Reduced BRCA1 transcript levels in freshly isolated blood leukocytes from BRCA1 mutation carriers is mutation specific
© The Author(s). 2016
Received: 26 November 2015
Accepted: 22 July 2016
Published: 17 August 2016
BRCA1 mutation carriers face a high lifetime risk of developing both breast and ovarian cancer. Haploinsufficiency is thought to predispose these women to cancer by reducing the pool of available BRCA1 transcript and protein, thereby compromising BRCA1 function. Whether or not cancer-free BRCA1 mutation carriers have lower messenger (m)RNA transcript levels in peripheral blood leukocytes has not been evaluated. The primary aim of this study was to characterize an association between BRCA1 mutation status and BRCA1 mRNA leukocyte expression levels among healthy women with a BRCA1 mutation.
RNA was extracted from freshly isolated peripheral blood leukocytes of 58 cancer-free, female participants (22 BRCA1 mutation carriers and 36 non-carriers). The expression levels of 236 cancer-associated genes, including BRCA1, were quantified using the Human Cancer Reference gene panel from the Nanostring Technologies nCounter Analysis System.
Multivariate modeling demonstrated that carrying a BRCA1 mutation was the most significant predictor of BRCA1 mRNA levels. BRCA1 mRNA levels were significantly lower in BRCA1 mutation carriers compared to non-carriers (146.7 counts vs. 175.1 counts; P = 0.002). Samples with BRCA1 mutations within exon 11 had lower BRCA1 mRNA levels than samples with mutations within the 5′ and 3′ regions of the BRCA1 gene (122.1 counts vs. 138.9 and 168.6 counts, respectively; P = 0.003). Unsupervised hierarchical clustering of gene expression profiles from freshly isolated blood leukocytes revealed that BRCA1 mutation carriers cluster more closely with other BRCA1 mutation carriers than with BRCA1 wild-type samples. Moreover, a set of 17 genes (including BRCA1) previously shown to be involved in carcinogenesis, were differentially expressed between BRCA1 mutation carriers and non-carriers.
Overall, these findings support the concept of BRCA1 haploinsufficiency wherein a specific mutation results in dosage-dependent alteration of BRCA1 at the transcriptional level. This study is the first to show a decrease in BRCA1 mRNA expression in freshly isolated blood leukocytes from healthy, unaffected BRCA1 mutation carriers.
KeywordsBRCA1 mRNA expression Hereditary breast and ovarian cancer Haploinsufficiency
Women with a mutation in the breast cancer susceptibility gene 1 (BRCA1) face a high lifetime risk of developing breast and ovarian cancer estimated to be as high as 80 % and 40 %, respectively [1–4]. BRCA1 regulates several key functions pertinent to cell survival, proliferation, and differentiation [5, 6]. In particular, BRCA1 helps maintain genomic stability by participating in the cellular DNA damage response through homologous recombination (HR)-mediated repair of double-stranded DNA breaks (DSBs) . There is accumulating evidence that BRCA1 haploinsufficiency is a driver of tumor predisposing events in BRCA1 mutation carriers .
For haploinsufficiency to be an early driver of BRCA1-associated cancer development, mutation-dependent reduction in BRCA1 expression levels should be associated with a loss of function [8–10]. Most studies that have characterized phenotypic alterations suggest that BRCA1 heterozygous cells have reduced functions in DNA damage repair, hormonal regulation, cell fate changes, transcriptional regulation and autophagy [11–21]; however, little is known about whether the abrogated functions observed in BRCA1 heterozygous cells are correlated with changes in BRCA1 transcript or protein levels [19, 22–24]. This is important in light of data suggesting that the type and location of a mutation can stratify cancer risk (i.e., breast vs. ovary), and the response to treatment [25–29].
