As medical science links certain genetic mutations with a greater variety of cancers, the names for these risk syndromes are falling out of step.
It’s more than just a name.
These outdated designations could keep the tests from being offered to many people and families whose health is at stake and who, based on the results, might benefit from preventive measures or more effective treatment.
The problem is addressed in a commentary in the July 3 edition of the scientific journal Nature. Here is the opinion piece.
The author is Dr. Colin C. Pritchard, associate professor of laboratory medicine at the University of Washington School of Medicine and head of precision diagnostics at the Brotman Baty Institute for Precision Medicine in Seattle.
He explained that a name like “hereditary breast and ovarian cancer syndrome” incorrectly suggests that only female organs are affected.
What is BRCA-1 and BRCA-2 Genetic Test?
- BRCA-1 and BRCA-2 test is a genetic blood test to detect mutation (harmful changes) in either of the two genes called BRCA-1 and BRCA-2 that belong to a class of genes known as tumor suppressors. The test includes DNA analysis and protein analysis to detect any harmful changes
- BRCA-1 is Breast Cancer susceptibility gene-1 and BRCA-2 is Breast Cancer susceptibility gene-2, respectively
- BRCA-1 and BRCA-2 are called tumor suppressor genes, because as normal cells these genes help prevent cancer by preventing any abnormal and uncontrolled cell growth
- These genes help maintain the stability of the cell’s genetic material (DNA). Harmful mutation of these genes affects their normal functioning and greatly increases the chances of development of hereditary breast and ovarian cancer in women. In men these harmful mutations increases the risk of breast cancer
- 5-10% of breast cancer and 10-15% of ovarian cancer (in US, amongst white women) have been linked to BRCA-1 and BRCA-2 mutations
- It is important to understand that not every woman with BRCA-1 and BRCA-2 mutation will develop breast and/or ovarian cancer. Likewise, not every case of breast and/or ovarian cancer is linked to BRCA-1 and BRCA-2 gene mutation
- The presence of BRCA-1 and BRCA-2 gene mutations increases the risk of developing breast cancer by up to five times. It also greatly increases the risk of developing ovarian cancer. However, since most of the data collected is through research on large families having individuals affected with cancers, this data may or may not apply to the general population
What are the Clinical Indications for performing the BRCA-1 and BRCA-2 Genetic Test?
Currently BRCA-1 and BRCA-2 mutation testing in not recommended for the general population. Also, there is no standard criterion for referring or recommending this test to any particular individual.
BRCA-1 or BRCA-2 tests may be ordered for individuals in the following category:
- Those having a history of breast cancer, at age 50 or less
- Those having a history of ovarian cancer, at any age
- Those having a personal history or a family history of cancer, in both breasts
- Those having a personal history or a family history of male breast cancer
- Individuals with 1 or more close relative diagnosed with breast cancer, before age 50
- Individuals with 3 or more close relatives diagnosed with breast cancer, at any age
- Individuals with 1 or more close relative diagnosed with ovarian cancer, at any age
- Individuals with a family history of both breast and ovarian cancers, either on mother’s side or on father’s side of the family
- Those having a personal history of breast cancer labeled as ‘triple negative’ (negative for estrogen receptor, progesterone receptor, and HER2/neu receptor)
- Ashkenazi Jewish descent individuals with 1 close relative diagnosed with breast and/or ovarian cancer
It is strongly recommended that individuals undergoing this test seek genetic counseling, prior to testing and after testing.
How is the Specimen Collected for BRCA-1 and BRCA-2 Genetic Test?
Sample required: Blood
Process: Insertion of needle into a vein (arm)
Preparation required: None; however, genetic counseling is strongly recommended before and after the test
What is the Significance of the BRCA-1 and BRCA-2 Genetic Test Result?
