Intronic alterations in BRCA1 and BRCA2: effect on mRNA splicing fidelity and expression.

Germline mutations in the human breast cancer susceptibility genes BRCA1 and BRCA2 account for the majority of hereditary breast and ovarian cancer. In spite of the large number of sequence variants identified in BRCA1 and BRCA2 mutation analyses, many of these genetic alterations are still classified as variants of unknown significance (VUS). In this study, we evaluated 12 BRCA1/2 intronic variants in order to differentiate their pathogenic or polymorphic effects on the mRNA splicing process. We detected the existence of aberrant splicing in three BRCA1 variants (c.301-2delA/IVS6-2delA, c.441+1G>A/IVS7+1G>A, and c.4986+6T>G/IVS16+6T>G) and two BRCA2 variants (c.8487+1G>A/IVS19+1G>A and c.8632-2A>G/IVS20-2A>G). All but one of the aberrant transcripts arise from mutations affecting the conserved splice acceptor or donor sequences and all would be predicted to result in expression of truncated BRCA1 or BRCA2 proteins. However, we demonstrated that four of these splice-site mutations (i.e., c.301-2delA, c.441+1G>A, c.4986+6T>G, and c.8632-2A>G) with premature termination codons were highly unstable and were unlikely to encode for abundant expression of a mutant protein. Three variants of BRCA1 (c.212+3A>G/IVS5+3A>G, c.593+8A>G/IVS9+8A>G, and c.4986-20A>G/IVS16-20A>G) and four variants of BRCA2 (c.516-19C>T/IVS6-19C>T, c.7976-4_7976_3delTT/IVS17-4delTT, c.8487+19A>G/IVS19+19A>G, and c.9256- 18C>A/IVS24- 18C>A) in our studies show no effects on the normal splicing process, and they are considered to be benign polymorphic alterations. Our studies help to clarify the aberrant splicing in BRCA1 and BRCA2 as well as provide information that can be used clinically to help counsel breast/ovarian cancer prone families.

Chen X ，Truong TT ，Weaver J ，Bove BA ，Cattie K ，Armstrong BA ，Daly MB ，Godwin AK ... -  《-》

RNA analysis of eight BRCA1 and BRCA2 unclassified variants identified in breast/ovarian cancer families from Spain.

Germ-line mutations in the breast cancer susceptibility genes BRCA1 and BRCA2 account for a large proportion of hereditary breast/ovarian cancer families. A large number of disease-causing germ-line mutations and variants of unknown pathological significance have been identified in both genes. The majority of these variants have been studied only in genomic DNA and their effects at the mRNA level have not been reported. Our aim was to ascertain the pathological effect of six BRCA1 and two BRCA2 sequence unclassified variants by RNA analysis. Three of the BRCA1 variants are novel: IVS18+5G>A, IVS20-6_IVS20-4del and IVS22-2A>G. Three BRCA1 mutations showed aberrant splicing: Ala1693del, IVS18+5G>A and IVS22-2A>G. The variants G1706A, S1715N and IVS20-6_IVS20-4del in BRCA1, and T2515I and IVS25+9A>C in BRCA2 led to normal transcripts. We compared these RNA results with those obtained from two theoretical splicing prediction methods. The consensus values for the splice sequences (Shapiro and Senapathy 1987) involved in three of the BRCA1 splicing site variants agreed with the RNA results, lending support to the validity of this model. Moreover, we used previously established exonic splicing enhancer (ESE) sequences to ascertain whether the four exonic variants studied fell within predicted ESE motifs and whether they would disrupt ESE functions. Our results suggest that the splicing predictions based on this method are not definitive and should be considered with caution. This work highlights the importance of studying mutations at DNA and RNA levels in order to clarify their pathological effect. This information is essential for providing efficient counseling for breast/ovarian cancer families.

Campos B ，Díez O ，Domènech M ，Baena M ，Balmaña J ，Sanz J ，Ramírez A ，Alonso C ，Baiget M ... -  《-》

Differentiating pathogenic mutations from polymorphic alterations in the splice sites of BRCA1 and BRCA2.

