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Soares de Lima Y, Arnau-Collell C, Muñoz J, Herrera-Pariente C, Moreira L, Ocaña T, Díaz-Gay M, Franch-Expósito S, Cuatrecasas M, Carballal S, Lopez-Novo A, Moreno L, Fernàndez G, Díaz de Bustamante A, Peters S, Sommer AK, Spier I, Te Paske IBAW, van Herwaarden YJ, Castells A, Bujanda L, Capellà G, Steinke-Lange V, Mahmood K, Joo JE, Arnold J, Parry S, Macrae FA, Winship IM, Rosty C, Cubiella J, Rodríguez-Alcalde D, Holinski-Feder E, de Voer R, Buchanan DD, Aretz S, Ruiz-Ponte C, Valle L, Balaguer F, Bonjoch L, Castellvi-Bel S. Germline mutations in WNK2 could be associated with serrated polyposis syndrome. J Med Genet 2023; 60:557-567. [PMID: 36270769 PMCID: PMC10313964 DOI: 10.1136/jmg-2022-108684] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Patients with serrated polyposis syndrome (SPS) have multiple and/or large serrated colonic polyps and higher risk for colorectal cancer. SPS inherited genetic basis is mostly unknown. We aimed to identify new germline predisposition factors for SPS by functionally evaluating a candidate gene and replicating it in additional SPS cohorts. METHODS After a previous whole-exome sequencing in 39 SPS patients from 16 families (discovery cohort), we sequenced specific genes in an independent validation cohort of 211 unrelated SPS cases. Additional external replication was also available in 297 SPS cases. The WNK2 gene was disrupted in HT-29 cells by gene editing, and WNK2 variants were transfected using a lentiviral delivery system. Cells were analysed by immunoblots, real-time PCR and functional assays monitoring the mitogen-activated protein kinase (MAPK) pathway, cell cycle progression, survival and adhesion. RESULTS We identified 2 rare germline variants in the WNK2 gene in the discovery cohort, 3 additional variants in the validation cohort and 10 other variants in the external cohorts. Variants c.2105C>T (p.Pro702Leu), c.4820C>T (p.Ala1607Val) and c.6157G>A (p.Val2053Ile) were functionally characterised, displaying higher levels of phospho-PAK1/2, phospho-ERK1/2, CCND1, clonogenic capacity and MMP2. CONCLUSION After whole-exome sequencing in SPS cases with familial aggregation and replication of results in additional cohorts, we identified rare germline variants in the WNK2 gene. Functional studies suggested germline WNK2 variants affect protein function in the context of the MAPK pathway, a molecular hallmark in this disease.
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Affiliation(s)
- Yasmin Soares de Lima
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Coral Arnau-Collell
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Jenifer Muñoz
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Cristina Herrera-Pariente
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Leticia Moreira
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Teresa Ocaña
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Marcos Díaz-Gay
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
- Department of Cellular and Molecular Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Sebastià Franch-Expósito
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miriam Cuatrecasas
- Department of Pathology, Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Tumor Bank-Biobank, Barcelona, Spain
| | - Sabela Carballal
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Anael Lopez-Novo
- Fundación Publica Galega de Medicina Xenómica (FPGMX), Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Lorena Moreno
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Guerau Fernàndez
- Department of Genetic and Molecular Medicine-IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, Center for Biomedical Research Network on Rare Diseases (CIBERER), Barcelona, Spain
| | | | - Sophia Peters
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Anna K Sommer
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Iris B A W Te Paske
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yasmijn J van Herwaarden
- Department of Gastroenterology and Hepatology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Antoni Castells
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Basque Country University (UPV/EHU), San Sebastian, Spain
| | - Gabriel Capellà
- Hereditary Cancer Program, Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
- MGZ - Center of Medical Genetics Center, Munich, Germany
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Parkville, Victoria, Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - JiHoon Eric Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Parkville, Victoria, Australia
| | - Julie Arnold
- New Zealand Familial Gastrointestinal Cancer Service, Auckland, New Zealand
| | - Susan Parry
- New Zealand Familial Gastrointestinal Cancer Service, Auckland, New Zealand
| | - Finlay A Macrae
- Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Parkville, Victoria, Australia
- Envoi Specialist Pathologists, Brisbane, Queensland, Australia
- University of Queensland, Brisbane, Queensland, Australia
| | - Joaquin Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | | | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
- MGZ - Center of Medical Genetics Center, Munich, Germany
| | - Richarda de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Clara Ruiz-Ponte
