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Vos N, Haghshenas S, van der Laan L, Russel PKM, Rooney K, Levy MA, Relator R, Kerkhof J, McConkey H, Maas SM, Vissers LELM, de Vries BBA, Pfundt R, Elting MW, van Hagen JM, Verbeek NE, Jongmans MCJ, Lakeman P, Rumping L, Bosch DGM, Vitobello A, Thauvin-Robinet C, Faivre L, Nambot S, Garde A, Willems M, Genevieve D, Nicolas G, Busa T, Toutain A, Gérard M, Bizaoui V, Isidor B, Merla G, Accadia M, Schwartz CE, Ounap K, Hoffer MJV, Nezarati MM, van den Boogaard MJH, Tedder ML, Rogers C, Brusco A, Ferrero GB, Spodenkiewicz M, Sidlow R, Mussa A, Trajkova S, McCann E, Mroczkowski HJ, Jansen S, Donker-Kaat L, Duijkers FAM, Stuurman KE, Mannens MMAM, Alders M, Henneman P, White SM, Sadikovic B, van Haelst MM. The detection of a strong episignature for Chung-Jansen syndrome, partially overlapping with Börjeson-Forssman-Lehmann and White-Kernohan syndromes. Hum Genet 2024:10.1007/s00439-024-02679-w. [PMID: 38787418 DOI: 10.1007/s00439-024-02679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Chung-Jansen syndrome is a neurodevelopmental disorder characterized by intellectual disability, behavioral problems, obesity and dysmorphic features. It is caused by pathogenic variants in the PHIP gene that encodes for the Pleckstrin homology domain-interacting protein, which is part of an epigenetic modifier protein complex. Therefore, we hypothesized that PHIP haploinsufficiency may impact genome-wide DNA methylation (DNAm). We assessed the DNAm profiles of affected individuals with pathogenic and likely pathogenic PHIP variants with Infinium Methylation EPIC arrays and report a specific and sensitive DNAm episignature biomarker for Chung-Jansen syndrome. In addition, we observed similarities between the methylation profile of Chung-Jansen syndrome and that of functionally related and clinically partially overlapping genetic disorders, White-Kernohan syndrome (caused by variants in DDB1 gene) and Börjeson-Forssman-Lehmann syndrome (caused by variants in PHF6 gene). Based on these observations we also proceeded to develop a common episignature biomarker for these disorders. These newly defined episignatures can be used as part of a multiclass episignature classifier for screening of affected individuals with rare disorders and interpretation of genetic variants of unknown clinical significance, and provide further insights into the common molecular pathophysiology of the clinically-related Chung-Jansen, Börjeson-Forssman-Lehmann and White-Kernohan syndromes.
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Affiliation(s)
- Niels Vos
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Liselot van der Laan
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Perle K M Russel
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Saskia M Maas
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Mariet W Elting
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Johanna M van Hagen
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Phillis Lakeman
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Lynne Rumping
- Center for Medical Genetics, Antwerp University Hospital, University of Antwerp, Drie Eikenstraat 655, 2650, Edegem, Belgium
| | - Danielle G M Bosch
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Antonio Vitobello
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, FHU-TRANSLAD, Unité Fonctionnelle Innovation en Diagnostic Génomique Des Maladies Rares, 21000, Dijon, France
| | - Christel Thauvin-Robinet
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, FHU-TRANSLAD, Unité Fonctionnelle Innovation en Diagnostic Génomique Des Maladies Rares, 21000, Dijon, France
- CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Déficiences Intellectuelles de Causes Rares», FHU-TRANSLAD, Dijon, France
| | - Laurence Faivre
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs», FHU-TRANSLAD, Dijon, France
| | - Sophie Nambot
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, FHU-TRANSLAD, Unité Fonctionnelle Innovation en Diagnostic Génomique Des Maladies Rares, 21000, Dijon, France
- CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs», FHU-TRANSLAD, Dijon, France
| | - Aurore Garde
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Déficiences Intellectuelles de Causes Rares», FHU-TRANSLAD, Dijon, France
| | - Marjolaine Willems
- INserm U1183, Department of Clinical Genetics, Montpellier University, 34090 CHU Montpellier, Montpellier, France
| | - David Genevieve
- INserm U1183, Department of Clinical Genetics, Montpellier University, 34090 CHU Montpellier, Montpellier, France
| | - Gaël Nicolas
- Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Univ Rouen Normandie, 76000, Rouen, France
| | - Tiffany Busa
- Department of Medical Genetics, Timone Hospital, Marseille, France
| | - Annick Toutain
- Genetics Department, University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | - Marion Gérard
- APHP, Department of Genetics, Robert Debré Hospital, 75019, Paris, France
| | - Varoona Bizaoui
- Clinical Genetics and Neurodevelopmental Disorders, Centre Hospitalier de L'Estran, 50170, Pontorson, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000, Nantes, France
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Foggia, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Maria Accadia
- Servizio di Genetica Medica, Ospedale Cardinale G. Panico, Tricase, LE, Italy
| | - Charles E Schwartz
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Katrin Ounap
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjan M Nezarati
- Genetics Program, North York General Hospital, Toronto, ON, M2K 1E1, Canada
| | | | | | | | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
- Unit of Medical Genetics, Città Della Salute e Della Scienza Hospital, Turin, Italy
| | - Giovanni B Ferrero
- Department of Clinical and Biological Science, University of Torino, Turin, Italy
| | | | - Richard Sidlow
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, CA, USA
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Torino, Turin, Italy
- Pediatric Clinical Genetics Unit, Regina Margherita Childrens' Hospital, Turin, Italy
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Emma McCann
- Liverpool Center for Genomic Medicine, Liverpool Women's Hospital, Liverpool, UK
| | - Henry J Mroczkowski
- Department of Pediatrics, Le Bonheur Children's Hospital, Memphis, TN, USA
- Division of Genetics, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sandra Jansen
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Laura Donker-Kaat
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Floor A M Duijkers
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Kyra E Stuurman
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Mariëlle Alders
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Peter Henneman
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada.
| | - Mieke M van Haelst
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands.
- Amsterdam UMC, Department of Paediatrics, Emma Children's Hospital, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Amsterdam UMC, Emma Center for Personalized Medicine, Amsterdam, The Netherlands.
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Vos N, Kleinendorst L, van der Laan L, van Uhm J, Jansen PR, van Eeghen AM, Maas SM, Mannens MMAM, van Haelst MM. Evaluation of 100 Dutch cases with 16p11.2 deletion and duplication syndromes; from clinical manifestations towards personalized treatment options. Eur J Hum Genet 2024:10.1038/s41431-024-01601-2. [PMID: 38605127 DOI: 10.1038/s41431-024-01601-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 03/03/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
The 16p11.2 deletion syndrome is a clinically heterogeneous disorder, characterized by developmental delay, intellectual disability, hyperphagia, obesity, macrocephaly and psychiatric problems. Cases with 16p11.2 duplication syndrome have similar neurodevelopmental problems, but typically show a partial 'mirror phenotype' with underweight and microcephaly. Various copy number variants (CNVs) of the chromosomal 16p11.2 region have been described. Most is known about the 'typical' 16p11.2 BP4-BP5 (29.6-30.2 Mb; ~600 kb) deletions and duplications, but there are also several published cohorts with more distal 16p11.2 BP2-BP3 CNVs (28.8-29.0 Mb; ~220 kb), who exhibit clinical overlap. We assessed 100 cases with various pathogenic 16p11.2 CNVs and compared their clinical characteristics to provide more clear genotype-phenotype correlations and raise awareness of the different 16p11.2 CNVs. Neurodevelopmental and weight issues were reported in the majority of cases. Cases with distal 16p11.2 BP2-BP3 deletion showed the most severe obesity phenotype (73.7% obesity, mean BMI SDS 3.2). In addition to the more well defined typical 16p11.2 BP4-BP5 and distal 16p11.2 BP2-BP3 CNVs, we describe the clinical features of five cases with other, overlapping, 16p11.2 CNVs in more detail. Interestingly, four cases had a second genetic diagnosis and 18 cases an additional gene variant of uncertain significance, that could potentially help explain the cases' phenotypes. In conclusion, we provide an overview of our Dutch cohort of cases with various pathogenic 16p11.2 CNVs and relevant second genetic findings, that can aid in adequately recognizing, diagnosing and counseling of individuals with 16p11.2 CNVs, and describe the personalized medicine for cases with these conditions.
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Affiliation(s)
- Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Lotte Kleinendorst
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Emma Center for Personalized Medicine, Meibergdreef 9, Amsterdam, The Netherlands
| | - Liselot van der Laan
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Jorrit van Uhm
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Philip R Jansen
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Agnies M van Eeghen
- Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Saskia M Maas
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Mieke M van Haelst
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands.
- Amsterdam UMC, University of Amsterdam, Emma Center for Personalized Medicine, Meibergdreef 9, Amsterdam, The Netherlands.
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van der Laan L, Lauffer P, Rooney K, Silva A, Haghshenas S, Relator R, Levy MA, Trajkova S, Huisman SA, Bijlsma EK, Kleefstra T, van Bon BW, Baysal Ö, Zweier C, Palomares-Bralo M, Fischer J, Szakszon K, Faivre L, Piton A, Mesman S, Hochstenbach R, Elting MW, van Hagen JM, Plomp AS, Mannens MMAM, Alders M, van Haelst MM, Ferrero GB, Brusco A, Henneman P, Sweetser DA, Sadikovic B, Vitobello A, Menke LA. DNA methylation episignature and comparative epigenomic profiling for Pitt-Hopkins syndrome caused by TCF4 variants. HGG Adv 2024; 5:100289. [PMID: 38571311 PMCID: PMC11087720 DOI: 10.1016/j.xhgg.2024.100289] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by pathogenic variants in TCF4, leading to intellectual disability, specific morphological features, and autonomic nervous system dysfunction. Epigenetic dysregulation has been implicated in PTHS, prompting the investigation of a DNA methylation (DNAm) "episignature" specific to PTHS for diagnostic purposes and variant reclassification and functional insights into the molecular pathophysiology of this disorder. A cohort of 67 individuals with genetically confirmed PTHS and three individuals with intellectual disability and a variant of uncertain significance (VUS) in TCF4 were studied. The DNAm episignature was developed with an Infinium Methylation EPIC BeadChip array analysis using peripheral blood cells. Support vector machine (SVM) modeling and clustering methods were employed to generate a DNAm classifier for PTHS. Validation was extended to an additional cohort of 11 individuals with PTHS. The episignature was assessed in relation to other neurodevelopmental disorders and its specificity was examined. A specific DNAm episignature for PTHS was established. The classifier exhibited high sensitivity for TCF4 haploinsufficiency and missense variants in the basic-helix-loop-helix domain. Notably, seven individuals with TCF4 variants exhibited negative episignatures, suggesting complexities related to mosaicism, genetic factors, and environmental influences. The episignature displayed degrees of overlap with other related disorders and biological pathways. This study defines a DNAm episignature for TCF4-related PTHS, enabling improved diagnostic accuracy and VUS reclassification. The finding that some cases scored negatively underscores the potential for multiple or nested episignatures and emphasizes the need for continued investigation to enhance specificity and coverage across PTHS-related variants.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Peter Lauffer
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Ananília Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Sylvia A Huisman
- Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Department of Pediatrics, Amsterdam, the Netherlands; Zodiak, Prinsenstichting, Purmerend, the Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Özlem Baysal
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christiane Zweier
- Department of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Department of Human Genetics, University of Bern, Inselspital Universitätsspital Bern, Bern, Switzerland
| | - María Palomares-Bralo
- Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | - Jan Fischer
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Katalin Szakszon
- Institute of Paediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laurence Faivre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD «Génétique des Anomalies du Développement», FHUTRANSLAD, Dijon, France; CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs», FHU-TRANSLDAD, Dijon, France
| | - Amélie Piton
- Genetic Diagnosis Laboratories, Strasbourg University Hospital, Strasbourg 67000, France
| | - Simone Mesman
- Swammerdam Institute for Life Sciences, FNWI, University of Amsterdam, Amsterdam, the Netherlands
| | - Ron Hochstenbach
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Mariet W Elting
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Johanna M van Hagen
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Astrid S Plomp
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Mieke M van Haelst
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Giovanni B Ferrero
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Peter Henneman
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - David A Sweetser
- Division of Medical Genetics and Metabolism and Center for Genomic Medicine, Massachusetts General for Children, Boston, MA, USA
| | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Leonie A Menke
- Amsterdam Reproduction & Development, Amsterdam, the Netherlands; Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Department of Pediatrics, Amsterdam, the Netherlands; Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Amsterdam, the Netherlands.
