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Altered regulation of BRCA1 exon 11 splicing is associated with breast cancer risk in carriers of BRCA1 pathogenic variants

Altered regulation of BRCA1 exon 11 splicing is associated with breast cancer risk in carriers of BRCA1 pathogenic variants
Altered regulation of BRCA1 exon 11 splicing is associated with breast cancer risk in carriers of BRCA1 pathogenic variants
Germline pathogenic variants in BRCA1 confer a high risk of developing breast and ovarian cancer. The BRCA1 exon 11 (formally exon 10) is one of the largest exons and codes for the nuclear localization signals of the corresponding gene product. This exon can be partially or entirely skipped during pre-mRNA splicing, leading to three major in-frame isoforms that are detectable in most cell types and tissue, and in normal and cancer settings. However, it is unclear whether the splicing imbalance of this exon is associated with cancer risk. Here we identify a common genetic variant in intron 10, rs5820483 (NC_000017.11:g.43095106_43095108dup), which is associated with exon 11 isoform expression and alternative splicing, and with the risk of breast cancer, but not ovarian cancer, in BRCA1 pathogenic variant carriers. The identification of this genetic effect was confirmed by analogous observations in mouse cells and tissue in which a loxP sequence was inserted in the syntenic intronic region. The prediction that the rs5820483 minor allele variant would create a binding site for the splicing silencer hnRNP A1 was confirmed by pull-down assays. Our data suggest that perturbation of BRCA1 exon 11 splicing modifies the breast cancer risk conferred by pathogenic variants of this gene.
BRCA1, breast cancer, isoform, risk, splicing, variant
1059-7794
1488-1502
Ruiz De Garibay, Gorka
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Fernandez‐garcia, Ignacio
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Mazoyer, Sylvie
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Leme De Calais, Flavia
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Ameri, Pietro
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Martinez‐ruiz, Sangeeta Haydeliz
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Damiola, Francesca
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Barjhoux, Laure
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Thomassen, Mads
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Andersen, Lars V. B.
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Herranz, Carmen
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Mateo, Francesca
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Palomero, Luis
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Espin, Roderic
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Gómez, Antonio
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García, Nadia
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Jimenez, Daniel
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Bonifaci, Núria
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Extremera, Ana I.
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Castaño, Julio
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Raya, Angel
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Eyras, Eduardo
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Puente, Xose S.
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Brunet, Joan
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Lázaro, Conxi
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Gemo,
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Cimba,
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Radice, Paolo
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Barnes, Daniel R.
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Antoniou, Antonis C.
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Spurdle, Amanda B.
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Hoya, Miguel
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Baralle, Diana
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Barcellos‐hoff, Mary Helen
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Pujana, Miquel A.
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Ruiz De Garibay, Gorka
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Fernandez‐garcia, Ignacio
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Mazoyer, Sylvie
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Leme De Calais, Flavia
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Ameri, Pietro
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Martinez‐ruiz, Sangeeta Haydeliz
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Damiola, Francesca
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Barjhoux, Laure
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Thomassen, Mads
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Andersen, Lars V. B.
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Herranz, Carmen
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Mateo, Francesca
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Palomero, Luis
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Espin, Roderic
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Gómez, Antonio
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García, Nadia
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Jimenez, Daniel
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Bonifaci, Núria
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Extremera, Ana I.
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Castaño, Julio
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Raya, Angel
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Eyras, Eduardo
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Puente, Xose S.
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Brunet, Joan
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Lázaro, Conxi
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Gemo,
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Cimba,
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Radice, Paolo
d5bff2d9-ed03-4a8e-a9ca-f896a1666e2c
Barnes, Daniel R.
eea80956-9c62-413a-b5fa-4d6df6d25f5d
Antoniou, Antonis C.
65739e70-823d-4acd-b99a-12c7b5521f34
Spurdle, Amanda B.
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Hoya, Miguel
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Baralle, Diana
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Barcellos‐hoff, Mary Helen
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Pujana, Miquel A.
b0b24c36-a004-449c-a1c6-ee75d82b08bf

