1
|
Hoorntje ET, Burns C, Marsili L, Corden B, Parikh VN, Te Meerman GJ, Gray B, Adiyaman A, Bagnall RD, Barge-Schaapveld DQCM, van den Berg MP, Bootsma M, Bosman LP, Correnti G, Duflou J, Eppinga RN, Fatkin D, Fietz M, Haan E, Jongbloed JDH, Hauer AD, Lam L, van Lint FHM, Lota A, Marcelis C, McCarthy HJ, van Mil AM, Oldenburg RA, Pachter N, Planken RN, Reuter C, Semsarian C, van der Smagt JJ, Thompson T, Vohra J, Volders PGA, van Waning JI, Whiffin N, van den Wijngaard A, Amin AS, Wilde AAM, van Woerden G, Yeates L, Zentner D, Ashley EA, Wheeler MT, Ware JS, van Tintelen JP, Ingles J. Variant Location Is a Novel Risk Factor for Individuals With Arrhythmogenic Cardiomyopathy Due to a Desmoplakin ( DSP) Truncating Variant. Circ Genom Precis Med 2023; 16:e003672. [PMID: 36580316 PMCID: PMC9946166 DOI: 10.1161/circgen.121.003672] [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] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Truncating variants in desmoplakin (DSPtv) are an important cause of arrhythmogenic cardiomyopathy; however the genetic architecture and genotype-specific risk factors are incompletely understood. We evaluated phenotype, risk factors for ventricular arrhythmias, and underlying genetics of DSPtv cardiomyopathy. METHODS Individuals with DSPtv and any cardiac phenotype, and their gene-positive family members were included from multiple international centers. Clinical data and family history information were collected. Event-free survival from ventricular arrhythmia was assessed. Variant location was compared between cases and controls, and literature review of reported DSPtv performed. RESULTS There were 98 probands and 72 family members (mean age at diagnosis 43±8 years, 59% women) with a DSPtv, of which 146 were considered clinically affected. Ventricular arrhythmia (sudden cardiac arrest, sustained ventricular tachycardia, appropriate implantable cardioverter defibrillator therapy) occurred in 56 (33%) individuals. DSPtv location and proband status were independent risk factors for ventricular arrhythmia. Further, gene region was important with variants in cases (cohort n=98; Clinvar n=167) more likely to occur in the regions resulting in nonsense mediated decay of both major DSP isoforms, compared with n=124 genome aggregation database control variants (148 [83.6%] versus 29 [16.4%]; P<0.0001). CONCLUSIONS In the largest series of individuals with DSPtv, we demonstrate that variant location is a novel risk factor for ventricular arrhythmia, can inform variant interpretation, and provide critical insights to allow for precision-based clinical management.
Collapse
Affiliation(s)
- Edgar T Hoorntje
- Department of Genetics, University Medical Centre Groningen, University of Groningen (E.T.H., G.J.t.M., J.D.H.J.).,Netherlands Heart Institute, Utrecht, the Netherlands (E.T.H., L.P.B., L.L., J.P.v.T.)
| | - Charlotte Burns
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (C.B., B.G., R.D.B., C.S.).,Faculty of Medicine and Health (C.B., B.G., R.D.B., J.D., C.S., L.Y., J.I.).,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia (C.B., B.G., C.S., L.Y., J.I.)
| | - Luisa Marsili
- Department of Clinical Genetics, Amsterdam University Medical Centre, location AMC, University of Amsterdam, the Netherlands (L.M., J.P.v.T.).,Clinique de Génétique, CHU Lille, Lille, France (L.M.)
| | - Ben Corden
- National Heart and Lung Institute and MRC London Institute of Medical Science, Imperial College London and Cardiovascular Research Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK (B.C., A.L., N.W., J.S.W.)
| | - Victoria N Parikh
- Stanford Centre for Inherited Cardiovascular Disease, Department of Medicine, Stanford University School of Medicine, CA (V.N.P., C.R., E.A.A., M.T.W.)
| | - Gerard J Te Meerman
- Department of Genetics, University Medical Centre Groningen, University of Groningen (E.T.H., G.J.t.M., J.D.H.J.)
| | - Belinda Gray
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (C.B., B.G., R.D.B., C.S.).,Faculty of Medicine and Health (C.B., B.G., R.D.B., J.D., C.S., L.Y., J.I.).,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia (C.B., B.G., C.S., L.Y., J.I.)
| | - Ahmet Adiyaman
- Department of Cardiology, Isala Heart Center, Zwolle (A.A.)