The test result may be negative, positive, or ambiguous/uncertain. These are described below:
Negative test result:
- A negative (or ‘true negative’) test result indicates that it is unlikely that an individual has an inherited susceptibility to cancer, associated with the gene BRCA-1 or BRCA-2. Sometimes, harmful mutations in BRCA-1 and BRCA-2 gene may not be detected by the test (termed as ‘false negative’)
- A negative test result does not mean that an individual will never get either breast or ovarian cancer. It indicates that the individual’s chances of getting breast/ovarian cancer are lower than somebody with a positive test result
- In other words, a true negative test result does not mean that an individual will not develop cancer; instead, the results are an indicator that the individual’s risk of cancer is probably similar to that of people in the general population.
Positive test result:
- A positive test result is an indicator that the individual has inherited the harmful mutation in BRCA-1 or BRCA-2 gene and therefore, has an increased risk of developing certain cancers, including breast and ovarian cancer
- A positive test result enables the individual make an informed decision about their future and in managing their cancer risk through steps such as: Undergoing frequent screening for early detection of cancer, prophylactic surgery, avoidance of certain behaviors associated with an increased risk of cancer, and the use of certain medications to prevent cancer
- The detection of such a harmful mutation can only inform the healthcare providers and the individual, that there is a risk of developing certain cancers; not if and when the cancers would develop
Ambiguous/uncertain test results:
- Tests results are sometimes classified as ambiguous/uncertain. If genetic testing indicates a change in BRCA-1 or BRCA-2 gene, which has not been previously tied to cancer in other people, it is labeled as ambiguous or uncertain
- It is sometimes difficult to conclude, if a specific DNA change affects a person’s risk of developing cancer. This is because each individual has certain genetic differences that are not associated with an increased risk for the disease
The laboratory test results are NOT to be interpreted as results of a “stand-alone” test. The test results have to be interpreted after correlating with suitable clinical findings and additional supplemental tests/information. Your healthcare providers will explain the meaning of your tests results, based on the overall clinical scenario.
Additional and Relevant Useful Information:
- Detection of harmful BRCA-1 and BRCA-2 mutations in women, also may increase their risk to a host of other cancers such as cervical, uterine, pancreatic, colon, stomach, gallbladder, bile duct cancer, and melanoma (a type of skin cancer)
- Detection of harmful BRCA-1 and BRCA-2 mutations in men, also may increase their risk to testicular, pancreatic, and early-onset prostate cancer
Certain medications that you may be currently taking may influence the outcome of the test. Hence, it is important to inform your healthcare provider, the complete list of medications (including any herbal supplements) you are currently taking. This will help the healthcare provider interpret your test results more accurately and avoid unnecessary chances of a misdiagnosis.
An estimated 19 million people worldwide carry mutations in these genes. Depending on the population, between 1 in 40 and 1 in 400 people have such a mutation.
Harmful mutations in BRCA1 and BRCA2 do encode for proteins associated with susceptibility to breast cancer and ovarian cancer, Pritchard said. What many people don’t realize is that mutations in these genes can also predispose people to lethal prostate cancer, pancreatic cancer and some forms of leukemia.
However, even when BRCA1 or BRCA2 gene mutations are discovered in a woman, her male relatives might not have the test recommended to them. Guidelines for prostate cancer, for example, have only recently been updated to recommend BRCA1 and BRCA2 screening.
“Testing is still not being done for the right people at the right time,” Pritchard said.
A study of a survey sample of 34,000 responders in the United States found that women were over 10 times more likely than men to be tested for BRCA1 and BRCA2 mutations.
Yet all sexes have the same mutation rate and the same chances of passing the mutation to their children.
Even when people are tested, Pritchard noted, they might not realize what the results mean for themselves or their family members.
Part of this misunderstanding comes from the mistaken belief that the mutation is passed only from mothers to their daughters.
Men who are diagnosed with the syndrome sometimes hide the information from their family out of fear of stigmatization.
Yet that information might help protect lives.
A man with late-stage prostate cancer, for instance, who knows that his sister has a BRCA1 mutation, might find that knowing he, too, has the same mutation, could open up more effective treatment options.
