The breast cancer type 1 susceptibility gene (BRCA1) is a tumor suppressor gene involved in many cellular processes, including genomic maintenance and DNA repair. Promoter methylation of or pathogenic variants in BRCA1 has been associated with the development of cancer, particularly breast and ovarian cancer.

Individuals with BRCA1 deficiency due to germline pathogenic variants of promoter methylation have an increased lifetime risk of breast and ovarian cancer. The presence of BRCA1 promoter methylation is a prognostic biomarker, associated with an unfavorable diagnosis. Fortunately, BRCA1 promoter methylation also indicates sensitivity towards platinum chemotherapy and PARP inhibitor (PARPi) treatment. 

The BRCA1 gene product plays a role in maintaining the genomic integrity in healthy cells through several pathways. The BRCA1 gene is located on chromosome 17q21 and encodes a 1863aa protein, containing a cysteine-rich RING domain, a zinc-binding domain commonly found in regulatory proteins and tandem BRCT domains. 

BRCT is a phosphopeptide domain, which mediates interactions with other proteins. The BRCA1 protein localizes to the nucleus of the cell, where it exists as a heterodimer with its obligatory binding partner BARD1, and together they function as an E3 ubiquitin ligase. The specific pathway in which the BRCA1 protein exerts its function is dependant on recruitment signals and the formation of specific protein complexes.

BRCA1 is perhaps most known for its role in the repair of double-stranded DNA breaks (DSBs). In these cases, BRCA1 is recruited to the DSB site, where it promotes homologous recombination repair, a high-fidelity DNA damage repair pathway. 

However, it is also involved in cell cycle checkpoint and centrosome regulation, transcriptional modulation, chromatin remodelling, and in the protection and repair of stailed and damaged replication forks. 

BRCA2 is the breast cancer type 2 susceptibility gene. BRCA2 is also involved in DNA damage repair of DSBs, and pathogenic variants in BRCA2  are associated with increased cancer risk. For more details, see the BRCA2 gene section of the MS-HRM resources. 

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BRCA1 gene in cancer 

Loss of BRCA1 function due to the presence of pathogenic variants is a well-known tumor-promoting event in specific, primarily hormone-sensitive tissues. It is thought that the DNA damage resulting from the loss of BRCA1 promotes tumorigenesis via an increased amount of random mutations and structural rearrangements in the genome, potentially resulting in the activation of oncogenes and inactivation of tumor suppressors. 

The emergence of a pathogenic variant in BRCA1 is a driving event in tumorigenesis, especially in breast and ovarian cancer, where deleterious BRCA1 alleles are prevalent, as well as in pancreatic cancer and prostate cancer.

The estimated frequency of mutated BRCA1 in healthy women os 0.11%, although it varies widely depending on country and population. Apart from tumors stemming from inherited pathogenic BRCA1 variants, sporadic cancers can also develop from somatic, pathogenic BRCA1 gene mutations. 

BRCA1 gene in breast cancer and ovarian cancer 

Factors known to increase the risk of breast and ovarian cancer include early menarche and delayed menopause, nulliparity, hormonal therapy, and genetic risk factors. The strongest risk factor for developing ovarian cancer is a family history of breast and ovarian cancer.

Inherited BRCA1 and BRCA2 pathogenic variants account for approximately 5-10% of breast cancers and up to 21% of ovarian cancers. The estimated lifetime risk of breast cancer ranges from 40% up to 90% for carriers of BRCA1 pathogenic variants and is slightly lower for carriers of BRCA2 pathogenic variants, both with an additional increased risk of contralateral breast cancer.

For carriers of BRCA1 and BRCA2 mutations, the estimated lifetime risk of ovarian cancer is 40-65% and 11-30%, respectively. BRCA1 deficiency is associated with early-onset development of aggressive of breast- and ovarian cancer types. BRCA1 pathogenic variants are associated with high-grade serous ovarian cancer (HGSOC), and a substantial fraction of BRCA1 deficient breast tumors are negative for the estrogen-, progesterone-, and HER2-receptors (triple-negative breast cancer, TNBC).

