Interferon-\u03b3 signaling is associated with BRCA1 loss-of-function mutations in high grade serous ovarian cancer

Horacio Cardenas,Kenneth P Nephew,Daniela Matei,Debabrata Chakravarti,Jessica Thomes Pepin,Guanglong Jiang,J Brandon Parker,Salvatore Condello,Yunlong Liu,Harikrishna Nakshatri

doi:10.1038/s41698-019-0103-4

Abstract

Loss-of-function mutations of the breast cancer type 1 susceptibility protein (BRCA1) are associated with breast (BC) and ovarian cancer (OC). To identify gene signatures regulated by epigenetic mechanisms in OC cells carrying BRCA1 mutations, we assessed cellular responses to epigenome modifiers and performed genome-wide RNA- and chromatin immunoprecipitation-sequencing in isogenic OC cells UWB1.289 (carrying a BRCA1 mutation, BRCA1-null) and UWB1.289 transduced with wild-type BRCA1 (BRCA1+). Increased sensitivity to histone deacetylase inhibitors (HDACi) was observed in BRCA1-null vs. BRCA1+ cells. Gene expression profiles of BRCA1-null vs. BRCA1+ cells and treated with HDACi were integrated with chromatin mapping of histone H3 lysine 9 or 27 acetylation. Gene networks activated in BRCA1-null vs. BRCA1 + OC cells related to cellular movement, cellular development, cellular growth and proliferation, and activated upstream regulators included TGFβ1, TNF, and IFN-γ. The IFN-γ pathway was altered by HDACi in BRCA1+ vs. BRCA1-null cells, and in BRCA1-mutated/or low vs. BRCA1-normal OC tumors profiled in the TCGA. Key IFN-γ-induced genes upregulated at baseline in BRCA1-null vs. BRCA1+OC and BC cells included CXCL10, CXCL11, and IFI16. Increased localization of STAT1 in the promoters of these genes occurred in BRCA1-null OC cells, resulting in diminished responses to IFN-γ or to STAT1 knockdown. The IFN-γ signature was associated with improved survival among OC patients profiled in the TCGA. In all, our results support that changes affecting IFN-γ responses are associated with inactivating BRCA1 mutations in OC. This signature may contribute to altered responses to anti-tumor immunity in BRCA1-mutated cells or tumors.

Highlights

Genetic or epigenetic inactivation of several tumor suppressor genes (TSGs), including TP53, PTEN, breast cancer type 1 susceptibility protein (BRCA1), BRCA2, DOK2, RB1, and others[1,2,3], are strongly associated with tumor initiation and progression of ovarian and breast cancers
Consistent with previous reports,[14,15] our findings support that BRCA1 mutations are associated with significant transcriptomic changes in ovarian cancer (OC) cells and tumors
We show that some of these changes are associated with distinct patterns of chromatin-associated H3K9 and H3K27 acetylated marks, leading to differences in cellular responses to histone deacetylase inhibitors (HDACi) and to an IFN-γ gene signature detectable in BRCA1-mutated cancer cells

Summary

INTRODUCTION

Genetic or epigenetic inactivation of several tumor suppressor genes (TSGs), including TP53, PTEN, BRCA1, BRCA2, DOK2, RB1, and others[1,2,3], are strongly associated with tumor initiation and progression of ovarian and breast cancers. We compared the transcriptome of OC cells carrying a loss of function BRCA1 mutation and cells in which BRCA1 was restored at baseline and in response to treatment with an HDAC inhibitor These analyses integrated with gene expression profiles of BRCA1-deficient (mutated BRCA1 or expression levels below the tenth quantile) or BRCA1-normal (not mutated BRCA1 and expression level above the first quartile) HGSOC tumors profiled in The Cancer Genome Atlas (TCGA) project[1] pointed to an IFN-γ. To determine whether the genomic changes observed between BRCA1 mutant and WT cells correlate with molecular profiles of human tumors, we analyzed gene expression measured by Agilent G4502A microarrays in HGSOC tumors from the TCGA1 program Expression levels of 3541 genes differed significantly (P < 0.01, ttest, FDR < 0.05) between BRCA1-deficient or mutated and BRCA1-

RESULTS

Cardenas et al 5

DISCUSSION

METHODS