Moving Beyond BRCA Mutations in Familial Breast Cancer

The concept of inherited breast cancer first brings to mind the BRCA genes. The 2 genes, BRCA1 and BRCA2, share about 2000 distinct mutations between them, and reports suggest that 1 in 400 to 800 people carry a pathogenic germline mutation in BRCA1 or BRCA2.¹ The phenotype of these mutations: nonfunctional BRCA1 or BRCA2 proteins or a complete lack of expression of the proteins. Late last year, the US Preventive Services Task Force provided an update to its 2005 recommendations, which was reported by Evidence-Based Oncology,² reaffirming the genetic risk assessment and BRCA mutation testing in women susceptible to breast and ovarian cancer, based on family history. The lack of expression, or an inactivating mutation, of a tumor suppressor, increases susceptibility to cancer. Germline mutations in BRCA1 and BRCA2 have historically been associated with the development of breast^3,4 and ovarian cancer,⁵ while recent studies have also identified the role in pancreatic cancer⁶ and colorectal cancer.⁷

However, the BRCA genes do not tell the whole tale—while women with BRCA mutations have an increased risk of breast cancer, mutations in other genes have been identified. These mutations do exist, though they are less prevalent and have a relatively smaller impact on the familial form of the disease. The rapid progress in bioinformatics has given momentum to the evaluation of the genetic profile of a large number of tumor samples, which can identify these rare mutations. One such project, a collaboration between researchers at the Huntsman Cancer Institute at the University of Utah and several other research organizations around the globe, discovered 4 new genes responsible for increased susceptibility to familial breast cancer: RINT1, MRE11A, RAD50, and NBN.⁸

Bioinformatics and Personalized Medicine

Targeted/personalized treatment is undoubtedly the future of cancer therapy. Our improved understanding of within-tumor and between-tumor heterogeneity has led to the development of interventions that can be tailored to an individual’s specific cancer subtype. However, the task is daunting—the complex nature of cancer, and the ease with which the tumors adapt, results in resistance phenomena that are at times hard to combat.

With this in mind, the National Cancer Institute (NCI) launched The Cancer Genome Atlas (TCGA) in collaboration with the National Human Genome Research Institute (NHGRI).⁹ The pilot, initiated in 2006, was designed to generate an atlas that would map the sea of changes that accompany a specific cancer type. Additionally, the data are accessible to researchers all around the world, which can help them make and validate their own discoveries, as well as fill up the gaps that exist in the current knowledge of a particular cancer type—a concept recently corroborated by researchers at the Broad Institute.¹⁰ In a study published in Nature that evaluated nearly 5000 tumor and matching normal tissue samples (many from TCGA), the authors identified nearly all the known cancer genes in the 21 tumor types being evaluated, in addition to 33 novel genes.¹⁰

The New Genes in Familial Breast Cancer

RINT-1

Going back to the recent discovery of genes responsible for breast cancer inheritance, the authors identified 3 as yet undiscovered mutations in Rad50 Interactor 1 (RINT-1). To follow up their findings, they conducted a mutation screen, which distinguished 29 carriers of rare, likely pathogenic variants—23 of these were identified in early-onset breast cancer cases and the remaining 6 were identified in matched controls. In families that had evidence of multiple cases of breast cancer, 4 additional carriers of rare genetic variants were identified. Additionally, RINT-1 mutations were also found to increase the carrier’s susceptibility to Lynch syndrome cancers (inherited cancer of the digestive tract), especially among relatives who had a cancer diagnosis at under 60 years of age.¹¹

RINT1 protein, expressed on the endoplasmic reticulum, the Golgi apparatus, and the centrosomes, has historically been identified as a cell cycle regulator that prevents tumor growth.¹² Disruptions in the expression of this protein were found to cause abnormalities during both the interphase and mitosis, with the mitotic events leading to cell death. Additionally, homozygous deletion of RINT-1 alleles (RINT-1-/-) resulted in embryonic lethality in mice, while the animals expressing heterozygous RINT-1 (RINT-1+/-) developed multiple tumors, emphasizing its role as a potential tumor suppressor.¹²