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (C.B., B.G., R.D.B., C.S.).,Faculty of Medicine and Health (C.B., B.G., R.D.B., J.D., C.S., L.Y., J.I.)
| | | | - Maarten P van den Berg
- Department of Cardiology, University of Groningen, University Medical Centre Groningen (M.P.v.d.B., G.v.W.)
| | - Marianne Bootsma
- Department of Cardiology, University of Leiden, Leiden University Medical Centre (M.B.)
| | - Laurens P Bosman
- Netherlands Heart Institute, Utrecht, the Netherlands (E.T.H., L.P.B., L.L., J.P.v.T.).,Department of Cardiology, University of Utrecht (L.P.B.)
| | - Gemma Correnti
- Adult Genetics Unit, Royal Adelaide Hospital and Faculty of Health and Medical Sciences, University of Adelaide (G.C.)
| | - Johan Duflou
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (C.B., B.G., R.D.B., C.S.)
| | | | - Diane Fatkin
- Victor Chang Cardiac Research Institute, Sydney (D.F.)
| | - Michael Fietz
- Department of Diagnostic Genomics, PathWest Laboratory, Medicine WA, Redlands, Australia (M.F.)
| | | | - Jan D H Jongbloed
- Department of Genetics, University Medical Centre Groningen, University of Groningen (E.T.H., G.J.t.M., J.D.H.J.)
| | - Arnaud D Hauer
- Department of Cardiology, Haga Teaching Hospital, the Hague (A.D.H.)
| | - Lien Lam
- Netherlands Heart Institute, Utrecht, the Netherlands (E.T.H., L.P.B., L.L., J.P.v.T.)
| | - Freyja H M van Lint
- Department of Genetics, University of Utrecht, University Medical Centre Utrecht, the Netherlands (F.H.M.v.L., J.P.v.T.)
| | - Amrit Lota
- National Heart and Lung Institute and MRC London Institute of Medical Science, Imperial College London and Cardiovascular Research Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK (B.C., A.L., N.W., J.S.W.)
| | - Carlo Marcelis
- Department of Clinical Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands (C.M.)
| | - Hugh J McCarthy
- Department of Clinical Genetics, Children's Hospital Westmead, Sydney, Australia (H.J.M.)
| | - Anneke M van Mil
- Department of Clinical Genetics, Leiden University Medical Centre (D.Q.C.M.B.-S., A.M.v.M.)
| | - Rogier A Oldenburg
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, the Netherlands (R.A.O.)
| | | | - R Nils Planken
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centre, Amsterdam, the Netherlands (R.N.P.)
| | - Chloe Reuter
- Stanford Centre for Inherited Cardiovascular Disease, Department of Medicine, Stanford University School of Medicine, CA (V.N.P., C.R., E.A.A., M.T.W.)
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (C.B., B.G., R.D.B., C.S.).,Faculty of Medicine and Health (C.B., B.G., R.D.B., J.D., C.S., L.Y., J.I.).,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia (C.B., B.G., C.S., L.Y., J.I.)
| | | | - Tina Thompson
- Department of Cardiology and Department of Genomic Medicine, Royal Melbourne Hospital (T.T., J.V., D.Z.)
| | - Jitendra Vohra
- Department of Cardiology and Department of Genomic Medicine, Royal Melbourne Hospital (T.T., J.V., D.Z.).,Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Australia (J.V., D.Z.)
| | - Paul G A Volders
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM) (P.G.A.V.)
| | | | - Nicola Whiffin
- National Heart and Lung Institute and MRC London Institute of Medical Science, Imperial College London and Cardiovascular Research Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK (B.C., A.L., N.W., J.S.W.)