His sons and daughters could be told that it is possible to inherit the mutation from their father, and be tested accordingly.
“The name ‘hereditary breast and ovarian cancer syndrome’ just doesn’t fit,” Pritchard said.
Pritchard proposed renaming the syndrome after Mary-Claire King, a geneticist who was among the first to recognize that cancer could be inherited along a single gene.
A professor of genome science and of medicine at the UW School of Medicine, King is a long-term advocate for BRCA1 and BRCA2 mutation testing to help prevent premature death from cancer.
King syndrome would have its precedent in other cancer risk syndromes, Pritchard said.
He mentioned Lynch syndrome, which acknowledges the late hereditary cancer research Henry T. Lynch. Healthcare providers stopped using the eponym and called it “non-polyposis colorectal cancer syndrome.” When that proved too limiting, Pritchard said, the name was reverted.
Pritchard outlined the benefits of changing HBOC to King syndrome. Removing the specificity of sex and type of cancer from the name would accommodate the evolution of scientific findings.
Mutations with similar actions and cancer-causing effects along the same DNA repair pathway could be linked to this syndrome.
A new name would also improve communication about the syndrome with patients and the public.
Pritchard believes that it could help people realize that the cancer risk syndrome occurs in all sexes, can be inherited along either the father’s or the mother’s side of the family, and that the cancer risk is not confined to the breasts or the ovaries.
The new name might also increase the likelihood that appropriate testing is done across all sexes.
Pritchard also hopes to spark a wider discussion about obsolete names for genetic risk syndromes.
For example, a mutation originally linked to gastric cancer has now been found to increase the odds of a certain type of breast cancer, and also certain congenital malformations, such as cleft palate.
Pritchard said his goal in writing the Nature opinion piece was to call attention to the need for easy, adaptable syndrome names to better explain the broader effects of cancer risk genes to individuals and their relatives.
Hereditary Breast and Ovarian Cancer (HBOC) Syndrome
Breast cancer is the most common cancer among women worldwide and ovarian cancer is the deadliest gynecological cancer. Mutations in high risk genes contribute to at least 10% and 15% of breast and ovarian cancer diagnoses, respectively, with cases frequently associated with a strong family history and early onset of disease.
Hereditary Breast and Ovarian Cancer (HBOC) Syndrome is an autosomal dominant syndrome, which is caused primarily by germline mutations in two genes: breast cancer susceptibility gene 1 (BRCA1), which was first described in 1994, and breast cancer susceptibility gene 2 (BRCA2), which was discovered one year later [1,2].
This syndrome is characterized by an increased risk for female and male breast cancer, ovarian cancer, and to a lesser extent, other cancers, such as prostate cancer, pancreatic cancer, and melanoma. For a heterozygous carrier, it has been reported that the lifetime risk is as high as 70% for breast and 20–40% for ovarian cancer [3,4,5].
Therefore, prophylactic surgeries, such as bilateral mastectomy and salpingo-oophorectomy, are effective risk reduction strategies.
Beyond the preventive aspects, understanding the mechanism of predisposition can help in the choice of treatment to improve the response and survival of patients.
Advances in translational research have confirmed the biological and preclinical evidences making it increasingly apparent that BRCA1/2 mutations are biomarkers that may predict the clinical response of breast and ovarian cancer patients to platinum salts and poly (ADP-ribose) polymerase (PARP) inhibitors [6,7,8,9,10,11].
Therefore, mutational status is becoming increasingly important for the management of BRCA related cancers as PARP inhibitors and BRCA1/2 mutation targeting seem to be a hopeful approach for this group of patients.
The BRCA1 gene encodes a nuclear protein of 1863 amino acids .
This protein contains a RING domain in the N-terminal region and two BRCT domains in its C-terminal region, through which it interacts with multiple partners, performing a variety of cellular functions that are particularly related to the DNA damage repair [14,15,16,17].