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van der Laan L, Karimi K, Rooney K, Lauffer P, McConkey H, Caro P, Relator R, Levy MA, Bhai P, Mignot C, Keren B, Briuglia S, Sobering AK, Li D, Vissers LELM, Dingemans AJM, Valenzuela I, Verberne EA, Misra-Isrie M, Zwijnenburg PJG, Waisfisz Q, Alders M, Sailer S, Schaaf CP, Mannens MMAM, Sadikovic B, van Haelst MM, Henneman P. DNA methylation episignature, extension of the clinical features, and comparative epigenomic profiling of Hao-Fountain syndrome caused by variants in USP7. Genet Med 2024; 26:101050. [PMID: 38126281 DOI: 10.1016/j.gim.2023.101050] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE Hao-Fountain syndrome (HAFOUS) is a neurodevelopmental disorder caused by pathogenic variants in USP7. HAFOUS is characterized by developmental delay, intellectual disability, speech delay, behavioral abnormalities, autism spectrum disorder, seizures, hypogonadism, and mild dysmorphic features. We investigated the phenotype of 18 participants with HAFOUS and performed DNA methylation (DNAm) analysis, aiming to generate a diagnostic biomarker. Furthermore, we performed comparative analysis with known episignatures to gain more insight into the molecular pathophysiology of HAFOUS. METHODS We assessed genomic DNAm profiles of 18 individuals with pathogenic variants and variants of uncertain significance (VUS) in USP7 to map and validate a specific episignature. The comparison between the USP7 cohort and 56 rare genetic disorders with earlier reported DNAm episignatures was performed with statistical and functional correlation. RESULTS We mapped a sensitive and specific DNAm episignature for pathogenic variants in USP7 and utilized this to reclassify the VUS. Comparative epigenomic analysis showed evidence of HAFOUS similarity to a number of other rare genetic episignature disorders. CONCLUSION We discovered a sensitive and specific DNAm episignature as a robust diagnostic biomarker for HAFOUS that enables VUS reclassification in USP7. We also expand the phenotypic spectrum of 9 new and 5 previously reported individuals with HAFOUS.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Karim Karimi
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Peter Lauffer
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Pilar Caro
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Pratibha Bhai
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Cyril Mignot
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France; Hôpital Armand Trousseau, Paris, France AND Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Boris Keren
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Silvana Briuglia
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Andrew K Sobering
- AU/UGA Medical Partnership Campus of the Medical College of Georgia, Athens, Georgia; Windward Islands Research and Education Foundation, True Blue, St. George's, Grenada; St. George's University School of Medicine, Department of Biochemistry, Grenada
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, University of Pennsylvania Perelman school of Medicine, Philadelphia, PA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Irene Valenzuela
- Àrea de Genètica Clínica i Malalties Minoritàries, Hospital Vall d'Hebron, Barcelona, Spain
| | - Eline A Verberne
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastian Sailer
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - Mieke M van Haelst
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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5
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van der Laan L, Hoekman DR, Wortelboer EJ, Mannens MMAM, Kooper AJA. Prenatal identification of an inverted duplicated 13q marker chromosome with a neocentromere. Mol Cytogenet 2023; 16:34. [PMID: 38031124 PMCID: PMC10687888 DOI: 10.1186/s13039-023-00666-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
In this case report, we describe a rare prenatal finding of a small marker chromosome. This marker chromosome corresponds to an inverted duplication of the 13q region 13q31.1q34 (or 13q31.1 → qter) with a neocentromere, detected during genetic analysis of a chorionic villus sample in a fetus with multiple congenital anomalies after a normal prenatal screening result by noninvasive prenatal testing.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel R Hoekman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Esther J Wortelboer
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Angelique J A Kooper
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
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6
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van der Laan L, Rooney K, Haghshenas S, Silva A, McConkey H, Relator R, Levy MA, Valenzuela I, Trujillano L, Lasa-Aranzasti A, Campos B, Castells N, Verberne EA, Maas S, Alders M, Mannens MMAM, van Haelst MM, Sadikovic B, Henneman P. Functional Insight into and Refinement of the Genomic Boundaries of the JARID2-Neurodevelopmental Disorder Episignature. Int J Mol Sci 2023; 24:14240. [PMID: 37762546 PMCID: PMC10531903 DOI: 10.3390/ijms241814240] [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: 08/17/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
JARID2 (Jumonji, AT-rich interactive domain 2) haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. It is characterized by intellectual disability, developmental delay, autistic features, behavior abnormalities, cognitive impairment, hypotonia, and dysmorphic features. JARID2 acts as a transcriptional repressor protein that is involved in the regulation of histone methyltransferase complexes. JARID2 plays a role in the epigenetic machinery, and the associated syndrome has an identified DNA methylation episignature derived from sequence variants and intragenic deletions involving JARID2. For this study, our aim was to determine whether patients with larger deletions spanning beyond JARID2 present a similar DNA methylation episignature and to define the critical region involved in aberrant DNA methylation in 6p22-p24 microdeletions. We examined the DNA methylation profiles of peripheral blood from 56 control subjects, 13 patients with (likely) pathogenic JARID2 variants or patients carrying copy number variants, and three patients with JARID2 VUS variants. The analysis showed a distinct and strong differentiation between patients with (likely) pathogenic variants, both sequence and copy number, and controls. Using the identified episignature, we developed a binary model to classify patients with the JARID2-neurodevelopmental syndrome. DNA methylation analysis indicated that JARID2 is the driver gene for aberrant DNA methylation observed in 6p22-p24 microdeletions. In addition, we performed analysis of functional correlation of the JARID2 genome-wide methylation profile with the DNA methylation profiles of 56 additional neurodevelopmental disorders. To conclude, we refined the critical region for the presence of the JARID2 episignature in 6p22-p24 microdeletions and provide insight into the functional changes in the epigenome observed when regulation by JARID2 is lost.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Ananília Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Irene Valenzuela
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Laura Trujillano
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Berta Campos
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Neus Castells
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Eline A. Verberne
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Saskia Maas
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mieke M. van Haelst
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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7
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Rooney K, van der Laan L, Trajkova S, Haghshenas S, Relator R, Lauffer P, Vos N, Levy MA, Brunetti-Pierri N, Terrone G, Mignot C, Keren B, Billette de Villemeur T, Volker-Touw CML, Verbeek N, van der Smagt JJ, Oegema R, Brusco A, Ferrero GB, Misra-Isrie M, Hochstenbach R, Alders M, Mannens MMAM, Sadikovic B, van Haelst MM, Henneman P. DNA methylation episignature and comparative epigenomic profiling of HNRNPU-related neurodevelopmental disorder. Genet Med 2023:100871. [PMID: 37120726 DOI: 10.1016/j.gim.2023.100871] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 01/19/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023] Open
Abstract
PURPOSE HNRNPU haploinsufficiency is associated with Developmental and Epileptic Encephalopathy 54. This neurodevelopmental disorder is characterized by developmental delay, intellectual disability, speech impairment, and early onset epilepsy. We performed genome-wide DNA methylation (DNAm) analysis in a cohort of individuals to develop a diagnostic biomarker and gain functional insights into the molecular pathophysiology of HNRNPU-related disorder. METHODS DNAm profiles of individuals carrying pathogenic HNRNPU variants, identified through an international multi-center collaboration, were assessed using Infinium Methylation EPIC arrays. Statistical and functional correlation analyses were performed comparing the HNRNPU cohort to 56 previously reported DNAm episignatures. RESULTS A robust and reproducible DNAm episignature and global DNAm profile were identified. Correlation analysis identified partial overlap and similarity of the global HNRNPU DNAm profile to several other rare disorders. CONCLUSION This study demonstrates new evidence of a specific and sensitive DNAm episignature associated with pathogenic heterozygous HNRNPU-variants, establishing its utility as a clinical biomarker for the expansion of the EpiSignTM diagnostic test.
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Affiliation(s)
- Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Peter Lauffer
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Niels Vos
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Translational Medicine, Federico II University, Naples, Italy
| | - Gaetano Terrone
- Department of Translational Medicine, Federico II University, Naples, Italy
| | - Cyril Mignot
- Assistance Publique-Hopitaux de Paris, Sorbonne Université, Departement de Génétique, Groupe Hospitalier Pitie-Salpetriere et Hopital Trousseau, Paris, France
| | - Boris Keren
- Assistance Publique-Hopitaux de Paris, Sorbonne Université, Departement de Génétique, Groupe Hospitalier Pitie-Salpetriere et Hopital Trousseau, Paris, France
| | | | - Catharina M L Volker-Touw
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nienke Verbeek
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jasper J van der Smagt
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Renske Oegema
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ron Hochstenbach
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Mieke M van Haelst
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
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8
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Verberne EA, Lo-A-Njoe SM, van Ginkel M, Zwolsman J, Nikkels S, Clement L, de Vroomen M, Wever MLG, Arends E, Holtsema H, Hajenius PJ, Moreta D, Ecury-Goossen GM, Mannens MMAM, de Walle HEK, Bergman JEH, van Haelst MM. Prevalence of congenital anomalies in the Dutch Caribbean islands of Aruba, Bonaire, and Curaçao. Birth Defects Res 2023; 115:595-604. [PMID: 36757056 DOI: 10.1002/bdr2.2153] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 02/10/2023]
Abstract
BACKGROUND Congenital anomalies represent an important global health issue. Data on the prevalence and pattern of congenital anomalies in the Caribbean region are scarce and lacking altogether in Aruba, Bonaire and Curaçao (ABC islands). METHODS We performed a population-based surveillance study to determine the prevalence of structural congenital anomalies in the ABC islands, including all live births and stillbirths between January 1, 2008 and December 31, 2017 with major congenital anomalies according to EUROCAT guide 1.5. Terminations of pregnancy for fetal anomaly were included as well. Cases were identified by active case ascertainment, using multiple sources including pediatric patient files and discharge letters, delivery records, and clinical genetic patient files. Total and subgroup prevalence rates were compared between the three islands and to the French West Indies and Northern Netherlands. RESULTS Total prevalence of congenital anomalies on the ABC islands was 242.97 per 10,000 births. Total prevalence of congenital anomalies in Bonaire (325.15 per 10,000 births) was higher compared to Aruba (233.29 per 10,000 births) and Curaçao (238.58 per 10,000 births), which was mainly attributable to a higher prevalence of limb anomalies, in particular polydactyly, in Bonaire. Total prevalence of congenital anomalies on the ABC islands was comparable to the French West Indies (248.69 per 10,000 births) but significantly lower compared to the Northern Netherlands (298.98 per 10,000 births). In the subgroup prevalence analysis, the prevalence of polydactyly and atrial septal defect on the ABC islands was significantly higher compared with the French West Indies and the Northern Netherlands, while the prevalence of congenital anomalies of the kidney and urinary tract and genetic disorders was significantly lower. CONCLUSIONS This is the first study to establish the prevalence and pattern of congenital anomalies on the ABC islands, which is important to inform healthcare managers and policymakers and to provide a basis for continuous surveillance of congenital anomalies.
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Affiliation(s)
- Eline A Verberne
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Manon van Ginkel
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jet Zwolsman
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sylke Nikkels
- Department of Pediatrics, Curaçao Medical Center, Willemstad, Curaçao
- Department of Pediatrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lauren Clement
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Maartje de Vroomen
- Department of Pediatrics, Fundashon Mariadal, Kralendijk, Bonaire, The Netherlands
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Maria L G Wever
- Department of Pediatrics, Dr. Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Eric Arends
- Department of Pediatrics, Dr. Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Hilda Holtsema
- Department of Obstetrics & Gynecology, Curaçao Medical Center, Willemstad, Curaçao
| | - Petra J Hajenius
- Department of Obstetrics and Gynecology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Obstetrics and Gynecology, Fundashon Mariadal, Kralendijk, Bonaire, The Netherlands
| | - Daphne Moreta
- Department of Obstetrics and Gynecology, Dr. Horacio E. Oduber Hospital, Oranjestad, Aruba
| | | | - Marcel M A M Mannens
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Hermien E K de Walle
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jorieke E H Bergman
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Mieke M van Haelst
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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9
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Krzyzewska IM, Lauffer P, Mul AN, Laan LVD, Yim AYFL, Cobben JM, Niklinski J, Chomczyk MA, Smigiel R, Mannens MMAM, Henneman P. Expression Quantitative Trait Methylation Analysis Identifies Whole Blood Molecular Footprint in Fetal Alcohol Spectrum Disorder (FASD). Int J Mol Sci 2023; 24:ijms24076601. [PMID: 37047575 PMCID: PMC10095438 DOI: 10.3390/ijms24076601] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Fetal alcohol spectrum disorder (FASD) encompasses neurodevelopmental disabilities and physical birth defects associated with prenatal alcohol exposure. Previously, we attempted to identify epigenetic biomarkers for FASD by investigating the genome-wide DNA methylation (DNAm) profiles of individuals with FASD compared to healthy controls. In this study, we generated additional gene expression profiles in a subset of our previous FASD cohort, encompassing the most severely affected individuals, to examine the functional integrative effects of altered DNAm status on gene expression. We identified six differentially methylated regions (annotated to the SEC61G, REEP3, ZNF577, HNRNPF, MSC, and SDHAF1 genes) associated with changes in gene expression (p-value < 0.05). To the best of our knowledge, this study is the first to assess whole blood gene expression and DNAm-gene expression associations in FASD. Our results present novel insights into the molecular footprint of FASD in whole blood and opens opportunities for future research into multi-omics biomarkers for the diagnosis of FASD.
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Affiliation(s)
- Izabela M. Krzyzewska
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Peter Lauffer
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Adri N. Mul
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Liselot van der Laan
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Andrew Y. F. Li Yim
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Jan Maarten Cobben
- Department of Pediatric Endocrinology and Faculty of Medicine, Northwest Thames Regional Genetics NHS, Imperial College, London SW7 2BX, UK
| | - Jacek Niklinski
- Department of Molecular Biology, Medical University of Bialystok, Jana Kilińskiego 1, 15-089 Białystok, Poland
| | - Monika A. Chomczyk
- Department of Molecular Biology, Medical University of Bialystok, Jana Kilińskiego 1, 15-089 Białystok, Poland
| | - Robert Smigiel
- Department of Genetics, Medical University of Wroclaw, Wybrzeże Ludwika Pasteura 1, 50-367 Wrocław, Poland
| | - Marcel M. A. M. Mannens
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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10
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van Jaarsveld RH, Reilly J, Cornips MC, Hadders MA, Agolini E, Ahimaz P, Anyane-Yeboa K, Bellanger SA, van Binsbergen E, van den Boogaard MJ, Brischoux-Boucher E, Caylor RC, Ciolfi A, van Essen TAJ, Fontana P, Hopman S, Iascone M, Javier MM, Kamsteeg EJ, Kerkhof J, Kido J, Kim HG, Kleefstra T, Lonardo F, Lai A, Lev D, Levy MA, Lewis MES, Lichty A, Mannens MMAM, Matsumoto N, Maya I, McConkey H, Megarbane A, Michaud V, Miele E, Niceta M, Novelli A, Onesimo R, Pfundt R, Popp B, Prijoles E, Relator R, Redon S, Rots D, Rouault K, Saida K, Schieving J, Tartaglia M, Tenconi R, Uguen K, Verbeek N, Walsh CA, Yosovich K, Yuskaitis CJ, Zampino G, Sadikovic B, Alders M, Oegema R. Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature. Genet Med 2023; 25:49-62. [PMID: 36322151 PMCID: PMC9825659 DOI: 10.1016/j.gim.2022.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
PURPOSE Pathogenic variants in genes involved in the epigenetic machinery are an emerging cause of neurodevelopment disorders (NDDs). Lysine-demethylase 2B (KDM2B) encodes an epigenetic regulator and mouse models suggest an important role during development. We set out to determine whether KDM2B variants are associated with NDD. METHODS Through international collaborations, we collected data on individuals with heterozygous KDM2B variants. We applied methylation arrays on peripheral blood DNA samples to determine a KDM2B associated epigenetic signature. RESULTS We recruited a total of 27 individuals with heterozygous variants in KDM2B. We present evidence, including a shared epigenetic signature, to support a pathogenic classification of 15 KDM2B variants and identify the CxxC domain as a mutational hotspot. Both loss-of-function and CxxC-domain missense variants present with a specific subepisignature. Moreover, the KDM2B episignature was identified in the context of a dual molecular diagnosis in multiple individuals. Our efforts resulted in a cohort of 21 individuals with heterozygous (likely) pathogenic variants. Individuals in this cohort present with developmental delay and/or intellectual disability; autism; attention deficit disorder/attention deficit hyperactivity disorder; congenital organ anomalies mainly of the heart, eyes, and urogenital system; and subtle facial dysmorphism. CONCLUSION Pathogenic heterozygous variants in KDM2B are associated with NDD and a specific epigenetic signature detectable in peripheral blood.
