Rare BRIP1 Missense Alleles Confer Risk for Ovarian and Breast Cancer

Abstract

Germline loss-of-function mutations in BRCA1 interacting protein C-terminal helicase 1 (BRIP1) are associated with ovarian carcinoma and may also contribute to breast cancer risk, particularly among patients who develop disease at an early age. Normal BRIP1 activity is required for DNA interstrand cross-link (ICL) repair and is thus central to the maintenance of genome stability. Although pathogenic mutations have been identified in BRIP1, genetic testing more often reveals missense variants, for which the impact on molecular function and subsequent roles in cancer risk are uncertain. Next-generation sequencing of germline DNA in 2,160 early-onset breast cancer and 1,199 patients with ovarian cancer revealed nearly 2% of patients carry a very rare missense variant (minor allele frequency < 0.0001) in BRIP1. This is 3-fold higher than the frequency of all rare BRIP1 missense alleles reported in more than 60,000 individuals of the general population (P < 0.0001, x 2 test). Using CRISPR-Cas9 gene editing technology and rescue assays, we functionally characterized 20 of these missense variants, focusing on the altered protein's ability to repair ICL damage. A total of 75% of the characterized variants rendered the protein hypomorph or null. In a clinical cohort of >117,000 patients with breast and ovarian cancer who underwent panel testing, the combined OR associated with BRIP1 hypomorph or null missense carriers compared with the general population was 2.30 (95% confidence interval, 1.60-3.30; P < 0.0001). These findings suggest that novel missense variants within the helicase domain of BRIP1 may confer risk for both breast and ovarian cancer and highlight the importance of functional testing for additional variants. Significance: Functional characterization of rare variants of uncertain significance in BRIP1 revealed that 75% demonstrate loss-of-function activity, suggesting rare missense alleles in BRIP1 confer risk for both breast and ovarian cancer.

DNA Repair and Ovarian Carcinogenesis: Impact on Risk, Prognosis and Therapy Outcome

“…It was previously associated with breast cancer risk [76][77][78][79] however, results from these studies are inconsistent and several other studies found no association of BRIP1 mutations and breast cancer risk [80,81]. It is one of the most common OvC susceptibility genes with 0.9-2.5% frequency in all patients carrying a mutation in this gene [62,[82][83][84]. A study from Weber-Lassalle et al on the loss of function BRIP1 mutations found that these mutations confer a high OvC risk in familial OvC patients as well as in late-onset OvC patients (OR = 20.97 and 29.91 respectively) [83].…”

Helicase-inactivating BRIP1 mutation yields Fanconi anemia with microcephaly and other congenital abnormalities

“…BRIP1 p.P47A, originally identified in a breast cancer patient and used as a negative control in our study, is also helicase-deficient (Cantor et al 2004). A recent study evaluated 18 additional BRIP1 missense mutations identified in ovarian and early-onset breast cancer patients for protein stability and effects on cell growth, cell cycle progression, and chromosome breakage in the presence of DNA damaging agents (Moyer et al 2020). Thirteen of these mutations were null or depleted in one or more of these functions, whereas five had fully normal function.…”

“…All BRIP1 truncating alleles yield loss of the helicase domain and are likely to lead to loss of protein (Levitus et al 2004;Levitus et al 2005;Levran et al 2005;Litman et al 2005;Steinberg-Shemer et al 2019). Missense alleles, which may retain at least partial protein expression and function (Levitus et al 2005;Bharti et al 2018;Moyer et al 2020), may cause a less severe phenotype. A recent analysis of genotype-phenotype associations in Fanconi anemia found an increased frequency of congenital abnormalities in patients with null genotypes compared to those with hypomorphic genotypes, suggesting that phenotypic severity may be influenced by the type of mutation (Fiesco-Roa et al 2019), although other studies have found conflicting results (Faivre et al 2000;Castella et al 2011;Steinberg-Shemer et al 2019).…”

“…Heterozygous BRIP1 loss-of-function mutations predispose to ovarian cancer (Rafnar et al 2011;Ramus et al 2015;Norquist et al 2016;Weber-Lassalle et al 2018), and current National Comprehensive Cancer Network guidelines indicate that risk-reducing salpingo-oophorectomy should be considered between the ages of 45-50 for women with these mutations (https://www.nccn.org/professionals/physician_gls/pdf/genetics_screening.pdf). These loss-of-function mutations include rare BRIP1 missense mutations that have been shown experimentally to have no or greatly reduced protective activity against DNA-damaging agents (Moyer et al 2020). BRIP1 p.R848H, with defective helicase activity, may also increase the risk of ovarian cancer.…”

History of DNA Helicases

“…Although the genetic linkage of DNA helicase defects to rare chromosomal instability disorders has been emphasized in this section, it should be stated that there are numerous studies documenting mutations in DNA helicase genes as being associated with cancers [400]. For example, a recent study established that rare missense alleles of BRIP1/FANCJ confer risk for breast as well as ovarian cancer [401]. This work is consistent with a previous study that truncating mutations in BRIP1/FANCJ confer susceptibility to breast cancer [402].…”