The BRCA2 gene also encodes a nuclear protein that is composed of 3418 residues . BRCA2, like BRCA1, is involved in DNA repair by homologous recombination, and it interacts with different partners (such as RAD51 and PALB2) to maintain the stability of the genome .
For the moment, three BRCA2 regions have been described as particularly important for homologous recombination function: N-terminal PALB2-binding site, BRC repeats (which correspond to eight consecutive motifs located in the central region of the protein and constitutes the principal RAD51 interaction site), and the C-terminal region (composed of three oligosaccharide binding folds, a helical domain, and a tower domain that together constitute the DNA binding region and contain a RAD51 binding domain) [18,19].
Although sequencing of these high penetrance genes BRCA1/2 has been available for over 20 years, after two decades of intense research, a pathogenic variant is identified in approximately 10% of tested families .
Despite the remarkable advances seen in the past years, for the majority of HBOC families, little is understood about the underlying molecular mechanisms of cancer susceptibility. New technologies are being developed to extensively search in parallel for a pathogenic variant in a panel of other genes related to the syndrome.
These high to moderate penetrance variants in known breast cancer related genes, such as TP53, PTEN, STK11, CDH1, ATM, BRIP1, PALB2, and RAD51 isoforms (RAD51C, D, B) may also contribute to hereditary predisposition, but altogether these variants only explain about 5% of the unsolved cases .
Additional attempts to identify breast cancer risk genes have uncovered a large number of low risk loci that generally map to gene regulatory regions. The remainder of the risk is therefore likely to be a combination of not yet identified high, moderate, or low risk variants located in the non-coding regions of the aforementioned genes or in currently unidentified breast cancer risk loci. It is noteworthy that current BRCA1/2 routine screening is limited to the coding region and intron/exon boundaries.
However, protein inactivating mutations may not be the only mechanism by which their function is altered. Reduction in gene expression by changes in trans acting factors (TFs) or cis-regulatory regions may achieve the same end as truncating mutations in the gene itself.
Since limited information currently exists about the impact of variants in BRCA1/2non-coding regions, the majority of variants that were identified in these regions remain unclassified.
Therefore, about 80% of BRCA1/2 gene screening remains negative, while introns and proximal untranslated regions remain relatively unexplored. However, evidence of non-coding variants impact on cancer risk and response to treatment begin to emerge .
Current technological sequencing advancements and development of bioinformatics tools has enabled the exploration and elucidation of the genome structure and non-coding DNA regions. The description of the functional elements of the human genome by the encyclopedia of DNA elements provided a better understanding of the human genome expression regulation and how regulatory data is encoded.
This effort demonstrated that most of the human genome is involved in gene expression regulation, while the small minority of the nucleotides (1.2%) encodes proteins within humans. The ENCODE project has also described thousands of regulatory active regions and showed that 90% of common variants fall outside the coding regions of the genes . Nevertheless, the majority of the studies to date have focused on the coding regions of the cancer related genes.
This article summarizes current knowledge of non-coding regulatory BRCA1/2 regions and the variants that are located in these regions.
Germline Cancer-Associated Variants in the Regulatory Regions
Until recently, most attention had been focused on the coding regions of the genes that are associated with cancer risk.
Exome sequencing of human genome and co-segregation studies have made evident that lots of disease-associated variants play a role in hereditary susceptibility.
Since coding changes do not explain all of the predisposition cases, the importance of the non-coding regions (including promoters, introns, intergenic sequences, and non-coding RNAs) in biological functions and hereditary predisposition must be considered.
Gathered evidence indicates that genetic variants in the non-coding but functional elements can contribute to the development of hereditary cancers.
The presence of variants in these regions can impact gene transcription by the creation or disruption of transcription factors binding sites, or by interfering with CpG island methylation which leads to an aberrant methylation pattern.
In addition, variants may have an impact at the post-transcriptional level, creating or disrupting microRNA 3′ complementary binding sites in 3′UTRs, and interfering with the stability of RNAs and microRNAs.