Regulation of BRCA1 gene expression is influenced by genetic and epigenetic mechanisms, and environmental factors such as genotoxic, hormonal, and metabolic stressors . Understanding the contribution of the mutation status to basal expression levels of the BRCA1 gene is a crucial step to delineating BRCA1 haploinsufficiency. Previous studies using immortalized lymphoblastoid cell lines have reported differential messenger RNA (mRNA) or protein expression in BRCA1 mutation carriers compared to non-carriers, suggesting a mutation-specific dosage effect [19, 24, 31]. In contrast, Feilotter et al.  did not find BRCA1 to be among the set of 43 genes that can predict BRCA1 mutation status by gene expression profiling. However, differences in BRCA1 mRNA expression may have been masked by the continuous proliferative state of immortalized lymphoblastoid cell lines used in these experiments [22, 32–37]. There are no studies, to our knowledge, that have evaluated BRCA1 transcript levels in freshly isolated blood leukocytes.
Notably, reduced BRCA1 protein expression in both inherited and sporadic forms of breast and ovarian cancer has been associated with a significant reduction in the levels of BRCA1 mRNA, thereby supporting the utility of BRCA1 transcript levels as a surrogate marker of BRCA1 function [38–40]. The overall goal of the current study was to evaluate the relationship between BRCA1 mutation status (and mutation type) and mRNA expression among women with and without a BRCA1 mutation, by studying freshly isolated blood leukocytes.
Study design and population
There were 58 women enrolled in the current study: 22 BRCA1 mutation carriers and 36 non-carriers. All women were 18 years of age or older, none had a personal history of cancer, and none were pregnant or breastfeeding. The first group included women with a BRCA1 mutation, identified from an existing database at the Familial Breast Cancer Research Unit, Women’s College Research Institute (WCRI, Toronto, Canada) who were contacted by letter. The second group included women from the general population who were recruited using various methods such as posters, newsletters or social media. A 30-minute study appointment was then scheduled at the WCRI for all the eligible participants. This research received approval from the Research Ethics Board at the Women’s College Hospital (number 2012-0055-B). All women provided informed consent to participate in the study by signing the provided consent form.
Data and biological sample collection
Study participants completed a questionnaire, which collected information on various exposures, including reproductive and lifestyle factors, medical history, and family history of cancer. Standardized procedures were used to collect measurements of weight (kg) and height (m) to calculate body mass index (BMI; kg/m2). A phlebotomist drew blood into two labeled EDTA-containing tubes (approximately 8 mL) by venipuncture. The samples were placed on ice and delivered immediately to the Women’s College Hospital research laboratory for RNA extraction.
RNA isolation and quantification
RNA was isolated from one of the two EDTA tubes using the LeukoLOCK Total RNA Isolation System (Ambion, USA). This system is optimized for use with human blood and offers the isolation of total RNA from the leukocyte population . In order to maximize RNA isolation yield, all samples were stabilized with RNALater® within 35 minutes of the blood draw. The nucleic acid content was quantified using the Nanodrop spectrophotometer (ThermoScientific). Total RNA quality and quantity was then determined using the Agilent 2100 Bioanalyzer (The Centre for Applied Genomics, Toronto, Canada). The resulting extracted RNA was stored at -80 °C until required for further analysis.
nCounter NanoString gene expression profiling
The nCounter Analysis System (NanoString Technologies) was used to measure mRNA gene expression (expressed as counts) at the University Health Network (Toronto, Canada)  using the Human Cancer Reference Kit consisting of 236 cancer-related genes. Briefly, the nCounter Analysis System probe library contains two sequence-specific probes, the capture probe and the reporter probe, for each gene of interest. Probe pairs are mixed with total RNA in one hybridization reaction, and then the structures are imaged with the use of fluorescent microscopy. Expression is measured by counting the number of unique color tags within the gene-probe tripartite structures and is reported as counts, a direct measure of the number of RNA transcripts of each gene of interest.
Data acquisition and normalization was carried out using the nSolver Analysis software version 2.0 (NanoString Technologies). Positive and negative controls were used to check for background expression. Reference housekeeping gene normalization was then performed to adjust counts relative to probes that are not expected to vary between samples or replicates, allowing meaningful comparisons between samples. We chose the set of housekeeping genes recommended by Nanostring, which comprised the following genes: CLTC (clathrin, heavy chain), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), GUSB (glucuronidase, beta), HPRT1 (hypoxanthine phosphoribosyltransferase 1), TUBB (tubulin, beta class 1), and PGK1 (phosphoglycerate kinase 1).
