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Fierheller CT, Alenezi WM, Serruya C, Revil T, Amuzu S, Bedard K, Subramanian DN, Fewings E, Bruce JP, Prokopec S, Bouchard L, Provencher D, Foulkes WD, El Haffaf Z, Mes-Masson AM, Tischkowitz M, Campbell IG, Pugh TJ, Greenwood CMT, Ragoussis J, Tonin PN. Molecular Genetic Characteristics of FANCI, a Proposed New Ovarian Cancer Predisposing Gene. Genes (Basel) 2023; 14:genes14020277. [PMID: 36833203 PMCID: PMC9956348 DOI: 10.3390/genes14020277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
FANCI was recently identified as a new candidate ovarian cancer (OC)-predisposing gene from the genetic analysis of carriers of FANCI c.1813C>T; p.L605F in OC families. Here, we aimed to investigate the molecular genetic characteristics of FANCI, as they have not been described in the context of cancer. We first investigated the germline genetic landscape of two sisters with OC from the discovery FANCI c.1813C>T; p.L605F family (F1528) to re-affirm the plausibility of this candidate. As we did not find other conclusive candidates, we then performed a candidate gene approach to identify other candidate variants in genes involved in the FANCI protein interactome in OC families negative for pathogenic variants in BRCA1, BRCA2, BRIP1, RAD51C, RAD51D, and FANCI, which identified four candidate variants. We then investigated FANCI in high-grade serous ovarian carcinoma (HGSC) from FANCI c.1813C>T carriers and found evidence of loss of the wild-type allele in tumour DNA from some of these cases. The somatic genetic landscape of OC tumours from FANCI c.1813C>T carriers was investigated for mutations in selected genes, copy number alterations, and mutational signatures, which determined that the profiles of tumours from carriers were characteristic of features exhibited by HGSC cases. As other OC-predisposing genes such as BRCA1 and BRCA2 are known to increase the risk of other cancers including breast cancer, we investigated the carrier frequency of germline FANCI c.1813C>T in various cancer types and found overall more carriers among cancer cases compared to cancer-free controls (p = 0.007). In these different tumour types, we also identified a spectrum of somatic variants in FANCI that were not restricted to any specific region within the gene. Collectively, these findings expand on the characteristics described for OC cases carrying FANCI c.1813C>T; p.L605F and suggest the possible involvement of FANCI in other cancer types at the germline and/or somatic level.
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Affiliation(s)
- Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Medical Laboratory Technology, Taibah University, Medina 42353, Saudi Arabia
| | - Corinne Serruya
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Setor Amuzu
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Karine Bedard
- Laboratoire de Diagnostic Moléculaire, Centre Hospitalier de l’Université de Montréal (CHUM), Montreal, QC H2X 3E4, Canada
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Deepak N. Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 1TN, UK
| | - Jeffrey P. Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Stephenie Prokopec
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Department of Medical Biology, Centres Intégrés Universitaires de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean Hôpital Universitaire de Chicoutimi, Saguenay, QC G7H 7K9, Canada
- Centre de Recherche du Centre Hospitalier l’Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Diane Provencher
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal and Institut du Cancer de Montréal, Montreal, QC H2X 0A9, Canada
- Division of Gynecologic Oncology, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - William D. Foulkes
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Department of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | - Zaki El Haffaf
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Anne-Marie Mes-Masson
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal and Institut du Cancer de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 1TN, UK
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Celia M. T. Greenwood
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, QC H3A 1Y7, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
- Correspondence:
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Alenezi WM, Fierheller CT, Serruya C, Revil T, Oros KK, Subramanian DN, Bruce J, Spiegelman D, Pugh T, Campbell IG, Mes-Masson AM, Provencher D, Foulkes WD, Haffaf ZE, Rouleau G, Bouchard L, Greenwood CMT, Ragoussis J, Tonin PN. Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases. Front Oncol 2023; 13:1111191. [PMID: 36969007 PMCID: PMC10030840 DOI: 10.3389/fonc.2023.1111191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023] Open
Abstract
Not all familial ovarian cancer (OC) cases are explained by pathogenic germline variants in known risk genes. A candidate gene approach involving DNA repair pathway genes was applied to identify rare recurring pathogenic variants in familial OC cases not associated with known OC risk genes from a population exhibiting genetic drift. Whole exome sequencing (WES) data of 15 OC cases from 13 families tested negative for pathogenic variants in known OC risk genes were investigated for candidate variants in 468 DNA repair pathway genes. Filtering and prioritization criteria were applied to WES data to select top candidates for further analyses. Candidates were genotyped in ancestry defined study groups of 214 familial and 998 sporadic OC or breast cancer (BC) cases and 1025 population-matched controls and screened for additional carriers in 605 population-matched OC cases. The candidate genes were also analyzed in WES data from 937 familial or sporadic OC cases of diverse ancestries. Top candidate variants in ERCC5, EXO1, FANCC, NEIL1 and NTHL1 were identified in 5/13 (39%) OC families. Collectively, candidate variants were identified in 7/435 (1.6%) sporadic OC cases and 1/566 (0.2%) sporadic BC cases versus 1/1025 (0.1%) controls. Additional carriers were identified in 6/605 (0.9%) OC cases. Tumour DNA from ERCC5, NEIL1 and NTHL1 variant carriers exhibited loss of the wild-type allele. Carriers of various candidate variants in these genes were identified in 31/937 (3.3%) OC cases of diverse ancestries versus 0-0.004% in cancer-free controls. The strategy of applying a candidate gene approach in a population exhibiting genetic drift identified new candidate OC predisposition variants in DNA repair pathway genes.
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Affiliation(s)
- Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Kathleen K. Oros
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
| | - Deepak N. Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jeffrey Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Dan Spiegelman
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Trevor Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Departement of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Division of Gynecologic Oncology, Université de Montréal, Montreal, QC, Canada
| | - William D. Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
- Department of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Service de Médecine Génique, Centre Hospitalier de l’Université de Montréal, Montreal, QC, Canada
| | - Guy Rouleau
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Medical Biology, Centres intégrés universitaires de santé et de services sociaux du Saguenay-Lac-Saint-Jean hôpital Universitaire de Chicoutimi, Saguenay, QC, Canada
- Centre de Recherche du Centre hospitalier l’Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Celia M. T. Greenwood
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- *Correspondence: Patricia N. Tonin,
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Alenezi WM, Fierheller CT, Revil T, Serruya C, Mes-Masson AM, Foulkes WD, Provencher D, El Haffaf Z, Ragoussis J, Tonin PN. Case Review: Whole-Exome Sequencing Analyses Identify Carriers of a Known Likely Pathogenic Intronic BRCA1 Variant in Ovarian Cancer Cases Clinically Negative for Pathogenic BRCA1 and BRCA2 Variants. Genes (Basel) 2022; 13:genes13040697. [PMID: 35456503 PMCID: PMC9032308 DOI: 10.3390/genes13040697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/01/2022] [Accepted: 04/14/2022] [Indexed: 12/04/2022] Open
Abstract
Background: Detecting pathogenic intronic variants resulting in aberrant splicing remains a challenge in routine genetic testing. We describe germline whole-exome sequencing (WES) analyses and apply in silico predictive tools of familial ovarian cancer (OC) cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants. Methods: WES data from 27 familial OC cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants and 53 sporadic early-onset OC cases were analyzed for pathogenic variants in BRCA1 or BRCA2. WES data from carriers of pathogenic BRCA1 or BRCA2 variants were analyzed for pathogenic variants in 10 other OC predisposing genes. Loss of heterozygosity analysis was performed on tumor DNA from variant carriers. Results: BRCA1 c.5407-25T>A intronic variant, identified in two affected sisters and one sporadic OC case, is predicted to create a new splice effecting transcription of BRCA1. WES data from BRCA1 c.5407-25T>A carriers showed no evidence of pathogenic variants in other OC predisposing genes. Sequencing the tumor DNA from the variant carrier showed complete loss of the wild-type allele. Conclusions: The findings support BRCA1 c.5407-25T>A as a likely pathogenic variant and highlight the importance of investigating intronic sequences as causal variants in OC families where the involvement of BRCA1 is highly suggestive.