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Affiliation(s)
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Marie-Claire Cornips
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Michael A Hadders
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy
| | - Priyanka Ahimaz
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Severine Audebert Bellanger
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Ton A J van Essen
- Department of Medical Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Paolo Fontana
- Medical Genetics Unit, A.O.R.N. San Pio, Benevento, Italy
| | - Saskia Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maria Iascone
- Laboratorio di Genetica Medica - ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Margaret M Javier
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Jun Kido
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Abbe Lai
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program and Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dorit Lev
- The Rina Mor Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach-Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Andre Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon; Institut Jérôme Lejeune, Paris, France
| | - Vincent Michaud
- Department of Medical Genetics, CHU Bordeaux, Bordeaux, France
| | - Evelina Miele
- Department of Pediatric Hematology and Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy
| | - Roberta Onesimo
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany; Center of Functional Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Sylvia Redon
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France; Université de Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Dmitrijs Rots
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Karen Rouault
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France; Université de Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Jolanda Schieving
- Department of Pediatric Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Romano Tenconi
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, Padova, Italy
| | - Kevin Uguen
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA
| | - Keren Yosovich
- Molecular Genetic Laboratory, Edith Wolfson Medical Center, Holon, Israel
| | - Christopher J Yuskaitis
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Giuseppe Zampino
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Faculty of Medicine and Surgery, Catholic University of Sacred Heart, Rome, Italy
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada.
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.
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11
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Holstege H, Hulsman M, Charbonnier C, Grenier-Boley B, Quenez O, Grozeva D, van Rooij JGJ, Sims R, Ahmad S, Amin N, Norsworthy PJ, Dols-Icardo O, Hummerich H, Kawalia A, Amouyel P, Beecham GW, Berr C, Bis JC, Boland A, Bossù P, Bouwman F, Bras J, Campion D, Cochran JN, Daniele A, Dartigues JF, Debette S, Deleuze JF, Denning N, DeStefano AL, Farrer LA, Fernández MV, Fox NC, Galimberti D, Genin E, Gille JJP, Le Guen Y, Guerreiro R, Haines JL, Holmes C, Ikram MA, Ikram MK, Jansen IE, Kraaij R, Lathrop M, Lemstra AW, Lleó A, Luckcuck L, Mannens MMAM, Marshall R, Martin ER, Masullo C, Mayeux R, Mecocci P, Meggy A, Mol MO, Morgan K, Myers RM, Nacmias B, Naj AC, Napolioni V, Pasquier F, Pastor P, Pericak-Vance MA, Raybould R, Redon R, Reinders MJT, Richard AC, Riedel-Heller SG, Rivadeneira F, Rousseau S, Ryan NS, Saad S, Sanchez-Juan P, Schellenberg GD, Scheltens P, Schott JM, Seripa D, Seshadri S, Sie D, Sistermans EA, Sorbi S, van Spaendonk R, Spalletta G, Tesi N, Tijms B, Uitterlinden AG, van der Lee SJ, Visser PJ, Wagner M, Wallon D, Wang LS, Zarea A, Clarimon J, van Swieten JC, Greicius MD, Yokoyama JS, Cruchaga C, Hardy J, Ramirez A, Mead S, van der Flier WM, van Duijn CM, Williams J, Nicolas G, Bellenguez C, Lambert JC. Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer's disease. Nat Genet 2022; 54:1786-1794. [PMID: 36411364 PMCID: PMC9729101 DOI: 10.1038/s41588-022-01208-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/19/2022] [Indexed: 11/22/2022]
Abstract
Alzheimer's disease (AD), the leading cause of dementia, has an estimated heritability of approximately 70%1. The genetic component of AD has been mainly assessed using genome-wide association studies, which do not capture the risk contributed by rare variants2. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals-16,036 AD cases and 16,522 controls. Next to variants in TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Additionally, the rare-variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential drivers of respective AD-genome-wide association study loci. Variants associated with the strongest effect on AD risk, in particular loss-of-function variants, are enriched in early-onset AD cases. Our results provide additional evidence for a major role for amyloid-β precursor protein processing, amyloid-β aggregation, lipid metabolism and microglial function in AD.
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Affiliation(s)
- Henne Holstege
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.
| | - Marc Hulsman
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.
| | - Camille Charbonnier
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Benjamin Grenier-Boley
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Olivier Quenez
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Detelina Grozeva
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Jeroen G J van Rooij
- Department of Neurology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Rebecca Sims
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Nuffield Department of Population Health Oxford University, Oxford, UK
| | - Penny J Norsworthy
- Medical Research Council Prion Unit at University College London, University College London Institute of Prion Diseases, London, UK
| | - Oriol Dols-Icardo
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Holger Hummerich
- Medical Research Council Prion Unit at University College London, University College London Institute of Prion Diseases, London, UK
| | - Amit Kawalia
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Philippe Amouyel
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Gary W Beecham
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Claudine Berr
- Université Montpellier, INSERM, Institute for Neurosciences of Montpellier, Montpellier, France
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anne Boland
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine Evry, Gif-sur-Yvette, France
| | - Paola Bossù
- Experimental Neuro-psychobiology Laboratory, Department of Clinical and Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico Santa Lucia Foundation, Rome, Italy
| | - Femke Bouwman
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Dominique Campion
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | | | - Antonio Daniele
- Department of Neuroscience, Catholic University of Sacred Heart, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | | | - Stéphanie Debette
- Université Bordeaux, INSERM, Bordeaux Population Health Research Center, Bordeaux, France
- Department of Neurology, Bordeaux University Hospital, Bordeaux, France
| | - Jean-François Deleuze
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine Evry, Gif-sur-Yvette, France
| | - Nicola Denning
- UKDRI Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Anita L DeStefano
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Lindsay A Farrer
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University, Boston, MA, USA
| | - Maria Victoria Fernández
- Neurogenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Psychiatry Department, Washington University School of Medicine, St Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Nick C Fox
- Dementia Research Centre, University College London Queen Square Institute of Neurology, London, UK
| | - Daniela Galimberti
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda, Ospedale Policlinico, Milan, Italy
- University of Milan, Milan, Italy
| | - Emmanuelle Genin
- Université Brest, INSERM, Etablissement Français du Sang, Centre Hospitalier Universitaire Brest, Unité Mixte de Recherche 1078, GGB, Brest, France
| | - Johan J P Gille
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Clive Holmes
- Clinical and Experimental Science, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - M Kamran Ikram
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Iris E Jansen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije University, Amsterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Marc Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Afina W Lemstra
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Alberto Lleó
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Lauren Luckcuck
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, the Netherlands
| | - Rachel Marshall
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Eden R Martin
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Carlo Masullo
- Institute of Neurology, Catholic University of the Sacred Heart, Rome, Italy
| | - Richard Mayeux
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Alun Meggy
- UKDRI Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Merel O Mol
- Department of Neurology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Adam C Naj
- Penn Neurodegeneration Genomics Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Valerio Napolioni
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Genomic and Molecular Epidemiology Laboratory, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Florence Pasquier
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, UMR1172, Resources and Research Memory Center (MRRC) of Distalz, Licend, Lille, France
| | - Pau Pastor
- Fundació Docència i Recerca MútuaTerrassa and Movement Disorders Unit, Department of Neurology, University Hospital MútuaTerrassa, Barcelona, Spain
- Memory Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Rachel Raybould
- UKDRI Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Richard Redon
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Centre National de la Recherche Scientifique, INSERM, l'institut du Thorax, Nantes, France
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Anne-Claire Richard
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Steffi G Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, Leipzig, Germany
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Stéphane Rousseau
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Natalie S Ryan
- Dementia Research Centre, University College London Queen Square Institute of Neurology, London, UK
| | - Salha Saad
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Pascual Sanchez-Juan
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Neurology Service, Marqués de Valdecilla University Hospital (University of Cantabria and IDIVAL), Santander, Spain
| | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Jonathan M Schott
- Dementia Research Centre, University College London Queen Square Institute of Neurology, London, UK
| | - Davide Seripa
- Laboratory for Advanced Hematological Diagnostics, Department of Hematology and Stem Cell Transplant, Lecce, Italy
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Psychiatry and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
| | - Daoud Sie
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Erik A Sistermans
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Resie van Spaendonk
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Gianfranco Spalletta
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico Santa Lucia Foundation, Rome, Italy
| | - Niccolo' Tesi
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Betty Tijms
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Sven J van der Lee
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Michael Wagner
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - David Wallon
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Neurology and CNRMAJ, Rouen, France
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aline Zarea
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Neurology and CNRMAJ, Rouen, France
| | - Jordi Clarimon
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - John C van Swieten
- Department of Neurology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Carlos Cruchaga
- Neurogenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Psychiatry Department, Washington University School of Medicine, St Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - John Hardy
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Psychiatry and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Simon Mead
- Medical Research Council Prion Unit at University College London, University College London Institute of Prion Diseases, London, UK
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Nuffield Department of Population Health Oxford University, Oxford, UK
| | - Julie Williams
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Gaël Nicolas
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France.
| | - Céline Bellenguez
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Jean-Charles Lambert
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France.
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12
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van der Laan L, Rooney K, Alders M, Relator R, McConkey H, Kerkhof J, Levy MA, Lauffer P, Aerden M, Theunis M, Legius E, Tedder ML, Vissers LELM, Koene S, Ruivenkamp C, Hoffer MJV, Wieczorek D, Bramswig NC, Herget T, González VL, Santos-Simarro F, Tørring PM, Denomme-Pichon AS, Isidor B, Keren B, Julia S, Schaefer E, Francannet C, Maillard PY, Misra-Isrie M, Van Esch H, Mannens MMAM, Sadikovic B, van Haelst MM, Henneman P. Episignature Mapping of TRIP12 Provides Functional Insight into Clark-Baraitser Syndrome. Int J Mol Sci 2022; 23:ijms232213664. [PMID: 36430143 PMCID: PMC9690904 DOI: 10.3390/ijms232213664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Clark-Baraitser syndrome is a rare autosomal dominant intellectual disability syndrome caused by pathogenic variants in the TRIP12 (Thyroid Hormone Receptor Interactor 12) gene. TRIP12 encodes an E3 ligase in the ubiquitin pathway. The ubiquitin pathway includes activating E1, conjugating E2 and ligating E3 enzymes which regulate the breakdown and sorting of proteins. This enzymatic pathway is crucial for physiological processes. A significant proportion of TRIP12 variants are currently classified as variants of unknown significance (VUS). Episignatures have been shown to represent a powerful diagnostic tool to resolve inconclusive genetic findings for Mendelian disorders and to re-classify VUSs. Here, we show the results of DNA methylation episignature analysis in 32 individuals with pathogenic, likely pathogenic and VUS variants in TRIP12. We identified a specific and sensitive DNA methylation (DNAm) episignature associated with pathogenic TRIP12 variants, establishing its utility as a clinical biomarker for Clark-Baraitser syndrome. In addition, we performed analysis of differentially methylated regions as well as functional correlation of the TRIP12 genome-wide methylation profile with the profiles of 56 additional neurodevelopmental disorders.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Peter Lauffer
- Department of Pediatric Endocrinology, Emma Children’s Hospital, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Mio Aerden
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Miel Theunis
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | | | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Mariette J. V. Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Nuria C. Bramswig
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Vanesa López González
- Sección Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, CIBERER, 30120 Murcia, Spain
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, 28029 Madrid, Spain
| | - Pernille M. Tørring
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Anne-Sophie Denomme-Pichon
- UF6254 Innovation en Diagnostic Genomique des Maladies Rares, 21070 Dijon, France
- Équipe Génétique des Anomalies du Développement (GAD), CHU Dijon-Bourgogne, 21000 Dijon, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France
| | - Boris Keren
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne Université, 75013 Paris, France
| | - Sophie Julia
- Service de Génétique Clinique, CHU Toulouse, 31300 Toulouse, France
| | - Elise Schaefer
- Service de Génétique Clinique, CHU Toulouse, 31300 Toulouse, France
| | - Christine Francannet
- Service de Genetique Medicale, CHU de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | | | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Hilde Van Esch
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
- Correspondence: (B.S.); (P.H.)
| | - Mieke M. van Haelst
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Correspondence: (B.S.); (P.H.)
