SpecificBRCAand immune configurations determine optimal response to platinum-based chemotherapy in triple negative breast and ovarian carcinomas
Authors: Menghi Francesca , Banda Kalyan , Kumar Pooja , Straub Robert , Dobrolecki Lacey , Rodriguez Isabel V. , Yost Susan E. , Chandok Harshpreet , Radke Marc R. , Zhu Angela S. , Somlo George , Yuan Yuan , Lewis Michael T. , Swisher Elizabeth M. , Liu Edison T. 
Published: August 2021

Loss of homologous recombination repair (HRR) via germline and somaticBRCA1orBRCA2gene mutations and viaBRCA1promoter methylation has been associated with better response to platinum agents and PARP inhibitors, in both triple negative breast cancer (TNBC) and ovarian carcinoma (OvCa). A major conundrum arising from recent clinical studies is why cancers withBRCA1promoter methylation (BRCA1meth) respond more poorly as compared to those bearing mutations inBRCA1andBRCA2(BRCAmut), given the biologically equivalent HRR deficiency in both states. We dissected this problem through detailed genomic analyses of primary TNBC and OvCa cohorts, as well as experimentation with patient-derived xenograft (PDX) models and genetically engineered cell lines. Using the precise genomic scar of the tandem duplicator phenotype as a precise genomic indicator of BRCA1 deficiency, we found that, in all cohorts,BRCA1mut andBRCA1meth cancers share an equivalent degree of BRCA1-linked genomic rearrangements. Nonetheless, we consistently found that patients withBRCAmut cancers, but not those withBRCA1meth cancers, had significantly better response outcomes when compared to those withBRCAproficient cancers. When fully promoter methylatedBRCA1PDX TNBCs were exposed to a single short course of platinum chemotherapy an unmethylatedBRCA1promoter allele emerged in resultant tumors associated with an increase inBRCA1expression. A separate analysis of PDXs derived from treatment naïve TNBCs featured complete methylation of theBRCA1promoter, whereas those derived from post-chemotherapy TNBCs invariably had only partial methylation. PDXs with partial methylation were significantly associated with lower response rates toin vivoplatinum-based therapy compared to those with complete promoter methylation. Using single cell clonal expansions from a partiallyBRCA1meth PDX, we confirmed that the reduced level of methylation was due to the demethylation of one of theBRCA1promoter alleles and not to the outgrowth of a non-methylated clone. Clinically, analysis of primary OvCas confirmed that high levels ofBRCA1methylation were significantly associated with reducedBRCA1gene expression whereas cancers with lower levels ofBRCA1methylation had expression levels approaching those found inBRCA1proficient cancers. These data suggest that unlikeBRCAmut cancers, where HRR deficiency is achieved via mutations that are genetically ‘fixed’,BRCA1meth cancers are highly adaptive to genotoxin exposure and more likely to recoverBRCA1expression, which may explain their poorer therapeutic response. We further found that an increased immune transcriptional signal, especially an elevated M1 macrophage signature, is associated with enhanced response to platinum-based chemotherapy only in patients withBRCAproficient cancers, in both TNBC and OvCa cohorts underscoring the importance of characterizing molecular heterogeneity to enhance predictive precision in assigning response probabilities in TNBC and OvCa.