A germline microRNA-based biomarker signature of immune-associated toxicity to anti-PD1/PDL1 therapy

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Background: Treatment with anti-PD1/anti-PDL1 agents is associated with toxicity termed immune related adverse events (iRAEs). While the prevalence of Grade 2 and higher iRAEs is approximately 25-30%, biomarkers have not been previously identified. We tested the hypothesis that functional, germ-line mutations would predict iRAEs. Methods: Four classifiers were trained on a set of 61 melanoma patients evaluated for toxicity and response. Subjects were classified as experiencing high toxicity (≥ Grade 2) vs low toxicity (< Grade 2). Performance of the classifiers was tested on a validation set of 89 cancer patients with a variety of cancer types, with the most common being GU and NSCLC. Classifiers were built for each treatment of marker data including classification trees, LASSO-regularized logistic regression, boosted trees (BT), and random forests. The final performance measures, accuracy, specificity, sensitivity, negative predictive value, positive predictive value, area under the curve (AUC), and F1 score, were reported on the categorical treatment of the training data using leave-one-out cross validation on the validation data. We also evaluated the association between our most significant toxicity biomarker and response to anti-PD1/PDL1 therapy. Results: Within the melanoma training sample, we found a biomarker signature where toxicity is predicted with 79.0% accuracy (F1 = .714, AUC = .827) using BT. The same biomarker panel also accurately predicted toxicity in the validation cohort with 85.6% accuracy (F1 = .760, AUC = .883). Of the most predictive biomarkers, three were in microRNA binding sites in RAC1, CD274, and KRAS, two in immune related genes IL2RA and FCGR2A, and one in the DNA repair gene ATM. Our most significant biomarker in RAC1 did not predict response to anti-PD1/PDL1 treatment (p=0.91). Conclusions: We have identified a germ-line biomarker signature which predicts Grade 2 or higher iRAEs for patients treated with anti-PD1/anti-PDL1 therapy, regardless of cancer type, and does not predict an increased likelihood of response to these therapies. These findings are an important step in defining how to better safely personalize immune therapy, whose use is growing rapidly.