{"doi":"10.1136/jitc-2022-005328","title":"Transcriptional and functional analyses of neoantigen-specific CD4 T cells during a profound response to anti-PD-L1 in metastatic Merkel cell carcinoma","abstract":"BACKGROUND: Merkel cell carcinoma (MCC) often responds to PD-1 pathway blockade, regardless of tumor-viral status (~80% of cases driven by the Merkel cell polyomavirus (MCPyV)). Prior studies have characterized tumor-specific T cell responses to MCPyV, which have typically been CD8, but little is known about the T cell response to UV-induced neoantigens. METHODS: A patient in her mid-50s with virus-negative (VN) MCC developed large liver metastases after a brief initial response to chemotherapy. She received anti-PD-L1 (avelumab) and had a partial response within 4 weeks. Whole exome sequencing (WES) was performed to determine potential neoantigen peptides. Characterization of peripheral blood neoantigen T cell responses was evaluated via interferon-gamma (IFNγ) ELISpot, flow cytometry and single-cell RNA sequencing. Tumor-resident T cells were characterized by multiplexed immunohistochemistry. RESULTS: WES identified 1027 tumor-specific somatic mutations, similar to the published average of 1121 for VN-MCCs. Peptide prediction with a binding cut-off of ≤100 nM resulted in 77 peptides that were synthesized for T cell assays. Although peptides were predicted based on class I HLAs, we identified circulating CD4 T cells targeting 5 of 77 neoantigens. In contrast, no neoantigen-specific CD8 T cell responses were detected. Neoantigen-specific CD4 T cells were undetectable in blood before anti-PD-L1 therapy but became readily detectible shortly after starting therapy. T cells produced robust IFNγ when stimulated by neoantigen (mutant) peptides but not by the normal (wild-type) peptides. Single cell RNAseq showed neoantigen-reactive T cells expressed the Th1-associated transcription factor (T-bet) and associated cytokines. These CD4 T cells did not significantly exhibit cytotoxicity or non-Th1 markers. Within the pretreatment tumor, resident CD4 T cells were also Th1-skewed and expressed T-bet. CONCLUSIONS: We identified and characterized tumor-specific Th1-skewed CD4 T cells targeting multiple neoantigens in a patient who experienced a profound and durable partial response to anti-PD-L1 therapy. To our knowledge, this is the first report of neoantigen-specific T cell responses in MCC. Although CD4 and CD8 T cells recognizing viral tumor antigens are often detectible in virus-positive MCC, only CD4 T cells recognizing neoantigens were detected in this patient. These findings suggest that CD4 T cells can play an important role in the response to anti-PD-(L)1 therapy.","journal":"Journal for ImmunoTherapy of Cancer","year":2022,"id":256760,"datarank":0.4493598410330987,"base_score":2.995732273553991,"endowment":2.995732273553991,"self_citation_contribution":0.4493598410330987,"citation_network_contribution":0.0,"self_endowment_contribution":0.4493598410330987,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":19,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9608,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":323050,"name":"Thomas H. Pulliam","orcid":"0000-0003-3511-6348","position":1,"is_corresponding":false},{"id":906630,"name":"Natalie V. Longino","orcid":null,"position":2,"is_corresponding":false},{"id":285792,"name":"Song Y. Park","orcid":"0000-0003-4366-1821","position":3,"is_corresponding":false},{"id":232690,"name":"Kimberly S. Smythe","orcid":"0000-0002-2329-8298","position":4,"is_corresponding":false},{"id":116079,"name":"Vladimir Makarov","orcid":null,"position":5,"is_corresponding":false},{"id":236122,"name":"Nadeem Riaz","orcid":"0000-0001-9873-5862","position":6,"is_corresponding":false},{"id":294665,"name":"Lichen Jing","orcid":"0000-0002-5938-4171","position":7,"is_corresponding":false},{"id":232694,"name":"Robert A. Amezquita","orcid":"0000-0001-6868-7193","position":8,"is_corresponding":false},{"id":296017,"name":"Jean S. Campbell","orcid":"0000-0002-9187-2204","position":9,"is_corresponding":false},{"id":18054,"name":"Raphaël Gottardo","orcid":"0000-0002-3867-0232","position":10,"is_corresponding":false},{"id":58596,"name":"Robert H. Pierce","orcid":"0000-0002-2677-144X","position":11,"is_corresponding":false},{"id":267765,"name":"Jaehyuk Choi","orcid":"0000-0003-2379-2226","position":12,"is_corresponding":false},{"id":69956,"name":"Timothy A. Chan","orcid":"0000-0002-9265-0283","position":13,"is_corresponding":false},{"id":294672,"name":"David M. Koelle","orcid":"0000-0003-1255-9023","position":14,"is_corresponding":false},{"id":287858,"name":"Paul Nghiem","orcid":"0000-0003-2784-963X","position":15,"is_corresponding":false},{"id":323051,"name":"Candice D. Church","orcid":"0000-0003-1582-8292","position":0,"is_corresponding":true}],"reference_count":57,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:25:25.728895Z","pmid":"36252564","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":[]}