In order to reduce breast cancer incidence and mortality, population-wide screening programs are employed. Additionally, genetic testing and counseling are recommended for patients at high risk, and to determine prognosis and treatment response in breast cancer patients.

Individuals at high breast cancer risk may additionally have an elective mastectomy to prevent disease. There is no effective screening method for ovarian cancer, but high-risk individuals can be identified via genetic testing, and they may subsequently undergo surgery to reduce the cancer risk.

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Role in cancer treatment

PLATINUM CHEMOTHERAPY

BRCA1 deficiency impairs the maintenance of genomic integrity, in part by preventing homologous recombination repair. Due to the lack of homologous recombination, BRCA1-deficient tumors are hypersensitive to alkylating and cross-linking agents, such as platinum salts. 

Platinum salts create inter- and intrastrand cross-links between the purine bases, distorting the helical DNA structure and preventing RNA transcription and DNA replication. 

Homologous recombination is necessary for the error-free resolution of these lesions. Hmologous recombination deficiency (HRD) can develop through germline or de novo loss-of-function mutations in BRCA1, by hypermethylation of the BRCA1 gene promoter, or pathogenic mutations in other genes involved in the homologous recombination pathway, exemplified by mutations in the BRCA2 gene. 

PARP INHIBITORS

Besides treatments that induce DNA damage, HRD tumors are also sensitive to treatments targeting the DNA damage response pathways. This is known as synthetic lethality, where two deficiencies individually do not affect viability, but are lethal when occurring together.

Synthetic lethality can be exploited clinically by the administration of PARPis, such as olaparib. PARPis inhibit the catalytic activity of PARP1, which normally binds to sites of single-strand DNA breaks and signal the need for DNA damage repair by poly-(ADP-ribosylation).

When inhibited, PARP1 cannot exert its function and stays bound to the DNA at the site of the damage, as a roadblock to transcriptional and replicational machinery.

Functional homologous recombination is needed to remove the lesion, and in HRD tumors, PARPi treatment results in the formation of mutations and structural rearrangements, and ultimately cell death.

Breast cancer patients treated with olaparib and talazoparib displayed increased progression-free survival, and the PARPis have been approved for the treatment of BRCA1 or BRCA2 mutated, HER2-negative, locally advanced, or metastatic breast cancer.

In ovarian cancer, PARPis can improve the prognosis of both primary and recurrent disease, and several PARPis are approved for maintenance therapies in first-line and recurrent disease, and as monotherapies.
Due to the sensitivity of HRD tumors towards platinum salts and PARPis, genetic testing can now inform treatment choice.

BRCA1 promoter hypermethylation in cancer

BRCA1 promoter hypermethylation causes HRD through transcriptional downregulation of BRCA1. Methylation of the BRCA1 promoter can be both a sporadic, somatic epimutation or a constitutional epimutation. Constitutional epimutations are epigenetic alterations that happen in utero, giving rise to epigenetic mosaicism and, in the case of BRCA1, an increased risk of cancer.  

Constitutional BRCA1 epimutations have been identified as predominantly monoallelic and present in corresponding levels in different tissues, suggesting clonal origin early in embryogenesis.

BRCA1 methylation is considered an early event in carcinogenesis and has been detected in up to 44% of sporadic human cancers, in 30% of TNBCs, and in 10-20% of HGSOCs. Additionally, a study of Arab women found 14.2% of breast cancer patients had BRCA1 promoter hypermethylation in their peripheral blood.

Other studies have identified BRCA1 methylation in the peripheral blood of 4-10% of cancer-free adult women and newborn girls, suggesting that BRCA1 methylation may predispose to tumorigenesis, similar to germline pathogenic BRCA1 variants.

