Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer.

Kyle C Strickland,Lauren L Ritterhouse,Dipanjan Chowdhury,Joyce F Liu,Brooke E Howitt,Judy E Garber,Alan D D’Andrea,Catherine J Wu,Panagiotis A Konstantinopoulos,Sachet A Shukla,Ursula A Matulonis,Scott Rodig

doi:10.18632/oncotarget.7277

Abstract

Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.

Highlights

Immune checkpoint inhibitors have demonstrated remarkable efficacy against hypermutated cancers such as melanomas, lung carcinomas and those with underlying mismatch repair-deficiency [1,2,3]
homologous recombination (HR) deficient high grade serous ovarian cancers (HGSOCs) exhibit higher neoantigen load compared to HR proficient tumors Initially, we compared the neoantigen load between BRCA1/2-mutated HGSOCs versus all remaining tumors in the The Cancer Genome Atlas (TCGA) dataset
Prediction of neoantigen load was performed using sequencing data from the ovarian TCGA dataset which included whole-exome sequencing data from 316 HGSOCs [11]. 71 of 316 samples were excluded from our analysis because they were comprised of only single-end reads using the SOLiD platform and not amenable to accurate HLA typing

Summary

Introduction

Immune checkpoint inhibitors (e.g., anti–PD-1 and anti–PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas, lung carcinomas and those with underlying mismatch repair-deficiency [1,2,3] One explanation for this effect is that tumors with higher mutational loads harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs) which is counterbalanced by overexpression of immune checkpoint modulators, such as PD-1 or PD-L1 [4,5,6,7]. BRCA1/2-mutated HGSOCs have been shown to possess a higher number of mutations compared to non-BRCA1/2-mutated tumors [18], with an elevated number of larger indels (up to 50 bp) with overlapping microhomology at breakpoint junctions [19] Given their higher mutational load and unique mutational signature, we hypothesized that BRCA1/2-mutated tumors may harbor more tumor-specific neoantigens, and, increased tumor-infiltrating lymphocytes (TILs) [7] as well as demonstrate increased expression of the immune checkpoint modulators, PD-1 and PD-L1

Methods

Results

Conclusion