Abstract 1775: The interaction of PD-L1, TMB, and genomic alterations in NSCLC
Authors: Goldberg Michael E. , Gay Laurie M. , Fabrizio David , Frampton Garrett M. , Elvin Julia A. , Ross Jeffrey S. , Miller Vincent A. , Stephens Philip J. , Albacker Lee A. 
Published: July 2017

Abstract
Introduction: In a cohort of non-small cell lung cancers (NSCLC), we identify new potential biomarkers that may predict response to checkpoint inhibitors through an analysis of genomics, PD-L1 protein expression, and tumor mutational burden (TMB).
Motivation: In cancer therapy, anti-PD-1/PD-L1 checkpoint inhibitors provide long term responses in a subset of patients. The current biomarker, PD-L1 IHC, is only partially successful in identifying responders. TMB, a measure of the number of mutations in a tumor’s genome, is an emerging biomarker that can predict response rates to checkpoint inhibition in addition to PD-L1 IHC. Higher TMB is thought to confer a higher probability of expressing a neoantigen protein recognizable by the immune system as non-self and therefore responding to checkpoint inhibition. While TMB represents the likelihood that tumor cells express immune-triggering neoantigens, PD-L1 expression represents one of many ways a tumor can evade immune response. We investigated the patterns of PD-L1 IHC staining and TMB in NSCLC.
Methods: We tabulated PD-L1 IHC stain statuses, TMB, and genomic alterations for 789 unique NSCLC tumor samples. Tumor cell PD-L1 expression was measured by IHC and scored for distribution (0, 1-24%, &gt; 24% of cells) and intensity (0, 1+, 2+) as Negative, Low Positive, or High Positive. Samples were tested with a comprehensive genomic profiling assay that identifies alterations in exons and select introns in 405 genes. TMB was calculated over 1.1 Mb by counting somatic, non-driver genomic alterations and scored as Low (&lt; 6 mut/Mb), Medium (&lt; 20, ≥ 6 mut/Mb), or High (≥ 20 mut/Mb).
Results: PD-L1 tumor staining was significantly correlated with TMB (P = 3.52e-4), although the correlation was not strong (Spearman’s rho = 0.12). To better explain discordant TMB/PD-L1, we ran Fisher’s exact tests to identify genes enriched for alterations in TMB-High/PDL1-Negative or TMB-Low/PD-L1-High Positive samples. The TMB-High/PD-L1-Negative subset preferentially harbored STK11 loss-of-function alterations with an odds ratio of 3.65 (P = 1.20e-3). The TMB-Low/PD-L1-High Positive subset exhibited enrichment for BRAF alterations with an odds ratio of 5.46 (P = 1.71e-3).
Conclusions: TMB-High tumors have high immunogenicity and often rely on PD-L1 expression as a means of immune evasion. Alterations in BRAF and other genes enriched in TMB-Low/PDL1-High Positive samples may trigger immune responses moderated by PD-L1 expression. Samples with these alterations, although often TMB-Low, may nevertheless respond to checkpoint inhibitors. Alterations in STK11 and other genes enriched in TMB-High/PD-L1-Negative samples may be implicated as non-PD-L1-based mechanisms for immune evasion. Although further ongoing analysis is required, our study suggests that the combination of TMB, PD-L1 staining, and genomics may provide the best prediction of response to checkpoint inhibitors.
Citation Format: Michael E. Goldberg, Laurie M. Gay, David Fabrizio, Garrett M. Frampton, Julia A. Elvin, Jeffrey S. Ross, Vincent A. Miller, Philip J. Stephens, Lee A. Albacker. The interaction of PD-L1, TMB, and genomic alterations in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1775. doi:10.1158/1538-7445.AM2017-1775