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Affiliation(s)
- Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
- Department of Medical Laboratory Technology, Taibah University, Medina 42353, Saudi Arabia
| | - Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
| | - Anne-Marie Mes-Masson
- Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada;
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada; (D.P.); (Z.E.H.)
| | - William D. Foulkes
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Department of Medical Genetics, McGill University Health Centre, Montreal, QC H3H 1P3, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1G5, Canada
| | - Diane Provencher
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada; (D.P.); (Z.E.H.)
- Division of Gynecologic Oncology, Université de Montréal, Montreal, QC H4A 3J1, Canada
| | - Zaki El Haffaf
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada; (D.P.); (Z.E.H.)
- Service de Médecine Génique, Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-(514)-934-1934 (ext. 44069)
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4
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Fierheller CT, Guitton-Sert L, Alenezi WM, Revil T, Oros KK, Gao Y, Bedard K, Arcand SL, Serruya C, Behl S, Meunier L, Fleury H, Fewings E, Subramanian DN, Nadaf J, Bruce JP, Bell R, Provencher D, Foulkes WD, El Haffaf Z, Mes-Masson AM, Majewski J, Pugh TJ, Tischkowitz M, James PA, Campbell IG, Greenwood CMT, Ragoussis J, Masson JY, Tonin PN. A functionally impaired missense variant identified in French Canadian families implicates FANCI as a candidate ovarian cancer-predisposing gene. Genome Med 2021; 13:186. [PMID: 34861889 PMCID: PMC8642877 DOI: 10.1186/s13073-021-00998-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Background Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic variants in other DNA repair pathway genes. Methods Whole exome sequencing was used to identify rare variants in HR genes in a BRCA1 and BRCA2 pathogenic variant negative OC family of French Canadian (FC) ancestry, a population exhibiting genetic drift. OC cases and cancer-free individuals from FC and non-FC populations were investigated for carrier frequency of FANCI c.1813C>T; p.L605F, the top-ranking candidate. Gene and protein expression were investigated in cancer cell lines and tissue microarrays, respectively. Results In FC subjects, c.1813C>T was more common in familial (7.1%, 3/42) than sporadic (1.6%, 7/439) OC cases (P = 0.048). Carriers were detected in 2.5% (74/2950) of cancer-free females though female/male carriers were more likely to have a first-degree relative with OC (121/5249, 2.3%; Spearman correlation = 0.037; P = 0.011), suggesting a role in risk. Many of the cancer-free females had host factors known to reduce risk to OC which could influence cancer risk in this population. There was an increased carrier frequency of FANCI c.1813C>T in BRCA1 and BRCA2 pathogenic variant negative OC families, when including the discovery family, compared to cancer-free females (3/23, 13%; OR = 5.8; 95%CI = 1.7–19; P = 0.005). In non-FC subjects, 10 candidate FANCI variants were identified in 4.1% (21/516) of Australian OC cases negative for pathogenic variants in BRCA1 and BRCA2, including 10 carriers of FANCI c.1813C>T. Candidate variants were significantly more common in familial OC than in sporadic OC (P = 0.04). Localization of FANCD2, part of the FANCI-FANCD2 (ID2) binding complex in the Fanconi anaemia (FA) pathway, to sites of induced DNA damage was severely impeded in cells expressing the p.L605F isoform. This isoform was expressed at a reduced level, destabilized by DNA damaging agent treatment in both HeLa and OC cell lines, and exhibited sensitivity to cisplatin but not to a poly (ADP-ribose) polymerase inhibitor. By tissue microarray analyses, FANCI protein was consistently expressed in fallopian tube epithelial cells and only expressed at low-to-moderate levels in 88% (83/94) of OC samples. Conclusions This is the first study to describe candidate OC variants in FANCI, a member of the ID2 complex of the FA DNA repair pathway. Our data suggest that pathogenic FANCI variants may modify OC risk in cancer families. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00998-5.
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Affiliation(s)
- Caitlin T Fierheller
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Laure Guitton-Sert
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Wejdan M Alenezi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Kathleen K Oros
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yuandi Gao
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Karine Bedard
- Laboratoire de Diagnostic Moléculaire, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada.,Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Suzanna L Arcand
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Supriya Behl
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Hubert Fleury
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Deepak N Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rachel Bell
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Division of Gynecologic Oncology, Université de Montréal, Montreal, Quebec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Paul A James
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,The Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Celia M T Greenwood
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada. .,Department of Medicine, McGill University, Montreal, Quebec, Canada.
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5
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Fierheller C, Alenezi WM, Serruya C, Revil T, Nadaf J, Mes-Masson AM, Provencher D, Foulkes WD, Haffaf ZE, Greenwood CMT, Masson JY, Ragoussis J, Tonin PN. Abstract 2056: The genomic landscape of carriers of rare variants in FANCI, a new candidate ovarian cancer predisposing gene. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The potentially pathogenic variant (PPV), FANCI c.1813C>T; p.L605F, in a new candidate ovarian cancer (OC) predisposing gene was discovered by whole exome sequencing (WES) of familial OC cases from the founder French Canadian (FC) population for discovering new OC predisposing genes. Modeling this variant in cellulo suggested this variant encodes an unstable protein. FANCI is an essential member upstream of the homologous recombination DNA repair pathway and intersects BRCA1 and BRCA2 function, proteins encoded by genes involved in hereditary OC. Investigating the FC founder population facilitates the discovery of PPVs as they are more likely to harbor recurrent variants due to common ancestors, increasing the likelihood of identifying candidate genes in cancer families.
To further support the candidacy of FANCI as a new OC predisposing gene, we investigated the germline landscape of c.1813C>T carrier FC OC cases for co-occurring PPVs in known or proposed new (emerging) OC predisposing genes or other genes involved in similar pathways (DNA repair).
Using WES of peripheral blood lymphocyte DNA, the genomic landscape of 10 FANCI carriers were investigated for heterozygous PPVs in 276 DNA repair pathways genes, which included known (BRCA1, BRCA2, MSH2, MLH1, MSH6, PMS2) and emerging (BRIP1, RAD51C, RAD51D) OC predisposing genes. Top ranking candidate variants (minor allele frequency <1%) were identified using 11 different in silico tools that assessed amino acid conversation or potential pathogenicity. Pathogenicity of known and emerging OC predisposing genes was assessed using BRCAExchange (www.brcaexchange.org) and ClinVar (www.ncbi.nlm.nih.gov/clinvar/). A similar analysis was done with WES data from 13 FC OC cases harboring pathogenic BRCA1/BRCA2 variants.