Student’s t test was used to compare continuous variables in mutation carriers and non-carriers and the chi-square test was used to test for differences in categorical variables. The Shapiro-Wilk test was used to verify the normality of BRCA1 mRNA expression. As expression of BRCA1 was normally distributed (P = 0.26), the Pearson correlation coefficient (ρ) was used to evaluate the correlation between BRCA1 mRNA expression, BRCA1 mutation status and various reproductive and lifestyle factors. Linear regression was used to evaluate the relationship between BRCA1 mutation status and mRNA expression, adjusting for significant predictors of BRCA1 mRNA levels including parity (parous/nulliparous), breastfeeding (ever/never), and menopausal status (premenopausal/postmenopausal). A significance level of P <0.05 was used as the criterion for including variables in the multivariate model.
We assigned the BRCA1 mutations into one of three mutation clusters reported to be differentially associated with the risk of breast vs. ovarian cancer: group 1 contained mutations in exons 1–10; group 2 contained mutations in exon 11; and group 3 contained mutations in exons 12–22 . One-way analysis of variance (ANOVA) was used to compare mean BRCA1 expression levels between the three mutation clusters.
Unsupervised hierarchical clustering was performed using Pearson-centered correlation metric with centroid linkage to categorize samples into homogenous groups based on similar levels of gene expression. Heat maps were generated using Java Treeview . Student’s t test was used to identify genes expressed differentially between BRCA1 mutation carriers and non-carriers by testing for differences in mean gene expression levels with a Benjamini-Hochberg false discovery rate of P < 0.05. The PathDIP database (http://ophid.utoronto.ca/pathDIP) was used to identify over-represented signaling pathways using data from significantly upregulated and downregulated genes through functional enrichment analysis. Statistical significance was defined at the level of P < 0.05 and all analyses were carried out using SPSS, IBM® SPSS® Statistics, version 23, 2015.
Characteristics of study participants
Characteristics of all study participants and stratified by BRCA1 mutation status
(n = 58)
(n = 36)
(n = 22)
Age (years), mean (range)
Ethnicity, n (%)
34 (59 %)
20 (56 %)
14 (64 %)
10 (17 %)
3 (8 %)
7 (32 %)
3 (5 %)
3 (8 %)
0 (0 %)
7 (12 %)
6 (17 %)
1 (4 %)
4 (7 %)
4 (11 %)
0 (0 %)
Parous, ever, n (%)
29 (50 %)
12 (33.3 %)
17 (77.3 %)
Breastfeeding, ever, n (%)a
23 (79 %)
10 (83 %)
13 (76 %)
Age at menarche (years), mean (SD)
Postmenopausal, n (%)
17 (29 %)
4 (11 %)
13 (59 %)
Current oral contraceptive use, yes, n (%)
6 (10 %)
4 (11 %)
2 (9 %)
Current smoking status, yes, n (%)
1 (2 %)
0 (0 %)
1 (5 %)
Current alcohol consumption, yes, n (%)
51 (88 %)
31 (86 %)
20 (91 %)
Prophylactic bilateral mastectomy, yes, n (%)
9 (16 %)
0 (0 %)
9 (41 %)
Prophylactic oophorectomy, yes, n (%)
14 (24 %)
1 (3 %)
13 (59 %)
Current hormone replacement therapy, yes, n (%)
10 (17 %)
3 (8 %)
7 (32 %)
BMI, kg/m2 (SD)
BRCA1 mRNA expression, mean (95 % CI)
164.3 (155, 173.5)
175.1 (163.4, 187)
146.7 (134.2, 159)
BRCA1 mutation status significantly contributes to lower overall BRCA1 expression levels
Correlation between reproductive or lifestyle factors and BRCA1 mRNA expression
Unstandardized B (95 % CI)
−0.63 (−1.3, 0.07)
−22.3 (−40, −4.8)
−12 (−22, −3)
Age at menarche
−3.7 (−10.2, 2.8)
−23.3 (−43, −4)
Current oral contraceptive use
−2.5 (−33, 30)
Current smoking status
−9.3 (−45, 26)
Current alcohol consumption
0.115 (−28, 28)
−15.3 (−41, 10)
−24 (−45, −3.4)
Current hormone replacement therapy use
0.5 (−11.8, 12.8)
Body mass index
0.445 (−1.5, 2.3)
−28.5 (−46, −11)