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Laboratory Clinical Genetics, Maastricht University Medical Centre (A.v.d.W.)
| | - Ahmad S Amin
- Department of Clinical and Experimental Cardiology, Heart Centre, Amsterdam University Medical Centre, location AMC, the Netherlands (A.S.A., A.A.M.W.)
| | - Arthur A M Wilde
- Department of Clinical and Experimental Cardiology, Heart Centre, Amsterdam University Medical Centre, location AMC, the Netherlands (A.S.A., A.A.M.W.)
| | - Gijs van Woerden
- Department of Cardiology, University of Groningen, University Medical Centre Groningen (M.P.v.d.B., G.v.W.)
| | - Laura Yeates
- Faculty of Medicine and Health (C.B., B.G., R.D.B., J.D., C.S., L.Y., J.I.).,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia (C.B., B.G., C.S., L.Y., J.I.).,Cardio Genomics Program at Centenary Institute, The University of Sydney (L.Y., J.I.)
| | - Dominica Zentner
- Department of Cardiology and Department of Genomic Medicine, Royal Melbourne Hospital (T.T., J.V., D.Z.).,Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Australia (J.V., D.Z.)
| | - Euan A Ashley
- Stanford Centre for Inherited Cardiovascular Disease, Department of Medicine, Stanford University School of Medicine, CA (V.N.P., C.R., E.A.A., M.T.W.)
| | - Matthew T Wheeler
- Stanford Centre for Inherited Cardiovascular Disease, Department of Medicine, Stanford University School of Medicine, CA (V.N.P., C.R., E.A.A., M.T.W.)
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Science, Imperial College London and Cardiovascular Research Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK (B.C., A.L., N.W., J.S.W.)
| | - J Peter van Tintelen
- Netherlands Heart Institute, Utrecht, the Netherlands (E.T.H., L.P.B., L.L., J.P.v.T.).,Department of Clinical Genetics, Amsterdam University Medical Centre, location AMC, University of Amsterdam, the Netherlands (L.M., J.P.v.T.).,Department of Genetics, University of Utrecht, University Medical Centre Utrecht, the Netherlands (F.H.M.v.L., J.P.v.T.)
| | - Jodie Ingles
- Faculty of Medicine and Health (C.B., B.G., R.D.B., J.D., C.S., L.Y., J.I.).,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia (C.B., B.G., C.S., L.Y., J.I.).,Cardio Genomics Program at Centenary Institute, The University of Sydney (L.Y., J.I.).,Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney (J.I.).,Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia (J.I.)
| |
Collapse
|
2
|
Leotti VB, de Vries JJ, Oliveira CM, de Mattos EP, Te Meerman GJ, Brunt ER, Kampinga HH, Jardim LB, Verbeek DS. CAG Repeat Size Influences the Progression Rate of Spinocerebellar Ataxia Type 3. Ann Neurol 2020; 89:66-73. [PMID: 32978817 DOI: 10.1002/ana.25919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVE In spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD), the expanded cytosine adenine guanine (CAG) repeat in ATXN3 is the causal mutation, and its length is the main factor in determining the age at onset (AO) of clinical symptoms. However, the contribution of the expanded CAG repeat length to the rate of disease progression after onset has remained a matter of debate, even though an understanding of this factor is crucial for experimental data on disease modifiers and their translation to clinical trials and their design. METHODS Eighty-two Dutch patients with SCA3/MJD were evaluated annually for 15 years using the International Cooperative Ataxia Rating Scale (ICARS). Using linear growth curve models, ICARS progression rates were calculated and tested for their relation to the length of the CAG repeat expansion and to the residual age at onset (RAO): The difference between the observed AO and the AO predicted on the basis of the CAG repeat length. RESULTS On average, ICARS scores increased 2.57 points/year of disease. The length of the CAG repeat was positively correlated with a more rapid ICARS progression, explaining 30% of the differences between patients. Combining both the length of the CAG repeat and RAO as comodifiers explained up to 47% of the interpatient variation in ICARS progression. INTERPRETATION Our data imply that the length of the expanded CAG repeat in ATXN3 is a major determinant of clinical decline, which suggests that CAG-dependent molecular mechanisms similar to those responsible for disease onset also contribute to the rate of disease progression in SCA3/MJD. ANN NEUROL 2021;89:66-73.