We identified 31 variants in 27 genes in FANCI c.1813C>T carriers. A previously known carrier of a pathogenic BRCA1 variant (c.2836_2837del; p.Ile946GlnfsTer5) was also identified in a familial case. No carriers of other pathogenic variants in known or emerging OC predisposing genes were found. However, FANCI carriers were found to carry at least one other PPV in a DNA repair pathway gene (range 2-9; average=4.1). There were no other carriers of variants in common among all OC cases, though at least 2 cases carried a variant in the same gene. FC OC cases harboring BRCA1/BRCA2 variants carried at least one other PPV in a DNA repair pathway gene (range 2-7; average 4).
It is possible that the identified variants influence or modify risk in conjunction with FANCI, though no PPV was identified in all carriers. As new cancer predisposing genes are identified it will become increasingly important to characterize the genetic context in which variants are identified. This will allow for further insight to clinical translatability once penetrance has been established.
Citation Format: Caitlin Fierheller, Wejdan M Alenezi, Corinne Serruya, Timothée Revil, Javad Nadaf, Anne-Marie Mes-Masson, Diane Provencher, William D Foulkes, Zaki El Haffaf, Celia M T Greenwood, Jean-Yves Masson, Jiannis Ragoussis, Patricia N Tonin. The genomic landscape of carriers of rare variants in FANCI, a new candidate ovarian cancer predisposing gene [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2056.
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Affiliation(s)
| | | | - Corinne Serruya
- 2The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Javad Nadaf
- 1McGill University, Montreal, Quebec, Canada
| | | | | | | | - Zaki El Haffaf
- 5Centre de recherche du Centre hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
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6
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Felicio PS, Grasel RS, Campacci N, de Paula AE, Galvão HCR, Torrezan GT, Sabato CS, Fernandes GC, Souza CP, Michelli RD, Andrade CE, Barros BDDF, Matsushita MM, Revil T, Ragoussis J, Couch FJ, Hart SN, Reis RM, Melendez ME, Tonin PN, Carraro DM, Palmero EI. Whole-exome sequencing of non-BRCA1/BRCA2 mutation carrier cases at high-risk for hereditary breast/ovarian cancer. Hum Mutat 2020; 42:290-299. [PMID: 33326660 PMCID: PMC7898723 DOI: 10.1002/humu.24158] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/25/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022]
Abstract
The current study aimed to identify new breast and/or ovarian cancer predisposition genes. For that, whole-exome sequencing (WES) was performed in the germline DNA of 52 non-BRCA1/BRCA2/TP53 mutation carrier women at high-risk for hereditary breast and ovarian cancer (HBOC). All variants were classified using information from population and disease specific databases, in silico prediction tools and the American College of Medical Genetics and Genomics (ACMG) criteria. Loss of heterozygosity (LOH) of tumor samples and segregation analyses were performed whenever possible. The variants identified were investigated in a second, independent cohort of 17 BC cases. Pathogenic/Likely Pathogenic variants were identified in known cancer genes such as CHEK2, MUTYH, PMS2, and RAD51C. Rare and potentially pathogenic variants were identified in DNA repair genes (FAN1, POLQ, and RAD54L) and other cancer-related genes such as DROSHA and SLC34A2. Interestingly, the variant c.149T>G in the FAN1 gene was identified in two unrelated families, and exhibited LOH in the tumor tissue of one of them. In conclusion, this is the largest Brazilian WES study involving families at high-risk for HBOC which has brought novel insights into the role of potentially new genetic risk factors for hereditary breast and ovarian cancer.
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Affiliation(s)
- Paula S Felicio
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Rebeca S Grasel
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Natalia Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Andre E de Paula
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | - Giovana T Torrezan
- Genomics and Molecular Biology Group, CIPE - A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Cristina S Sabato
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Gabriela C Fernandes
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristiano P Souza
- Department of Oncogenetics, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Carlos E Andrade
- Department of Oncogenetics, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Marcus M Matsushita
- Department of Pathology, Barretos Cancer Hospital Barretos, Sao Paulo, Brazil
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, University of McGill, Montreal, Canada
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Steven N Hart
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Matias E Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Pele Little Prince Research Institute, Curitiba, Brazil.,Faculdades Pequeno Príncipe, Curitiba, Brazil
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, Canada.,Department of Medicine, McGill University, Montreal, Canada.,Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Dirce M Carraro
- Genomics and Molecular Biology Group, CIPE - A. C. Camargo Cancer Center, São Paulo, Brazil.,Genomic Diagnostic Center, AC Camargo Cancer Center, São Paulo, Brazil
| | - Edenir I Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Pele Little Prince Research Institute, Curitiba, Brazil.,Faculdades Pequeno Príncipe, Curitiba, Brazil
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7
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Rivera B, Nadaf J, Fahiminiya S, Apellaniz-Ruiz M, Saskin A, Chong AS, Sharma S, Wagener R, Revil T, Condello V, Harra Z, Hamel N, Sabbaghian N, Muchantef K, Thomas C, de Kock L, Hébert-Blouin MN, Bassenden AV, Rabenstein H, Mete O, Paschke R, Pusztaszeri MP, Paulus W, Berghuis A, Ragoussis J, Nikiforov YE, Siebert R, Albrecht S, Turcotte R, Hasselblatt M, Fabian MR, Foulkes WD. DGCR8 microprocessor defect characterizes familial multinodular goiter with schwannomatosis. J Clin Invest 2020; 130:1479-1490. [PMID: 31805011 DOI: 10.1172/jci130206] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/26/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUNDDICER1 is the only miRNA biogenesis component associated with an inherited tumor syndrome, featuring multinodular goiter (MNG) and rare pediatric-onset lesions. Other susceptibility genes for familial forms of MNG likely exist.METHODSWhole-exome sequencing of a kindred with early-onset MNG and schwannomatosis was followed by investigation of germline pathogenic variants that fully segregated with the disease. Genome-wide analyses were performed on 13 tissue samples from familial and nonfamilial DGCR8-E518K-positive tumors, including MNG, schwannomas, papillary thyroid cancers (PTCs), and Wilms tumors. miRNA profiles of 4 tissue types were compared, and sequencing of miRNA, pre-miRNA, and mRNA was performed in a subset of 9 schwannomas, 4 of which harbor DGCR8-E518K.RESULTSWe identified c.1552G>A;p.E518K in DGCR8, a microprocessor component located in 22q, in the kindred. The variant identified is a somatic hotspot in Wilms tumors and has been identified in 2 PTCs. Copy number loss of chromosome 22q, leading to loss of heterozygosity at the DGCR8 locus, was found in all 13 samples harboring c.1552G>A;p.E518K. miRNA profiling of PTCs, MNG, schwannomas, and Wilms tumors revealed a common profile among E518K hemizygous tumors. In vitro cleavage demonstrated improper processing of pre-miRNA by DGCR8-E518K. MicroRNA and RNA profiling show that this variant disrupts precursor microRNA production, impacting populations of canonical microRNAs and mirtrons.CONCLUSIONWe identified DGCR8 as the cause of an unreported autosomal dominant mendelian tumor susceptibility syndrome: familial multinodular goiter with schwannomatosis.FUNDINGCanadian Institutes of Health Research, Compute Canada, Alex's Lemonade Stand Foundation, the Mia Neri Foundation for Childhood Cancer, Cassa di Sovvenzioni e Risparmio fra il Personale della Banca d'Italia, and the KinderKrebsInitiative Buchholz/Holm-Seppensen.
