Mutational Load (ML) and T-cell-inflamed Microenvironment As Predictors of Response to Pembrolizumab.

1 Background: ML is associated with response to anti CTLA-4 and PD-1/L1 immunotherapies in some cancers, likely due to increased tumor antigenicity via generation of neoepitopes not subject to central immune tolerance. An IFNγ centric gene expression profile (GEP), characteristic of a T cell inflamed microenvironment, is also related to response to PD-1/PD-L1 therapies. The association between ML and outcome, and independent predictive values of ML and GEP in pembrolizumab treated patients across 21 tumor types were assessed. Methods: Whole exome and RNA sequencing were performed on FFPE specimens pooled from 2 multicohort advanced solid tumor trials (KEYNOTE 012 [n = 39] and 028 [n = 80]). The previously defined GEP score is a weighted sum of normalized expression values for 18 genes. ML and neoantigen analysis tools included GATK, MuTect and NetMHC. Statistical testing was adjusted for multiple testing. ML and GEP association was also explored in Moffitt and TCGA datasets. Results: ML and neoantigen load were significantly associated with objective response (OR) (AUROC = 0.76 and 0.78; p = 0.0036 and 0.0083, respectively). Median numbers of mutations were 180 in responders and 61 in nonresponders. The overall response rate (ORR) in all patients was 15%. At a ML cutoff of 102 (based on ROC Curve YoudenIndex), the ORR was 32.3% (prevalence 31.0%; NPV 92.8%). GEP was also significantly associated with OR (AUROC = 0.76; p = 0.0071). ML and GEP were modestly correlated (r = 0.28), consistent with associations between ML and GEP in Moffitt (r = 0.11) and TCGA databases (r = 0.29). When jointly modeled, ML was significantly associated with response (p = 0.0078) after adjusting for GEP (also significant; p = 0.0251). Data from additional patients will also be presented. Conclusions: These data show that ML and GEP are independently predictive biomarkers of response to pembrolizumab in multiple tumor types, suggesting that tumor antigenicity and T cell infiltration may provide complementary information for expected pembrolizumab activity. As measures of distinct, yet common features of a PD-1 checkpoint blockade responsive tumor, ML and GEP may have utility in characterizing responses to anti PD-1 and other cancer immunotherapies. Clinical trial information: NCT01848834; NCT02054806.