We performed extensive transcriptional profiling of intratumoral immune infiltrates of 25 melanoma patients by massively parallel single cell RNA sequencing of 46,612 immune cells which passed quality control filtering, yielding profiles of 29,825 T and NK cells. While immune cell subtypes were largely shared across most patients, their relative abundance differed considerably between patients, even when disease stage and treatment background were matched. Notably, in spite of this variability in abundance, conserved trajectories of CD8 cells were observed, consistent with an ongoing differentiation process driven by interactions within the tumor microenvironment.
In particular, CD8 positive T cells were observed in two separate subsets, with only one of these transitioning into a dysfunctional T cell pool that is characterized by both known and novel regulatory molecules, and that includes molecules shared with CD4 Treg. Coupled single cell T cell receptor (TCR) sequencing and transcriptional profiling revealed that dysfunctional T cells display the highest level of clonal expansion. Furthermore, analysis of a cell cycle transcriptional signature, as well as flow cytometric analysis of Ki-67 expression and cell cycle progression, provided evidence for ongoing proliferation within this dysfunctional T cell compartment. This proliferative capacity was mainly associated with initial buildup of the dysfunctional program, whereas more advanced dysfunctional cells lost this proliferative signature. In contrast, a discrete pool of cytotoxic CD8 cells showed little evidence of proliferation and was unlinked to the dysfunctional T cell pool, as based on both TCR sharing data and gene module analysis. Collectively, our data suggest that the dysfunctional CD8 T cell pool should be considered a dynamically differentiating and active cell compartment that is likely to drive tumor-reactivity across patients. In-depth models of regulation of this T cell compartment should lead to the identification of novel immune modulatory pathways and optimization of T cell-based cancer therapies.
To exploit and disseminate our results, I have attended the following conferences:
• Third CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference, September 6 - 9, 2017, Germany
• SINGLE CELL GENOMICS 2017, October 16-18, 2017, Israel
• Cell-WIS Symposium: Next Gen Immunology, February 11-14, 2018, Israel
• Forth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference, 2018, USA
• SINGLE CELL GENOMICS, 2018, USA
• Cell Symposia: Single Cells: Technology to Biology, 2019, Singapore
I also published the results of the project in the Cell journal, with a statement in the Acknowledgment that “Hanjie Li is funded by the Marie Curie Individual Fellowship (EU project 746382 - SCALTIE)”. The results were reported by Weizmann Institute website and Netherland Cancer Institute website.