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Affiliation(s)
- Barbara Rivera
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Javad Nadaf
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Somayyeh Fahiminiya
- Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada
| | - Maria Apellaniz-Ruiz
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Avi Saskin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Division of Medical Genetics, Department of Medicine, McGill University Health Centre and Jewish General Hospital, Montreal, Quebec, Canada
| | - Anne-Sophie Chong
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Sahil Sharma
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Rabea Wagener
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Génome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - Vincenzo Condello
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Zineb Harra
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nancy Hamel
- Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada
| | - Nelly Sabbaghian
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Karl Muchantef
- Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada.,Pediatric Radiology, Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Muenster, Muenster, Germany
| | - Leanne de Kock
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | | | - Hannah Rabenstein
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Ozgur Mete
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Ralf Paschke
- Department of Medicine.,Department of Oncology.,Department of Pathology.,Biochemistry and Molecular Biology Institute, and.,Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Marc P Pusztaszeri
- Department of Pathology, Jewish General Hospital, Montreal, Quebec, Canada
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Muenster, Muenster, Germany
| | - Albert Berghuis
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada.,Génome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Steffen Albrecht
- Department of Pathology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Robert Turcotte
- Division of Orthopedic Surgery (Experimental Surgery), McGill University, Montreal, Quebec, Canada.,Department of Surgical Oncology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Muenster, Muenster, Germany
| | - Marc R Fabian
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - William D Foulkes
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Division of Medical Genetics, Department of Medicine, McGill University Health Centre and Jewish General Hospital, Montreal, Quebec, Canada
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8
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Savage P, Blanchet-Cohen A, Revil T, Badescu D, Saleh SMI, Wang YC, Zuo D, Liu L, Bertos NR, Munoz-Ramos V, Basik M, Petrecca K, Asselah J, Meterissian S, Guiot MC, Omeroglu A, Kleinman CL, Park M, Ragoussis J. A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer. Cell Rep 2018; 21:1140-1149. [PMID: 29091754 DOI: 10.1016/j.celrep.2017.10.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/04/2017] [Accepted: 10/03/2017] [Indexed: 12/29/2022] Open
Abstract
Therapies targeting epidermal growth factor receptor (EGFR) have variable and unpredictable responses in breast cancer. Screening triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), we identify a subset responsive to EGFR inhibition by gefitinib, which displays heterogeneous expression of wild-type EGFR. Deep single-cell RNA sequencing of 3,500 cells from an exceptional responder identified subpopulations displaying distinct biological features, where elevated EGFR expression was significantly enriched in a mesenchymal/stem-like cellular cluster. Sorted EGFRhi subpopulations exhibited enhanced stem-like features, including ALDH activity, sphere-forming efficiency, and tumorigenic and metastatic potential. EGFRhi cells gave rise to EGFRhi and EGFRlo cells in primary and metastatic tumors, demonstrating an EGFR-dependent expansion and hierarchical state transition. Similar tumorigenic EGFRhi subpopulations were identified in independent PDXs, where heterogeneous EGFR expression correlated with gefitinib sensitivity. This provides new understanding for an EGFR-dependent hierarchy in TNBC and for patient stratification for therapeutic intervention.
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Affiliation(s)
- Paul Savage
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC H3G 0B1, Canada; Department of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Alexis Blanchet-Cohen
- Lady Davis Research Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada; McGill University and Genome Québec Innovation Centre, Montréal, QC H3A 1A4, Canada
| | - Dunarel Badescu
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada; McGill University and Genome Québec Innovation Centre, Montréal, QC H3A 1A4, Canada
| | - Sadiq M I Saleh
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC H3G 0B1, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Yu-Chang Wang
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada; McGill University and Genome Québec Innovation Centre, Montréal, QC H3A 1A4, Canada
| | - Dongmei Zuo
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC H3G 0B1, Canada
| | - Leah Liu
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC H3G 0B1, Canada
| | - Nicholas R Bertos
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC H3G 0B1, Canada
| | - Valentina Munoz-Ramos
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC H3G 0B1, Canada
| | - Mark Basik
- Lady Davis Research Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Oncology, McGill University, Montréal, QC H4A 3T2, Canada; Department of Surgery, McGill University, Montréal, QC H3G 1A4, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 2B4, Canada
| | - Jamil Asselah
- Department of Oncology, McGill University, Montréal, QC H4A 3T2, Canada
| | - Sarkis Meterissian
- Department of Oncology, McGill University, Montréal, QC H4A 3T2, Canada; Department of Surgery, McGill University, Montréal, QC H3G 1A4, Canada
| | | | - Atilla Omeroglu
- Department of Pathology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Claudia L Kleinman
- Lady Davis Research Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada; Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Morag Park
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC H3G 0B1, Canada; Department of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada; Department of Oncology, McGill University, Montréal, QC H4A 3T2, Canada; Department of Pathology, McGill University, Montréal, QC H3A 2B4, Canada.
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada; McGill University and Genome Québec Innovation Centre, Montréal, QC H3A 1A4, Canada; Center of Innovation in Personalized Medicine, Cancer and Mutagen Unit, King Fahd Center for Medical Research, Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia.
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9
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Sabbaghian N, Digilio MC, Blue GM, Revil T, Winlaw DS, Foulkes WD. Analysis of DICER1
in familial and sporadic cases of transposition of the great arteries. CONGENIT HEART DIS 2018; 13:401-406. [DOI: 10.1111/chd.12578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/22/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Nelly Sabbaghian
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital; Montréal Quebec Canada
| | - Maria C. Digilio
- Department of Medical Genetics; Bambino Gesù Pediatric Hospital; Rome Italy
| | - Gillian M. Blue
- Heart Centre for Children, The Children's Hospital at Westmead; Westmead New South Wales Australia
- University of Sydney; Sydney New South Wales Australia
| | - Timothée Revil
- McGill University and Genome Quebec Innovation Centre; Montréal Quebec Canada
| | - David S. Winlaw
- Heart Centre for Children, The Children's Hospital at Westmead; Westmead New South Wales Australia
- University of Sydney; Sydney New South Wales Australia
| | - William D. Foulkes
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital; Montréal Quebec Canada
- Cancer Research Program; Research Institute of the McGill University Health Centre, McGill University; Montréal Quebec Canada
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10
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Gilbert L, Revil T, Meunier C, Jardon K, Zeng X, Martins C, Arseneau J, Fu L, North K, Schiavi A, Ehrensperger E, Artho G, Lee T, Morris D, Ragoussis J. The empress of subterfuge: cancer of the fallopian tube presenting with malapropism. Lancet 2017; 390:1003-1004. [PMID: 28872014 DOI: 10.1016/s0140-6736(17)31586-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/18/2017] [Accepted: 05/09/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Lucy Gilbert
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, McGill University Health Centre, Montreal, QC, Canada.
