Identification of BRCA1 Deficiency Using Multi-Analyte Estimation of BRCA1 and Its Repressors in FFPE Tumor Samples from Patients with Triple Negative Breast Cancer

Abstract

PurposeApart from germ-line BRCA1-mutated breast cancers, a significant proportion of women with sporadic triple negative breast cancer (TNBC) sub-type are known to harbour varying levels of BRCA1-dysfuction. There is currently no established diagnostic method to identify these patients.MethodsThe analysis was performed on 183 primary breast cancer tumor specimens from our longitudinal case-series archived as formalin-fixed-paraffin-embedded (FFPE) blocks comprising 71 TNBCs and 112 Hormone receptor positive HER2 negative (HR+HER2-) tumors. Transcript levels of BRCA1 and two of its repressors ID4 and microRNA182 were determined by TaqMan quantitative PCR. BRCA1 protein was detected immunohistochemically with the MS110 antibody.ResultsThe representation of BRCA1 and its repressor ID4 as a ratio led to improved separation of TNBCs from HR+HER2- compared to either measure by itself. We then dichotomised the continuous distribution of each of the three measurements (Protein, MIRNA and transcript:repressor ratio) into categories of deficient (0) and adequate (1). A composite BRCA1 Deficiency Score (BDS) was computed by the addition of the score for all three measures. Samples deficient on 2 or more measures were deemed to be BRCA1 deficient; and 40% of all TNBCs met this criterion.ConclusionWe propose here a simple multi-level assay of BRCA1 deficiency using the BRCA1:ID4 ratio as a critical parameter that can be performed on FFPE samples in clinical laboratories by the estimation of only 3 bio-markers. The ease of testing will hopefully encourage adoption and clinical validation.

BRCA1 Promoter Hypermethylation is Associated with Good Prognosis and Chemosensitivity in Triple-Negative Breast Cancer

“…In the study by Al-Mula et al, the same weak correlation was found between IHC protein evaluation and mRNA levels quantification, using real-time RT-PCR [42]. Reported correlations with epigenetic inactivation through promoter hypermethylation varied, from good correlations in high-grade ovarian serous carcinoma [43] to weak in BC [44]. BRCA1 IHC evaluation suffers from considerable run-to-run variability [41].…”

ID4 controls luminal lineage commitment in normal mammary epithelium and inhibits BRCA1 function in basal-like breast cancer

“…The majority of the literature is based on Crippa et al (2014) ID4 expression is inversely correlated with miR-342 and (Turner et al 2007, Thike et al 2015, Korlimarla et al 2016. Beger and coworkers (2001) subsequently characterised the regulators of BRCA1 gene expression and identified ID4 as an upstream regulator of the BRCA1 promoter using an inverse genomics approach in luminal breast cancer cell lines.…”

Evaluation of DNA and RNA quality from archival formalin‐fixed paraffin‐embedded tissue for next‐generation sequencing – Retrospective study in Japanese single institution

“…[5][6][7][8][9] As the evaluation of gene abnormalities by IHC is limited, genetic analysis methods, such as fluorescence in situ hybridization and polymerase chain reaction (PCR), have been increasingly used in the detection of point mutations, insertion/deletions, and formation of fusion genes. [10][11][12][13][14][15][16][17][18][19][20] In addition, there are diverse types of cancer-specific target molecules, and a large number of molecular target drugs have been developed and used clinically. Hence, cancer prognosis has significantly improved.…”