ASO Author Reflections: High BRCA2 Gene Expression is Associated with Aggressive and Highly Proliferative Breast Cancer

Abstract

Background. Mutations of BRCA genes are the most studied in breast cancer, but the clinical relevance of BRCA2 gene expression has been less well studied. Given that BRCA2 is a DNA repair gene, we hypothesized that high BRCA2 expression is associated with highly proliferative and aggressive biology in breast cancer. Materials and Methods. A total of 4342 breast cancer patients were analyzed from The Cancer Genome Atlas (TCGA, n = 1069) as the testing cohort and Gene Expression Omnibus (GEO) dataset GSE96058 (n = 3273) as a validation cohort. Results. There was no relationship between BRCA2 mutation and BRCA2 gene expression. BRCA2 high expression breast cancer was associated with higher Nottingham grade (p\\ 0.001), with high proliferation (MKI67, p\\ 0.001), and with higher intratumor heterogeneity, homologous recombination deficiency, mutation rate, fraction altered, and neoantigens (all p\\ 0.001). BRCA2 high expression was associated with E2F1, RB1, PALB2, and PARP, as well as cell proliferation-related gene sets, E2F targets, G2M checkpoints, and mitotic spindle, and with less ESR1 and ER response early and late gene sets. They were associated with significantly reduced number of stroma cells and with high infiltration of both favorable and unfavorable immune cells. BRCA2 high expression significantly correlated with response to olaparib, a PARP inhibitor, and inversely with cyclophosphamide in ERpositive/HER2-negative tumors, but not in TNBC. Conclusions. BRCA2 high gene expression was associated with highly proliferative and aggressive breast cancer that was highly immunogenic with better response to PARP inhibitors in ER-positive patients. BRCA2 gene expression may become a candidate marker for aggressive biology and to tailor specific treatment strategies in the future. Mutations in BRCA1 and BRCA2 are among the most well-studied mutations associated with hereditary forms of breast cancer. We know that BRCA1 and BRCA2 function as tumor suppressor genes that are functionally recessive. BRCA2 is the larger of the two genes, located on chromosome 13q12-13 and primarily mediating homologous recombination. The role of BRCA2 is mainly as a DNA repair gene, mediating double-stranded DNA repair and thus chromosomal stability. Breast cancers associated with BRCA mutations have unique clinical and pathological characteristics. It is known that BRCA-mutated cancers are more frequently of the triple-negative subtype and are sensitive to platinum agent chemotherapy. PARP inhibitors act on BRCA1and BRCA2-defective tumors on the Vikas Satyananda and Masanori Oshi have contributed equally to this work. Society of Surgical Oncology 2021 First Received: 22 February 2021 Accepted: 4 April 2021 K. Takabe, MD, PhD, FACS e-mail: [email protected] Ann Surg Oncol https://doi.org/10.1245/s10434-021-10063-5 basis of ‘‘synthetic lethality’’, and they have been approved by the Food and Drug Administration (FDA) for use in BRCA-mutated breast cancers. Given the decreased cost of genome and gene sequencing and advances in the field of bioinformatics, we are in an era of personalized medicine. Technological advances have further allowed us to look at individual aberrations in cancer genes that make them susciptible to particular drugs and have enabled us to offer patients therapies and trials with the most benefit. Unlike BRCA2 mutation, the clinical relevance of BRCA2 gene expression has been less well studied. We have shown that breast cancers with high mutation rate gain aggressive phenotypes but counterbalanced by increased anticancer immunity; at the same time, excessive DNA damage kills the cells. We hypothesized that high BRCA2 gene expression with enhanced DNA repair is associated with highly proliferative breast cancer that responds better to neoadjuvant chemotherapy and PARP inhibitors. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) cohorts were analyzed to test this hypothesis. MATERIALS AND METHODS Clinical Data Acquisition The clinical, pathological, and gene expression levels of patients with breast cancer from The Cancer Genome Atlas (TCGA) were retrieved through cBioPortal as described previously. A total of 1069 female breast cancer patients from TCGA were included in the study. Gene Expression Omnibus (GEO) dataset GSE96058 (n = 3273) was used as a validation cohort. Instituitonal review board approval at Roswell Park Cancer Institute was waived as we used publicly available deidentified databases. Gene Set Enrichment Analysis Gene set enrichment analysis (GSEA) was performed as previously reported using publicly available software from Broad Institute (http://software.broadinstitute.org/gsea/inde x.jsp). The hallmark gene sets enriched in BRCA2 gene were compared with those that had low expression. A false discovery rate (FDR) of 0.25 was used as recommended. Signaling Pathway Score, Immune Cell Composition, Cytolytic Activity Score, and Immune-Related Scores We calculated hallmark gene sets score, including E2F targets, G2M checkpoint, p53 pathway, and estrogen response early and late signaling, by gene set variation analysis (GSVA), as we previously reported. xCell, a computation algorithm, was used to estimate the cell composition of immune cells within the tumor, as previously reported. Cytolytic activity (CYT) was calculated using the geometric mean of granzyme A and perforin 1 expression values, as reported previously by Rooney et al. Immune-related scores such as interferon-c response, tumor infiltration lymphocyte regional fraction, and T-cell receptor (TCR) richness, as well as intratumor heterogeneity, silent and non-silent mutation rate, neoantigens, and homologous recombinant deficiency (HRD) were calculated per previously reported study by Thorsson et al. Drug Response Analyses The correlation between BRCA2 gene expression and drug response was evaluated using 27 breast cancer cell lines with both comprehensive transcriptome and drug response data from the Cancer Cell Line Encyclopedia (CCLE) and Cancer Therapeutics Response Portal (CTRP) via the DepMap portal. Statistical Analysis All statistical analyses were performed using R software (http://www.r-project.org/). p-Value\\0.05 was considered statistically significant.