| | - Timothée Revil
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Charles Meunier
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Kris Jardon
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, McGill University Health Centre, Montreal, QC, Canada
| | - Xing Zeng
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, McGill University Health Centre, Montreal, QC, Canada
| | - Claudia Martins
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, McGill University Health Centre, Montreal, QC, Canada
| | - Jocelyne Arseneau
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Lili Fu
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Krystle North
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, McGill University Health Centre, Montreal, QC, Canada
| | - Alicia Schiavi
- Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, McGill University Health Centre, Montreal, QC, Canada
| | - Eric Ehrensperger
- Division of Neurology, McGill University Health Centre, Montreal, QC, Canada
| | - Giovanni Artho
- Department of Radiology, McGill University Health Centre, Montreal, QC, Canada
| | - Todd Lee
- Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - David Morris
- Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
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11
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de Kock L, Rivera B, Revil T, Thorner P, Goudie C, Bouron-Dal Soglio D, Choong CS, Priest JR, van Diest PJ, Tanboon J, Wagner A, Ragoussis J, Choong PF, Foulkes WD. Sequencing of DICER1 in sarcomas identifies biallelic somatic DICER1 mutations in an adult-onset embryonal rhabdomyosarcoma. Br J Cancer 2017; 116:1621-1626. [PMID: 28524158 PMCID: PMC5518865 DOI: 10.1038/bjc.2017.147] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 12/18/2022] Open
Abstract
Background: Sarcomas are rare and heterogeneous cancers. We assessed the contribution of DICER1 mutations to sarcoma development. Methods: The coding region of DICER1 was sequenced in 67 sarcomas using a custom Fluidigm Access Array. The RNase III domains were Sanger sequenced in six additional sarcomas to identify hotspot DICER1 variants. Results: The median age of sarcoma diagnosis was 45.7 years (range: 3 months to 87.4 years). A recurrent embryonal rhabdomyosarcoma (ERMS) of the broad ligament, first diagnosed at age 23 years, harboured biallelic pathogenic somatic DICER1 variants (1 truncating and 1 RNase IIIb missense). We identified nine other DICER1 variants. One somatic variant (p.L1070V) identified in a pleomorphic sarcoma and one germline variant (c.2257-7A>G) may be pathogenic, but the others are considered to be benign. Conclusions: We show that deleterious DICER1 mutations underlie the genetic basis of only a small fraction of sarcomas, in particular ERMS of the urogenital tract.
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Affiliation(s)
- Leanne de Kock
- Department of Human Genetics, McGill University, 1205 Dr. Penfield Avenue, Stewart Biology Building, Room N5/13, Montréal, QC H3A 1B1, Canada.,Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, 3755 Cote Sainte Catherine Road, Montréal, QC H3T 1E2, Canada
| | - Barbara Rivera
- Department of Human Genetics, McGill University, 1205 Dr. Penfield Avenue, Stewart Biology Building, Room N5/13, Montréal, QC H3A 1B1, Canada.,Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, 3755 Cote Sainte Catherine Road, Montréal, QC H3T 1E2, Canada
| | - Timothée Revil
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montréal, QC H3A 0G4, Canada
| | - Paul Thorner
- Division of Pathology, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Catherine Goudie
- Department of Paediatrics, McGill University, 1001 Décarie Boulevard, Montréal, QC H4A 3J1, Canada
| | | | - Catherine S Choong
- Princess Margaret Hospital for Children, Roberts Road, Subiaco, WA 6008, Australia.,The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | | | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht 3584 CX, The Netherlands
| | - Jantima Tanboon
- Department of Pathology, Siriraj Hospital, Bangkok Noi, Bangkok 10700, Thailand.,Faculty of Medicine, Mahidol University, Bangkok Noi, Bangkok 10700, Thailand
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC University Medical Center, Wytemaweg 80, Rotterdam 3015 CN, The Netherlands
| | - Jiannis Ragoussis
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montréal, QC H3A 0G4, Canada
| | - Peter Fm Choong
- Department of Surgery, St. Vincent's Hospital Melbourne, University of Melbourne, 41 Victoria Parade, Melbourne, VIC 3065, Australia
| | - William D Foulkes
- Department of Human Genetics, McGill University, 1205 Dr. Penfield Avenue, Stewart Biology Building, Room N5/13, Montréal, QC H3A 1B1, Canada.,Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, 3755 Cote Sainte Catherine Road, Montréal, QC H3T 1E2, Canada.,Department of Medical Genetics, Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montréal, QC H4A 3J1, Canada
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12
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Savage P, Saleh SMI, Wang YC, Revil T, Badescu D, Liu L, Iacucci E, Zuo D, Bertos N, Munoz-Ramos V, Asselah J, Meterissian S, Omeroglu A, Hébert S, Kleinman C, Park M, Ragoussis J. Abstract P1-06-11: A targetable EGFR-driven tumor-initiating program in breast cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-06-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Inter- and intra-tumour heterogeneity underlies variability in therapeutic response. Although targeting of the epidermal growth factor receptor (EGFR) in breast cancer has failed to demonstrate clinical efficacy at the population level, complete and durable responses have been reported at low frequencies. The molecular determinants of these responses are unknown, but are of importance in the era of precision medicine.
Results: We performed a patient-derived xenograft (PDX) clinical trial with gefitinib in a breast cancer PDX cohort. Consistent with clinical trial data, gefitinib exhibited limited efficacy across most models. One PDX, however, demonstrated a complete and durable (>6 months) clinical response, and was subject to deep molecular profiling to identify determinants of response. Exome sequencing revealed no single nucleotide variants or copy number alterations in EGFR pathway members. EGFR was differentially expressed between the two major cellular subpopulations identified by single-cell RNAseq and this cellular heterogeneity in EGFR expression was validated immunohistochemically. Fluorescence-activated cell sorting of the EGFRhi subpopulation revealed cells with enhanced stem-like properties, including ALDH activity, sphere-forming capacity in vitro, ability to form tumours in vivo and seeding lung micrometastases from orthotopically transplanted tumours. Tumourspheres derived from EGFRhi cells developed into mixed EGFRhi and EGFRlo subpopulations, as did macrometastases, supporting that EGFRhi subpopulation can self-renew and re-populate. Analysis of expressed SNVs in the single-cell RNAseq data, filtered by variants identified from exome sequencing, showed no clonal segregation, supporting a non-clonal origin of the functionally distinct EGFRhi and EGFRlo subpopulations. This EGFR-driven tumour initiating cell program was observed in independent PDX models, some which showed growth inhibition in response to gefitinib.
Conclusions: Using bulk and single-cell genomic profiling, we identified and functionally validated an EGFR-driven tumour-initiating program in a subset of aggressive breast tumours, which may be predictive of gefitinib sensitivity. This contradicts traditional beliefs that good therapeutic targets are homogenously expressed, in that we show that a target displaying intra-tumour heterogeneity can be effective so long that it is expressed in the tumour-initiating population.
Citation Format: Savage P, Saleh SMI, Wang Y-C, Revil T, Badescu D, Liu L, Iacucci E, Zuo D, Bertos N, Munoz-Ramos V, Asselah J, Meterissian S, Omeroglu A, Hébert S, Kleinman C, Park M, Ragoussis J. A targetable EGFR-driven tumor-initiating program in breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-06-11.