- Fundación Publica Galega de Medicina Xenómica (FPGMX), Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Laura Valle
- Hereditary Cancer Program, Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francesc Balaguer
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Laia Bonjoch
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Sergi Castellvi-Bel
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
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Bonjoch L, Soares de Lima Y, Díaz-Gay M, Dotti I, Muñoz J, Moreira L, Carballal S, Ocaña T, Cuatrecasas M, Ortiz O, Castells A, Pellisé M, Balaguer F, Salas A, Alexandrov LB, Castellví-Bel S. Unraveling the impact of a germline heterozygous POLD1 frameshift variant in serrated polyposis syndrome. Front Mol Biosci 2023; 10:1119900. [PMID: 36756361 PMCID: PMC9900627 DOI: 10.3389/fmolb.2023.1119900] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Serrated polyposis syndrome (SPS) is one of the most frequent polyposis syndromes characterized by an increased risk for developing colorectal cancer (CRC). Although SPS etiology has been mainly associated with environmental factors, germline predisposition to SPS could also be relevant for cases with familial aggregation or a family history of SPS/CRC. After whole-exome sequencing of 39 SPS patients from 16 families, we identified a heterozygous germline frameshift variant in the POLD1 gene (c.1941delG, p.(Lys648fs*46)) in a patient with SPS and CRC. Tumor presented an ultra-hypermutated phenotype and microsatellite instability. The POLD1 germline variant segregated in three additional SPS-affected family members. We attempted to create yeast and cellular models for this variant but were no viable. Alternatively, we generated patient-derived organoids (PDOs) from healthy rectal tissue of the index case, as well as from a control donor. Then, we challenged PDOs with a DNA-damaging agent to induce replication stress. No significant differences were observed in the DNA damage response between control and POLD1-Lys648fs PDOs, nor specific mutational signatures were observed. Our results do not support the pathogenicity of the analyzed POLD1 frameshift variant. One possible explanation is that haplosufficiency of the wild-type allele may be compensating for the absence of expression of the frameshift allele. Overall, future work is required to elucidate if functional consequences could be derived from POLD1 alterations different from missense variants in their proofreading domain. To our knowledge, our study presents the first organoid model for germline POLD1 variants and establishes the basis for its use as a model for disease in SPS, CRC and other malignancies.
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Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, UC San Diego, La Jolla, CA, United States
| | - Isabella Dotti
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Sabela Carballal
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | - Oswaldo Ortiz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Maria Pellisé
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, UC San Diego, La Jolla, CA, United States
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
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Soares de Lima Y, Arnau-Collell C, Díaz-Gay M, Bonjoch L, Franch-Expósito S, Muñoz J, Moreira L, Ocaña T, Cuatrecasas M, Herrera-Pariente C, Carballal S, Moreno L, Díaz de Bustamante A, Castells A, Bujanda L, Cubiella J, Rodríguez-Alcalde D, Balaguer F, Castellví-Bel S. Germline and Somatic Whole-Exome Sequencing Identifies New Candidate Genes Involved in Familial Predisposition to Serrated Polyposis Syndrome. Cancers (Basel) 2021; 13:929. [PMID: 33672345 PMCID: PMC7927050 DOI: 10.3390/cancers13040929] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
The serrated polyposis syndrome (SPS) is the most common and yet underdiagnosed colorectal polyposis syndrome. It is characterized by multiple and/or large colonic serrated polyps and a higher associated risk for colorectal cancer (CRC). The main objective of this study was to identify new candidate genes involved in the germline predisposition to SPS/CRC. Thirty-nine SPS patients from 16 families (≥2 patients per family) were recruited without alterations in well-known hereditary CRC genes, and germline and somatic whole-exome sequencing were performed. Germline rare variants with plausible pathogenicity, located in genes involved in cancer development, senescence and epigenetic regulation were selected. Somatic mutational profiling and signature analysis was pursued in one sample per family, when possible. After data filtering, ANXA10, ASXL1, CFTR, DOT1L, HIC1, INO80, KLF3, MCM3AP, MCM8, PDLIM2, POLD1, TP53BP1, WNK2 and WRN were highlighted as the more promising candidate genes for SPS germline predisposition with potentially pathogenic variants shared within families. Somatic analysis characterized mutational profiles in advanced serrated polyps/tumors, revealing a high proportion of hypermutated samples, with a prevalence of clock-like mutational signatures in most samples and the presence of DNA mismatch repair-defective signatures in some cases. In conclusion, we identified new candidate genes to be involved in familial SPS. Further functional studies and replication in additional cohorts are required to confirm the selected candidates.
