Journal Article

Transcriptional and functional analyses of neoantigen-specific CD4 T cells during a profound response to anti-PD-L1 in metastatic Merkel cell carcinoma

Riaz, Nadeem, Pulliam, Thomas, Church, Candice, Park, Song Y, Longino, Natalie, Campbell, Jean S, Smythe, Kimberly S, Gottardo, Raphael, Jing, Lichen, Makarov, Vladimir, Koelle, David M, Choi, Jaehyuk, Nghiem, Paul, Chan, Timothy A, Amezquita, Robert, Pierce, Robert H

2022

Overview

BackgroundMerkel 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.MethodsA 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.ResultsWES 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.ConclusionsWe 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.

• Publisher: BMJ Publishing Group Ltd,BMJ Publishing Group LTD,BMJ Publishing Group
• Subject: adaptive immunity / Antibodies / Antigens / Antigens, Viral, Tumor / Basic Tumor Immunology / Biopsy / Cancer / Cancer therapies / Carcinoma, Merkel Cell - drug therapy / Carcinoma, Merkel Cell - genetics / CD4-Positive T-Lymphocytes / Chemotherapy / Cloning / Cytokines / Female / Gene expression / Humans / immunity, cellular / Immunotherapy / Interferon-gamma / Ligands / Lymphocytes / Merkel cell polyomavirus / Metastasis / Monoclonal antibodies / Peptides / Programmed Cell Death 1 Receptor - antagonists & inhibitors / Response rates / Skin cancer / skin neoplasms / Skin Neoplasms - drug therapy / Skin Neoplasms - genetics / Transcription Factors / Tumors