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Affiliation(s)
- P Savage
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - SMI Saleh
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Y-C Wang
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - T Revil
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - D Badescu
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - L Liu
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - E Iacucci
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - D Zuo
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - N Bertos
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - V Munoz-Ramos
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - J Asselah
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - S Meterissian
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - A Omeroglu
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - S Hébert
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - C Kleinman
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - M Park
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - J Ragoussis
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada; Genome Québec Innovation Centre, McGill University, Montreal, QC, Canada; McGill University Health Centre, Montreal, QC, Canada; Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
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de Kock L, Bah I, Revil T, Bérubé P, Wu MK, Sabbaghian N, Priest JR, Ragoussis J, Foulkes WD. Deep Sequencing Reveals Spatially Distributed Distinct Hot Spot Mutations in DICER1-Related Multinodular Goiter. J Clin Endocrinol Metab 2016; 101:3637-3645. [PMID: 27459524 DOI: 10.1210/jc.2016-1328] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
CONTEXT Nontoxic multinodular goiter (MNG) occurs frequently, but its genetic etiology is not well established. Familial MNG and MNG occurring with ovarian Sertoli-Leydig cell tumor are associated with germline DICER1 mutations. We recently identified second somatic DICER1 ribonuclease (RNase) IIIb mutations in two MNGs. OBJECTIVE The objective of the study was to investigate the occurrence of somatic DICER1 mutations and mutational clonality in MNG. PATIENTS MNGs from 15 patients (10 with and five without germline DICER1 mutations) were selected based on tissue availability. DESIGN Core biopsies/scrapings (n = 70) were obtained, sampling areas of follicular hyperplasia, hyperplasia within colloid pools, unremarkable thyroid parenchyma, and areas of thyroid parenchyma, not classified. After capture with a Fluidigm access array, the coding sequence of DICER1 was deep sequenced using DNA from each core/scraping. RESULTS All germline DICER1-mutated cases were found to harbor at least one RNase III mutation. Specifically, we identified 12 individually distinct DICER1 RNase IIIb hot spot mutations in 32 of the follicular hyperplasia or hyperplasia within colloid pools cores/scrapings. These mutations are predicted to affect the metal-ion binding residues at positions p.Glu1705, p.Asp1709, p.Gly1809, p.Asp1810, and p.Glu1813. Somatic RNase IIIb mutations were identified in the 10 DICER1 germline mutated MNGs as follows: two cases contained one somatic mutation, five cases contained two mutations, and three cases contained three distinct somatic hot spot mutations. No RNase IIIb mutations were identified in the MNGs from individuals without germline DICER1 mutations. CONCLUSIONS This study demonstrates that nodules within MNG occurring in DICER1 syndrome are associated with spatially distributed somatic DICER1 RNase IIIb mutations.
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Affiliation(s)
- Leanne de Kock
- Departments of Human Genetics (L.d.K., M.K.W., W.D.F.), Pathology (I.B.), Oncology (W.D.F.), McGill University; Department of Medical Genetics, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (L.d.K., M.K.W., N.S., W.D.F.); Research Institute of the McGill University Health Centre (L.d.K., W.D.F.); McGill University and Genome Québec Innovation Centre (T.R., P.B., J.R.), Montréal, Québec, Canada; and (J.R.P.), Minneapolis, Minnesota, USA
| | - Ismaël Bah
- Departments of Human Genetics (L.d.K., M.K.W., W.D.F.), Pathology (I.B.), Oncology (W.D.F.), McGill University; Department of Medical Genetics, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (L.d.K., M.K.W., N.S., W.D.F.); Research Institute of the McGill University Health Centre (L.d.K., W.D.F.); McGill University and Genome Québec Innovation Centre (T.R., P.B., J.R.), Montréal, Québec, Canada; and (J.R.P.), Minneapolis, Minnesota, USA
| | - Timothée Revil
- Departments of Human Genetics (L.d.K., M.K.W., W.D.F.), Pathology (I.B.), Oncology (W.D.F.), McGill University; Department of Medical Genetics, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (L.d.K., M.K.W., N.S., W.D.F.); Research Institute of the McGill University Health Centre (L.d.K., W.D.F.); McGill University and Genome Québec Innovation Centre (T.R., P.B., J.R.), Montréal, Québec, Canada; and (J.R.P.), Minneapolis, Minnesota, USA
| | - Pierre Bérubé
- Departments of Human Genetics (L.d.K., M.K.W., W.D.F.), Pathology (I.B.), Oncology (W.D.F.), McGill University; Department of Medical Genetics, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (L.d.K., M.K.W., N.S., W.D.F.); Research Institute of the McGill University Health Centre (L.d.K., W.D.F.); McGill University and Genome Québec Innovation Centre (T.R., P.B., J.R.), Montréal, Québec, Canada; and (J.R.P.), Minneapolis, Minnesota, USA
| | - Mona K Wu
- Departments of Human Genetics (L.d.K., M.K.W., W.D.F.), Pathology (I.B.), Oncology (W.D.F.), McGill University; Department of Medical Genetics, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (L.d.K., M.K.W., N.S., W.D.F.); Research Institute of the McGill University Health Centre (L.d.K., W.D.F.); McGill University and Genome Québec Innovation Centre (T.R., P.B., J.R.), Montréal, Québec, Canada; and (J.R.P.), Minneapolis, Minnesota, USA
| | - Nelly Sabbaghian
- Departments of Human Genetics (L.d.K., M.K.W., W.D.F.), Pathology (I.B.), Oncology (W.D.F.), McGill University; Department of Medical Genetics, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (L.d.K., M.K.W., N.S., W.D.F.); Research Institute of the McGill University Health Centre (L.d.K., W.D.F.); McGill University and Genome Québec Innovation Centre (T.R., P.B., J.R.), Montréal, Québec, Canada; and (J.R.P.), Minneapolis, Minnesota, USA
| | - John R Priest
- Departments of Human Genetics (L.d.K., M.K.W., W.D.F.), Pathology (I.B.), Oncology (W.D.F.), McGill University; Department of Medical Genetics, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (L.d.K., M.K.W., N.S., W.D.F.); Research Institute of the McGill University Health Centre (L.d.K., W.D.F.); McGill University and Genome Québec Innovation Centre (T.R., P.B., J.R.), Montréal, Québec, Canada; and (J.R.P.), Minneapolis, Minnesota, USA
| | - Jiannis Ragoussis
- Departments of Human Genetics (L.d.K., M.K.W., W.D.F.), Pathology (I.B.), Oncology (W.D.F.), McGill University; Department of Medical Genetics, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (L.d.K., M.K.W., N.S., W.D.F.); Research Institute of the McGill University Health Centre (L.d.K., W.D.F.); McGill University and Genome Québec Innovation Centre (T.R., P.B., J.R.), Montréal, Québec, Canada; and (J.R.P.), Minneapolis, Minnesota, USA
| | - William D Foulkes
- Departments of Human Genetics (L.d.K., M.K.W., W.D.F.), Pathology (I.B.), Oncology (W.D.F.), McGill University; Department of Medical Genetics, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (L.d.K., M.K.W., N.S., W.D.F.); Research Institute of the McGill University Health Centre (L.d.K., W.D.F.); McGill University and Genome Québec Innovation Centre (T.R., P.B., J.R.), Montréal, Québec, Canada; and (J.R.P.), Minneapolis, Minnesota, USA
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de Kock L, Wang YC, Revil T, Badescu D, Rivera B, Sabbaghian N, Wu M, Weber E, Sandoval C, Hopman SMJ, Merks JHM, van Hagen JM, Bouts AHM, Plager DA, Ramasubramanian A, Forsmark L, Doyle KL, Toler T, Callahan J, Engelenberg C, Bouron-Dal Soglio D, Priest JR, Ragoussis J, Foulkes WD. High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome. J Med Genet 2015; 53:43-52. [DOI: 10.1136/jmedgenet-2015-103428] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/18/2015] [Indexed: 12/30/2022]
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15
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Revil T, Jerome-Majewska LA. During embryogenesis, esrp1 expression is restricted to a subset of epithelial cells and is associated with splicing of a number of developmentally important genes. Dev Dyn 2013; 242:281-90. [PMID: 23233200 DOI: 10.1002/dvdy.23918] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2012] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Development of a mature organism from a single cell requires a series of important morphological changes, which is in part regulated by alternative splicing. In this article, we report the expression of Esrp1 during early mouse embryogenesis, a splicing factor implicated in epithelial to mesenchymal transitions. RESULTS By qRT-PCR, we find higher expression of Esrp1 and Esrp2 in placenta compared to the embryos. We also find a correlation between the expression of Esrp1 and alternative splicing of several known target exons. Using in situ RNA hybridization we show that while Esrp1 expression is ubiquitous in embryonic day (E)6.5 mouse embryos, expression becomes restricted to the chorion and definitive endoderm starting at E7.5. Esrp1 expression was consistently restricted to a subset of epithelial cell types in developing embryos from E9.5 to E13.5. CONCLUSIONS Our results suggest that Esrp1 could play an important role in the morphological changes underlying embryogenesis of the placenta and embryo.
