Effect of chemokine signaling signatures on resolving discrepancy between TMB and checkpoint expression.

Abstract

3131 Background: Tumor mutation burden (TMB) and PD1/L1 expression are independent biomarkers for immune checkpoint blockade therapy, as seen in the Checkmate227 trial. Here we explore whether chemokine activity, an intermediate step between neoantigen presentation and immune-infiltration, can resolve this lack of association between existing biomarkers. We further use this novel biomarker to corroborate recent findings from Crowther et al. for a role of MHC class 1-related gene ( MR1) downregulation in immune evasion. Methods: 1,395 clinical samples from the NantHealth database with matched tumor:normal whole exomes and deep whole-transcriptomic sequencing (> 200M reads) were available for analysis. The most common indications in the cohort were Breast (18%), Colon (9.8%), Lung (7.8%), Soft-tissue/Sarcomas (7.7%), and Pancreatic (6.1%). TMB was calculated by counting non-synonymous exonic mutations as per Rizvi, 2015. Immune-infiltration and chemokine signaling were inferred from RNAseq expression of published immune-cell-specific genesets (Bindea, 2013) and chemokine ligands (Nagarsheth, 2017) respectively. Significant associations between TMB, chemokine activity, immune-infiltration, and checkpoint expression were analyzed by ranksums test and corrected for multiple-hypothesis testing using Benjamini-Hochberg adjustment. Results: As expected, TMB and PD1/L1 mRNA expression were not correlated in this cohort (r = 0.08 and r = 0.07 respectively). 36.3% of patients classified as highly immune-infiltrated by unsupervised clustering of immune-cell scores, and this subgroup significantly overexpressed all 11 targetable checkpoint genes analyzed including PD1, PDL1, CTLA4, IDO1, and VISTA (adj. p 9.7e-68 to 4e-168). There was no association between immune-infiltrated samples and TMB (t = 0.9, p = 0.35). Twice as many patients classified as chemokine-active (70.0%) and there was significant agreement between immune-infiltrated and chemokine-active patients (OR = 34.8, p = 6.5e-81). Interestingly, there was a weak but significant association between high chemokine-activity and increased TMB (t = 3.3, p = 0.001). Within patients that were chemokine-active but lacked immune-infiltration, MR1 expression was significantly depleted (t = -10.7, p = 1e-26). Conclusions: Chemokine signatures can help resolve discordance between TMB and checkpoint expression. Analysis of discordance between chemokine-active but immune-depleted tumors may aid in identifying targets for converting from cold to hot tumor microenvironments.