Collapse
Affiliation(s)
- Vanessa B Leotti
- Departamento de Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Epidemiologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jeroen J de Vries
- Expertise Center Movement Disorders Groningen, Department of Neurology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Camila M Oliveira
- Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Eduardo P de Mattos
- Department of Biomedical Science of Cell & Systems, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerard J Te Meerman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ewout R Brunt
- Expertise Center Movement Disorders Groningen, Department of Neurology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Harm H Kampinga
- Department of Biomedical Science of Cell & Systems, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Laura B Jardim
- Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Departamento de Medicina Interna, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| |
Collapse
|
3
|
Johansson LF, de Weerd HA, de Boer EN, van Dijk F, Te Meerman GJ, Sijmons RH, Sikkema-Raddatz B, Swertz MA. NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing. BMC Bioinformatics 2018; 19:531. [PMID: 30558531 PMCID: PMC6296037 DOI: 10.1186/s12859-018-2557-8] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/04/2018] [Indexed: 12/30/2022] Open
Abstract
Background Various algorithms have been developed to predict fetal trisomies using cell-free DNA in non-invasive prenatal testing (NIPT). As basis for prediction, a control group of non-trisomy samples is needed. Prediction accuracy is dependent on the characteristics of this group and can be improved by reducing variability between samples and by ensuring the control group is representative for the sample analyzed. Results NIPTeR is an open-source R Package that enables fast NIPT analysis and simple but flexible workflow creation, including variation reduction, trisomy prediction algorithms and quality control. This broad range of functions allows users to account for variability in NIPT data, calculate control group statistics and predict the presence of trisomies. Conclusion NIPTeR supports laboratories processing next-generation sequencing data for NIPT in assessing data quality and determining whether a fetal trisomy is present. NIPTeR is available under the GNU LGPL v3 license and can be freely downloaded from https://github.com/molgenis/NIPTeR or CRAN. Electronic supplementary material The online version of this article (10.1186/s12859-018-2557-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. .,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Hendrik A de Weerd
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,School of Bioscience, Systems biology research center, University of Skövde, Skövde, Sweden
| | - Eddy N de Boer
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Freerk van Dijk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard J Te Meerman
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| |
Collapse
|
4
|
Hoorntje ET, Bollen IA, Barge-Schaapveld DQ, van Tienen FH, Te Meerman GJ, Jansweijer JA, van Essen AJ, Volders PG, Constantinescu AA, van den Akker PC, van Spaendonck-Zwarts KY, Oldenburg RA, Marcelis CL, van der Smagt JJ, Hennekam EA, Vink A, Bootsma M, Aten E, Wilde AA, van den Wijngaard A, Broers JL, Jongbloed JD, van der Velden J, van den Berg MP, van Tintelen JP. Lamin A/C-Related Cardiac Disease: Late Onset With a Variable and Mild Phenotype in a Large Cohort of Patients With the Lamin A/C p.(Arg331Gln) Founder Mutation. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.116.001631. [PMID: 28790152 DOI: 10.1161/circgenetics.116.001631] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 02/20/2016] [Accepted: 05/08/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Interpretation of missense variants can be especially difficult when the variant is also found in control populations. This is what we encountered for the LMNA c.992G>A (p.(Arg331Gln)) variant. Therefore, to evaluate the effect of this variant, we combined an evaluation of clinical data with functional experiments and morphological studies. METHODS AND RESULTS Clinical data of 23 probands and 35 family members carrying this variant were retrospectively collected. A time-to-event analysis was performed to compare the course of the disease with carriers of other LMNA mutations. Myocardial biopsies were studied with electron microscopy and by measuring force development of the sarcomeres. Morphology of the nuclear envelope was assessed with immunofluorescence on cultured fibroblasts. The phenotype in probands and family members was characterized by atrioventricular conduction disturbances (61% and 44%, respectively), supraventricular arrhythmias (69% and 52%, respectively), and dilated cardiomyopathy (74% and 14%, respectively). LMNA p.(Arg331Gln) carriers had a significantly better outcome regarding the composite end point (malignant ventricular arrhythmias, end-stage heart failure, or death) compared with carriers of other pathogenic LMNA mutations. A shared haplotype of 1 Mb around LMNA suggested a common founder. The combined logarithm of the odds score was 3.46. Force development in membrane-permeabilized cardiomyocytes was reduced because of decreased myofibril density. Structural nuclear LMNA-associated envelope abnormalities, that is, blebs, were confirmed by electron microscopy and immunofluorescence microscopy. CONCLUSIONS Clinical, morphological, functional, haplotype, and segregation data all indicate that LMNA p.(Arg331Gln) is a pathogenic founder mutation with a phenotype reminiscent of other LMNA mutations but with a more benign course.