Moreover, the elucidation of three-dimensional (3D) chromatin structure reveals a complex network of interactions within the regulatory regions of the genome that includes long-range interactions between functionally coordinated domains lying hundreds of kilobases upstream or downstream of their target [24,25].
Therefore, non-coding sequence alterations may also influence this model of regulation.
As non-coding sequences correspond to 98% of the genome, the identification of regions with a greater chance of bearing a variant that contributes to disease should be prioritized.
Since transcriptional activity is correlated with less condensed chromatin regions, regulatory elements are often located in DNAse I hypersensitive sites.
Furthermore, regions that are conserved in mammals, containing multiple binding sites for known transcription factors are most likely to be functional and present a higher probability of containing disease-associated variants .
Bioinformatics, experimental, and population-based approaches are complementary in identifying and validating key regulatory regions of the genome.
There is increasing data associating germline non-coding variants with cancer risk. Additionally, most cancer-associated single nucleotide variants (SNVs) that were identified through genome-wide association studies are located in non-coding regions, some of them with a proven role in gene expression regulation [26,27].
As examples: (i) a germline variant in the promoter of TERT(telomerase reverse transcriptase) gene (c.-57T>G) significantly increased promoter activity.
This variant co-segregated with cancer in a family with 14 melanoma cases who were not carriers of germline mutations in the two known melanoma genes, CDKN2A and CDK4 .
The variant increases TERT expression, probably by the creation of a new binding site for Ets, Elk1, and Elk4 transcription factors.
Interestingly, the 5′UTR MLH1 variant c.-27C>A is an example of a non-coding sequence change associated with an epigenetic modification.
Additionally, it was proved that an enhancer region, which is located in the intergenic sequence on chromosome 8q24, interacts with MYC proto-oncogene, even though it is located 335kb from this gene.
A variant located there (rs6983267) is associated with colorectal cancer risk via the disruption of transcription factor 7-like2 (TCFL2) binding site, a co activator of the Wnt-β catenin pathway .
A priority now is to identify the full spectrum of non-coding variants that contribute to disease and then determine their impact of gene function and disease risk. Indeed, as subtle quantitative effects are expected, it is challenging but important to define a threshold of effect that classifies these non-coding variants as “pathogenic variants” to allow for accurate genetic counseling.
Regulatory Regions in BRCA1 and BRCA2 Genes
BRCA1 and BRCA2 expression are controlled at the transcriptional and post-transcriptional levels. The key transcriptional regulatory elements are housed in gene promoters, introns, and long-range elements, while the key post-transcriptional control elements are predominantly located in 5′ and 3′ untranslated regions (UTRs).
Both genes are expressed in a cell cycle regulated manner, with low levels of proteins being observed in G0 and early G1 phases before entry into S phase, and high levels are maintained through the S and G2 phases of the cell cycle [36,37].
BRCA1 is a tumor suppressor gene that is located on chromosome 17q21 involved in DNA error-free repair by homologous recombination.
The core promoter of BRCA1 includes the non-coding exon 1 and part of intron 1 of BRCA1, as well as the exon 1 and part of intron 1 of the neighboring gene NBR2 (chr17: 43,168,800–43,172,601).
BRCA1 expression is complex with its transcription controlled by two different promoters, α and β, located upstream from the alternative first exon 1A (121bp) and 1B (378bp), respectively.
These transcripts differ by the 5′UTR (exon 1) and they are expressed in a tissue specific fashion: exon 1B is only expressed in breast cancer while exon 1A transcripts are present in both normal or tumor tissue. The maintenance of the correct ratio between the two transcripts has the potential to be important for normal regulation and function. In vitro studies show that this structural difference is related to a lower translation efficiency of 5′UTR-a in comparison with 5′UTR-b .
The more efficient BRCA1 promoter (α) consists of a region of 200 base pairs, upstream of the start site, which functions as a bidirectional transcriptional element able to direct expression in either the BRCA1 or NBR2 direction.