BRCA1 methylated cancers present phenotypically similar to cancers with BRCA1 pathogenic variants, although they only have a modest effect compared to germline pathogenic BRCA1 variants. This is likely due to the mosaic nature of constitutional epimutations, compared to germline variants, which typically affect all cells in the organism.

BRCA1 promoter methylation is particularly associated with TNBCs, HGSOC, and poor survival. Fortunately, this epimutation is also associated with patient responsiveness to platinum chemotherapy and PARPi treatment.

Extending routine clinical analyses to include BRCA1 methylation might optimize treatment selection in advanced breast and ovarian cancer.

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Fanconi anemia

BRCA1 and BRCA2 are a part of the Fanconi anemia pathway. This means that certain pathogenic variants in BRCA1 and BRCA2 can predispose to Fanconi anemia. BRCA2 is a part of the Fanconi complex (FANCD2), and BRCA1 plays a critical role downstream of this complex.

Fanconi anemia is a genetic chromosomal instability disorder characterized by physical abnormalities and bone marrow failure and is associated with increased cancer risk. Clinically, physical abnormalities include microcephaly, short stature, abnormal skin pigmentation, and skeletal malformations, as well as progressive bone marrow failure within the first decade.

Treatments include surgery, androgen therapy, synthetic growth factors, and bone marrow transplant.

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How MethylDetect can assist you in your research

At MethylDetect, we can provide you with ready-to-use kits for DNA methylation analysis of your target of interest. 

In our catalog, we offer more than 850 EpiMelt assays. In Products, you will find EpiMelt kits targeting genes relevant for BRCA1 research, such as, but not limited to, BRCA1, BRCA2, PALB2, RAD51, and ATM.

The EpiMelt assay kits are based on the Methylation-Sensitive High-Resolution Melting (MS-HRM) technology and can be used with standard laboratory equipment for qPCR and melting assessment. Each EpiMelt assay kit comes with a unique control system, securing high sensitivity.

Please consult our catalog at Products, and the protocol at Assay Protocol MethylDetect, for further information on setting up the EpiMelt analysis in your laboratory. 

Custom-Tailored EpiMelt Kits

If your target gene is not found in our portfolio, we offer to design and produce EpiMelt test kits tailored to target specific areas of the genome. Following methylation-specific array screening analyses, you may have identified targets, which are not yet described in the literature.

In collaboration with you, we can design and produce EpiMelt test kits targeting these specific genomic areas, and tailor the kit to fulfill your needs. We take into account if your samples are FFPE tissue, liquid biopsies, or high-quality DNA. Custom-Tailored EpiMelt assays are always performed in close collaboration with you. 

For further information, please contact us at info@methyldetect.com 

Further reading 

Al-Moghrabi, N. et al. (2014). The molecular significance of methylated BRCA1 promoter in white blood cells of cancer-free females. BMC Cancer, 14, 830.

Daly, M. B. et al. (2021). Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic, Version 2.2021, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw, 19(1), 77-102.

Hu, C. et al. (2021). A Population-Based Study of Genes Previously Implicated in Breast Cancer. New England Journal of Medicine, 384(5), 440-451.

Krishnan, R. et al. (2021). BRCA1 and Metastasis: Outcome of Defective DNA Repair. Cancers (Basel), 14(1).

Lønning, P. E. et al. (2019). Constitutional Mosaic Epimutations – a hidden cause of cancer? Cell Stress, 3(4), 118-135.

Lønning, P. E. et al. (2022). Constitutional BRCA1 Methylation and Risk of Incident Triple-Negative Breast Cancer and High-grade Serous Ovarian Cancer. JAMA Oncol, 8(11), 1579-1587.

Takaoka, M., & Miki, Y. (2018). BRCA1 gene: function and deficiency. International Journal of Clinical Oncology, 23(1), 36-44.

Tarsounas, M., & Sung, P. (2020). The antitumorigenic roles of BRCA1-BARD1 in DNA repair and replication. Nat Rev Mol Cell Biol, 21(5), 284-299.