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13
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Levy MA, Relator R, McConkey H, Pranckeviciene E, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Ferilli M, Fletcher RS, Cherick F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Plomp AS, Poulton C, Reilly J, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, John MS, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci TB, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Campion D, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Heron D, Husson T, Kernohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vincent M, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Hum Mutat 2022; 43:1609-1628. [PMID: 35904121 DOI: 10.1002/humu.24446] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 12/06/2021] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022]
Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Erinija Pranckeviciene
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Mariet W Elting
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Marco Ferilli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Florian Cherick
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, The Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000, Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | | | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | | | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Delphine Heron
- AP-HP, Département de Génétique Médicale, Groupe Hospitalier Pitié Salpétrière, Paris, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, UK, and Sheffield Children's Hospital NHS Foundation Trust
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Dept of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Marie Vincent
- Service de génétique Médicale, CHU Nantes, France.,Institut du thorax, INSERM, CNRS, UNIV Nantes, 44007, Nantes, France
| | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
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14
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Verberne EA, Westermann JM, de Vries TI, Ecury-Goossen GM, Lo-A-Njoe SM, Manshande ME, Faries S, Veenhuis HD, Philippi P, Falix FA, Rosina-Angelista I, Ponson-Wever M, Rafael-Croes L, Thorsen P, Arends E, de Vroomen M, Nagelkerke SQ, Tilanus M, van der Veken LT, Huijsdens-van Amsterdam K, van der Kevie-Kersemaekers AM, Alders M, Mannens MMAM, van Haelst MM. Genetic care in geographically isolated small island communities: 8 years of experience in the Dutch Caribbean. Am J Med Genet A 2022; 188:1777-1791. [PMID: 35253369 PMCID: PMC9314971 DOI: 10.1002/ajmg.a.62708] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/25/2022] [Accepted: 02/12/2022] [Indexed: 11/16/2022]
Abstract
Worldwide, there are large inequalities in genetic service delivery. In 2011, we established a bi‐annual joint pediatric‐genetics clinic with a visiting clinical geneticist in the Dutch Caribbean. This retrospective study evaluates the yield of diagnostic testing and the clinical utility of a diagnosis for patients with rare diseases on these relatively isolated, resource‐limited islands. A total of 331 patients that were referred to the clinical geneticist between November 2011 and November 2019 and had genetic testing were included in this study. A total of 508 genetic tests were performed on these patients. Microarray, next‐generation sequencing gene panels, and single‐gene analyses were the most frequently performed genetic tests. A molecularly confirmed diagnosis was established in 33% of patients (n = 108). Most diagnosed patients had single nucleotide variants or small insertions and/or deletions (48%) or copy number variants (34%). Molecular diagnostic yield was highest in patients referred for seizures and developmental delay/intellectual disability. The genetic diagnosis had an impact on clinical management in 52% of patients. Referrals to other health professionals and changes in therapy were the most frequently reported clinical consequences. In conclusion, despite limited financial resources, our genetics service resulted in a reasonably high molecular diagnostic yield. Even in this resource‐limited setting, a genetic diagnosis had an impact on clinical management for the majority of patients. Our approach with a visiting clinical geneticist may be an example for others who are developing genetic services in similar settings.
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Affiliation(s)
- Eline A Verberne
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jonne M Westermann
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Tamar I de Vries
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Medical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | | | | | - Sonja Faries
- Department of Pediatrics, Curaçao Medical Center, Willemstad, Curaçao
| | - Hans D Veenhuis
- Department of Pediatrics, Curaçao Medical Center, Willemstad, Curaçao
| | - Patricia Philippi
- Department of Pediatrics, Curaçao Medical Center, Willemstad, Curaçao
| | - Farah A Falix
- Department of Pediatrics, Curaçao Medical Center, Willemstad, Curaçao
| | | | - Maria Ponson-Wever
- Department of Pediatrics, Dr. Horacio E. Oduber Hospital, Oranjestad, Aruba
| | | | - Patricia Thorsen
- Department of Pediatrics, Dr. Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Eric Arends
- Department of Pediatrics, Dr. Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Maartje de Vroomen
- Department of Pediatrics, Fundashon Mariadal, Kralendijk, Bonaire, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sietse Q Nagelkerke
- Department of Pediatrics, Fundashon Mariadal, Kralendijk, Bonaire, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijn Tilanus
- Department of Pediatrics, St. Maarten Medical Center, Cay Hill, St. Maarten
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Karin Huijsdens-van Amsterdam
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Anne-Marie van der Kevie-Kersemaekers
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Mieke M van Haelst
- Department of Human Genetics and Amsterdam Reproduction & Development research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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15
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Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders. HGG Adv 2022; 3:100075. [PMID: 35047860 PMCID: PMC8756545 DOI: 10.1016/j.xhgg.2021.100075] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [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: 07/12/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, UK
| | | | - Mariet W Elting
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Florian Cherik
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, the Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Kristin D Kerrnohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
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16
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Chilunga FP, Henneman P, Venema A, Meeks KAC, Requena-Méndez A, Beune E, Mockenhaupt FP, Smeeth L, Bahendeka S, Danquah I, Klipstein-Grobusch K, Adeyemo A, Mannens MMAM, Agyemang C. Genome-wide DNA methylation analysis on C-reactive protein among Ghanaians suggests molecular links to the emerging risk of cardiovascular diseases. NPJ Genom Med 2021; 6:46. [PMID: 34117263 PMCID: PMC8196035 DOI: 10.1038/s41525-021-00213-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/22/2020] [Accepted: 05/20/2021] [Indexed: 12/28/2022] Open
Abstract
Molecular mechanisms at the intersection of inflammation and cardiovascular diseases (CVD) among Africans are still unknown. We performed an epigenome-wide association study to identify loci associated with serum C-reactive protein (marker of inflammation) among Ghanaians and further assessed whether differentially methylated positions (DMPs) were linked to CVD in previous reports, or to estimated CVD risk in the same population. We used the Illumina Infinium® HumanMethylation450 BeadChip to obtain DNAm profiles of blood samples in 589 Ghanaians from the RODAM study (without acute infections, not taking anti-inflammatory medications, CRP levels < 40 mg/L). We then used linear models to identify DMPs associated with CRP concentrations. Post-hoc, we evaluated associations of identified DMPs with elevated CVD risk estimated via ASCVD risk score. We also performed subset analyses at CRP levels ≤10 mg/L and replication analyses on candidate probes. Finally, we assessed for biological relevance of our findings in public databases. We subsequently identified 14 novel DMPs associated with CRP. In post-hoc evaluations, we found that DMPs in PC, BTG4 and PADI1 showed trends of associations with estimated CVD risk, we identified a separate DMP in MORC2 that was associated with CRP levels ≤10 mg/L, and we successfully replicated 65 (24%) of previously reported DMPs. All DMPs with gene annotations (13) were biologically linked to inflammation or CVD traits. We have identified epigenetic loci that may play a role in the intersection between inflammation and CVD among Ghanaians. Further studies among other Africans are needed to confirm our findings.
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Affiliation(s)
- Felix P Chilunga
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam Reproduction & Development research institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Amsterdam Reproduction & Development research institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ana Requena-Méndez
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Global Public Health, Karolinska Institutet, Solna, Sweden
| | - Erik Beune
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank P Mockenhaupt
- Institute of Tropical Medicine and International Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Liam Smeeth
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Silver Bahendeka
- Department of Medicine, MKPGMS-Uganda Martyrs University, Kampala, Uganda
| | - Ina Danquah
- Heidelberg Institute of Global Health (HIGH), Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Kerstin Klipstein-Grobusch
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Amsterdam Reproduction & Development research institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
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17
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Ensink JBM, Keding TJ, Henneman P, Venema A, Papale LA, Alisch RS, Westerman Y, van Wingen G, Zantvoord J, Middeldorp CM, Mannens MMAM, Herringa RJ, Lindauer RJL. Differential DNA Methylation Is Associated With Hippocampal Abnormalities in Pediatric Posttraumatic Stress Disorder. Biol Psychiatry Cogn Neurosci Neuroimaging 2021; 6:1063-1070. [PMID: 33964519 DOI: 10.1016/j.bpsc.2021.04.016] [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] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/01/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Recent findings in neuroimaging and epigenetics offer important insights into brain structures and biological pathways of altered gene expression associated with posttraumatic stress disorder (PTSD). However, it is unknown to what extent epigenetic mechanisms are associated with PTSD and its neurobiology in youth. METHODS In this study, we combined a methylome-wide association study and structural neuroimaging measures in a Dutch cohort of youths with PTSD (8-18 years of age). We aimed to replicate findings in a similar independent U.S. cohort. RESULTS We found significant methylome-wide associations for pediatric PTSD (false discovery rate p < .05) compared with non-PTSD control groups (traumatized and nontraumatized youths). Methylation differences on nine genes were replicated, including genes related to glucocorticoid functioning. In both cohorts, methylation on OLFM3 gene was further associated with anterior hippocampal volume. CONCLUSIONS These findings point to molecular pathways involved in inflammation, stress response, and neuroplasticity as potential contributors to neural abnormalities and provide potentially unique biomarkers and treatment targets for pediatric PTSD.
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Affiliation(s)
- Judith B M Ensink
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Department of Child and Adolescent Psychiatry, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Academic Centre for Child and Adolescent Psychiatry, De Bascule, Amsterdam, the Netherlands; Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Taylor J Keding
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Andrea Venema
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Ligia A Papale
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Yousha Westerman
- Academic Centre for Child and Adolescent Psychiatry, De Bascule, Amsterdam, the Netherlands
| | - Guido van Wingen
- Department of Psychiatry, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands
| | - Jasper Zantvoord
- Department of Psychiatry, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands
| | - Christel M Middeldorp
- Children's Health Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Marcel M A M Mannens
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Ryan J Herringa
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin.
| | - Ramon J L Lindauer
- Department of Child and Adolescent Psychiatry, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Academic Centre for Child and Adolescent Psychiatry, De Bascule, Amsterdam, the Netherlands
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18
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Li Yim AYF, Ferrero E, Maratou K, Lewis HD, Royal G, Tough DF, Larminie C, Mannens MMAM, Henneman P, de Jonge WJ, van de Sande MGH, Gerlag DM, Prinjha RK, Tak PP. Novel Insights Into Rheumatoid Arthritis Through Characterization of Concordant Changes in DNA Methylation and Gene Expression in Synovial Biopsies of Patients With Differing Numbers of Swollen Joints. Front Immunol 2021; 12:651475. [PMID: 33968050 PMCID: PMC8100206 DOI: 10.3389/fimmu.2021.651475] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
In this study, we sought to characterize synovial tissue obtained from individuals with arthralgia and disease-specific auto-antibodies and patients with established rheumatoid arthritis (RA), by applying an integrative multi-omics approach where we investigated differences at the level of DNA methylation and gene expression in relation to disease pathogenesis. We performed concurrent whole-genome bisulphite sequencing and RNA-Sequencing on synovial tissue obtained from the knee and ankle from 4 auto-antibody positive arthralgia patients and thirteen RA patients. Through multi-omics factor analysis we observed that the latent factor explaining the variance in gene expression and DNA methylation was associated with Swollen Joint Count 66 (SJC66), with patients with SJC66 of 9 or more displaying separation from the rest. Interrogating these observed differences revealed activation of the immune response as well as dysregulation of cell adhesion pathways at the level of both DNA methylation and gene expression. We observed differences for 59 genes in particular at the level of both transcript expression and DNA methylation. Our results highlight the utility of genome-wide multi-omics profiling of synovial samples for improved understanding of changes associated with disease spread in arthralgia and RA patients, and point to novel candidate targets for the treatment of the disease.
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Affiliation(s)
- Andrew Y. F. Li Yim
- R&D GlaxoSmithKline, Stevenage, United Kingdom
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction & Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | | | | | | | | | | | - Marcel M. A. M. Mannens
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction & Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction & Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Department of Surgery, University Clinic of Bonn, Bonn, Germany
| | - Marleen G. H. van de Sande
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam Institute for Infection & Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Institute for Infection & Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | | | - Paul P. Tak
- R&D GlaxoSmithKline, Stevenage, United Kingdom
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam Institute for Infection & Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Department of Rheumatology, Ghent University, Ghent, Belgium
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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19
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Verberne EA, Ecury-Goossen GM, Manshande ME, Ponson-Wever M, de Vroomen M, Tilanus M, Mannens MMAM, Henneman L, van Haelst MM. Clinical and community genetics services in the Dutch Caribbean. J Community Genet 2021; 12:497-501. [PMID: 33751485 PMCID: PMC7943254 DOI: 10.1007/s12687-021-00515-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/11/2020] [Accepted: 03/01/2021] [Indexed: 10/26/2022] Open
Abstract
The Caribbean part of the Kingdom of the Netherlands consists of six islands: Aruba, Bonaire, Curaçao, St. Maarten, St. Eustatius, and Saba. Because of their small size and relative remoteness, they face several economic and healthcare challenges, including limited access to genetics services. In this article, we provide an overview of the clinical and community genetics services that are available in the Dutch Caribbean. In particular, we describe our joint pediatric-genetics clinic with a visiting clinical geneticist that was established in 2011 to provide clinical genetics services for the pediatric population of the Dutch Caribbean.
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Affiliation(s)
- Eline A Verberne
- Department of Clinical Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - Maria Ponson-Wever
- Department of Pediatrics, Dr. Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Maartje de Vroomen
- Department of Pediatrics, Fundashon Mariadal, Kralendijk, Bonaire, The Netherlands.,Department of Pediatrics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Martijn Tilanus
- Department of Pediatrics, St. Maarten Medical Center, Cay Hill, St. Maarten
| | - Marcel M A M Mannens
- Department of Clinical Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Mieke M van Haelst
- Department of Clinical Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands. .,Department of Clinical Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands.
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20
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Sadikovic B, Levy MA, Kerkhof J, Aref-Eshghi E, Schenkel L, Stuart A, McConkey H, Henneman P, Venema A, Schwartz CE, Stevenson RE, Skinner SA, DuPont BR, Fletcher RS, Balci TB, Siu VM, Granadillo JL, Masters J, Kadour M, Friez MJ, van Haelst MM, Mannens MMAM, Louie RJ, Lee JA, Tedder ML, Alders M. Correction: Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet Med 2021; 23:2228. [PMID: 33637969 PMCID: PMC9119201 DOI: 10.1038/s41436-021-01130-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Andrea Venema
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Victoria Mok Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jennefer Masters
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Mike Kadour
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | | | - Mieke M van Haelst
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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21
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Sadikovic B, Levy MA, Kerkhof J, Aref-Eshghi E, Schenkel L, Stuart A, McConkey H, Henneman P, Venema A, Schwartz CE, Stevenson RE, Skinner SA, DuPont BR, Fletcher RS, Balci TB, Siu VM, Granadillo JL, Masters J, Kadour M, Friez MJ, van Haelst MM, Mannens MMAM, Louie RJ, Lee JA, Tedder ML, Alders M. Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet Med 2021; 23:1065-1074. [PMID: 33547396 PMCID: PMC8187150 DOI: 10.1038/s41436-020-01096-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 01/23/2023] Open
Abstract
Purpose We describe the clinical implementation of genome-wide DNA methylation analysis in rare disorders across the EpiSign diagnostic laboratory network and the assessment of results and clinical impact in the first subjects tested. Methods We outline the logistics and data flow between an integrated network of clinical diagnostics laboratories in Europe, the United States, and Canada. We describe the clinical validation of EpiSign using 211 specimens and assess the test performance and diagnostic yield in the first 207 subjects tested involving two patient subgroups: the targeted cohort (subjects with previous ambiguous/inconclusive genetic findings including genetic variants of unknown clinical significance) and the screening cohort (subjects with clinical findings consistent with hereditary neurodevelopmental syndromes and no previous conclusive genetic findings). Results Among the 207 subjects tested, 57 (27.6%) were positive for a diagnostic episignature including 48/136 (35.3%) in the targeted cohort and 8/71 (11.3%) in the screening cohort, with 4/207 (1.9%) remaining inconclusive after EpiSign analysis. Conclusion This study describes the implementation of diagnostic clinical genomic DNA methylation testing in patients with rare disorders. It provides strong evidence of clinical utility of EpiSign analysis, including the ability to provide conclusive findings in the majority of subjects tested.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Andrea Venema
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Victoria Mok Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jennefer Masters
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Mike Kadour
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | | | - Mieke M van Haelst
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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22
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Vos N, Oussaada SM, Cooiman MI, Kleinendorst L, Ter Horst KW, Hazebroek EJ, Romijn JA, Serlie MJ, Mannens MMAM, van Haelst MM. Bariatric Surgery for Monogenic Non-syndromic and Syndromic Obesity Disorders. Curr Diab Rep 2020; 20:44. [PMID: 32729070 PMCID: PMC7391392 DOI: 10.1007/s11892-020-01327-7] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW The global prevalence of obesity has increased rapidly over the last decades, posing a severe threat to human health. Currently, bariatric surgery is the most effective therapy for patients with morbid obesity. It is unknown whether this treatment is also suitable for patients with obesity due to a confirmed genetic defect (genetic obesity disorders). Therefore, this review aims to elucidate the role of bariatric surgery in the treatment of genetic obesity. RECENT FINDINGS In monogenic non-syndromic obesity, an underlying genetic defect seems to be the most important factor determining the efficacy of bariatric surgery. In syndromic obesity, bariatric surgery result data are scarce, and even though some promising follow-up results have been reported, caution is required as patients with more severe behavioral and developmental disorders might have poorer outcomes. There is limited evidence in support of bariatric surgery as a treatment option for genetic obesity disorders; hence, no strong statements can be made regarding the efficacy and safety of these procedures for these patients. However, considering that patients with genetic obesity often present with life-threatening obesity-related comorbidities, we believe that bariatric surgery could be considered a last-resort treatment option in selected patients.
