Using scRNAseq data from patients with ICI-treated melanoma, Bae et al. profiled conventional CD4+ T cells (excluding Tregs and proliferative cells) at the lesion level. A cytotoxic cluster was enriched in responders, and an exhausted, Treg-like cluster was detected in all samples, and trended towards enrichment in non-responders (NRs). Two clusters dually enhanced in cytotoxicity and exhaustion genes also trended towards enrichment in NRs. Trajectory analysis suggested a cluster characterized by migratory genes as a precursor to the cytotoxic/exhausted clusters, along with a potential transition of a unique exhausted cluster to the Treg-like state.

Contributed by Morgan Janes

ABSTRACT: Although checkpoint immunotherapy has primarily focused on CD8⁺ T cells, emerging evidence highlights an important role for cytotoxic CD4⁺ T cells in mediating therapeutic responses. However, research on the functional properties of cytotoxic CD4⁺ T cells in the context of immunotherapy is still at an early stage and remains insufficiently defined. Utilizing single-cell RNA-sequencing datasets obtained from metastatic melanoma patients treated with checkpoint inhibitors targeting PD-1 and/or CTLA-4, we performed transcriptomic profiling of conventional CD4⁺ T cells, excluding proliferative and regulatory (FOXP3⁺) subsets, and compared responders and non-responders as distinct groups. Importantly, our analysis identified distinct clusters that discriminate between responders and non-responders, with cytotoxic CD4⁺ T cells occupying a central position within these clusters. In responder-specific clusters, cytotoxic CD4⁺ T cells exhibited features of early activation, whereas clusters specific to non-responders were characterized by an exhausted phenotype. Notably, non-responder-specific clusters were positioned proximally to Treg-like clusters, suggesting a potential transition from cytotoxic to regulatory CD4⁺ T cell states in non-responders. Our findings reinforce the emerging concept that cytotoxic CD4⁺ T cells play a central role in mediating immunotherapy responses. These results provide a foundation for the development of predictive biomarkers and novel therapeutic strategies aimed at modulating CD4⁺ T cell differentiation.

Author Info: (1) Center for Food and Nutritional Genomics, Kyungpook National University, Daegu, 41566, Republic of Korea. Department of Food Science and Nutrition, Kyungpook National Universit

Author Info: (1) Center for Food and Nutritional Genomics, Kyungpook National University, Daegu, 41566, Republic of Korea. Department of Food Science and Nutrition, Kyungpook National University, Daegu, 41566, Republic of Korea. Omixplus, LLC, Austin, TX, 78750, USA. (2) Department of Biology, Kyungpook National University, Daegu, 41566, Republic of Korea. (3) School of Artificial Intelligence, Kyungpook National University, Daegu, 41566, Republic of Korea. (4) Omixplus, LLC, Austin, TX, 78750, USA. (5) Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA. (6) Center for Food and Nutritional Genomics, Kyungpook National University, Daegu, 41566, Republic of Korea. eykwon@knu.ac.kr. Department of Food Science and Nutrition, Kyungpook National University, Daegu, 41566, Republic of Korea. eykwon@knu.ac.kr. Center for Beautiful Aging, Kyungpook National University, Daegu, 41566, Republic of Korea. eykwon@knu.ac.kr.