There is some evidence to suggest that these two genes, separated by little more than 200 bp, are reciprocally regulated and present divergent transcription .
BRCA1promoter contains: a RIBS element that acts as an activator and possesses multi subunit EtsGA-binding protein binding sites , a CREB binding site that is a strong positive transcriptional element , a CAAT box , and an E2F binding site .
Since no estrogen responsive element (ERE) was identified in BRCA1 promoter α, the stimulation of BRCA1 expression by estrogen seems to result from an indirect effect of estrogen. In contrast, an ERE was described in BRCA1 promoter β, so, in this case, the estrogen stimulation effect is due to estrogen bound to the DNA and a subsequently interaction with the transcription machinery to stimulate transcription [39,47].
In addition to promoter elements, upstream repressor elements were also described in regions upstream of the start of transcription and translation .
Gene promoter methylation has been proposed as an alternative mechanism for the transcriptional silencing of cancer-associated genes . As a typical example, epigenetic silencing of MLH1 that is associated with inherited variants leading to promoter methylation was described in familial colorectal cancers [32,50,51,52].
BRCA1 promoter methylation appears to be more relevant for sporadic than for hereditary breast and ovarian cancers [53,54,55]. It is an uncommon event among BRCA mutation carriers. For the BRCA1 gene, it was detected in about 3%and 11% of breast  and ovarian carcinomas , respectively.
There is limited information about regulatory elements outside of the BRCA1 promoter. Suen and Goss localized a 36-bp repressor element in the first intron of BRCA1 .
Wardrop and Brown subsequently described two evolutionarily conserved regions rich of TF binding sites in the second BRCA1 intron that mediates both the activation and repression of the BRCA1 gene . In addition, we reported recently the enhancer property of an intronic sequence that is located in the intron 12 of BRCA1 .
The BRCA1 3′ untranslated region (3′UTR) has been shown to be important for post-transcriptional regulation and this has been exemplified by a variety of variants located there that negatively regulate mRNA translation, probably by the disruption or creation of complementary MicroRNAs binding sites [59,60,61,62].
It is located −66 to +129 from the transcriptional start site, and corresponds to a region rich in CG nucleotides and with several TF binding sites, including E-box, Ets/E2F, and SP1. BRCA2 promoter is induced by NFκB and Elf1 [63,64], while repressed by P53, PARP1, and SLUG [65,66,67].
Recently, functional studies that were based on micro deletions mapped other regulatory promoter regions with up and down-regulating elements . Like BRCA1, BRCA2 is expressed in a cell cycle-regulated manner and the estrogen induction is also an indirect effect of mitogenic activity.
Low protein levels are observed in G0 and early G1 phases, while peak levels are reached in late G1, S, and G2 phases of the cell cycle. Misra et al. described the bi-directional activity of BRCA2promoter, similar to that of BRCA1.
It was shown that the forward and reverse promoter activity regulates both BRCA2 and ZAR2 transcription, respectively.
Interestingly, during the G0 and G1 phase of cell cycle, this promoter is 8–20 times more active in the reverse orientation, increasing the production of the ZAR2 protein that binds to the promoter and silencing BRCA2 expression. Whereas, during the pre-division phases (S/G2), the forward activity is 5–8 times higher and the ZAR2 is trapped in the cytoplasm .
Evidence suggests that promoter hypermethylation is not an obvious contributor to BRCA2related cancers .
For now, little information about BRCA2 non-coding regions is available. A few cis-acting intronic polymorphisms that alter the binding of transcription factors at regulatory sites have been described , as well as one 3′UTR variant (BRCA2c.*172G>A), but with no clear evidence of pathogenicity .
More information: Colin C. Pritchard. New name for breast-cancer syndrome could help to save lives, Nature (2019). DOI: 10.1038/d41586-019-02015-7
Journal information: Nature
Provided by University of Washington