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Affiliation(s)
- Yasmin Soares de Lima
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Coral Arnau-Collell
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Marcos Díaz-Gay
- Moores Cancer Center, Department of Cellular and Molecular Medicine, Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA;
| | - Laia Bonjoch
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Sebastià Franch-Expósito
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Jenifer Muñoz
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Leticia Moreira
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Teresa Ocaña
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Miriam Cuatrecasas
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Pathology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Tumor Bank-Biobank, Hospital Clínic, 08036 Barcelona, Spain;
| | - Cristina Herrera-Pariente
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Sabela Carballal
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Lorena Moreno
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | | | - Antoni Castells
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Basque Country University (UPV/EHU), 20014 San Sebastián, Spain;
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 32005 Ourense, Spain;
| | | | - Francesc Balaguer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Sergi Castellví-Bel
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
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4
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Herrera-Pariente C, Capó-García R, Díaz-Gay M, Carballal S, Muñoz J, Llach J, Sánchez A, Bonjoch L, Arnau-Collell C, Soares de Lima Y, Golubicki M, Jung G, Lozano JJ, Castells A, Balaguer F, Bujanda L, Castellví-Bel S, Moreira L. Identification of New Genes Involved in Germline Predisposition to Early-Onset Gastric Cancer. Int J Mol Sci 2021; 22:1310. [PMID: 33525650 PMCID: PMC7866206 DOI: 10.3390/ijms22031310] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/24/2022] Open
Abstract
The genetic cause for several families with gastric cancer (GC) aggregation is unclear, with marked relevance in early-onset patients. We aimed to identify new candidate genes involved in GC germline predisposition. Whole-exome sequencing (WES) of germline samples was performed in 20 early-onset GC patients without previous germline mutation identified. WES was also performed in nine tumor samples to analyze the somatic profile using SigProfilerExtractor tool. Sequencing germline data were filtered to select those variants with plausible pathogenicity, rare frequency and previously involved in cancer. Then, a manual filtering was performed to prioritize genes according to current knowledge and function. These genetic variants were prevalidated with Integrative Genomics Viewer 2.8.2 (IGV). Subsequently, a further selection step was carried out according to function and information obtained from tumor samples. After IGV and selection step, 58 genetic variants in 52 different candidate genes were validated by Sanger sequencing. Among them, APC, FAT4, CTNND1 and TLR2 seem to be the most promising genes because of their role in hereditary cancer syndromes, tumor suppression, cell adhesion and Helicobacter pylori recognition, respectively. These encouraging results represent the open door to the identification of new genes involved in GC germline predisposition.
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Affiliation(s)
- Cristina Herrera-Pariente
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Roser Capó-García
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Marcos Díaz-Gay
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sabela Carballal
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Jenifer Muñoz
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Joan Llach
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Ariadna Sánchez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Laia Bonjoch
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Coral Arnau-Collell
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Yasmin Soares de Lima
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Mariano Golubicki
- Oncology Section, Hospital of Gastroenterology “Dr. C. B. Udaondo”, C1264 Buenos Aires, Argentina;
- Molecular Biology Laboratory, Hospital of Gastroenterology “Dr. C. B. Udaondo”, C1264 Buenos Aires, Argentina
| | - Gerhard Jung
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Juan José Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Spain;
| | - Antoni Castells
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Francesc Balaguer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Luis Bujanda
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Biodonostia Health Research Institute, Basque Country University (UPV/EHU), 20014 San Sebastián, Spain;
| | - Sergi Castellví-Bel
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
| | - Leticia Moreira
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (C.H.-P.); (R.C.-G.); (M.D.-G.); (S.C.); (J.M.); (J.L.); (A.S.); (L.B.); (C.A.-C.); (Y.S.d.L.); (G.J.); (A.C.); (F.B.)