Collapse
Affiliation(s)
| | - Ilse A Bollen
- For the author affiliations, please see the Appendix
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aryan Vink
- For the author affiliations, please see the Appendix
| | | | - Emmelien Aten
- For the author affiliations, please see the Appendix
| | | | | | - Jos L Broers
- For the author affiliations, please see the Appendix
| | | | | | | | | |
Collapse
|
5
|
Van Der Werf CS, Wabbersen TD, Hsiao NH, Paredes J, Etchevers HC, Kroisel PM, Tibboel D, Babarit C, Schreiber RA, Hoffenberg EJ, Vekemans M, Zeder SL, Ceccherini I, Lyonnet S, Ribeiro AS, Seruca R, Te Meerman GJ, van Ijzendoorn SCD, Shepherd IT, Verheij JBGM, Hofstra RMW. CLMP is required for intestinal development, and loss-of-function mutations cause congenital short-bowel syndrome. Gastroenterology 2012; 142:453-462.e3. [PMID: 22155368 DOI: 10.1053/j.gastro.2011.11.038] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 10/24/2011] [Accepted: 11/22/2011] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Short-bowel syndrome usually results from surgical resection of the small intestine for diseases such as intestinal atresias, volvulus, and necrotizing enterocolitis. Patients with congenital short-bowel syndrome (CSBS) are born with a substantial shortening of the small intestine, to a mean length of 50 cm, compared with a normal length at birth of 190-280 cm. They also are born with intestinal malrotation. Because CSBS occurs in many consanguineous families, it is considered to be an autosomal-recessive disorder. We aimed to identify and characterize the genetic factor causing CSBS. METHODS We performed homozygosity mapping using 610,000 K single-nucleotide polymorphism arrays to analyze the genomes of 5 patients with CSBS. After identifying a gene causing the disease, we determined its expression pattern in human embryos. We also overexpressed forms of the gene product that were and were not associated with CSBS in Chinese Hamster Ovary and T84 cells and generated a zebrafish model of the disease. RESULTS We identified loss-of-function mutations in Coxsackie- and adenovirus receptor-like membrane protein (CLMP) in CSBS patients. CLMP is a tight-junction-associated protein that is expressed in the intestine of human embryos throughout development. Mutations in CLMP prevented its normal localization to the cell membrane. Knock-down experiments in zebrafish resulted in general developmental defects, including shortening of the intestine and the absence of goblet cells. Because goblet cells are characteristic for the midintestine in zebrafish, which resembles the small intestine in human beings, the zebrafish model mimics CSBS. CONCLUSIONS Loss-of-function mutations in CLMP cause CSBS in human beings, likely by interfering with tight-junction formation, which disrupts intestinal development. Furthermore, we developed a zebrafish model of CSBS.
Collapse
Affiliation(s)
- Christine S Van Der Werf
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Niens M, Visser L, Nolte IM, van der Steege G, Diepstra A, Cordano P, Jarrett RF, Te Meerman GJ, Poppema S, van den Berg A. Serum chemokine levels in Hodgkin lymphoma patients: highly increased levels of CCL17 and CCL22. Br J Haematol 2008; 140:527-36. [PMID: 18275430 DOI: 10.1111/j.1365-2141.2007.06964.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hodgkin lymphoma (HL) is characterized by a minority of neoplastic Hodgkin-Reed Sternberg (HRS) cells surrounded by a non-neoplastic reactive infiltrate. As immunological mechanisms appear to be crucial in classical HL pathogenesis, altered serum chemokine levels might be related to disease activity. Serum levels of nine chemokines were examined in 163 untreated HL patients and 334 controls. We investigated single nucleotide polymorphisms (SNPs) for association with serum CCL17 (thymus and activation-regulated chemokine, TARC) levels and HL susceptibility. Serum CCL17 and CCL22 (macrophage-derived chemokine, MDC) levels were significantly increased in 82% and 57% of the HL patients. Nodular sclerosis cases showed increased serum CCL17 and CCL22 levels (P < 0.001) and serum levels were correlated with Ann Arbor stage. Of nine patients with pre- and post-treatment serum samples, the majority showed decreased CCL17 and CCL22 levels after treatment. HRS cells expressed CCL17 and CCL22 in 77% and 75% of 74 cases. Three SNPs showed a trend of increased serum CCL17 levels with minor alleles in controls, but were not associated with HL susceptibility. CCL17 and CCL22 were the only chemokines with increased serum levels in the vast majority of HL patients, which provides further insight into the molecular mechanism(s) leading to infiltrations of reactive lymphocytes in HL.
