Abstract Background Patients with high numbers of neoepitopes responds better to immunotherapy, but the correlation to response is imperfect, indicating that multiple layers of modulation and/or suppression plays a role in triggering an ongoing immune response. The STING/cGAS pathway senses cytosolic DNA and interact with P53 to trigger the innate immune system. Cytosolic DNA may be generated through chromosomal instability (CIN), a hallmark of cancer associated with poor prognosis. Here we investigate the interplay between tumour infiltrating lymphocytes (TILs) and CIN in a bladder cancer cohort from the The Cancer Genome Atlas. Methods Measures of CIN (Marquard AM, 2015, Biomark Res, Burrell RA, Nature 2013) were determined based on ASCAT segmented SNP6 data. TILs were estimated from RNAseq data as described (Danaher P, Journal for ImmunoTherapy of Cancer, 2017). CIN and TIL scores were subjected to hierarchical clustering to determine groups of high and low CIN and TIL. Results We performed hierarchical clustering separately on measures of CIN and measures of TILs, revealing for each analysis a low, intermediate and high group. To improve signal, we discarded samples in the intermediate group. This resulted in samples classified into four groups, as high/low CIN and high/low TILs. Biological characterization revealed the high CIN-low TIL group as an outlier, with fewer mutations overall, relatively higher expression of STING, and low proliferation. Kaplan-Meier analysis shows how overall survival associates with both CIN and TILs, with high-CIN associating with poor survival in high-TIL samples, but with improved survival in low-TIL samples. Conclusions Mobilization of the immune system to fight cancer is currently revolutionizing patient treatment. The adaptive immune system recognizes cancer neoepitopes and may drive an anti-cancer response. Stratifying tumours into high and low levels of CIN and TILs shows subgroup-specific biological variation potentially indicating how a dysfunctional STING/cGAS pathway may result in a reduced activation of the innate immune response with an association to overall survival. These observations need further confirmation in larger cohorts, and the implications of CIN must be explored in the context of immuno-oncology agents. Legal entity responsible for the study The authors. Funding Aarhus University Research Foundation. Disclosure All authors have declared no conflicts of interest.
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