Preprint Club
A cross-institutional Journal Club Initiative

Keywords

• T-cell dysfunction

• ICB

• CD8 T-cells

• DNA Damage Response

Main Findings

• Authors identified a cohort of patients with MSI-H, MMRd or hypermutated uterine cancers being treated with immune checkpoint inhibitor against PD-1,nivolumab. These patients usually have high tumor mutation burden (due to MMR defects) as well as large infiltration of expanding T-cells and should respond well to immune checkpoint blockade(ICB).

• A subset of patients within the cohort did not respond to therapy, even though they had high tumor mutation burden (TMB)and proliferating T-cells that were similar to clinical responders in their ability to divide and proliferate, leading to the hypothesis that there are T-cell intrinsic differences in response to proliferation and genotoxic stress that could be causing differential outcomes in response to ICB

• To interrogate this, they developed a high dimensional, single-cell platform using flow cytometry to profile 7 different memory T-cell states as well as DNA Damage Response (DDR)pathways(using pATM,γH2AX, PARP1 andMSH2)activated upon induction of proliferative stress, UV and irradiation

• Using patient samples, they saw that pATM was differentially upregulated in proliferating cells(Ki67+ cells)within clinical responders, particularly in Tex cells that are the target for anti PD1 therapy

• They created ATM null CD8 T-cells using CRISPR and performed RNA seq to identify genes that are differentially upregulated in response to proliferative stress using gene set enrichment in ATMKO vs WT CD8 T cells. Using these genes that were specifically activated, they created an ATM-Responder Gene Signature(ARGS).

• Authors then looked at cohorts of Uterine Corpus Endometrial Carcinoma, Colorectal adenocarcinoma, and Skin Cutaneous Melanoma in The Cancer Genome Atlas. They found that patients who have a higher expression of ARGS genes are associated with better overall survival

• Overall, the authors identified patterns of DNA Damage Response (DDR)defects in different CD8 subsets that make them more likely to respond to PD-1 blockade and showed that the ability to induce ATM activation (pATM) inCD8 T-cells during PD-1 blockade is more robust in clinical responders

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Limitations​

• Small sample size

• Data limited to peripheral T-cells

• Did not look at other cells in the immune compartment

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Significance/Novelty

What is the novelty of the preprint for the field specific?

• Showed that patients treated with chemotherapy/radiation may have increased genome instability and altered T-cell function based on changes in DDR that were previously unexplored.

• Uncovered a previously unknown effect of DDR that is intrinsic to CD8 T-cells and is higher in responders across multiple cancer types.

• DDRd have mostly been implicated in tumour cell biology but this paper shows its importance in the functioning of T-cells, especially upon rapid proliferation and replicative stress which is induced after ICB.

• Developed a platform to assay changes in DDR as well as T-cell differentiation and activation.

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How does the result of the preprint matter for general immunologists and/or patients?

• Reiterates that having high TMB and infiltration of CD8 T-cells is not enough for response to therapy and proposes alternative biomarkers/ pathways that can be used for better prediction of response to therapy.

• Shows the importance of T-cell intrinsic functionality in response to therapy-pATM may be used as a biomarker to help select patients that will respond better to PD1 blockade.

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Credit

Reviewed by Prerna Suri as part of the cross-institutional journal club of the Immunology Institute of the Icahn School of Medicine, Mount Sinai, and the Kennedy Institute of Rheumatology, University of Oxford.