mi","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China","institution_ids":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152987809","display_name":"Jinghua Zhu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210128482","display_name":"Jiangsu Cancer Hospital","ror":"https://ror.org/03108sf43","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128482"]},{"id":"https://openalex.org/I83519826","display_name":"Nanjing Medical University","ror":"https://ror.org/059gcgy73","country_code":"CN","type":"education","lineage":["https://openalex.org/I83519826"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinghua Zhu","raw_affiliation_strings":["Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, China","institution_ids":["https://openalex.org/I4210128482","https://openalex.org/I83519826"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100541453","display_name":"Zhu Dai","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhu Dai","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China","institution_ids":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028744762","display_name":"Ruyue Yang","orcid":"https://orcid.org/0009-0006-7394-0329","observed_orcids":["https://orcid.org/0009-0006-7394-0329"]},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruyue Yang","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China","institution_ids":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152968869","display_name":"Dongmei Tian","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongmei Tian","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China","institution_ids":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023713769","display_name":"\u66f9\u56fd\u6625","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210128482","display_name":"Jiangsu Cancer Hospital","ror":"https://ror.org/03108sf43","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128482"]},{"id":"https://openalex.org/I83519826","display_name":"Nanjing Medical University","ror":"https://ror.org/059gcgy73","country_code":"CN","type":"education","lineage":["https://openalex.org/I83519826"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guochun Cao","raw_affiliation_strings":["Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, China","institution_ids":["https://openalex.org/I4210128482","https://openalex.org/I83519826"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023799242","display_name":"Zhongdang XIAO","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhongdang Xiao","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China","institution_ids":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5023713769","https://openalex.org/A5023799242"],"corresponding_institution_ids":["https://openalex.org/I4210128482","https://openalex.org/I4387154005","https://openalex.org/I76569877","https://openalex.org/I83519826"],"apc_list":{"value":2900,"currency":"CHF","value_usd":3499},"apc_paid":{"value":2900,"currency":"CHF","value_usd":3499},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.68744396,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"18","first_page":"8338","last_page":"8338"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.9063000082969666,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.9063000082969666,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.07649999856948853,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.004399999976158142,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cd8-t-cells","display_name":"CD8+ T cells","score":0.9739999771118164},{"id":"https://openalex.org/keywords/tumor-infiltrating-lymphocytes","display_name":"tumor-infiltrating lymphocytes","score":0.8450000286102295},{"id":"https://openalex.org/keywords/clonal-expansion","display_name":"clonal expansion","score":0.8360000252723694},{"id":"https://openalex.org/keywords/tcr-clonotypes","display_name":"TCR clonotypes","score":0.8379999995231628},{"id":"https://openalex.org/keywords/t-cell-exhaustion","display_name":"T cell exhaustion","score":0.7139999866485596},{"id":"https://openalex.org/keywords/t-cell-differentiation","display_name":"T cell differentiation","score":0.8270000219345093},{"id":"https://openalex.org/keywords/t-cell-proliferation","display_name":"T cell proliferation","score":0.5},{"id":"https://openalex.org/keywords/pancreatic-ductal-adenocarcinoma","display_name":"pancreatic ductal adenocarcinoma","score":0.843999981880188},{"id":"https://openalex.org/keywords/tcr-repertoire","display_name":"T cell receptor repertoire","score":0.45100000500679016},{"id":"https://openalex.org/keywords/prognostic-signature","display_name":"prognostic signature","score":0.6290000081062317},{"id":"https://openalex.org/keywords/overall-survival","display_name":"overall survival","score":0.492000013589859}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5859000086784363},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5418000221252441},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4571000039577484},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.44999998807907104},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38690000772476196},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.38609999418258667},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3756999969482422},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3675000071525574},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.31459999084472656},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.3003000020980835},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.2980000078678131},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.2840000092983246},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.2833999991416931},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.28119999170303345},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.27970001101493835},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.2736999988555908},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.2630999982357025},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.25200000405311584},{"id":"https://openalex.org/C81885089","wikidata":"https://www.wikidata.org/wiki/Q189082","display_name":"Cell culture","level":2,"score":0.2513999938964844}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008213","descriptor_name":"Lymphocyte