The DNA Repair Proteins: MRE11A, RAD50, NBN

Mutations in the MRE11A-RAD50-Nibrin (MRN) protein complex, a major player in DNA double-strand break repair, were also found to increase breast cancer susceptibility. Although defects in the MRN complex have previously been shown to predispose individuals to breast cancer,¹³ the exact mechanism of the defect is not clear. In the recent study published in Breast Cancer Research, the authors queried if the defect was a result of protein truncation or an expression of a missense protein. Further, they examined whether some of the rare MRN variants are responsible for intermediate-risk breast cancer susceptibility alleles.¹⁴

The results of this study, which evaluated samples from diverse ethnic groups, led the authors to conclude that MRE11A, RAD50, and NBN (Nbs1) are indeed intermediate-risk breast cancer susceptibility genes that should be included on cancer susceptibility diagnostic gene panels. Although truncation variants of these proteins were discovered in the patient samples, a significantly higher proportion of missense mutations were identified. However, the authors think that the data are insufficient to establish a clinically actionable classification of individual variants observed in the study.¹⁴

PALB2

The partner and localizer of BRCA2 (PALB2) protein, initially recognized as a BRCA2 binding partner, was later found to interact with BRCA1 as well.^15,16 Responsible for Fanconi’s anemia following a biallelic loss-of-function mutation, the monoallelic loss-of-function mutation of PALB2 is a risk factor for breast cancer as well as pancreatic cancer.¹⁷ While analyses have provided risk estimates on loss-of-function PALB2 mutations and familial breast cancer, a recent paper published in the New England Journal of Medicine took up the task of obtaining more precise and robust estimates, based on data collected across different locations within the United Kingdom—362 individuals across multiple generations of 154 families, and with different family histories.¹⁸ These individuals, who expressed truncated mutants, splice variants, or deletion mutants of PALB2, were 8 to 9 times more likely to develop breast cancer relative to the general population if they were below 40 years of age. Susceptibility reduced, however, with age: those in the 40-to-60-year age group were 6 to 8 times more likely to develop the disease, while those over 60 years of age were 5 times more likely to develop breast cancer.

The authors concluded that loss-of-function mutations in PALB2 are an important determinant of hereditary breast cancer, although the risk of developing the disease in these individuals could overlap with BRCA2 mutation carriers.¹⁸

Implications for the Patient

Some of the diagnostic panels that are currently available include some of these genes (Table),^19,20,21 since they have all been associated with breast cancer. Inventia’s

“High-risk hereditary breast cancer” panel, for example, is a 7-gene panel that includes PALB2, along with the BRCA genes. Myriad, which has been in the genetic testing marketplace for some time now, has developed the “Myriad myRisk Hereditary Cancer” panel—a 25-gene panel that points to susceptibility of an individual to familial cancers of the breast, ovary, endometrium, prostate, stomach, skin, and pancreas, and colorectal cancer.22 The panel includes BRCA1, BRCA2, PALB2, and NBN, among other genes, to identify the risk for familial breast cancer.²³ Myriad also markets the BRACAnalysis test, which evaluates mutations only in the BRCA genes to identify hereditary risk of breast and ovarian cancer.²⁴

Several health insurance plans cover counseling and testing costs, if individuals decide to go that route. However, to reduce the risk of unnecessary testing, insurance companies like Cigna and Priority Health have mandated pre-testing genetic counseling for hereditary conditions—including breast cancer—from an independent genetic

counselor.^25,26 Additionally, the Affordable Care Act has made provisions for new health plans to provide coverage of physician-recommended counseling and BRCA-testing costs.²⁷

EBO

The tools are out there—the requirement is raising awareness in the population to appropriately utilize them. Individuals who have had cancer or those who have a known family history of cancer would be ideal candidates for such testing. However, the process should be aided by a genetic counselor, who can evaluate the person’s family tree to determine the need for testing. With newer genes being identified and validated in large and diverse populations, these panels will definitely expand.References

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2. Dangi-Garimella S. USPSTF recommends BRCA testing in women based on familial history. Am J Manag Care. 2014;20(SP5):SP137-SP139.

3. Miki Y, Swensen J, Shattuck-Eidens D, et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science. 1994;266(5182):66-71.

4. Wooster R, Bignell G, Lancaster J, et al. Identification of the breast cancer susceptibility gene BRCA2. Nature. 1995;378(6559):789-792.

5. Girolimetti G, Perrone AM, Santini D, et al. BRCA-associated ovarian cancer: from molecular genetics to risk management. Biomed Res Int. 2014;2014:article id 787143.