Ruiz De Garibay, Gorka, Fernandez‐garcia, Ignacio, Mazoyer, Sylvie, Leme De Calais, Flavia, Ameri, Pietro, Martinez‐ruiz, Sangeeta Haydeliz, Damiola, Francesca, Barjhoux, Laure, Thomassen, Mads, Andersen, Lars V. B., Herranz, Carmen, Mateo, Francesca, Palomero, Luis, Espin, Roderic, Gómez, Antonio, García, Nadia, Jimenez, Daniel, Bonifaci, Núria, Extremera, Ana I., Castaño, Julio, Raya, Angel, Eyras, Eduardo, Puente, Xose S., Brunet, Joan, Lázaro, Conxi, Gemo, , Cimba, , Radice, Paolo, Barnes, Daniel R., Antoniou, Antonis C., Spurdle, Amanda B., Hoya, Miguel, Baralle, Diana, Barcellos‐hoff, Mary Helen and Pujana, Miquel A. (2021) Altered regulation of BRCA1 exon 11 splicing is associated with breast cancer risk in carriers of BRCA1 pathogenic variants. Human Mutation, 42 (11), 1488-1502. (doi:10.1002/humu.24276).

Record type: Article

Abstract

Germline pathogenic variants in BRCA1 confer a high risk of developing breast and ovarian cancer. The BRCA1 exon 11 (formally exon 10) is one of the largest exons and codes for the nuclear localization signals of the corresponding gene product. This exon can be partially or entirely skipped during pre-mRNA splicing, leading to three major in-frame isoforms that are detectable in most cell types and tissue, and in normal and cancer settings. However, it is unclear whether the splicing imbalance of this exon is associated with cancer risk. Here we identify a common genetic variant in intron 10, rs5820483 (NC_000017.11:g.43095106_43095108dup), which is associated with exon 11 isoform expression and alternative splicing, and with the risk of breast cancer, but not ovarian cancer, in BRCA1 pathogenic variant carriers. The identification of this genetic effect was confirmed by analogous observations in mouse cells and tissue in which a loxP sequence was inserted in the syntenic intronic region. The prediction that the rs5820483 minor allele variant would create a binding site for the splicing silencer hnRNP A1 was confirmed by pull-down assays. Our data suggest that perturbation of BRCA1 exon 11 splicing modifies the breast cancer risk conferred by pathogenic variants of this gene.