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Affiliation(s)
- Niels Vos
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, The Netherlands
| | - Sabrina M Oussaada
- Department of Endocrinology and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Mellody I Cooiman
- Department of Bariatric Surgery, Rijnstate Hospital and Vitalys Clinic, Arnhem, The Netherlands
| | - Lotte Kleinendorst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, The Netherlands
| | - Kasper W Ter Horst
- Department of Endocrinology and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Eric J Hazebroek
- Department of Bariatric Surgery, Rijnstate Hospital and Vitalys Clinic, Arnhem, The Netherlands
| | - Johannes A Romijn
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Mireille J Serlie
- Department of Endocrinology and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, The Netherlands
| | - Mieke M van Haelst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, The Netherlands.
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands.
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23
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Verberne EA, Faries S, Mannens MMAM, Postma AV, van Haelst MM. Expanding the phenotype of biallelic RNPC3 variants associated with growth hormone deficiency. Am J Med Genet A 2020; 182:1952-1956. [PMID: 32462814 PMCID: PMC7496482 DOI: 10.1002/ajmg.a.61632] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/21/2022]
Abstract
Pathogenic variants in components of the minor spliceosome have been associated with several human diseases. Recently, it was reported that biallelic RNPC3 variants lead to severe isolated growth hormone deficiency and pituitary hypoplasia. The RNPC3 gene codes for the U11/U12‐65K protein, a component of the minor spliceosome. The minor spliceosome plays a role in the splicing of minor (U12‐type) introns, which are present in ~700–800 genes in humans and represent about 0.35% of all introns. Here, we report a second family with biallelic RNPC3 variants in three siblings with a growth hormone deficiency, central congenital hypothyroidism, congenital cataract, developmental delay/intellectual deficiency and delayed puberty. These cases further confirm the association between biallelic RNPC3 variants and severe postnatal growth retardation due to growth hormone deficiency. Furthermore, these cases show that the phenotype of this minor spliceosome‐related disease might be broader than previously described.
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Affiliation(s)
- Eline A Verberne
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sonja Faries
- Department of Pediatrics, Curaçao Medical Center, Willemstad, Curacao
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex V Postma
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Mieke M van Haelst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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24
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Struijk RB, Dorssers LCJ, Henneman P, Rijlaarsdam MA, Venema A, Jongejan A, Mannens MMAM, Looijenga LHJ, Repping S, van Pelt AMM. Comparing genome-scale DNA methylation and CNV marks between adult human cultured ITGA6+ testicular cells and seminomas to assess in vitro genomic stability. PLoS One 2020; 15:e0230253. [PMID: 32176716 PMCID: PMC7075560 DOI: 10.1371/journal.pone.0230253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
Autologous transplantation of spermatogonial stem cells is a promising new avenue to restore fertility in infertile recipients. Expansion of the initial spermatogonial stem cell pool through cell culturing is a necessary step to obtain enough cells for effective repopulation of the testis after transplantation. Since in vitro propagation can lead to (epi-)genetic mutations and possibly malignant transformation of the starting cell population, we set out to investigate genome-wide DNA methylation status in uncultured and cultured primary testicular ITGA6+ sorted cells and compare them with germ cell tumor samples of the seminoma subtype. Seminomas displayed a severely global hypomethylated profile, including loss of genomic imprinting, which we did not detect in cultured primary testicular ITGA6+ cells. Differential methylation analysis revealed altered regulation of gamete formation and meiotic processes in cultured primary testicular ITGA6+ cells but not in seminomas. The pivotal POU5F1 marker was hypomethylated in seminomas but not in uncultured or cultured primary testicular ITGA6+ cells, which is reflected in the POU5F1 mRNA expression levels. Lastly, seminomas displayed a number of characteristic copy number variations that were not detectable in primary testicular ITGA6+ cells, either before or after culture. Together, the data show a distinct DNA methylation patterns in cultured primary testicular ITGA6+ cells that does not resemble the pattern found in seminomas, but also highlight the need for more sensitive methods to fully exclude the presence of malignant cells after culture and to further study the epigenetic events that take place during in vitro culture.
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Affiliation(s)
- Robert B. Struijk
- Center for Reproductive Medicine, Research Institute Reproduction and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Lambert C. J. Dorssers
- Department of Pathology, Erasmus MC University Medical Center, Rotterdam, and Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Martin A. Rijlaarsdam
- Department of Pathology, Erasmus MC University Medical Center, Rotterdam, and Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Center for Reproductive Medicine, Research Institute Reproduction and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcel M. A. M. Mannens
- Department of Clinical Genetics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Leendert H. J. Looijenga
- Department of Pathology, Erasmus MC University Medical Center, Rotterdam, and Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sjoerd Repping
- Center for Reproductive Medicine, Research Institute Reproduction and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ans M. M. van Pelt
- Center for Reproductive Medicine, Research Institute Reproduction and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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25
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Meeks KAC, Henneman P, Venema A, Addo J, Bahendeka S, Burr T, Danquah I, Galbete C, Mannens MMAM, Mockenhaupt FP, Owusu-Dabo E, Rotimi CN, Schulze MB, Smeeth L, Spranger J, Zafarmand MH, Adeyemo A, Agyemang C. Epigenome-wide association study in whole blood on type 2 diabetes among sub-Saharan African individuals: findings from the RODAM study. Int J Epidemiol 2020; 48:58-70. [PMID: 30107520 DOI: 10.1093/ije/dyy171] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) results from a complex interplay between genetics and the environment. Several epigenome-wide association studies (EWAS) have found DNA methylation loci associated with T2D in European populations. However, data from African populations are lacking. We undertook the first EWAS for T2D among sub-Saharan Africans, aiming at identifying ubiquitous and novel DNA methylation loci associated with T2D. METHODS The Illumina 450k DNA-methylation array was used on whole blood samples of 713 Ghanaian participants (256 with T2D, 457 controls) from the cross-sectional Research on Obesity and Diabetes among African Migrants (RODAM) study. Differentially methylated positions (DMPs) for T2D and HbA1c were identified through linear regression analysis adjusted for age, sex, estimated cell counts, hybridization batch, array position and body mass index (BMI). We also did a candidate analysis of previously reported EWAS loci for T2D in non-African populations, identified through a systematic literature search. RESULTS Four DMPs [cg19693031 (TXNIP), cg04816311 (C7orf50), cg00574958 (CPT1A), cg07988171 (TPM4)] were associated with T2D after correction for inflation by possible systematic biases. The most strongly associated DMP-cg19693031, TXNIP (P = 2.6E-19) -showed hypomethylation in T2D cases compared with controls. Two out of the four DMPs [cg19693031 (TXNIP), cg04816311 (C7orf50)] remained associated with T2D after adjustment for BMI, and one locus [cg07988171 (TPM4)] that has not been reported previously. CONCLUSIONS In this first EWAS for T2D in sub-Saharan Africans, we have identified four DMPs at epigenome-wide level, one of which is novel. These findings provide insight into the epigenetic loci that underlie the burden of T2D in sub-Saharan Africans.
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Affiliation(s)
- Karlijn A C Meeks
- Department of Public Health, Amsterdam Public Health Research Institute, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Research Institute for Reproduction and Development, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Research Institute for Reproduction and Development, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Juliet Addo
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Silver Bahendeka
- Mother Kevin Postgraduate Medical School (MKPGMS), Uganda Martyrs University, Kampala, Uganda
| | - Tom Burr
- Genomics Department, Source BioScience, Nottingham, UK
| | - Ina Danquah
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany.,Institute for Social Medicine, Epidemiology and Health Economics, Charité - Universitaetsmedizin Berlin, Berlin, Germany
| | - Cecilia Galbete
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Research Institute for Reproduction and Development, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank P Mockenhaupt
- Institute of Tropical Medicine and International Health, Charité - University Medicine Berlin, Berlin, Germany
| | - Ellis Owusu-Dabo
- School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Liam Smeeth
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Joachim Spranger
- Department of Endocrinology and Metabolism, Charité - University Medicine Berlin, Berlin, Germany.,Partner site Berlin, German Centre for Cardiovascular Research (DZHK), Berlin, Germany.,Center for Cardiovascular Research (CCR), Charité - University Medicine Berlin, Berlin, Germany
| | - Mohammad H Zafarmand
- Department of Public Health, Amsterdam Public Health Research Institute, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Charles Agyemang
- Department of Public Health, Amsterdam Public Health Research Institute, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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26
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Chilunga FP, Henneman P, Requena-Méndez A, Meeks K, Beune E, Mannens MMAM, Agyemang C. Hyperuricaemia and its association with 10-year risk of cardiovascular disease among migrant and non-migrant African populations: the RODAM study. Trop Med Int Health 2019; 25:496-505. [PMID: 31825117 DOI: 10.1111/tmi.13362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE In the advent of rapid urbanisation, migration and epidemiological transition, the extent to which serum uric acid (sUA) affects cardiovascular disease (CVD) risk among Africans is not well understood. We assessed differences in sUA levels and associations with CVD risk among migrant Ghanaians in Europe and non-migrant Ghanaians in rural and urban Ghana. METHODS Baseline data from 633 rural, 916 urban and 2315 migrant participants (40-70 years) from the cross-sectional RODAM study were analysed. Hyperuricaemia was defined as sUA >7 mg/dl in men and >6 mg/dl in women. The 10-year risk of atherosclerotic cardiovascular disease (ASCVD) was calculated using the American College of Cardiology (ACC)/American Heart Association (AHA) risk score which takes into account ethnic minority populations. High CVD risk was defined as ASCVD risk scores ≥7.5%. Logistic regressions were used to assess associations between hyperuricaemia and CVD risk. RESULTS Prevalence for hyperuricaemia in rural, urban and migrant participants was 17.4%, 19.1% and 31.7% for men, and 15.9%, 18.2% and 33.2% for women, respectively. Hyperuricaemia was positively associated with elevated CVD risk among rural residents (adjusted OR for men 3.28, 95% CI: 1.21-8.96, 6.36, 95% CI: 2.98-13.56 for women), urban residents (1.12, 95% CI: 0.45-2.81 for men, 2.11, 95% CI: 1.26-3.52 for women) and migrants (1.73, 95% CI: 1.01-2.96 for men, 4.61, 95% CI: 3.05-6.97 for women). CONCLUSION Our study shows variations of sUA levels in different African contexts. Hyperuricaemia is associated with elevated 10-year CVD risk in both migrants and non-migrants. Further studies should identify factors driving associations between sUA and CVD risk in Africans.
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Affiliation(s)
- Felix P Chilunga
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ana Requena-Méndez
- ISGlobal, Barcelona Centre for International Health Research, Hospital Clinic-University of Barcelona, Barcelona, Spain
| | - Karlijn Meeks
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Erik Beune
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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Chen HJ, Li Yim AYF, Griffith GR, de Jonge WJ, Mannens MMAM, Ferrero E, Henneman P, de Winther MPJ. Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo. Front Immunol 2019; 10:2887. [PMID: 31921150 PMCID: PMC6917623 DOI: 10.3389/fimmu.2019.02887] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 07/15/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Macrophages are heterogeneous leukocytes regulated in a tissue- and disease-specific context. While in vitro macrophage models have been used to study diseases empirically, a systematic analysis of the transcriptome thereof is lacking. Here, we acquired gene expression data from eight commonly-used in vitro macrophage models to perform a meta-analysis. Specifically, we obtained gene expression data from unstimulated macrophages (M0) and macrophages stimulated with lipopolysaccharides (LPS) for 2–4 h (M-LPSearly), LPS for 24 h (M-LPSlate), LPS and interferon-γ (M-LPS+IFNγ), IFNγ (M-IFNγ), interleukin-4 (M-IL4), interleukin-10 (M-IL10), and dexamethasone (M-dex). Our meta-analysis identified consistently differentially expressed genes that have been implicated in inflammatory and metabolic processes. In addition, we built macIDR, a robust classifier capable of distinguishing macrophage activation states with high accuracy (>0.95). We classified in vivo macrophages with macIDR to define their tissue- and disease-specific characteristics. We demonstrate that alveolar macrophages display high resemblance to IL10 activation, but show a drop in IFNγ signature in chronic obstructive pulmonary disease patients. Adipose tissue-derived macrophages were classified as unstimulated macrophages, but acquired LPS-activation features in diabetic-obese patients. Rheumatoid arthritis synovial macrophages exhibit characteristics of IL10- or IFNγ-stimulation. Altogether, we defined consensus transcriptional profiles for the eight in vitro macrophage activation states, built a classification model, and demonstrated the utility of the latter for in vivo macrophages.