About 4% of all BRCA1 and BRCA2 alterations reported to the Breast Information Core database are splice site variants. Only a limited number of them have been studied at the RNA level. By BRCA1 and BRCA2 mutation analysis of breast/ovarian cancer families, we identified two novel and eight previously reported potential splice site mutations, never characterized at the cDNA level before. RT-PCR was performed to determine whether these variants disrupted correct splicing. To ensure efficient detection of transcripts containing premature termination codons, a nonsense-mediated mRNA decay inhibitor was added to the lymphoblastoid cell lines of the patients before RNA extraction. We found that BRCA1 IVS3+3A>C, 4304G>A (in the last codon of exon 12), and IVS19+2delT and BRCA2 IVS6+1G>A, IVS23-2A>G, and IVS24+1G>A lead to aberrant transcripts in lymphocytes. Therefore, they were considered to be true pathogenic mutations, predisposing carriers to cancers of the hereditary breast/ovarian cancer syndrome. BRCA2 IVS24-16T>C is a frequent polymorphism in linkage disequilibrium, with a polymorphic stop codon in exon 27, K3326X. BRCA1 IVS2-14C>T and BRCA2 IVS9-5insT and IVS25+9A>C represent rare variants, not disrupting normal splicing in blood lymphocytes. However, some of the alterations may act differently, qualitatively and/or quantitatively, in breast or ovarian tissues. The data provided in this paper allowed more accurate risk estimation of patients and relatives carrying the mutations described herein and have facilitated genetic counseling. Furthermore, our study is important for a better understanding of splicing mechanisms and revealed new patterns of alternative splicing in BRCA1 and BRCA2.

Claes K ，Poppe B ，Machackova E ，Coene I ，Foretova L ，De Paepe A ，Messiaen L ... -  《GENES CHROMOSOMES & CANCER》

Intronic variants in BRCA1 and BRCA2 that affect RNA splicing can be reliably selected by splice-site prediction programs.

A large number of sequence variants identified in BRCA1 and BRCA2 cannot be distinguished as either disease-causing mutations or neutral variants. These so-called unclassified variants (UVs) include variants that are located in the intronic sequences of BRCA1 and BRCA2. The purpose of this study was to assess the use of splice-site prediction programs (SSPPs) to select intronic variants in BRCA1 and BRCA2 that are likely to affect RNA splicing. We performed in vitro molecular characterization of RNA of six intronic variants in BRCA1 and BRCA2. In four cases (BRCA1, c.81-6T>A and c.4986+5G>T; BRCA2, c.7617+2T>G and c.8754+5G>A) a deleterious effect on RNA splicing was seen, whereas the c.135-15_-12del variant in BRCA1 showed no effect on RNA splicing. In the case of the BRCA2 c.68-7T>A variant, RNA analysis was not sufficient to establish the clinical significance. Six SSPPs were used to predict whether an effect on RNA splicing was expected for these six variants as well as for 23 intronic variants in BRCA1 for which the effect on RNA splicing has been published. Out of a total of 174 predictions, 161 (93%) were informative (i.e., the wild-type splice-site was recognized). No false-negative predictions were observed; an effect on RNA splicing was always predicted by these programs. In four cases (2.5%) a false-positive prediction was observed. For DNA diagnostic laboratories, these programs are therefore very useful to select intronic variants that are likely to affect RNA splicing for further analysis.

Vreeswijk MP ，Kraan JN ，van der Klift HM ，Vink GR ，Cornelisse CJ ，Wijnen JT ，Bakker E ，van Asperen CJ ，Devilee P ... -  《-》

RNA-based analysis of BRCA1 and BRCA2 gene alterations.

Bonatti F ，Pepe C ，Tancredi M ，Lombardi G ，Aretini P ，Sensi E ，Falaschi E ，Cipollini G ，Bevilacqua G ，Caligo MA ... -  《cancer genetics and cytogenetics》