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RuizdeGaribay_MainText_072321 - Accepted Manuscript
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Accepted/In Press date: 19 August 2021
e-pub ahead of print date: 22 August 2021
Published date: 1 November 2021
Additional Information: Funding Information: The study of the wild‐type allele was first proposed and led by Dr. Olga Sinilnikova in CIMBA. We dedicate this study to her memory. The paper is also dedicated to Dr. David L. Kleinberg, who contributed to the study of the BRCA1 mouse model. The authors acknowledge Dr. Weifeng Ruan for his contributions to early studies related to this project, the Experimental Pathology Core Laboratory at NYU School of Medicine for tissue sectioning and staining, the VA Medical Center Animal Facility, and Ms. Clara Montesino for help with the animal experiments. The results are partly based upon data generated by the TCGA Research Network ( https://www.cancer.gov/tcga ), and we express our gratitude to the TCGA consortium and coordinators for producing the data and clinical information used in our study. The ICO‐IDIBELL research was supported by the Generalitat de Catalunya (SGR 2017‐449, 2017‐899 and 2017‐1282; PERIS MedPerCan and PFI‐Salut SLT017‐20‐000076; URDCat; and CERCA programme for IDIBELL institutional support), Carlos III Institute of Health (ISCIII), funded by FEDER funds—a way to build Europe—(Ministry of Science, Innovation, and Universities; grants PI16/00563, PI18/01029, PI19/00553, and PI21/01306; CIBERONC and CIBER‐BBN) and Ministry of Economy and Competitiveness‐MINECO (grants RTI2018‐095377‐B‐100 and RD16/0011/0024). G.R.G. was supported by an IDIBELL post‐residency fellowship. The work at NYU was supported by DOD Breast Cancer Research Program funding to D.L.K. (W81XWH‐11‐1‐0779) and M.H.B.‐H. (W81XWH‐11‐1‐780), and a Novartis Investigator‐Initiated Grant to D.L.K. (CSOM230BUS03). The Baralle laboratory is supported by D.B.'s NIHR Research Professorship (RP‐2016‐07‐011). A.B.S. is supported by an NHMRC Investigator Fellowship (APP: 1177524) and P.R. is supported by funds from the Italian Association for Cancer Research (AIRC; IG number 22093). BRCA1 Funding Information: The study of the BRCA1 wild-type allele was first proposed and led by Dr. Olga Sinilnikova in CIMBA. We dedicate this study to her memory. The paper is also dedicated to Dr. David L. Kleinberg, who contributed to the study of the BRCA1 mouse model. The authors acknowledge Dr. Weifeng Ruan for his contributions to early studies related to this project, the Experimental Pathology Core Laboratory at NYU School of Medicine for tissue sectioning and staining, the VA Medical Center Animal Facility, and Ms. Clara Montesino for help with the animal experiments. The results are partly based upon data generated by the TCGA Research Network (https://www.cancer.gov/tcga), and we express our gratitude to the TCGA consortium and coordinators for producing the data and clinical information used in our study. The ICO-IDIBELL research was supported by the Generalitat de Catalunya (SGR 2017-449, 2017-899 and 2017-1282; PERIS MedPerCan and PFI-Salut SLT017-20-000076; URDCat; and CERCA programme for IDIBELL institutional support), Carlos III Institute of Health (ISCIII), funded by FEDER funds?a way to build Europe?(Ministry of Science, Innovation, and Universities; grants PI16/00563, PI18/01029, PI19/00553, and PI21/01306; CIBERONC and CIBER-BBN) and Ministry of Economy and Competitiveness-MINECO (grants RTI2018-095377-B-100 and RD16/0011/0024). G.R.G. was supported by an IDIBELL post-residency fellowship. The work at NYU was supported by DOD Breast Cancer Research Program funding to D.L.K. (W81XWH-11-1-0779) and M.H.B.-H. (W81XWH-11-1-780), and a Novartis Investigator-Initiated Grant to D.L.K. (CSOM230BUS03). The Baralle laboratory is supported by D.B.'s NIHR Research Professorship (RP-2016-07-011). A.B.S. is supported by an NHMRC Investigator Fellowship (APP: 1177524) and P.R. is supported by funds from the Italian Association for Cancer Research (AIRC; IG number 22093). Funding Information: M.A.P. was the recipient of an unrestricted research grant from Roche Pharma for the development of the ProCURE ICO research program. X.S.P. is a cofounder of and has an ownership interest (including stock and patents) in DREAMgenics. Publisher Copyright: © 2021 Wiley Periodicals LLC
Keywords: BRCA1, breast cancer, isoform, risk, splicing, variant

Identifiers

Local EPrints ID: 451037
URI: http://eprints.soton.ac.uk/id/eprint/451037
ISSN: 1059-7794
PURE UUID: bb3cd985-ba17-4074-a8a7-6b52e0130307
ORCID for Diana Baralle: ORCID iD orcid.org/0000-0003-3217-4833

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Date deposited: 03 Sep 2021 16:33
Last modified: 17 Mar 2024 06:47

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Contributors

Author: Gorka Ruiz De Garibay
Author: Ignacio Fernandez‐garcia
Author: Sylvie Mazoyer
Author: Flavia Leme De Calais
Author: Pietro Ameri
Author: Sangeeta Haydeliz Martinez‐ruiz
Author: Francesca Damiola
Author: Laure Barjhoux
Author: Mads Thomassen
Author: Lars V. B. Andersen
Author: Carmen Herranz
Author: Francesca Mateo
Author: Luis Palomero
Author: Roderic Espin
Author: Antonio Gómez
Author: Nadia García
Author: Daniel Jimenez
Author: Núria Bonifaci
Author: Ana I. Extremera
Author: Julio Castaño
Author: Angel Raya
Author: Eduardo Eyras
Author: Xose S. Puente
Author: Joan Brunet
Author: Conxi Lázaro
Author: Gemo
Author: Cimba
Author: Paolo Radice
Author: Daniel R. Barnes
Author: Antonis C. Antoniou
Author: Amanda B. Spurdle
Author: Miguel Hoya
Author: Diana Baralle ORCID iD
Author: Mary Helen Barcellos‐hoff
Author: Miquel A. Pujana

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