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Affiliation(s)
- Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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McDonald-McGinn DM, Fahiminiya S, Revil T, Nowakowska BA, Suhl J, Bailey A, Mlynarski E, Lynch DR, Yan AC, Bilaniuk LT, Sullivan KE, Warren ST, Emanuel BS, Vermeesch JR, Zackai EH, Jerome-Majewska LA. Hemizygous mutations in SNAP29 unmask autosomal recessive conditions and contribute to atypical findings in patients with 22q11.2DS. J Med Genet 2012; 50:80-90. [PMID: 23231787 PMCID: PMC3585484 DOI: 10.1136/jmedgenet-2012-101320] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder, affecting an estimated 1 : 2000–4000 live births. Patients with 22q11.2DS have a broad spectrum of phenotypic abnormalities which generally includes congenital cardiac abnormalities, palatal anomalies, and immunodeficiency. Additional findings, such as skeletal anomalies and autoimmune disorders, can confer significant morbidity in a subset of patients. 22q11.2DS is a contiguous gene DS and over 40 genes are deleted in patients; thus deletion of several genes within this region contributes to the clinical features. Mutations outside or on the remaining 22q11.2 allele are also known to modify the phenotype. Methods We utilised whole exome, targeted exome and/or Sanger sequencing to examine the genome of 17 patients with 22q11.2 deletions and phenotypic features found in <10% of affected individuals. Results and conclusions In four unrelated patients, we identified three novel mutations in SNAP29, the gene implicated in the autosomal recessive condition cerebral dysgenesis, neuropathy, ichthyosis and keratoderma (CEDNIK). SNAP29 maps to 22q11.2 and encodes a soluble SNARE protein that is predicted to mediate vesicle fusion at the endoplasmic reticulum or Golgi membranes. This work confirms that the phenotypic variability observed in a subset of patients with 22q11.2DS is due to mutations on the non-deleted chromosome, which leads to unmasking of autosomal recessive conditions such as CEDNIK, Kousseff, and a potentially autosomal recessive form of Opitz G/BBB syndrome. Furthermore, our work implicates SNAP29 as a major modifier of variable expressivity in 22q11.2 DS patients.
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Affiliation(s)
- Donna M McDonald-McGinn
- Division of Human Genetics, The Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Revil T, Gaffney D, Dias C, Majewski J, Jerome-Majewska LA. Alternative splicing is frequent during early embryonic development in mouse. BMC Genomics 2010; 11:399. [PMID: 20573213 PMCID: PMC2898759 DOI: 10.1186/1471-2164-11-399] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 06/23/2010] [Indexed: 12/20/2022] Open
Abstract
Background Alternative splicing is known to increase the complexity of mammalian transcriptomes since nearly all mammalian genes express multiple pre-mRNA isoforms. However, our knowledge of the extent and function of alternative splicing in early embryonic development is based mainly on a few isolated examples. High throughput technologies now allow us to study genome-wide alternative splicing during mouse development. Results A genome-wide analysis of alternative isoform expression in embryonic day 8.5, 9.5 and 11.5 mouse embryos and placenta was carried out using a splicing-sensitive exon microarray. We show that alternative splicing and isoform expression is frequent across developmental stages and tissues, and is comparable in frequency to the variation in whole-transcript expression. The genes that are alternatively spliced across our samples are disproportionately involved in important developmental processes. Finally, we find that a number of RNA binding proteins, including putative splicing factors, are differentially expressed and spliced across our samples suggesting that such proteins may be involved in regulating tissue and temporal variation in isoform expression. Using an example of a well characterized splicing factor, Fox2, we demonstrate that changes in Fox2 expression levels can be used to predict changes in inclusion levels of alternative exons that are flanked by Fox2 binding sites. Conclusions We propose that alternative splicing is an important developmental regulatory mechanism. We further propose that gene expression should routinely be monitored at both the whole transcript and the isoform level in developmental studies
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Affiliation(s)
- Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
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Revil T, Gaffney D, Dias C, Majewski J, Jerome-Majewska LA. Alternative splicing of genes expressed during early embryonic development. Dev Biol 2009. [DOI: 10.1016/j.ydbio.2009.05.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Revil T, Pelletier J, Toutant J, Cloutier A, Chabot B. Heterogeneous nuclear ribonucleoprotein K represses the production of pro-apoptotic Bcl-xS splice isoform. J Biol Chem 2009; 284:21458-67. [PMID: 19520842 DOI: 10.1074/jbc.m109.019711] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Bcl-x pre-mRNA is alternatively spliced to produce the anti-apoptotic Bcl-x(L) and the pro-apoptotic Bcl-x(S) isoforms. By performing deletion mutagenesis on a human Bcl-x minigene, we have identified a novel exonic element that controls the use of the 5' splice site of Bcl-x(S). The proximal portion of this element acts as a repressor and is located downstream of an enhancer. Further mutational analysis provided a detailed topological map of the regulatory activities revealing a sharp transition between enhancer and repressor sequences. Portions of the enhancer can function when transplanted in another alternative splicing unit. Chromatography and immunoprecipitation assays indicate that the silencer element interacts with heterogeneous ribonucleoprotein particle (hnRNP) K, consistent with the presence of putative high affinity sites for this protein. Finally, down-regulation of hnRNP K by RNA interference enhanced splicing to Bcl-x(S), an effect seen only when the sequences bound by hnRNP K are present. Our results therefore document a clear role for hnRNP K in preventing the production of the pro-apoptotic Bcl-x(S) splice isoform.