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Affiliation(s)
- Hung-Jen Chen
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Andrew Y F Li Yim
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Epigenetics Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom
| | - Guillermo R Griffith
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Marcel M A M Mannens
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Enrico Ferrero
- Computational Biology, Target Sciences, GlaxoSmithKline, Stevenage, United Kingdom
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Menno P J de Winther
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Institute for Cardiovascular Prevention (IPEK), Ludwig Maximilians University, Munich, Germany
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28
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Krzyzewska IM, Maas SM, Henneman P, Lip KVD, Venema A, Baranano K, Chassevent A, Aref-Eshghi E, van Essen AJ, Fukuda T, Ikeda H, Jacquemont M, Kim HG, Labalme A, Lewis SME, Lesca G, Madrigal I, Mahida S, Matsumoto N, Rabionet R, Rajcan-Separovic E, Qiao Y, Sadikovic B, Saitsu H, Sweetser DA, Alders M, Mannens MMAM. A genome-wide DNA methylation signature for SETD1B-related syndrome. Clin Epigenetics 2019; 11:156. [PMID: 31685013 PMCID: PMC6830011 DOI: 10.1186/s13148-019-0749-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/22/2019] [Indexed: 01/02/2023] Open
Abstract
SETD1B is a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 (H3K4) and is responsible for the epigenetic control of chromatin structure and gene expression. De novo microdeletions encompassing this gene as well as de novo missense mutations were previously linked to syndromic intellectual disability (ID). Here, we identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases. We demonstrate the clinical utility of this unique epi-signature by reclassifying previously identified SETD1B VUS (variant of uncertain significance) in two patients.
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Affiliation(s)
- I M Krzyzewska
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - S M Maas
- Amsterdam UMC, Department of Pediatrics, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - P Henneman
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - K V D Lip
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - A Venema
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - K Baranano
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - A Chassevent
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - E Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada
| | - A J van Essen
- University Medical Centre Groningen, University of Groningen, Department of Medical Genetics, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - T Fukuda
- Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - H Ikeda
- National Epilepsy Centre, NHO, Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - M Jacquemont
- Department of medical genetics, CHU La Reunion-Groupe Hospitalier Sud Reunion, La Reunion, France
| | - H-G Kim
- Neurological Disorder Center Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - A Labalme
- Department of medical genetics, Hospices Civils de Lyon, Bron, France
| | - S M E Lewis
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - G Lesca
- Department of medical genetics, Hospices Civils de Lyon, Bron, France
| | - I Madrigal
- Biochemistry and Molecular Genetics Service, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Center for Biomedical Network Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - S Mahida
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - N Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - R Rabionet
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, av diagonal 643, 08028, Barcelona, Spain
| | - E Rajcan-Separovic
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - Y Qiao
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - B Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada
| | - H Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - D A Sweetser
- MassGeneral Hospital, Division of Medical Genetics and Metabolism, 175 Cambridge St, Suite 500, Boston, Massachusetts, 02114, USA
| | - M Alders
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
| | - M M A M Mannens
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
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29
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Mannens MMAM. [Clinical implications of epigenetic changes]. Ned Tijdschr Geneeskd 2019; 163:D4123. [PMID: 31609563] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Inherited and acquired changes in DNA can influence the coding for gene products (proteins). When the function of a protein is disturbed, this may lead to disease. DNA in chromatin can be condensed or be arranged in an open structure. The activity of genes is significantly affected by the accessibility to DNA by transcription factors and other proteins involved in the transcription of genes. The accessibility of DNA is regulated by epigenetic processes, including methylation of cytosine. In these circumstances the nucleic sequence of the DNA does not change. Nevertheless, disturbances of these processes can also culminate in disease. Epigenetic changes to DNA are reversible. This offers opportunities for treatment and recovery in conditions that are a result of disturbed epigenetic processes.
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30
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Krzyzewska IM, Alders M, Maas SM, Bliek J, Venema A, Henneman P, Rezwan FI, Lip KVD, Mul AN, Mackay DJG, Mannens MMAM. Genome-wide methylation profiling of Beckwith-Wiedemann syndrome patients without molecular confirmation after routine diagnostics. Clin Epigenetics 2019; 11:53. [PMID: 30898153 PMCID: PMC6429826 DOI: 10.1186/s13148-019-0649-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 12/18/2018] [Accepted: 03/06/2019] [Indexed: 11/16/2022] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) is caused due to the disturbance of imprinted genes at chromosome 11p15. The molecular confirmation of this syndrome is possible in approximately 85% of the cases, whereas in the remaining 15% of the cases, the underlying defect remains unclear. The goal of our research was to identify new epigenetic loci related to BWS. We studied a group of 25 patients clinically diagnosed with BWS but without molecular conformation after DNA diagnostics and performed a whole genome methylation analysis using the HumanMethylation450 Array (Illumina).We found hypermethylation throughout the methylome in two BWS patients. The hypermethylated sites in these patients overlapped and included both non-imprinted and imprinted regions. This finding was not previously described in any BWS-diagnosed patient.Furthermore, one BWS patient exhibited aberrant methylation in four maternally methylated regions-IGF1R, NHP2L1, L3MBTL, and ZDBF2-that overlapped with the differentially methylated regions found in BWS patients with multi-locus imprinting disturbance (MLID). This finding suggests that the BWS phenotype can result from MLID without detectable methylation defects in the primarily disease-associated loci (11p15). Another patient manifested small but significant aberrant methylation in disease-associated loci at 11p near H19, possibly confirming the diagnosis in this patient.
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Affiliation(s)
- I M Krzyzewska
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - M Alders
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - S M Maas
- Amsterdam UMC, University of Amsterdam, Department of Pediatrics, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - J Bliek
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - A Venema
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - P Henneman
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - F I Rezwan
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - K V D Lip
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - A N Mul
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - D J G Mackay
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - M M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction & Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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31
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Li Yim AYF, de Bruyn JR, Duijvis NW, Sharp C, Ferrero E, de Jonge WJ, Wildenberg ME, Mannens MMAM, Buskens CJ, D’Haens GR, Henneman P, te Velde AA. A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients. PLoS One 2018; 13:e0209656. [PMID: 30589872 PMCID: PMC6307755 DOI: 10.1371/journal.pone.0209656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The chronic remitting and relapsing intestinal inflammation characteristic of Crohn's disease frequently leads to fibrosis and subsequent stenosis of the inflamed region. Approximately a third of all Crohn's disease patients require resection at some stage in their disease course. As the pathogenesis of Crohn's disease associated fibrosis is largely unknown, a strong necessity exists to better understand the pathophysiology thereof. METHODS In this study, we investigated changes of the DNA methylome and transcriptome of ileum-derived fibroblasts associated to the occurrence of Crohn's disease associated fibrosis. Eighteen samples were included in a DNA methylation array and twenty-one samples were used for RNA sequencing. RESULTS Most differentially methylated regions and differentially expressed genes were observed when comparing stenotic with non-inflamed samples. By contrast, few differences were observed when comparing Crohn's disease with non-Crohn's disease, or inflamed with non-inflamed tissue. Integrative methylation and gene expression analyses revealed dysregulation of genes associated to the PRKACA and E2F1 network, which is involved in cell cycle progression, angiogenesis, epithelial to mesenchymal transition, and bile metabolism. CONCLUSION Our research provides evidence that the methylome and the transcriptome are systematically dysregulated in stenosis-associated fibroblasts.
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Affiliation(s)
- Andrew Y. F. Li Yim
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom
| | - Jessica R. de Bruyn
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Gastroenterology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Nicolette W. Duijvis
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Catriona Sharp
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom
| | - Enrico Ferrero
- Computational Biology, Target Sciences, GlaxoSmithKline, Stevenage, United Kingdom
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Manon E. Wildenberg
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Marcel M. A. M. Mannens
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Christianne J. Buskens
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Geert R. D’Haens
- Department of Gastroenterology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Anje A. te Velde
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- * E-mail:
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32
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Chilunga FP, Boateng D, Henneman P, Beune E, Requena-Méndez A, Meeks K, Smeeth L, Addo J, Bahendeka S, Danquah I, Schulze MB, Klipstein-Grobusch K, Mannens MMAM, Agyemang C. Perceived discrimination and stressful life events are associated with cardiovascular risk score in migrant and non-migrant populations: The RODAM study. Int J Cardiol 2018; 286:169-174. [PMID: 30638750 DOI: 10.1016/j.ijcard.2018.12.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 09/01/2018] [Revised: 11/28/2018] [Accepted: 12/19/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND Psychosocial stress could be an underlying factor for emerging risk of cardiovascular diseases (CVD) in Africans. We assessed the association between psychosocial stress and estimated CVD risk among non-migrant Ghanaians and migrant Ghanaians living in Europe. METHODS Data from the Research on Obesity and Diabetes among African Migrants (RODAM) study, involving 2315 migrant and 1549 non-migrants aged 40-70 years were used for this study. Psychosocial stress included self-reported stress at work and home, recent negative life events and perceived discrimination. CVD risk was estimated using the pooled cohort equations with estimates ≥7.5% over 10 years defining high CVD risk. Adjusted Odds Ratios (AOR) and 95% confidence intervals (95% CI) were calculated by logistic regression with adjustments for socioeconomic status. RESULTS Prevalence for migrant and non-migrants were; 72.5% and 84.9% for psychosocial stress and 35.9% and 27.4% for high estimated CVD risk. Stress at work and home was not associated with a high estimated CVD risk in either group. Recent negative life events were associated with a high estimated CVD risk in non-migrants only (AOR 1.29, 95%CI 1.02-1.68, p = 0.048). Higher levels of perceived discrimination were associated with a high estimated CVD risk in migrants only (AOR 2.74, 95%CI 1.95-3.86, p < 0.001). CONCLUSIONS Among migrant populations, higher levels of perceived discrimination were associated with a high estimated CVD risk, and this was also true for recent negative life events among non-migrant populations. Further research is needed to identify context specific mechanisms that underlie associations between psychological characteristics and CVD risk.
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Affiliation(s)
- Felix P Chilunga
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, the Netherlands.
| | - Daniel Boateng
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, the Netherlands; School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Erik Beune
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Ana Requena-Méndez
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Spain
| | - Karlijn Meeks
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Liam Smeeth
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Juliet Addo
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Ina Danquah
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universitaet zu Berlin, Berlin Institute of Health, Institute for Social Medicine, Epidemiology and Health Economics, Germany
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Kerstin Klipstein-Grobusch
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, the Netherlands; Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Charles Agyemang
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, the Netherlands
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33
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Stalman SE, Solanky N, Ishida M, Alemán-Charlet C, Abu-Amero S, Alders M, Alvizi L, Baird W, Demetriou C, Henneman P, James C, Knegt LC, Leon LJ, Mannens MMAM, Mul AN, Nibbering NA, Peskett E, Rezwan FI, Ris-Stalpers C, van der Post JAM, Kamp GA, Plötz FB, Wit JM, Stanier P, Moore GE, Hennekam RC. Genetic Analyses in Small-for-Gestational-Age Newborns. J Clin Endocrinol Metab 2018; 103:917-925. [PMID: 29342293 DOI: 10.1210/jc.2017-01843] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/09/2018] [Indexed: 12/15/2022]
Abstract
CONTEXT Small for gestational age (SGA) can be the result of fetal growth restriction, which is associated with perinatal morbidity and mortality. Mechanisms that control prenatal growth are poorly understood. OBJECTIVE The aim of the current study was to gain more insight into prenatal growth failure and determine an effective diagnostic approach in SGA newborns. We hypothesized that one or more copy number variations (CNVs) and disturbed methylation and sequence variants may be present in genes associated with fetal growth. DESIGN A prospective cohort study of subjects with a low birth weight for gestational age. SETTING The study was conducted at an academic pediatric research institute. PATIENTS A total of 21 SGA newborns with a mean birth weight below the first centile and a control cohort of 24 appropriate-for-gestational-age newborns were studied. INTERVENTIONS Array comparative genomic hybridization, genome-wide methylation studies, and exome sequencing were performed. MAIN OUTCOME MEASURES The numbers of CNVs, methylation disturbances, and sequence variants. RESULTS The genetic analyses demonstrated three CNVs, one systematically disturbed methylation pattern, and one sequence variant explaining SGA. Additional methylation disturbances and sequence variants were present in 20 patients. In 19 patients, multiple abnormalities were found. CONCLUSION Our results confirm the influence of a large number of mechanisms explaining dysregulation of fetal growth. We concluded that CNVs, methylation disturbances, and sequence variants all contribute to prenatal growth failure. These genetic workups can be an effective diagnostic approach in SGA newborns.
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Affiliation(s)
- Susanne E Stalman
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Nita Solanky
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Miho Ishida
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Cristina Alemán-Charlet
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Sayeda Abu-Amero
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Marielle Alders
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Lucas Alvizi
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - William Baird
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Charalambos Demetriou
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Peter Henneman
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Chela James
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Lia C Knegt
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Lydia J Leon
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Adi N Mul
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Nicole A Nibbering
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Emma Peskett
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Faisal I Rezwan
- Department of Human Development and Health, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Carrie Ris-Stalpers
- Department of Gynecology and Obstetrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Joris A M van der Post
- Department of Gynecology and Obstetrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerdine A Kamp
- Department of Pediatrics, Tergooi Hospitals, Blaricum, The Netherlands
| | - Frans B Plötz
- Department of Pediatrics, Tergooi Hospitals, Blaricum, The Netherlands
| | - Jan M Wit
- Department of Pediatrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Philip Stanier
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Gudrun E Moore
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Raoul C Hennekam
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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34
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Abstract
OBJECTIVES Hypertrophic cardiomyopathy (HCM) is an inherited cardiac disorder that affects over one in 500 persons worldwide. The autosomal dominant transmission of HCM implies that many relatives are at risk for HCM associated morbidity and mortality, therefore genetic testing and counselling is of great importance. However, in only 50-60% of the patients a mutation is found, which hampers predictive genetic testing in relatives. In HCM patients in whom the causal mutation has not been identified (yet), phenocopies of HCM - i.e. diseases that mimic HCM - could be responsible for the HCM phenotype. One of the HCM phenocopies is transthyretin amyloidosis (ATTR), caused by mutations in the transthyretin (TTR) gene. METHODS From 697 HCM index patients referred to our cardiogenetics outpatient clinic and tested for HCM associated genes between January 1997 and December 2012, we selected the ones without a detected causal mutation (n = 345). In these patients, additional DNA analysis of the TTR gene was performed. RESULTS In four patients (1.2%), a TTR mutation was detected (E7G, V30M, T119M, V122I). The E7G mutation is probably a non-pathogenic mutation. The T119M mutation is a known TTR mutation, but does not cause a cardiac phenotype. So in two (0.6%) patients, TTR analysis identified the cause of their HCM. CONCLUSIONS ATTR should always be considered in patients with unexplained HCM, especially because of the great benefit of an early diagnosis regarding treatment and prognosis.