6. Golan T, Kanji ZS, Epelbaum R, et al. Overall survival and clinical characteristics of pancreatic cancer in BRCA mutation carriers [published online July 29, 2014]. Br J Cancer. doi: 10.1038/bjc.2014.418.

7. Phelan CM, Iqbal J, Lynch HT, et al. Incidence of colorectal cancer in BRCA1 and BRCA2 mutation carriers: results from a follow-up study. Br J Cancer. 2014;110(2):530-534.

8. Four new genes confirmed to increase familial breast cancer risk: one gene also increases risk for other cancers [press release]. Salt Lake City, UT: University of Utah; June 4, 2014. http://healthcare.utah.edu/huntsmancancerinstitute/newsroom/current-press-releases/four-newgenes-increase-breast-cancer-risk.php.

9. The Cancer Genome Atlas: program overview. National Cancer Institute website. http://cancergenome.nih.gov/abouttcga/overview. Accessed August 25, 2014.

10. Lawrence MS, Stojanov P, Mermel CH, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014;505(7484):495-501.

11. Park DJ, Tao K, Le Calvez-Kelm F, et al. Rare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancers. Cancer Discov. 2014;4(7):804-815.

12. Lin X, Liu CC, Gao Q, Zhang X, Wu G, Lee WH. RINT-1 serves as a tumor suppressor and maintains Golgi dynamics and centrosome integrity for cell survival. Mol Cell Biol. 2007;27(13):4905-4916.

13. Bartkova J, Tommiska J, Oplustilova L, et al. Aberrations of the MRE11-RAD50-NBS1 DNA damage sensor complex in human breast cancer: MRE11 as a candidate familial cancerpredisposing gene. Mol Oncol. 2008;2(4):296-316.

14. Damiola F, Pertesi M, Oliver J, et al. Rare key functional domain missense substitutions in MRE11A, RAD50, and NBN contribute to breast cancer susceptibility: results from a Breast Cancer Family Registry case-control mutation-screening study. Breast Cancer Res. 2014;16(3):R58.

15. Xia B, Sheng Q, Nakanishi, K, et al. Control of BRCA2 cellular and clinical functions by a nuclear partner, PALB2. Mol Cell. 2006;22(6):719-729.

16. Zhang F, Ma J, Wu J, et al. PALB2 links BRCA1 and BRCA2 in the DNA-damage response. Curr Biol. 2009;19(6):524-529.

17. Tischkowitz M, Xia B. PALB2/FANCN: recombining cancer and Fanconi anemia. Cancer Res. 2010;70(19):7353-7359.

18. Antoniou AC, Casadei S, Heikkinen T, et al. Breast-cancer risk in families with mutations in PALB2. N Engl J Med. 2014;371(6):497-506.

19. High-risk hereditary breast cancers. Invitae website. https://www.invitae.com/en/physician/panel-detail/PNL0009/. Accessed August 27, 2014.

20. myRisk clinical handbook. https://myriadweb.s3.amazonaws.com/myRisk/myRisk-Clinical-Handbook-web.pdf. Accessed August 27, 2014.

21. BreastNext. Ambry Genetics website. http://www.ambrygen.com/tests/breastnext. Accessed August 27, 2014.

22. Myriad myRisk Hereditary Cancer. Myriad website. http://www.myriad.com/productsservices/hereditary-cancers/myrisk-hereditarycancer/. Accessed August 26, 2014.

23. myRisk clinical handbook. Myriad website. https://myriad-web.s3.amazonaws.com/myRisk/myRisk-Clinical-Handbook-web.pdf. Accessed August 27, 2014.

24. BRACAnalysis. Myriad website. http://www.myriad.com/products-services/hereditarycancers/bracanalysis/. Accessed August 27, 2014.

25. Genetic testing and counseling program. Cigna website. http://www.cigna.com/healthcare-professionals/resources-forhealth-care-professionals/genetic-testing andcounseling-program. Accessed August 27, 2014.

26. Genetics: counseling, testing, screening.Priority Health website. https://www.priorityhealth.com/provider/manual/auths/~/media/documents/medical-policies/91540.pdf.

Accessed August 27, 2014.

27. Preventive services covered under the Affordable Care Act. US Department of Health and Human Services website. http://www.hhs.gov/healthcare/facts/factsheets/2010/07/preventive-services-list.html#CoveredPreventiveServicesforWomenIncludingPregnantWomen. Updated September 27, 2012. Accessed August 27, 2014.

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