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Affiliation(s)
- Timothée Revil
- RNA/RNP Group, Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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Fisette JF, Michelle L, Revil T, Chabot B. [Guiding and integrating to control and diversify splicing]. Med Sci (Paris) 2009; 25:175-80. [PMID: 19239850 DOI: 10.1051/medsci/2009252175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recent studies directed at understanding alternative splicing control have produced an expanding list of regulators that can enhance or silence the use of splice sites by binding to specific sequences. A fine balance in the expression and the combinatorial use of these factors would help to adapt splicing decisions to a variety of situations. Additional levels of control are provided by tightly connecting the activity of alternative splicing factors with other cellular processes such as signal transduction and transcription. Combining classical experiments and high-throughput approaches is now confirming the important contribution of alternative splicing to proteomic diversity while helping to decipher the underlying networks of splicing regulation.
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Affiliation(s)
- Jean-François Fisette
- Chaire de recherche du Canada en génomique fonctionnelle, Groupe ARN, Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
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Cloutier P, Toutant J, Shkreta L, Goekjian S, Revil T, Chabot B. Antagonistic Effects of the SRp30c Protein and Cryptic 5 ′ Splice Sites on the Alternative Splicing of the Apoptotic Regulator Bcl-x. J Biol Chem 2008; 283:21315-24. [DOI: 10.1074/jbc.m800353200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Revil T, Toutant J, Shkreta L, Garneau D, Cloutier P, Chabot B. Protein kinase C-dependent control of Bcl-x alternative splicing. Mol Cell Biol 2007; 27:8431-41. [PMID: 17923691 PMCID: PMC2169420 DOI: 10.1128/mcb.00565-07] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 05/07/2007] [Accepted: 09/19/2007] [Indexed: 02/07/2023] Open
Abstract
The alternative splicing of Bcl-x generates the proapoptotic Bcl-x(S) protein and the antiapoptotic isoform Bcl-x(L). Bcl-x splicing is coupled to signal transduction, since ceramide, hormones, and growth factors alter the ratio of the Bcl-x isoforms in different cell lines. Here we report that the protein kinase C (PKC) inhibitor and apoptotic inducer staurosporine switches the production of Bcl-x towards the x(S) mRNA isoform in 293 cells. The increase in Bcl-x(S) elicited by staurosporine likely involves signaling events that affect splicing decisions, because it requires active transcription and no new protein synthesis and is independent of caspase activation. Moreover, the increase in Bcl-x(S) is reproduced with more specific inhibitors of PKC. Alternative splicing of the receptor tyrosine kinase gene Axl is similarly affected by staurosporine in 293 cells. In contrast to the case for 293 cells, PKC inhibitors do not influence the alternative splicing of Bcl-x and Axl in cancer cell lines, suggesting that these cells have sustained alterations that uncouple splicing decisions from PKC-dependent signaling. Using minigenes, we show that an exonic region located upstream of the Bcl-x(S) 5' splice site is important to mediate the staurosporine shift in Bcl-x splicing. When transplanted to other alternative splicing units, portions of this region confer splicing modulation and responsiveness to staurosporine, suggesting the existence of factors that couple splicing decisions with PKC signaling.
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Affiliation(s)
- Timothée Revil
- RNA/RNP Group, Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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Abstract
Proteins of the heterogeneous nuclear ribonucleoparticles (hnRNP) family form a structurally diverse group of RNA binding proteins implicated in various functions in metazoans. Here we discuss recent advances supporting a role for these proteins in precursor-messenger RNA (pre-mRNA) splicing. Heterogeneous nuclear RNP proteins can repress splicing by directly antagonizing the recognition of splice sites, or can interfere with the binding of proteins bound to enhancers. Recently, hnRNP proteins have been shown to hinder communication between factors bound to different splice sites. Conversely, several reports have described a positive role for some hnRNP proteins in pre-mRNA splicing. Moreover, cooperative interactions between bound hnRNP proteins may encourage splicing between specific pairs of splice sites while simultaneously hampering other combinations. Thus, hnRNP proteins utilize a variety of strategies to control splice site selection in a manner that is important for both alternative and constitutive pre-mRNA splicing.
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Revil T, Shkreta L, Chabot B. [Pre-mRNA alternative splicing in cancer: functional impact, molecular mechanisms and therapeutic perspectives]. Bull Cancer 2006; 93:909-19. [PMID: 16980234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Accepted: 06/21/2006] [Indexed: 05/11/2023]
Abstract
For most of the 25,000 human genes, the removal of introns by pre-messenger RNA splicing represents an essential step towards the production of functional messenger RNAs. Moreover, a majority of pre-messenger RNAs is alternatively spliced to yield different messenger RNAs. Cancer cells often display aberrant profiles of alternative splicing producing isoforms that can stimulate cell proliferation and migration or improve resistance to apoptosis. While mutations at splice sites or in splicing control elements have been identified, changes are also caused by alterations in the expression of proteins that affect splice site selection. Current challenges consist in documenting the functional diversity generated by alternative splicing and its contribution to different types of cancers. The development of innovative approaches aimed at reprogramming alternative splicing offers promising perspectives in cancer therapy.
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Affiliation(s)
- Timothée Revil
- Groupe ARN, Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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Garneau D, Revil T, Fisette JF, Chabot B. Heterogeneous nuclear ribonucleoprotein F/H proteins modulate the alternative splicing of the apoptotic mediator Bcl-x. J Biol Chem 2005; 280:22641-50. [PMID: 15837790 DOI: 10.1074/jbc.m501070200] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bcl-x is a member of the Bcl-2 family of proteins that are key regulators of apoptosis. The Bcl-x pre-mRNA is alternatively spliced to yield Bcl-x(S) and Bcl-x(L), two isoforms that have been associated, respectively, with the promotion and the prevention of apoptosis. We have investigated some of the elements and factors involved in the production of these two splice variants. Deletion mutagenesis using a human Bcl-x minigene identifies two regions in exon 2 that modulate Bcl-x 5'-splice site selection in human HeLa cells. One region (B3) is located upstream of the Bcl-x(L) 5'-splice site and enforces Bcl-x(L) production in cells and splicing extracts. The other region (B2) is located immediately downstream of the 5'-splice site of Bcl-x(S) and favors Bcl-x(S) production in vivo and in vitro. A 30-nucleotide G-rich element (B2G) is responsible for the activity of the B2 element. We show that recombinant heterogeneous nuclear ribonucleoprotein (hnRNP) F and H proteins bind to B2G, and mutating the G stretches abolishes binding. Moreover, the addition of hnRNP F to a HeLa extract improved the production of the Bcl-x(S) variant in a manner that was dependent on the integrity of the G stretches in B2G. Consistent with the in vitro results, small interfering RNA-mediated RNA interference targeting hnRNP F and H decreased the Bcl-x(S)/Bcl-x(L) ratio of plasmid-derived and endogenously produced Bcl-x transcripts. Our results document a positive role for the hnRNP F/H proteins in the production of the proapoptotic regulator Bcl-x(S.).
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Affiliation(s)
- Daniel Garneau
- RNA/RNP Group, Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec, Canada
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