Acquired High Tumor Mutational Burden and Activity of Immunotherapy after Targeted Therapy in Microsatellite Stable Colorectal Cancer

Abstract Purpose: Microsatellite stable (MSS) colorectal cancers, in contrast to microsatellite instability–high colorectal cancers, have few mutations and are insensitive to immune checkpoint blockade (ICB). Colorectal cancers treated with targeted agents often acquire a high number of genomic alterations at progression. We asked whether targeted therapy could be used to generate a high tumor mutational burden (TMB) in MSS colorectal cancer and sensitize these tumors to ICB. Experimental Design: In patients with MSS metastatic colorectal cancer treated with targeted therapy, we evaluated baseline and progression TMB and response to ICB for patients whose tumors developed high TMB. We determined types of alterations, mutational signatures, neoantigenicity, and clonality associated with emergent genomic alterations in cases of acquired high TMB. Results: Among 26 cases, nine acquired high TMB at progression. Three of these patients received ICB but none had a response. In the TMB-high cases, we found no induction of tumor-infiltrating lymphocytes or PD-L1 expression. Acquired genomic alterations consisted predominantly of single-nucleotide variants, were enriched for single base substitution 17a/b mutational signature, and did not enhance predicted MHC class I binding. TMB was higher in plasma, driven by highly subclonal acquired alterations, compared with tissue samples, which harbored few resistance alterations. Conclusions: A substantial number of MSS colorectal cancers acquire high TMB following targeted therapy. However, this change is not associated with sensitization to ICB. The high TMB is due to subclonal alterations unique to individual disease sites that are inadequate to elicit a robust antitumor immune response.