High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types

Abstract

High tumor mutation burden (TMB-H) has been proposed as a predictive biomarker for response to immune checkpoint blockade (ICB), largely due to the potential for tumor mutations to generate immunogenic neoantigens. Despite recent pan-cancer approval of ICB treatment for any TMB-H tumor, as assessed by the targeted FoundationOne CDx assay in nine tumor types, the utility of this biomarker has not been fully demonstrated across all cancers. Data from over 10000 patient tumors included in The Cancer Genome Atlas were used to compare approaches to determine TMB and identify the correlation between predicted neoantigen load and CD8 T cells. Association of TMB with ICB treatment outcomes was analyzed by both objective response rates (ORRs, N= 1551) and overall survival (OS, N= 1936). In cancer types where CD8 T-cell levels positively correlated with neoantigen load, such as melanoma, lung,and bladder cancers, TMB-H tumors exhibited a 39.8% ORR to ICB [95% confidence interval (CI) 34.9-44.8], which was significantly higher than that observed in low TMB (TMB-L) tumors [odds ratio (OR)= 4.1, 95% CI 2.9-5.8, P < 2× 10-16]. In cancer types that showed no relationship between CD8 T-cell levels and neoantigen load, such as breast cancer, prostate cancer, and glioma, TMB-H tumors failed to achieve a 20% ORR (ORR= 15.3%, 95% CI 9.2-23.4, P= 0.95), and exhibited a significantly lower ORR relative to TMB-L tumors (OR= 0.46, 95% CI 0.24-0.88, P= 0.02). Bulk ORRs were not significantly different between the two categories of tumors (P= 0.10) for patient cohorts assessed. Equivalent results were obtained by analyzing OS and by treating TMB as a continuous variable. Our analysis failed to support application of TMB-H as a biomarker for treatment with ICB in all solid cancer types. Further tumor type-specific studies are warranted.