Collapse
Affiliation(s)
- Marijke Niens
- Department of Medical Genetics, Unviersity Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Nolte IM, de Vries AR, Spijker GT, Jansen RC, Brinza D, Zelikovsky A, Te Meerman GJ. Association testing by haplotype-sharing methods applicable to whole-genome analysis. BMC Proc 2007; 1 Suppl 1:S129. [PMID: 18466471 PMCID: PMC2367507 DOI: 10.1186/1753-6561-1-s1-s129] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [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: 01/09/2023] Open
Abstract
We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS test, which tests whether a case and a control haplotype show less sharing than two random haplotypes. The significance of the HSS is determined using a variance estimate from the theory of U-statistics, whereas the significance of the CROSS test is estimated from a sequential randomization procedure. Both methods are fast and hence practical, even for whole-genome screens with high marker densities. We analyzed data sets of Problems 2 and 3 of Genetic Analysis Workshop 15 and compared HSS and CROSS to conventional association methods. Problem 2 provided a data set of 2300 single-nucleotide polymorphisms (SNPs) in a 10-Mb region of chromosome 18q, which had shown linkage evidence for rheumatoid arthritis. The CROSS test detected a significant association at approximately position 4407 kb. This was supported by single-marker association and HSS. The CROSS test outperformed them both with respect to significance level and signal-to-noise ratio. A 20-kb candidate region could be identified. Problem 3 provided a simulated 10 k SNP data set covering the whole genome. Three known candidate regions for rheumatoid arthritis were detected. Again, the CROSS test gave the most significant results. Furthermore, both the HSS and the CROSS showed better fine-mapping accuracy than straightforward haplotype association. In conclusion, haplotype sharing methods, particularly the CROSS test, show great promise for identifying disease gene loci.
Collapse
Affiliation(s)
- Ilja M Nolte
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - André R de Vries
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Geert T Spijker
- Deparment of Dermatology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, the Netherlands
| | - Dumitru Brinza
- Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, Georgia 30303-3086, USA
| | - Alexander Zelikovsky
- Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, Georgia 30303-3086, USA
| | - Gerard J Te Meerman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| |
Collapse
|
8
|
Abstract
Ovarian cancer is a heterogeneous disease with respect to histopathology, molecular biology, and clinical outcome. In advanced stages, surgery and chemotherapy result in an approximately 25% overall 5-year survival rate, pointing to a strong need to identify subgroups of patients that may benefit from targeted innovative molecular therapy. This review summarizes: (a) microarray research identifying gene-expression profiles in ovarian cancer; (b) the methodological flaws in the available microarray studies; and (c) applications of pathway analysis to define new molecular subgroups. Microarray technology now permits the analysis of expression levels of thousands of genes. So far seven studies have aimed to identify a genetic profile that can predict survival/clinical outcome and/or response to platinum-based therapy. To date, the clinical evidence of prognostic microarray studies has only reached the level of small retrospective studies, and there are other issues that may explain the nonreproducibility among the reported prognostic profiles, such as overfitting, technical platform differences, and accuracy of measurements. We consider pathway analysis a promising new strategy. The accumulation of small differential expressions within a meaningful molecular regulatory network might lead to a critical threshold level, resulting in ovarian cancer. Microarray technologies have already provided valuable expression data for classifying ovarian cancer and the first clues about which molecular changes in ovarian cancer could be exploited in new treatment strategies. Further improvements in technology as well as in study design, combined with pathway analysis, will allow us to detect even more subtle tumor expression differences among subgroups of ovarian cancer patients. Disclosure of potential conflicts of interest is found at the end of this article.