The mutation status is the most significant contributor to reduced BRCA1 mRNA levels after adjusting for parity, breastfeeding, and menopause
B Coefficient (95 % CI)
179 (128.4, 207.5)
−22.5 (−43.3, −1.7)
3.5 (−28, 35)
−9.3 (−24, 5.6)
−3.5 (−28, 20)
As BRCA1 mutation status was the most significant contributor to reduced BRCA1 mRNA expression counts in the univariate analysis, we also evaluated this relationship after adjusting for parity, breastfeeding, menopause, and oophorectomy. Covariates were selected based on the univariate analysis showing statistically significant correlations with BRCA1 mRNA counts (Table 2 and Additional file 2: Table S2). For the final regression model, parity, breastfeeding, menopause and mutation status were included in the analysis. As oophorectomy results in menopause, it was excluded from the analysis to prevent over-adjustment. Multivariate modeling demonstrated that carrying a BRCA1 mutation remained the most significant predictor of BRCA1 mRNA levels (Table 3). After adjusting for other important covariates, women with a BRCA1 mutation had 22.5 lower counts of BRCA1 mRNA levels compared to non-carriers (P = 0.04). These data suggest that BRCA1 mutation status alone predicts BRCA1 mRNA expression levels.
BRCA1 mRNA expression levels are mutation specific
Overview of BRCA1 mutation type and association with nonsense-mediated decay
aNonsense-mediated decay (NMD)
Deletion Exon 1-2
Deletion Exon 4-6
3748G > T
BRCA1 mutation carriers have similar gene expression profiles
A summary of genes significantly downregulated in samples of BRCA1 mutation carriers compared to non-carriers (Benjamini-Hochberg false discovery rate < 0.05 using the t-test)
c-Src tyrosine kinase
Neuroblastoma RAS viral (v-ras) oncogene homolog
Transforming growth factor, beta receptor II
Xeroderma pigmentosum, complementation group C
Breast cancer 1, early onset
Cyclin-dependent kinase 16
Topoisomerase (DNA) I
Tumor necrosis factor (ligand) superfamily, member 10
A summary of genes significantly upregulated in samples of BRCA1 mutation carriers compared to non-carriers (Benjamini-Hochberg false discovery rate < 0.05 using the t test)
Clathrin, heavy chain (Hc)
Fms-related tyrosine kinase 3
LIM domain only 2
V-Rel avian reticuloendotheliosis viral oncogene homolog
Breakpoint cluster region
Protein tyrosine phosphatase, non-receptor type 11
Tumor necrosis factor superfamily, member 10B
Transforming growth factor, beta 1
The goal of the current study was to evaluate whether BRCA1 mRNA expression levels are reduced in the leukocytes of women with a BRCA1 mutation. We found that carrying a BRCA1 mutation was the most significant predictor of BRCA1 mRNA levels. BRCA1 mRNA levels were significantly lower in mutation carriers compared to non-carriers (146.7 counts vs. 175.1 counts; P = 0.002). Furthermore, mutations within exon 11 were associated with lower mRNA expression levels compared to mutations within the 5′ and 3′ regions of the BRCA1 gene (122 counts vs. 138 and 167 counts, respectively; P = 0.003). In addition, 17 other genes in a panel of 236 genes, some of which have been previously shown to be involved in breast and ovarian carcinogenesis, were also differentially expressed between the two groups of women. Overall, these findings support the concept of BRCA1 haploinsufficiency, whereby a dosage-dependent effect of the BRCA1 gene is associated with molecular alterations at the transcriptional level. Reduced BRCA1 mRNA expression levels were previously reported in BRCA1-associated cancer . To our knowledge, this is the first study to identify lower BRCA1 expression in leukocytes from healthy, unaffected BRCA1 mutation carriers. Whether lower BRCA1 transcript levels translate to changes in protein levels or to carcinogenesis remains to be determined.