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5
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Bonjoch L, Franch-Expósito S, Garre P, Belhadj S, Muñoz J, Arnau-Collell C, Díaz-Gay M, Gratacós-Mulleras A, Raimondi G, Esteban-Jurado C, Soares de Lima Y, Herrera-Pariente C, Cuatrecasas M, Ocaña T, Castells A, Fillat C, Capellá G, Balaguer F, Caldés T, Valle L, Castellví-Bel S. Germline Mutations in FAF1 Are Associated With Hereditary Colorectal Cancer. Gastroenterology 2020; 159:227-240.e7. [PMID: 32179092 DOI: 10.1053/j.gastro.2020.03.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/19/2020] [Accepted: 03/08/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS A significant proportion of colorectal cancer (CRC) cases have familial aggregation but little is known about the genetic factors that contribute to these cases. We performed an exhaustive functional characterization of genetic variants associated with familial CRC. METHODS We performed whole-exome sequencing analyses of 75 patients from 40 families with a history of CRC (including early-onset cases) of an unknown germline basis (discovery cohort). We also sequenced specific genes in DNA from an external replication cohort of 473 families, including 488 patients with colorectal tumors that had normal expression of mismatch repair proteins (validation cohort). We disrupted the Fas-associated factor 1 gene (FAF1) in DLD-1 CRC cells using CRISPR/Cas9 gene editing; some cells were transfected with plasmids that express FAF1 missense variants. Cells were analyzed by immunoblots, quantitative real-time polymerase chain reaction, and functional assays monitoring apoptosis, proliferation, and assays for Wnt signaling or nuclear factor (NF)-kappa-B activity. RESULTS We identified predicted pathogenic variant in the FAF1 gene (c.1111G>A; p.Asp371Asn) in the discovery cohort; it was present in 4 patients of the same family. We identified a second variant in FAF1 in the validation cohort (c.254G>C; p.Arg85Pro). Both variants encoded unstable FAF1 proteins. Expression of these variants in CRC cells caused them to become resistant to apoptosis, accumulate beta-catenin in the cytoplasm, and translocate NF-kappa-B to the nucleus. CONCLUSIONS In whole-exome sequencing analyses of patients from families with a history of CRC, we identified variants in FAF1 that associate with development of CRC. These variants encode unstable forms of FAF1 that increase resistance of CRC cells to apoptosis and increase activity of beta-catenin and NF-kappa-B.
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Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Pilar Garre
- Molecular Oncology Laboratory, Centro Investigación Biomédica en Red de Cáncer (CIBERONC). Hospital Clínico San Carlos. Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Sami Belhadj
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Marcos Díaz-Gay
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Anna Gratacós-Mulleras
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Giulia Raimondi
- Gene Therapy and Cancer, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat de Barcelona, Barcelona, Spain
| | - Clara Esteban-Jurado
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Herrera-Pariente
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Fillat
- Gene Therapy and Cancer, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat de Barcelona, Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Centro Investigación Biomédica en Red de Cáncer (CIBERONC). Hospital Clínico San Carlos. Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.
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6
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Arnau-Collell C, Soares de Lima Y, Díaz-Gay M, Muñoz J, Carballal S, Bonjoch L, Moreira L, Lozano JJ, Ocaña T, Cuatrecasas M, Díaz de Bustamante A, Castells A, Capellà G, Bujanda L, Cubiella J, Rodríguez-Alcalde D, Balaguer F, Ruiz-Ponte C, Valle L, Moreno V, Castellvi-Bel S. Colorectal cancer genetic variants are also associated with serrated polyposis syndrome susceptibility. J Med Genet 2020; 57:677-682. [PMID: 32170005 PMCID: PMC7525772 DOI: 10.1136/jmedgenet-2019-106374] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 06/13/2019] [Revised: 01/10/2020] [Accepted: 01/22/2020] [Indexed: 12/14/2022]
Abstract
Background Serrated polyposis syndrome (SPS) is a clinical entity characterised by large and/ormultiple serrated polyps throughout the colon and increased risk for colorectal cancer (CRC). The basis for SPS genetic predisposition is largely unknown. Common, low-penetrance genetic variants have been consistently associated with CRC susceptibility, however, their role in SPS genetic predisposition has not been yet explored. Objective The aim of this study was to evaluate if common, low-penetrance genetic variants for CRC risk are also implicated in SPS genetic susceptibility. Methods A case-control study was performed in 219 SPS patients and 548 asymptomatic controls analysing 65 CRC susceptibility variants. A risk prediction model for SPS predisposition was developed. Results Statistically significant associations with SPS were found for seven genetic variants (rs4779584-GREM1, rs16892766-EIF3H, rs3217810-CCND2, rs992157-PNKD1/TMBIM1, rs704017-ZMIZ1, rs11196172-TCF7L2, rs6061231-LAMA5). The GREM1 risk allele was remarkably over-represented in SPS cases compared with controls (OR=1.573, 1.21–2.04, p value=0.0006). A fourfold increase in SPS risk was observed when comparing subjects within the highest decile of variants (≥65) with those in the first decile (≤50). Conclusions Genetic variants for CRC risk are also involved in SPS susceptibility, being the most relevant ones rs4779584-GREM1, rs16892766-EIF3H and rs3217810-CCND2.