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Affiliation(s)
- Alexa M C Vermeer
- a Department of Clinical Genetics , Academic Medical Center , Amsterdam , The Netherlands.,b Department of Clinical and Experimental Cardiology, Heart Center , Academic Medical Center , Amsterdam , The Netherlands
| | - Anneloes Janssen
- a Department of Clinical Genetics , Academic Medical Center , Amsterdam , The Netherlands
| | - Peter C Boorsma
- a Department of Clinical Genetics , Academic Medical Center , Amsterdam , The Netherlands
| | - Marcel M A M Mannens
- a Department of Clinical Genetics , Academic Medical Center , Amsterdam , The Netherlands
| | - Arthur A M Wilde
- b Department of Clinical and Experimental Cardiology, Heart Center , Academic Medical Center , Amsterdam , The Netherlands.,c Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University , Jeddah , Kingdom of Saudi Arabia
| | - Imke Christiaans
- a Department of Clinical Genetics , Academic Medical Center , Amsterdam , The Netherlands
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Jansweijer JA, Nieuwhof K, Russo F, Hoorntje ET, Jongbloed JDH, Lekanne Deprez RH, Postma AV, Bronk M, van Rijsingen IAW, de Haij S, Biagini E, van Haelst PL, van Wijngaarden J, van den Berg MP, Wilde AAM, Mannens MMAM, de Boer RA, van Spaendonck-Zwarts KY, van Tintelen JP, Pinto YM. Truncating titin mutations are associated with a mild and treatable form of dilated cardiomyopathy. Eur J Heart Fail 2016; 19:512-521. [PMID: 27813223 DOI: 10.1002/ejhf.673] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [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: 04/02/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 11/09/2022] Open
Abstract
AIMS Truncating titin mutations (tTTN) occur in 25% of dilated cardiomyopathy (DCM) cases, but the phenotype and severity of disease they cause have not yet been systematically studied. We studied whether tTTN variants are associated with a clinically distinguishable form of DCM. METHODS AND RESULTS We compared clinical data on DCM probands and relatives with a tTTN mutation (n = 45, n = 73), LMNA mutation (n = 28, n = 29), and probands who tested negative for both genes [idiopathic DCM (iDCM); n = 60]. Median follow-up was at least 2.5 years in each group. TTN subjects presented with DCM at higher age than LMNA subjects (probands 47.9 vs. 40.4 years, P = 0.004; relatives 59.8 vs. 47.0 years, P = 0.01), less often developed LVEF <35% [probands hazard ratio (HR) 0.38, P = 0.002], had higher age of death (probands 70.4 vs. 59.4 years, P < 0.001; relatives 74.1 vs. 58.4 years, P = 0.008), and had better composite outcome (malignant ventricular arrhythmia, heart transplantation, or death; probands HR 0.09, P < 0.001; relatives HR 0.21, P = 0.02) than LMNA subjects and iDCM subjects (HR 0.36, P = 0.07). An LVEF increase of at least 10% occurred in 46.9% of TTN subjects after initiation of standard heart failure treatment, while this only occurred in 6.5% of LMNA subjects (P < 0.001) and 18.5% of iDCM subjects (P = 0.02). This was confirmed in families with co-segregation, in which the 10% point LVEF increase occurred in 55.6% of subjects (P = 0.003 vs. LMNA, P = 0.079 vs. iDCM). CONCLUSIONS This study shows that tTTN-associated DCM is less severe at presentation and more amenable to standard therapy than LMNA mutation-induced DCM or iDCM.
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Affiliation(s)
- Joeri A Jansweijer
- AMC Heart Center, Department of Clinical and Experimental Cardiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Karin Nieuwhof
- Department of Clinical Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Francesco Russo
- Department of Clinical Genetics, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Edgar T Hoorntje
- Department of Clinical Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jan D H Jongbloed
- Department of Clinical Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ronald H Lekanne Deprez
- Department of Clinical Genetics, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex V Postma
- Department of Anatomy, Embryology and Physiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Marieke Bronk
- Department of Clinical Genetics, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Ingrid A W van Rijsingen
- AMC Heart Center, Department of Clinical and Experimental Cardiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Simone de Haij
- Department of Clinical Genetics, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Elena Biagini
- Department of Cardiology, S. Orsola-Malpighi Hospital, Bologna University, Italy
| | | | | | - Maarten P van den Berg
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arthur A M Wilde
- AMC Heart Center, Department of Clinical and Experimental Cardiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Rudolf A de Boer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Karin Y van Spaendonck-Zwarts
- Department of Clinical Genetics, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - J Peter van Tintelen
- Department of Clinical Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Clinical Genetics, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Yigal M Pinto
- AMC Heart Center, Department of Clinical and Experimental Cardiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
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Li Yim AYF, Duijvis NW, Zhao J, de Jonge WJ, D'Haens GRAM, Mannens MMAM, Mul ANPM, Te Velde AA, Henneman P. Peripheral blood methylation profiling of female Crohn's disease patients. Clin Epigenetics 2016; 8:65. [PMID: 27279921 PMCID: PMC4897922 DOI: 10.1186/s13148-016-0230-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 01/22/2016] [Accepted: 05/22/2016] [Indexed: 01/17/2023] Open
Abstract
Background Crohn’s disease (CD) is a chronic inflammatory disorder belonging to the inflammatory bowel diseases (IBD). CD affects distinct parts of the gastrointestinal tract, leading to symptoms including diarrhea, fever, abdominal pain, weight loss, and anemia. The aim of this study was to assess whether the DNA methylome of peripheral blood cells can be associated with CD in women. Methods Samples were obtained from 18 female patients with histologically confirmed ileal or ileocolic CD and 25 healthy age- and gender-matched controls (mean age and standard deviation: 30.5 ± 6.5 years for both groups). Genome-wide DNA methylation was determined using the Illumina HumanMethylation 450k BeadChip. Results Our analysis implicated 4287 differentially methylated positions (DMPs; corrected p < 0.05) that are associated to 2715 unique genes. Gene ontology enrichment analysis revealed significant enrichment of our DMPs in immune response processes and inflammatory pathways. Of the 4287 DMPs, 32 DMPs were located on chromosome X with several hits for MIR223 and PABPC5. Comparison with previously performed (epi)genome-wide studies revealed that we replicated 33 IBD-associated genes. In addition to DMPs, we found eight differentially methylated regions (DMRs). Conclusions CD patients display a characteristic DNA methylation landscape, with the differentially methylated genes being implicated in immune response. Additionally, DMPs were found on chromosome X suggesting X-linked manifestations of CD that could be associated with female-specific symptoms. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0230-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Y F Li Yim
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Academic Medical Center Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Epinova Discovery Performance Unit, GlaxoSmithKline, Stevenage, UK
| | - Nicolette W Duijvis
- Tytgat Institute for Liver & Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - Jing Zhao
- Tytgat Institute for Liver & Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver & Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - Geert R A M D'Haens
- Department of Gastroenterology, Academic Medical Center, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Academic Medical Center Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Adri N P M Mul
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Academic Medical Center Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Anje A Te Velde
- Tytgat Institute for Liver & Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Academic Medical Center Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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Rump P, Jazayeri O, van Dijk-Bos KK, Johansson LF, van Essen AJ, Verheij JBGM, Veenstra-Knol HE, Redeker EJW, Mannens MMAM, Swertz MA, Alizadeh BZ, van Ravenswaaij-Arts CMA, Sinke RJ, Sikkema-Raddatz B. Whole-exome sequencing is a powerful approach for establishing the etiological diagnosis in patients with intellectual disability and microcephaly. BMC Med Genomics 2016; 9:7. [PMID: 26846091 PMCID: PMC4743197 DOI: 10.1186/s12920-016-0167-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/25/2016] [Indexed: 12/19/2022] Open
Abstract
Background Clinical and genetic heterogeneity in monogenetic disorders represents a major diagnostic challenge. Although the presence of particular clinical features may aid in identifying a specific cause in some cases, the majority of patients remain undiagnosed. Here, we investigated the utility of whole-exome sequencing as a diagnostic approach for establishing a molecular diagnosis in a highly heterogeneous group of patients with varied intellectual disability and microcephaly. Methods Whole-exome sequencing was performed in 38 patients, including three sib-pairs, in addition to or in parallel with genetic analyses that were performed during the diagnostic work-up of the study participants. Results In ten out of these 35 families (29 %), we found mutations in genes already known to be related to a disorder in which microcephaly is a main feature. Two unrelated patients had mutations in the ASPM gene. In seven other patients we found mutations in RAB3GAP1, RNASEH2B, KIF11, ERCC8, CASK, DYRK1A and BRCA2. In one of the sib-pairs, mutations were found in the RTTN gene. Mutations were present in seven out of our ten families with an established etiological diagnosis with recessive inheritance. Conclusions We demonstrate that whole-exome sequencing is a powerful tool for the diagnostic evaluation of patients with highly heterogeneous neurodevelopmental disorders such as intellectual disability with microcephaly. Our results confirm that autosomal recessive disorders are highly prevalent among patients with microcephaly. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0167-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick Rump
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Omid Jazayeri
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Krista K van Dijk-Bos
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands. .,Department of Genetics, University of Groningen, University Medical Centre Groningen, Genomics Coordination Centre, Groningen, The Netherlands.
| | - Anthonie J van Essen
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Johanna B G M Verheij
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Egbert J W Redeker
- Department of Clinical Genetics, University of Amsterdam, Academic Medical Centre, Amsterdam, The Netherlands.
| | - Marcel M A M Mannens
- Department of Clinical Genetics, University of Amsterdam, Academic Medical Centre, Amsterdam, The Netherlands.
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Genomics Coordination Centre, Groningen, The Netherlands.
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.
| | - Conny M A van Ravenswaaij-Arts
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
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Meeks KAC, Stronks K, Beune EJAJ, Adeyemo A, Henneman P, Mannens MMAM, Nicolaou M, Peters RJG, Rotimi CN, Snijder MB, Agyemang C. Prevalence of type 2 diabetes and its association with measures of body composition among African residents in the Netherlands--The HELIUS study. Diabetes Res Clin Pract 2015; 110:137-46. [PMID: 26432411 DOI: 10.1016/j.diabres.2015.09.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/29/2015] [Accepted: 09/12/2015] [Indexed: 02/05/2023]
Abstract
AIMS To compare type 2 diabetes prevalence among three ethnic groups resident in the Netherlands: Ghanaians, African Surinamese and Dutch origin. Secondly, to determine the contribution of measures of body composition to ethnic differences in type 2 diabetes. METHODS Baseline data from Ghanaian (n=1873), African Surinamese (n=2189) and Dutch (n=2151) origin participants of the HELIUS study (aged 18-70 years) were analyzed. Type 2 diabetes was determined according to the WHO criteria. Logistic regression tested ethnic differences in type 2 diabetes and the contribution of body fat percentage and waist-to-hip ratio. RESULTS Among men, type 2 diabetes prevalence was higher in Ghanaians (14.9%) than in African Surinamese (10.4%) and Dutch (5.0%). Among women, type 2 diabetes prevalence in Ghanaian (11.1%) was higher than in Dutch (2.3%), but similar to African Surinamese (11.5%). After adjusting for age, body fat percentage and waist-to-hip ratio, the odds ratios for having type 2 diabetes were 1.55 (95% CI: 1.12-2.15) for Ghanaian men compared with African Surinamese and 4.19 (95% CI: 2.86-6.12) compared with Dutch. Among women these odds ratios were 0.94 (95% CI: 0.70-1.26) and 4.78 (95% CI: 2.82-8.11). CONCLUSIONS The higher prevalence of type 2 diabetes among Ghanaian compared with African Surinamese men suggests a need to distinguish between African descent populations when assessing their type 2 diabetes risk. The higher odds for type 2 diabetes among Ghanaians cannot be attributed to differences in body composition. Further research on the contribution of lifestyle factors as well as genetic and epigenetic factors is needed to identify the reasons for the observed disparities.
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Affiliation(s)
- Karlijn A C Meeks
- Department of Public Health, Academic Medical Center/University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
| | - Karien Stronks
- Department of Public Health, Academic Medical Center/University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
| | - Erik J A J Beune
- Department of Public Health, Academic Medical Center/University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, MD, United States.
| | - Peter Henneman
- Department of Clinical Genetics, Academic Medical Center/University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Academic Medical Center/University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
| | - Mary Nicolaou
- Department of Public Health, Academic Medical Center/University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
| | - Ron J G Peters
- Department of Cardiology, Academic Medical Center/University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, MD, United States.
| | - Marieke B Snijder
- Department of Public Health, Academic Medical Center/University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
| | - Charles Agyemang
- Department of Public Health, Academic Medical Center/University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
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Alders M, Maas SM, Kadouch DJM, van der Lip K, Bliek J, van der Horst CMAM, Mannens MMAM. Methylation analysis in tongue tissue of BWS patients identifies the (EPI)genetic cause in 3 patients with normal methylation levels in blood. Eur J Med Genet 2014; 57:293-7. [PMID: 24704790 DOI: 10.1016/j.ejmg.2014.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [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: 11/21/2013] [Accepted: 03/25/2014] [Indexed: 10/25/2022]
Abstract
The Beckwith-Wiedemann syndrome is caused by disturbed imprinting of genes at 11p15.5. Routine diagnostic testing for Beckwith-Wiedemann syndrome (BWS) includes methylation analysis of the imprinting centers ICR1 and ICR2 in DNA extracted from lymphocytes. In approximately 15% of BWS patients the diagnosis cannot be molecularly confirmed. In this study we determined the methylation status in resected tongue tissue of 11 BWS patients and compared this to the genetic defects found by routine diagnostic screening of blood lymphocytes. In all three patients with normal methylation levels in blood, aberrant methylation patterns were found in tongue tissue. In two patients a UPD was detected and the third case had hypermethylation of ICR1. This result shows that tissue specific mosaic (epi)genetic changes, not present in blood, is the underlying defect in at least a subset of BWS patients without a molecular diagnosis after standard genetic testing.