Emerging evidence from epidemiologic studies, from human tissue culture model systems and from murine studies supports a continuum of tumor suppression where BRCA1 expression levels might be tightly correlated with function . Recently, Pathania et al. reported that human breast epithelial and skin fibroblast cells from BRCA1 mutation carriers had lower BRCA1 protein levels that were associated with haploinsufficiency for stalled replication fork repair/replication stress and conditional haploinsufficiency for HR-DSB . Under concurrent forms of stress, such as UV and IR that require BRCA1 mediated HR-DSB, the pool of available BRCA1 is not sufficient to repair all the damage, thereby leading to the accumulation of small genomic aberrations. When these aberrations reach a threshold above which the damage is irreparable, genomic instability ensues and drives malignant transformation . Consequently, identifying BRCA1 mutations that result in low basal expression levels might help stratify cancer risk. More recently, Sedic et al. showed that BRCA1 mutation carriers exhibit cell-type-specific haploinsufficiency for genomic instability, whereby human mammary epithelial cells from BRCA1 mutation carriers had shorter telomeres that contributed to premature senescence compared to non-carriers . If these in vitro findings translate to mammary epithelial cells having a reduced life span in vivo, then additional genomic alterations are required to bypass premature senescence. Whether BRCA1 expression levels can predict cells that are at increased risk of escaping senescence remains to be determined.
A number of epidemiologic reports suggest tumor type predisposition differs according to the position of the BRCA1 mutation [27–29]. In an analysis of 60 families with a history of breast or ovarian cancer, Gayther et al. showed that BRCA1 mutations mapping up to and including exon 12 were linked to a higher ratio of ovarian to breast cancers compared to mutations mapping to the C-terminal portion of the BRCA1 gene . Moreover, using genotype-phenotype correlations in 356 families with pathogenic BRCA1 mutations, Thompson et al. showed that the ovarian to breast cancer ratio was higher with mutations in the central region of the BRCA1 gene (nucleotides 2401-4190; predominantly within exon 11) . In a systemic analysis of 19,581 carriers of BRCA1 mutations, Rebbeck et al. identified that mutation clusters mapped to the 5′ (BCCR1, c.179 to c.505) and 3′ (BCCR2, c.4328 to c.4945 and BCCR2′, c.5261 to c.5563) regions of BRCA1 were associated with increased breast cancer risk, while mutations mapped to exon 11 were associated with increased ovarian cancer risk .
In the current study, we showed that mutations within exon 11 had the lowest mRNA expression levels compared to mutations within the 5′ and 3′ regions of the BRCA1 gene, with nonsense-mediated decay being the most likely mechanism mediating mutation-dependent reduced transcript level readout. It remains to be determined how mutation-dependent modulation of BRCA1 expression levels affects the different functions of BRCA1, i.e., which mutations confer a dominant negative role compared to mutations that retain partial wild-type BRCA1 function, whether functions involving domains within exon 11 are more relevant to ovarian epithelium function and whether those within domains of the 3′ and 5′ regions more relevant to breast epithelium functioning .
Conditional Brca1 mouse models have also provided insight into functional correlates of different BRCA1 mutations. Mouse strains carrying loss of Brca1 and heterozygous p53 mutations are conditionally targeted to mammary epithelial cells using Cre-lox system. Shakya et al. showed that introduction of a brca1 mutation I26A, which impairs E3 ubiquitin ligase activity but maintains the interaction with Bard1, does not lead to tumor formation; whereas mutation of the BRCT domain (S1598F) that disrupts phosphoprotein binding resulted in a high rate of tumor formation . Drost et al. demonstrated that the Brca1 (C61G) missense mutation, which impairs BRCA1/BARD1 heterodimerization and ubiquitin ligase activity, resulted in mammary tumors that were resistant to cisplatin and PARP inhibitors compared to Brca1 null mice . Overall, these studies suggest that all BRCA1 mutations are not equivalent in their tumorigenic potential, and consequently, cancer risk assessment might be mutation specific.
The present study also highlights BRCA1 mutation status as a significant classifier based on global gene expression profiling. Pathway enrichment analysis revealed gene expression alterations that are tissue specific, including genes that mediate acute/chronic leukemia. Interestingly, enrichment of genes involved in Toll-like receptor signaling and IL-2-mediated signaling in BRCA1 mutation carriers, suggests that changes in the immune microenvironment might occur early on in heterozygous cells and may be useful for targeted prevention strategies. Furthermore, downregulated genes were enriched in DNA damage response pathways, thereby supporting the growing evidence for BRCA1 haploinsufficiency in DNA damage repair as a potential early tumor predisposing event.