Collapse
Affiliation(s)
- Rudolf S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
9
|
de Jong MM, Nolte IM, Te Meerman GJ, van der Graaf WTA, Oosterom E, Bruinenberg M, Steege GVD, Oosterwijk JC, van der Hout AH, Boezen HM, Schaapveld M, Kleibeuker JH, de Vries EGE. No increased susceptibility to breast cancer from combined CHEK2 1100delC genotype and the HLA class III region risk factors. Eur J Cancer 2005; 41:1819-23. [PMID: 16043347 DOI: 10.1016/j.ejca.2005.04.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [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: 02/18/2005] [Accepted: 04/08/2005] [Indexed: 12/19/2022]
Abstract
CHEK2 is low-penetrance breast cancer susceptibility gene. The 1100delC mutation may interact with variants/mutations in other breast cancer susceptibility loci. We identified a risk haplotype in the HLA class III region in breast cancer patients [de Jong MM, Nolte IM, de Vries EGE, et al. The HLA class III subregion is responsible for an increased breast cancer risk. Hum Mol Genet 2003, 12, 2311-2319] and tested whether it interacted with 1100delC mutation. The CHEK2 1100delC mutation was analysed in the same series of patients and controls as in the HLA breast cancer study. In 962 unselected breast cancer patients, the 1100delC mutation was observed in 2.9% and in 367 controls in 1.4% (NS). The highest 1100delC frequency occurred in high-risk (4.4%), followed by moderate-risk (3.8%), and lowest in low genetic risk patients (2.4%, P(trend) 0.029). In HLA risk haplotype carriers no increased breast cancer risk was observed in the presence of 1100delC mutation. Patients more often had one than both genetic risk factors. The 1100delC mutation and the HLA risk haplotype confer increased breast cancer risks, but an interactive effect on breast cancer between both factors is unlikely. In contrast, the effect of 1100delC mutation on breast cancer risk was limited to individuals without HLA risk haplotype, suggesting a mutual excluding effect between these risk factors.
Collapse
Affiliation(s)
- Mirjam M de Jong
- Department of Medical Oncology, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Zoodsma M, Nolte IM, Te Meerman GJ, De Vries EGE, Van der Zee AGJ. HLA genes and other candidate genes involved in susceptibility for (pre)neoplastic cervical disease. Int J Oncol 2005; 26:769-84. [PMID: 15703836] [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] [Indexed: 05/01/2023] Open
Abstract
This review focuses on common and genetic risk factors such as HLA and other genes that may be involved in susceptibility for (pre)neoplastic cervical disease. The goal of this review is the evaluation of polymorphisms that are either associated with cervical intraepithelial neoplasia (CIN) and/or cervical cancer. A pooled analysis was performed for DQA1, DQB1 and DRB1 alleles and 10 other genes that have been evaluated in more than one study. An association, either an increased or a decreased risk, with CIN and cervical cancer at a 5% significance level was found for 15 HLA II alleles. Four polymorphisms (Tp53, IL-10, CYP2D6 and the MTHFR) exhibited an increased CIN and cervical cancer risk. However, only the pooled analysis of the DQB1 alleles, the HLA-DR specificities and Tp53 genes had sufficiently large sample sizes to confirm or exclude the proposed association. Our data indicate that further analysis in larger sample sizes, especially for genes other than the HLA genes, is necessary to describe the exact relations between these genes and susceptibility for CIN and cervical cancer with an adequate power.
Collapse
Affiliation(s)
- Margreet Zoodsma
- Department of Gynecology, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | | | | | | | | |
Collapse
|
11
|
de Jong MM, Nolte IM, Te Meerman GJ, van der Graaf WTA, Mulder MJ, van der Steege G, Bruinenberg M, Schaapveld M, Niessen RC, Berends MJW, Sijmons RH, Hofstra RMW, de Vries EGE, Kleibeuker JH. Colorectal cancer and theCHEK2 1100delC mutation. Genes Chromosomes Cancer 2005; 43:377-82. [PMID: 15852425 DOI: 10.1002/gcc.20195] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The CHEK2 1100delC mutation was recently identified as a low-penetrance breast cancer susceptibility allele. The mutation occurred more frequently in families with clustering of breast and colorectal cancers (CRCs) than in families with clustering of breast cancer only. Hence, the 1100delC mutation could also be a low-penetrance CRC susceptibility allele. To test this hypothesis, we examined the mutation in 629 unselected CRC cases, 230 controls, and 105 selected CRCs diagnosed in patients before age 50. The mutation was observed in 1.6% of unselected patients and in 0.3% of controls (Not significant (NS)). After stratifying unselected patients according to defined genetic risk (on the basis of age at diagnosis and family history of colorectal and endometrial cancer), the highest frequency was observed in high-risk patients (12.5%), followed by moderate-risk patients (3.3%), and was lowest in low-risk patients (1.0%, P(trend) 0.014). In selected patients, 1.6% carried the mutation (NS). Subgroup analyses for tumor localization, gender, and age at diagnosis did not reveal an association with the 1100delC genotype. In addition, a pooled analysis, combining data of one published study in unselected CRC cases and our study, also did not reveal an association. In conclusion, the frequency of the 1100delC genotype was neither significantly increased in unselected CRC patients nor in selected CRC patients diagnosed before age 50. However, after stratifying unselected CRC patients according to defined genetic risk, a significant trend of increasing frequency was observed. Together, the results are consistent with a low-penetrance effect (OR 1.5-2.0) of the CHEK2 1100delC on CRC risk. Large case-control studies are required to clarify the exact role of the CHEK2 1100delC mutation in CRC.