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Affiliation(s)
- Coral Arnau-Collell
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Marcos Díaz-Gay
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Sabela Carballal
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Laia Bonjoch
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Juan José Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | | | - Antoni Castells
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Gabriel Capellà
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Basque Country University (UPV/EHU), San Sebastian, Spain
| | - Joaquin Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Ourense, Spain
| | | | - Francesc Balaguer
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica_USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO); Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL); Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP); Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Sergi Castellvi-Bel
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Barcelona, Spain
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7
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Toma C, Díaz-Gay M, Franch-Expósito S, Arnau-Collell C, Overs B, Muñoz J, Bonjoch L, Soares de Lima Y, Ocaña T, Cuatrecasas M, Castells A, Bujanda L, Balaguer F, Cubiella J, Caldés T, Fullerton JM, Castellví-Bel S. Using linkage studies combined with whole-exome sequencing to identify novel candidate genes for familial colorectal cancer. Int J Cancer 2019; 146:1568-1577. [PMID: 31525256 PMCID: PMC7004061 DOI: 10.1002/ijc.32683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 04/18/2019] [Accepted: 08/23/2019] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) is a complex disorder for which the majority of the underlying germline predisposition factors remain still unidentified. Here, we combined whole‐exome sequencing (WES) and linkage analysis in families with multiple relatives affected by CRC to identify candidate genes harboring rare variants with potential high‐penetrance effects. Forty‐seven affected subjects from 18 extended CRC families underwent WES. Genome‐wide linkage analysis was performed under linear and exponential models. Suggestive linkage peaks were identified on chromosomes 1q22–q24.2 (maxSNP = rs2134095; LODlinear = 2.38, LODexp = 2.196), 7q31.2–q34 (maxSNP = rs6953296; LODlinear = 2.197, LODexp = 2.149) and 10q21.2–q23.1 (maxSNP = rs1904589; LODlinear = 1.445, LODexp = 2.195). These linkage signals were replicated in 10 independent sets of random markers from each of these regions. To assess the contribution of rare variants predicted to be pathogenic, we performed a family‐based segregation test with 89 rare variants predicted to be deleterious from 78 genes under the linkage intervals. This analysis showed significant segregation of rare variants with CRC in 18 genes (weighted p‐value > 0.0028). Protein network analysis and functional evaluation were used to suggest a plausible candidate gene for germline CRC predisposition. Etiologic rare variants implicated in cancer germline predisposition may be identified by combining traditional linkage with WES data. This approach can be used with already available NGS data from families with several sequenced members to further identify candidate genes involved germline predisposition to disease. This approach resulted in one candidate gene associated with increased risk of CRC but needs evidence from further studies. What's new? Inherited genetic factors are thought to account for more than one‐third of colorectal cancer (CRC) cases. Most predisposing genetic factors, however, remain unidentified. Here, genome‐wide linkage analysis using whole‐exome sequencing (WES) data was performed in families with marked CRC aggregation. The combined linkage‐sequencing approach identified possible linkage peaks on chromosomes 1q22‐q24.2, 7q31.2‐q34, and 10q21.2‐q23.1. Analyses of potentially pathogenic variants revealed significant segregation of rare variants in 18 genes, while functional analyses identified a plausible candidate gene for germline CRC predisposition. The findings underscore the utility of linkage analysis employing WES for the discovery of candidate genes for disease predisposition.
