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A Population of Tumor-Infiltrating CD4+ T-cells Co-expressing CD38 and CD39 is Associated with Checkpoint Inhibitor Resistance

ABSTRACT: We previously showed that elevated peripheral blood frequencies of a population of T-cells defined by the marker set CD3+CD4+CD127-GARP-CD38+CD39+ were associated with checkpoint immunotherapy resistance in metastatic melanoma patients. In this study we sought to further understand the role(s) of this population of ectoenzyme expressing T-cells (Teee). Using RNA-sequencing and flow cytometry to evaluate Teee from the peripheral blood of metastatic melanoma patients, we found that Teee were proliferative, apoptotic, had exhaustion associated phenotypes, and had high expression of inhibitory molecules. Co-culture of patient Teee with autologous T-cells in vitro resulted in suppression of proliferation of the target T-cells. Using single-cell RNA-sequencing datasets, we identified distinct clusters of cells with a Teee gene signature present in melanoma, non-small cell lung cancer and bladder cancer patients’ tumors. Teee were not present in healthy bladder tissue. Using multispectral immunofluorescence of melanoma patient FFPE tumor samples, we were able to identify CD4+ T-cells co-expressing CD38 and CD39 in the tumor microenvironment, which preferentially associated with Ki67- CD8+ T-cells. Finally, we found that high baseline intra-tumor frequencies of cells with a Teee gene signature were associated with checkpoint immunotherapy resistance and poor overall survival in metastatic melanoma patients. These results build upon our previous findings, demonstrating that a novel population of CD4+ T-cells co-expressing CD38 and CD39 are found in the periphery and tumor of patients and are associated with checkpoint immunotherapy resistance.

ORGANISM(S): Homo sapiens

PROVIDER: GSE224099 | GEO | 2023/07/17

REPOSITORIES: GEO

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Project description:Checkpoint blockade therapy using antibodies targeting CTLA4, PD1 or PDL1 have changed the way cancer patients with advanced disease are being treated, as evident by their FDA approval in a wide variety of malignancies, and their ability to induce high response rates when compared to conventional therapies (e.g. chemotherapy). However, even in melanoma, despite the high response rate, most patients are refractory to therapy or acquire resistance in 10-12 months. To identify key immunological elements coupled with response or resistance to checkpoint immunotherapy, we performed an unbiased analysis on 16,291 CD45+ immune cells from 32 patients (48 samples) treated with checkpoint therapy (anti-PD1=37; anti-PD1/CTLA4=11), using single cell transcriptomics. Initial unsupervised clustering of all CD45+ cells identified 11 clusters. When examining the association of these clusters with clinical outcome, we found that two clusters (B-cells, p=0.005; memory T-cells, p=0.03) were significantly enriched in responder lesions while 4 clusters (monocytes/macrophages, p=0.003; dendritic cells, p=0.015; exhausted CD8+ T-cells, p=0.005; and exhausted/cell-cycle lymphocytes, 1.3x10-5) are enriched in non-responder lesions. Next, by leveraging our unbiased single cell approach, we identified not only clusters but also specific markers associated with either responder lesions (PLAC8, LTB, LY9, SELL, TCF7, IGKC and CCR7) or non-responder ones (CCL3, CD38, HAVCR2, ENTPD1 and WARS), many of which were not previously reported to be associated with clinical outcome to checkpoint therapy. Due to the importance of CD8+ T-cells in controlling tumors, the significant association of T-cell states with clinical outcome, and their high abundance in melanoma tumors, we next focused our analysis on CD8+ T-cells and identified 2 main clusters CD8_G (with increased expression of genes linked to memory) and CD8_B (enriched for genes linked to cell dysfunction), that were significantly enriched in responder (CD8_G, p=1.4x10-6) and non-responder (CD8_B, p=0.005) lesions, respectively. Since cells with both states coexist in each of the responder and non-responder lesions, we decided to calculate the ratio between the number of cells in these 2 clusters and observed a significant separation between responders (CD8_G/CD8_B>1) and non-responders (CD8_G/CD8_B<1) when looking at all samples, baseline or post samples separately. Similar results were detected when looking at the expression of a single transcription factor, TCF7, in CD8 T-cells in an independent cohort (n=43) using a simple immunofluorescence assay. Additionally, we validated the identity and function of some of the newly identified cell states as well as their epigenetic landscape, and found that cells expressing the inhibitory molecules CD39 and TIM3, on top of being enriched in non-responder lesions, are likely to play a crucial role in T-cell exhaustion in melanoma. Collectively, our study provides extensive unbiased data in human tumors for discovery of predictors and therapeutic targets to checkpoint immunotherapy.

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A Population of Tumor-Infiltrating CD4+ T-cells Co-expressing CD38 and CD39 is Associated with Checkpoint Inhibitor Resistance

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