Collapse
Affiliation(s)
- Mirjam M de Jong
- Department of Gastroenterology, University of Groningen Medical Center, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
de Jong MM, Nolte IM, de Vries EGE, Schaapveld M, Kleibeuker JH, Oosterom E, Oosterwijk JC, van der Hout AH, van der Steege G, Bruinenberg M, Boezen HM, Te Meerman GJ, van der Graaf WTA. The HLA class III subregion is responsible for an increased breast cancer risk. Hum Mol Genet 2003; 12:2311-9. [PMID: 12915440 DOI: 10.1093/hmg/ddg245] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [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: 11/14/2022] Open
Abstract
BRCA1 and BRCA2 germline mutations account for <5% of breast cancer cases. Less penetrant breast cancer susceptibility genes are likely to exist. Earlier studies have suggested involvement of the HLA region. The HLA region was genotyped with 24 microsatellite markers and markers for two single nucleotide polymorphisms (SNPs) in TNFalpha and TNFbeta, in germline DNA from 956 breast cancer patients and 1271 family-based controls. Association analyses and the haplotype sharing statistic (HSS) were used to search for differences in haplotype sharing between patients and controls. Based on criteria known to influence genetic breast cancer risk, patients were divided into groups of high, moderate and low risk. The HSS revealed a significant difference in mean haplotype sharing between patients and controls for four consecutive markers (D6S2671, TNFa, D6S2672 and MICA), the highest being at D6S2671 (P=0.017). Subgroup analyses showed that moderate-risk patients were responsible for this difference, with the strongest association for D6S2672 (P=0.0009). A single haplotype was more frequent and longer in moderate-risk patients than in controls. The results were confirmed with association analyses. Individuals homozygous for haplotype 110-184 (D6S2672-MICA) were observed in 9.0% of moderate-risk patients and 1.5% of controls [odds ratio (OR)=7.14], while heterozygotes were at a lower risk (OR=1.41), suggesting a recessive effect. No association was observed between the two SNPs in TNFalpha (-308) and TNFbeta (intron 1) and breast cancer risk. The results reveal a potential role of the HLA class III subregion in susceptibility to breast cancer in patients at moderate familial risk.
Collapse
Affiliation(s)
- Mirjam M de Jong
- Department of Medical Oncology, University Medical Center Groningen, Hanzeplein 1, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Sonneveld DJA, Lutke Holzik MF, Nolte IM, Sleijfer DT, van der Graaf WTA, Bruinenberg M, Sijmons RH, Hoekstra HJ, Te Meerman GJ. Testicular carcinoma and HLA Class II genes. Cancer 2002; 95:1857-63. [PMID: 12404278 DOI: 10.1002/cncr.10903] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The association with histocompatibility antigens (HLA), in particular Class II genes (DQB1, DRB1), has recently been suggested to be one of the genetic factors involved in testicular germ cell tumor (TGCT) development. The current study, which uses genotyping of microsatellite markers, was designed to replicate previous associations. METHODS In 151 patients, along with controls comprising parents or spouses, the HLA region (particularly Class II) on chromosome 6p21 was genotyped for a set of 15 closely linked microsatellite markers. RESULTS In both patients and controls, strong linkage disequilibrium was observed in the genotyped region, indicating that similar haplotypes are likely to be identical by descent. However, association analysis and the transmission disequilibrium test did not show significant results. Haplotype sharing statistics, a haplotype method that derives extra information from phase and single marker tests, did not show differences in haplotype sharing between patients and controls. CONCLUSION The current genotyping study did not confirm the previously reported association between HLA Class II genes and TGCT. As the HLA alleles for which associations were reported are also prevalent in the Dutch populations, these associations are likely to be nonexistent or much weaker than previously reported.
Collapse
Affiliation(s)
- Dirk J A Sonneveld
- Department of Surgical Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|