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Affiliation(s)
- Claudio Toma
- Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Marcos Díaz-Gay
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Bronwyn Overs
- Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Laia Bonjoch
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Basque Country University (UPV/EHU), San Sebastian, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, CIBERONC (Centro de Investigacion Biomedica en Red de Cancer), IdISSC, Madrid, Spain
| | - Janice M Fullerton
- Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
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8
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Toma C, Díaz-Gay M, Soares de Lima Y, Arnau-Collell C, Franch-Expósito S, Muñoz J, Overs B, Bonjoch L, Carballal S, Ocaña T, Cuatrecasas M, Díaz de Bustamante A, Castells A, Bujanda L, Cubiella J, Balaguer F, Rodríguez-Alcalde D, Fullerton JM, Castellví-Bel S. Identification of a Novel Candidate Gene for Serrated Polyposis Syndrome Germline Predisposition by Performing Linkage Analysis Combined With Whole-Exome Sequencing. Clin Transl Gastroenterol 2019; 10:e00100. [PMID: 31663907 PMCID: PMC6919450 DOI: 10.14309/ctg.0000000000000100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/19/2019] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Serrated polyposis syndrome (SPS) is a complex disorder with a high risk of colorectal cancer for which the germline factors remain largely unknown. Here, we combined whole-exome sequencing (WES) and linkage studies in families with multiple members affected by SPS to identify candidate genes harboring rare variants with higher penetrance effects. METHODS Thirty-nine affected subjects from 16 extended SPS families underwent WES. Genome-wide linkage analysis was performed under linear and exponential models. The contribution of rare coding variants selected to be highly pathogenic was assessed using the gene-based segregation test. RESULTS A significant linkage peak was identified on chromosome 3p25.2-p22.3 (maxSNP = rs2293787; LODlinear = 2.311, LODexp = 2.11), which logarithm of the odds (LOD) score increased after fine mapping for the same marker (maxSNP = rs2293787; LODlinear = 2.4, LODexp = 2.25). This linkage signal was replicated in 10 independent sets of random markers from this locus. To assess the contribution of rare variants predicted to be pathogenic, we performed a family-based segregation test with 11 rare variants predicted to be deleterious from 10 genes under the linkage intervals. This analysis showed significant segregation of rare variants with SPS in CAPT7, TMEM43, NGLY1, and FBLN2 genes (weighted P value > 0.007). DISCUSSION Protein network analysis suggested FBLN2 as the most plausible candidate genes for germline SPS predisposition. Etiologic rare variants implicated in disease predisposition may be identified by combining traditional linkage with WES data. This powerful approach was effective for the identification of a new candidate gene for hereditary SPS.
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Affiliation(s)
- Claudio Toma
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Marcos Díaz-Gay
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Bronwyn Overs
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Laia Bonjoch
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sabela Carballal
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | | | - Antoni Castells
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Basque Country University (UPV/EHU), San Sebastián, Spain
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | | | - Janice M. Fullerton
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
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9
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Soares de Lima Y, Chiabai M, Shen J, Córdoba MS, Versiani BR, Benício ROA, Pogue R, Mingroni-Netto RC, Lezirovitz K, Pic-Taylor A, Mazzeu JF, Oliveira SF. Syndromic hearing loss molecular diagnosis: Application of massive parallel sequencing. Hear Res 2018; 370:181-188. [PMID: 30390570 DOI: 10.1016/j.heares.2018.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/19/2018] [Accepted: 10/14/2018] [Indexed: 12/17/2022]
Abstract
Syndromic hearing loss accounts for approximately 30% of all cases of hearing loss due to genetic causes. Mutation screening in known genes is important because it potentially sheds light on the genetic etiology of hearing loss and helps in genetic counseling of families. In this study, we describe a customized Ion AmpliSeq Panel, specifically designed for the investigation of syndromic hearing loss. The Ion AmpliSeq Panel was customized to cover the coding sequences of 52 genes. Twenty-four patients were recruited: 17 patients with a clinical diagnosis of a known syndrome, and seven whose clinical signs did not allow identification of a syndrome. Of 24 patients sequenced, potentially causative mutations were found in nine, all of which belonged to the group with a previous clinical diagnostic and none in the group not clinically diagnosed. We were able to provide conclusive molecular diagnosis to six patients, constituting a diagnostic rate of 25% (6/24). In the group of patients with a suspected clinical diagnosis, the diagnostic rate was 35% (6/17). Of the nine different mutations identified, three are novel, and were found in patients with Waardenburg, Treacher Collins and CHARGE syndromes. Since all patients with a conclusive molecular diagnosis through this panel had a previous suspected clinical diagnosis, our results suggest that this panel was more effective in diagnosing this group of patients. Therefore, the panel demonstrated effectiveness in molecular diagnosis when compared to others in the literature, especially for patients with a defined clinical diagnosis.
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Affiliation(s)
- Yasmin Soares de Lima
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasília, Brazil; Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil.
| | - Marcela Chiabai
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Brazil.
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Mara S Córdoba
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil.
| | - Beatriz R Versiani
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil.
| | | | - Robert Pogue
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Brazil.
| | - Regina Célia Mingroni-Netto
- Centro de Estudos do Genoma Humano, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Karina Lezirovitz
- Laboratório de Otorrinolaringologia - LIM32, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil.
| | - Aline Pic-Taylor
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasília, Brazil; Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil.
| | - Juliana F Mazzeu
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil; Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.
| | - Silviene F Oliveira
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasília, Brazil; Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil.
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