Data from A Population of Tumor-Infiltrating CD4<sup>+</sup> T Cells Co-Expressing CD38 and CD39 Is Associated with Checkpoint Inhibitor Resistance

AbstractPurpose:

We previously showed that elevated frequencies of peripheral blood CD3⁺CD4⁺CD127⁻GARP⁻CD38⁺CD39⁺ T cells were associated with checkpoint immunotherapy resistance in patients with metastatic melanoma. In the present study, we sought to further investigate this population of ectoenzyme-expressing T cells (T_eee).

Experimental Design:

T_eee derived from the peripheral blood of patients with metastatic melanoma were evaluated by bulk RNA-sequencing (RNA-seq) and flow cytometry. The presence of T_eee in the tumor microenvironment was assessed using publically available single-cell RNA-seq datasets of melanoma, lung, and bladder cancers along with multispectral immunofluorescent imaging of melanoma patient formalin-fixed, paraffin-embedded specimens. Suppressive function of T_eee was determined by an in vitro autologous suppression assay.

Results:

T_eee had phenotypes associated with proliferation, apoptosis, exhaustion, and high expression of inhibitory molecules. Cells with a T_eee gene signature were present in tumors of patients with melanoma, lung, and bladder cancers. CD4⁺ T cells co-expressing CD38 and CD39 in the tumor microenvironment were preferentially associated with Ki67⁻ CD8⁺ T cells. Co-culture of patient T_eee with autologous T cells resulted in decreased proliferation of target T cells. High baseline intratumoral frequencies of T_eee were associated with checkpoint immunotherapy resistance and poor overall survival in patients with metastatic melanoma.

Conclusions:

These results demonstrate that a novel population of CD4⁺ T cells co-expressing CD38 and CD39 is found both in the peripheral blood and tumor of patients with melanoma and is associated with checkpoint immunotherapy resistance.