Strengths of the current study include the use of RNA from blood leukocytes that was stabilized within 30 minutes of collection, resulting in high quality RNA (mean RNA integrity number, RIN = 8.7), and the use of the NanoString nCounter Analysis System to quantify mRNA expression, which helps to achieve high validity, reproducibility, and sensitivity . The primary limitation of our study is that the BRCA1 expression analysis was not allele-specific, i.e., the lower mRNA counts in leukocytes of BRCA1 mutation carriers extend beyond nonsense-mediated decay of the mutant allele to include mechanisms, such as microRNA-mediated regulation of expression levels of wild-type or mutant-type alleles, and altered expression levels of regulators of BRCA1 mRNA levels in BRCA1 mutation carriers vs. non-carriers. Future studies using RNA sequencing, which can discriminate between levels of the wild-type and mutant allele are warranted. Other limitations include the relatively small sample size that allowed for the evaluation of a narrow spectrum of BRCA1 mutations and their effects on BRCA1 gene expression levels.
Collectively, these data support the concept of BRCA1 haploinsufficiency, whereby BRCA1 heterozygous cells have lower BRCA1 mRNA expression levels. Since the evaluation of BRCA1 protein levels as a surrogate marker of BRCA1 haploinsufficiency posits a challenge, especially in freshly isolated leukocytes, our study highlights the role of using BRCA1 mRNA levels as an indicator of prospective BRCA1 functional levels. Factors that increase BRCA1 levels to a normal level might restore BRCA1 function. We recently demonstrated that daily oral supplementation with 3,3′-diindolylmethane (i.e., DIM) for 4–6 weeks resulted in a significant 34 % increase in BRCA1 mRNA expression in leukocytes from women with a BRCA1 mutation . Elsewhere, sedentary behavior was associated with significantly lower BRCA1 mRNA levels in women with and without a mutation . These studies provide important mechanistic insight into how a lifestyle factor may mediate cancer risk in this high-risk population.
In summary, our findings suggest that BRCA1 mutation status is a significant predictor of lower BRCA1 mRNA levels in peripheral blood leukocytes. In turn, this may provide a feasible tool whereby modulation of BRCA1 levels through different interventions can be monitored in the clinical setting or can stratify risk. The possibility of mitigating the effect of an inherited deleterious BRCA1 mutation by increasing the physiologic expression of the gene and normalizing protein levels represents a clinically important paradigm shift in the prevention strategies available to these high-risk women.
AGE-RAGE, advanced glycation end products-receptor for advanced glycation end products; ANOVA, analysis of variance; BCCR, breast cancer cluster region; BRCA1, Breast cancer 1, early onset; DSB, double strand break; HR, homologous recombination; HR-DSB, homologous recombination mediated repair of double-stranded DNA breaks; HRT, hormone replacement therapy; mRNA, messenger RNA; NMD, nonsense mediated decay; PTC, premature termination codon; WCRI, Women’s College Research Institute
JK is the recipient of a Cancer Care Ontario Research Chair in Population Studies. JK and MA are recipients of a Canadian Cancer Society Career Development Award in Prevention. SAN and IJ are recipients of a Tier I Canada Research Chair. LS is the recipient of a Tier II Canada Research Chair. This study was supported by a Cancer Care Ontario Population Studies Research Network Pilot Study grant. The authors would like to thank Jennifer Cruickshank for her valuable comments on this manuscript.
JK, SAN, MA, RC, and LS conceived and designed the study. JK was involved in the management and funding of the study. RC and RP enrolled the study participants, collected data and biological specimens and performed the processing of the specimens as well as RNA extraction. RC, MK, and IJ performed the statistical analyses. RC and JK drafted the manuscript and were both involved in data analysis and interpretation of the results. All authors contributed to the critical revision and editing of the manuscript. All authors read and approved the final version of the manuscript.
The authors declare that they have no competing interests.
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