Activation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016246","descriptor_name":"Lymphocytes, Tumor-Infiltrating","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D016246","descriptor_name":"Lymphocytes, Tumor-Infiltrating","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018414","descriptor_name":"CD8-Positive T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D018414","descriptor_name":"CD8-Positive T-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.3390/ijms27188338","doi":"https://doi.org/10.3390/ijms27188338","is_oa":true,"landing_page_url":"https://doi.org/10.3390/ijms27188338","pdf_url":null,"source":{"id":"https://openalex.org/S10623703","display_name":"International Journal of Molecular Sciences","issn_l":"1422-0067","issn":["1422-0067","1661-6596"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","medline","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Molecular Sciences","raw_type":"journal-article"},{"id":"pmid:42794764","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42794764","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International journal of molecular sciences","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13607992","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13607992/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Int J Mol Sci","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/ijms27188338","doi":"https://doi.org/10.3390/ijms27188338","is_oa":true,"landing_page_url":"https://doi.org/10.3390/ijms27188338","pdf_url":null,"source":{"id":"https://openalex.org/S10623703","display_name":"International Journal of Molecular Sciences","issn_l":"1422-0067","issn":["1422-0067","1661-6596"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","medline","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Molecular Sciences","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.9476000070571899,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320336297","display_name":"Jiangsu Cancer Hospital","ror":"https://ror.org/03108sf43"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1973639800","https://openalex.org/W1977281284","https://openalex.org/W1978518799","https://openalex.org/W2068046103","https://openalex.org/W2105381977","https://openalex.org/W2163660115","https://openalex.org/W2304211375","https://openalex.org/W2747877289","https://openalex.org/W2800392236","https://openalex.org/W2916020270","https://openalex.org/W2951506174","https://openalex.org/W2953151710","https://openalex.org/W3005326482","https://openalex.org/W3040324319","https://openalex.org/W3132661792","https://openalex.org/W3185560091","https://openalex.org/W4200327459","https://openalex.org/W4200468913","https://openalex.org/W4223424723","https://openalex.org/W4281984900","https://openalex.org/W4282929459","https://openalex.org/W4320896665","https://openalex.org/W4323546617","https://openalex.org/W4376133743","https://openalex.org/W4379514197","https://openalex.org/W4388072673","https://openalex.org/W4388692479","https://openalex.org/W4392561142","https://openalex.org/W4394923725","https://openalex.org/W4404832583","https://openalex.org/W4404860427","https://openalex.org/W4407107918","https://openalex.org/W4413521152","https://openalex.org/W4414361072","https://openalex.org/W4415134225","https://openalex.org/W7172512187"],"related_works":["https://openalex.org/W7154576613","https://openalex.org/W7207757320","https://openalex.org/W4414710011","https://openalex.org/W4308399148","https://openalex.org/W3214468520","https://openalex.org/W7163525010","https://openalex.org/W7213910781","https://openalex.org/W7167236848","https://openalex.org/W7126743234","https://openalex.org/W4392561142"],"abstract_inverted_index":{"Tumor-infiltrating":[0],"CD8+":[1,42,55,99,109,114,159,215],"T":[2,56,110,160],"cells":[3,57,161],"are":[4],"transcriptionally":[5],"heterogeneous,":[6],"and":[7,28,49,65,69,97,102,144,153,183,188,198,212,218],"robust":[8],"features":[9,226],"linking":[10],"their":[11],"clonal":[12,47],"dynamics":[13],"to":[14,40,132,178,181,185,193,196,200],"experimentally":[15,141],"defined":[16],"tumor":[17,50],"reactivity":[18],"remain":[19],"incompletely":[20],"characterized.":[21],"We":[22],"integrated":[23],"single-cell":[24,37],"RNA":[25],"sequencing":[26,32],"(scRNA-seq)":[27],"paired":[29],"T-cell":[30,43,100,115,216],"receptor":[31],"(scTCR-seq)":[33],"data":[34],"from":[35,147,162,176,191],"31":[36],"immune":[38],"datasets":[39],"characterize":[41],"states":[44,68,217],"associated":[45,72],"with":[46,73],"expansion":[48],"reactivity.":[51],"Across":[52],"cancers,":[53],"HLA-II-expressing":[54],"were":[58,70],"enriched":[59],"in":[60,93,107,125,155],"activated,":[61],"cytotoxic,":[62],"proliferative,":[63],"exhausted,":[64],"terminally":[66],"differentiated":[67],"preferentially":[71],"expanded":[74,214],"TCR":[75],"clonotypes.":[76],"Pseudotime":[77],"analysis":[78],"indicated":[79],"that":[80],"HLA-II":[81,168,205],"expression":[82,206],"occurs":[83],"along":[84],"late":[85],"differentiation":[86],"states.":[87],"HLA-DR":[88],"blockade":[89],"reduced":[90],"CD25":[91],"upregulation":[92],"activated":[94,211],"mixed":[95],"PBMC":[96],"purified":[98,108],"cultures":[101],"attenuated":[103],"CellTrace":[104],"CFSE":[105],"dilution":[106],"cells.":[111],"An":[112],"HLA-II-associated":[113,224],"signature":[116],"showed":[117],"cancer-type-dependent":[118],"survival":[119,124],"associations,":[120],"including":[121],"longer":[122],"overall":[123],"several":[126],"cohorts.":[127],"To":[128],"evaluate":[129],"its":[130],"contribution":[131],"tumor-reactivity":[133],"prediction,":[134],"an":[135],"expansion-pretrained":[136],"DNN":[137],"was":[138],"adapted":[139],"using":[140],"annotated":[142,158],"tumor-reactive":[143,230],"non-tumor-reactive":[145],"clonotypes":[146],"six":[148,167],"pancreatic":[149],"ductal":[150],"adenocarcinoma":[151],"samples":[152],"evaluated":[154],"2225":[156],"functionally":[157],"three":[163,173],"held-out":[164],"samples.":[165],"Adding":[166],"genes":[169],"improved":[170,189],"ROC-AUC":[171],"across":[172],"feature":[174,209],"panels":[175],"0.540":[177],"0.781,":[179],"0.626":[180],"0.732,":[182],"0.838":[184],"0.878,":[186],"respectively,":[187],"PR-AUC":[190],"0.570":[192],"0.739,":[194],"0.640":[195],"0.718,":[197],"0.799":[199],"0.869.":[201],"These":[202],"findings":[203],"identify":[204],"as":[207],"a":[208],"of":[210,223],"clonally":[213],"support":[219],"the":[220],"complementary":[221],"value":[222],"transcriptional":[225],"for":[227],"prioritizing":[228],"candidate":[229],"TCRs.":[231]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-09-27T00:00:00"}