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Affiliation(s)
- Mariëlle Alders
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands.
| | - Saskia M Maas
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands; Department of Pediatrics, Academic Medical Center, Amsterdam, The Netherlands
| | - Daniël J M Kadouch
- Department of Dermatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Karin van der Lip
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Jet Bliek
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Marcel M A M Mannens
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
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Joustra SD, Schoenmakers N, Persani L, Campi I, Bonomi M, Radetti G, Beck-Peccoz P, Zhu H, Davis TME, Sun Y, Corssmit EP, Appelman-Dijkstra NM, Heinen CA, Pereira AM, Varewijck AJ, Janssen JAMJL, Endert E, Hennekam RC, Lombardi MP, Mannens MMAM, Bak B, Bernard DJ, Breuning MH, Chatterjee K, Dattani MT, Oostdijk W, Biermasz NR, Wit JM, van Trotsenburg ASP. The IGSF1 deficiency syndrome: characteristics of male and female patients. J Clin Endocrinol Metab 2013; 98:4942-52. [PMID: 24108313 DOI: 10.1210/jc.2013-2743] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Ig superfamily member 1 (IGSF1) deficiency was recently discovered as a novel X-linked cause of central hypothyroidism (CeH) and macro-orchidism. However, clinical and biochemical data regarding growth, puberty, and metabolic outcome, as well as features of female carriers, are scarce. OBJECTIVE Our objective was to investigate clinical and biochemical characteristics associated with IGSF1 deficiency in both sexes. METHODS All patients (n = 42, 24 males) from 10 families examined in the university clinics of Leiden, Amsterdam, Cambridge, and Milan were included in this case series. Detailed clinical data were collected with an identical protocol, and biochemical measurements were performed in a central laboratory. RESULTS Male patients (age 0-87 years, 17 index cases and 7 from family studies) showed CeH (100%), hypoprolactinemia (n = 16, 67%), and transient partial GH deficiency (n = 3, 13%). Pubertal testosterone production was delayed, as were the growth spurt and pubic hair development. However, testicular growth started at a normal age and attained macro-orchid size in all evaluable adults. Body mass index, percent fat, and waist circumference tended to be elevated. The metabolic syndrome was present in 4 of 5 patients over 55 years of age. Heterozygous female carriers (age 32-80 years) showed CeH in 6 of 18 cases (33%), hypoprolactinemia in 2 (11%), and GH deficiency in none. As in men, body mass index, percent fat, and waist circumference were relatively high, and the metabolic syndrome was present in 3 cases. CONCLUSION In male patients, the X-linked IGSF1 deficiency syndrome is characterized by CeH, hypoprolactinemia, delayed puberty, macro-orchidism, and increased body weight. A subset of female carriers also exhibits CeH.
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Affiliation(s)
- S D Joustra
- MD, Department of Endocrinology and Metabolism C7-Q, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
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Postma AV, Alders M, Sylva M, Bilardo CM, Pajkrt E, van Rijn RR, Schulte-Merker S, Bulk S, Stefanovic S, Ilgun A, Barnett P, Mannens MMAM, Moorman AFM, Oostra RJ, van Maarle MC. Mutations in the T (brachyury) gene cause a novel syndrome consisting of sacral agenesis, abnormal ossification of the vertebral bodies and a persistent notochordal canal. J Med Genet 2013; 51:90-7. [PMID: 24253444 DOI: 10.1136/jmedgenet-2013-102001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND The T gene (brachyury gene) is the founding member of the T-box family of transcription factors and is vital for the formation and differentiation of the mesoderm and the axial development of all vertebrates. RESULTS We report here on four patients from three consanguineous families exhibiting sacral agenesis, a persistent notochordal canal and abnormal ossification of the vertebral bodies, and the identification and characterisation of their underlying genetic defect. Given the consanguineous nature and the similarity of the phenotypes between the three families, we performed homozygosity mapping and identified a common 4.1 Mb homozygous region on chromosome 6q27, containing T, brachyury homologue (mouse) or T. Sequencing of T in the affected individuals led to the identification of a homozygous missense mutation, p.H171R, in the highly conserved T-box. The homozygous mutation results in diminished DNA binding, increased cell growth, and interferes with the normal expression of genes involved in ossification, notochord maintenance and axial mesoderm development. CONCLUSIONS We have identified a shared homozygous mutation in three families in T and linked it to a novel syndrome consisting of sacral agenesis, a persistent notochordal canal and abnormal ossification of the vertebral bodies. We suggest that screening for the ossification of the vertebrae is warranted in patients with sacral agenesis to evaluate the possible causal involvement of T.
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Affiliation(s)
- A V Postma
- Department of Anatomy, Embryology & Physiology, Academic Medical Centre, Amsterdam, The Netherlands
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Hofman N, Tan HL, Alders M, Kolder I, de Haij S, Mannens MMAM, Lombardi MP, Dit Deprez RHL, van Langen I, Wilde AAM. Yield of molecular and clinical testing for arrhythmia syndromes: report of 15 years' experience. Circulation 2013; 128:1513-21. [PMID: 23963746 DOI: 10.1161/circulationaha.112.000091] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [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] [Indexed: 12/28/2022]
Abstract
BACKGROUND Sudden cardiac death is often caused by inherited arrhythmia syndromes, particularly if it occurs at a young age. In 1996, we started a cardiogenetics clinic aimed at diagnosing such syndromes and providing timely (often presymptomatic) treatment to families in which such syndromes or sudden cardiac death existed. We studied the yield of DNA testing for these syndromes using a candidate-gene approach over our 15 years of experience. METHODS AND RESULTS We analyzed the yield of DNA testing. In subanalyses, we studied differences in the yield of DNA testing over time, between probands with isolated or familial cases and between probands with or without clear disease-specific clinical characteristics. In cases of sudden unexplained death (antemortem or postmortem analysis of the deceased not performed or providing no diagnosis), we analyzed the yield of cardiological investigations. Among 7021 individuals who were counseled, 6944 from 2298 different families (aged 41 ± 19 years; 49% male) were analyzed. In 702 families (31%), a possible disease-causing mutation was detected. Most mutations were found in families with long-QT syndrome (47%) or hypertrophic cardiomyopathy (46%). Cascade screening revealed 1539 mutation-positive subjects. The mutation detection rate decreased over time, in part because probands with a less severe phenotype were studied, and was significantly higher in familial than in isolated cases. We counseled 372 families after sudden unexplained death; in 29% of them (n=108), an inherited arrhythmia syndrome was diagnosed. CONCLUSIONS The proportion of disease-causing mutations found decreased over time, in part because probands with a less severe phenotype were studied. Systematic screening of families identified many (often presymptomatic) mutation-positive subjects.
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Affiliation(s)
- Nynke Hofman
- Department of Clinical Genetics (N.H., M.A., S.d.H., M.M.A.M.M., M.P.L., R.H.L.d.D., I.v.L.), Department of Cardiology (H.L.T., A.A.M.W.), and Department of Epidemiology, Biostatistics, and Bioinformatics (I.K.), Academic Medical Center, Amsterdam, The Netherlands
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Mook ORF, Haagmans MA, Soucy JF, van de Meerakker JBA, Baas F, Jakobs ME, Hofman N, Christiaans I, Lekanne Deprez RH, Mannens MMAM. Targeted sequence capture and GS-FLX Titanium sequencing of 23 hypertrophic and dilated cardiomyopathy genes: implementation into diagnostics. J Med Genet 2013; 50:614-26. [PMID: 23785128 PMCID: PMC3756457 DOI: 10.1136/jmedgenet-2012-101231] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [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] [Indexed: 01/25/2023]
Abstract
BACKGROUND Genetic evaluation of cardiomyopathies poses a challenge. Multiple genes are involved but no clear genotype-phenotype correlations have been found so far. In the past, genetic evaluation for hypertrophic (HCM) and dilated (DCM) cardiomyopathies was performed by sequential screening of a very limited number of genes. Recent developments in sequencing have increased the throughput, enabling simultaneous screening of multiple genes for multiple patients in a single sequencing run. OBJECTIVE Development and implementation of a next generation sequencing (NGS) based genetic test as replacement for Sanger sequencing. METHODS AND RESULTS In order to increase the number of genes that can be screened in a shorter time period, we enriched all exons of 23 of the most relevant HCM and DCM related genes using on-array multiplexed sequence capture followed by massively parallel pyrosequencing on the GS-FLX Titanium. After optimisation of array based sequence capture it was feasible to reliably detect a large panel of known and unknown variants in HCM and DCM patients, whereby the unknown variants could be confirmed by Sanger sequencing. CONCLUSIONS The rate of detection of (pathogenic) variants in both HCM and DCM patients was increased due to a larger number of genes studied. Array based target enrichment followed by NGS showed the same accuracy as Sanger sequencing. Therefore, NGS is ready for implementation in a diagnostic setting.
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Affiliation(s)
- Olaf R F Mook
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands.
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van de Meerakker JBA, Christiaans I, Barnett P, Lekanne Deprez RH, Ilgun A, Mook ORF, Mannens MMAM, Lam J, Wilde AAM, Moorman AFM, Postma AV. A novel alpha-tropomyosin mutation associates with dilated and non-compaction cardiomyopathy and diminishes actin binding. Biochim Biophys Acta 2012; 1833:833-9. [PMID: 23147248 DOI: 10.1016/j.bbamcr.2012.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/30/2012] [Accepted: 11/02/2012] [Indexed: 10/27/2022]
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is characterized by idiopathic dilatation and systolic contractile dysfunction of the ventricle(s) leading to an impaired systolic function. The origin of DCM is heterogeneous, but genetic transmission of the disease accounts for up to 50% of the cases. Mutations in alpha-tropomyosin (TPM1), a thin filament protein involved in structural and regulatory roles in muscle cells, are associated with hypertrophic cardiomyopathy (HCM) and very rarely with DCM. METHODS AND RESULTS Here we present a large four-generation family in which DCM is inherited as an autosomal dominant trait. Six family members have a cardiomyopathy with the age of diagnosis ranging from 5 months to 52 years. The youngest affected was diagnosed with dilated and non-compaction cardiomyopathy (NCCM) and died at the age of five. Three additional children died young of suspected heart problems. We mapped the phenotype to chromosome 15 and subsequently identified a missense mutation in TPM1, resulting in a p.D84N amino acid substitution. In addition we sequenced 23 HCM/DCM genes using next generation sequencing. The TPM1 p.D84N was the only mutation identified. The mutation co-segregates with all clinically affected family members and significantly weakens the binding of tropomyosin to actin by 25%. CONCLUSIONS We show that a mutation in TPM1 is associated with DCM and a lethal, early onset form of NCCM, probably as a result of diminished actin binding caused by weakened charge-charge interactions. Consequently, the screening of TPM1 in patients and families with DCM and/or (severe, early onset forms of) NCCM is warranted. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Cardiac Pathways of Differentiation, Metabolism and Contraction.
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van den Wijngaard A, Volders P, Van Tintelen JP, Jongbloed JDH, van den Berg MP, Lekanne Deprez RH, Mannens MMAM, Hofmann N, Slegtenhorst M, Dooijes D, Michels M, Arens Y, Jongbloed R, Smeets BJM. Recurrent and founder mutations in the Netherlands: cardiac Troponin I (TNNI3) gene mutations as a cause of severe forms of hypertrophic and restrictive cardiomyopathy. Neth Heart J 2011; 19:344-51. [PMID: 21533915 PMCID: PMC3144325 DOI: 10.1007/s12471-011-0135-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [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: 01/29/2023] Open
Abstract
BACKGROUND About 2-7% of familial cardiomyopathy cases are caused by a mutation in the gene encoding cardiac troponin I (TNNI3). The related clinical phenotype is usually severe with early onset. Here we report on all currently known mutations in the Dutch population and compared these with those described in literature. METHODS TheTNNI3 gene was screened for mutations in all coding exons and flanking intronic sequences in a large cohort of cardiomyopathy patients. All Dutch index cases carrying a TNNI3 mutation that are described in this study underwent extensive cardiological evaluation and were listed by their postal codes. RESULTS In 30 families, 14 different mutations were identified. Three TNNI3 mutations were found relatively frequently in both familial and non-familial cases of hypertrophic cardiomyopathy (HCM) or restrictive cardiomyopathy (RCM). Haplotype analysis showed that p.Arg145Trp and p.Ser166Phe are founder mutations in the Netherlands, while p.Glu209Ala is not. The majority of Dutch TNNI3 mutations were associated with a HCM phenotype. Mean age at diagnosis was 36.5 years. Mutations causing RCM occurred less frequently, but were identified in very young children with a poor prognosis. CONCLUSION In line with previously published data, we found TNNI3 mutations to be rare and associated with early onset and severe clinical presentation.
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Affiliation(s)
- A van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands,
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46
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Christiaans I, Nannenberg EA, Dooijes D, Jongbloed RJE, Michels M, Postema PG, Majoor-Krakauer D, van den Wijngaard A, Mannens MMAM, van Tintelen JP, van Langen IM, Wilde AAM. Founder mutations in hypertrophic cardiomyopathy patients in the Netherlands. Neth Heart J 2011; 18:248-54. [PMID: 20505798 DOI: 10.1007/bf03091771] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In this part of a series on cardiogenetic founder mutations in the Netherlands, we review the Dutch founder mutations in hypertrophic cardiomyopathy (HCM) patients. HCM is a common autosomal dominant genetic disease affecting at least one in 500 persons in the general population. Worldwide, most mutations in HCM patients are identified in genes encoding sarcomeric proteins, mainly in the myosin-binding protein C gene (MYBPC3, OMIM #600958) and the beta myosin heavy chain gene (MYH7, OMIM #160760). In the Netherlands, the great majority of mutations occur in the MYBPC3, involving mainly three Dutch founder mutations in the MYBPC3 gene, the c.2373_2374insG, the c.2864_2865delCT and the c.2827C>T mutation. In this review, we describe the genetics of HCM, the genotype-phenotype relation of Dutch founder MYBPC3 gene mutations, the prevalence and the geographic distribution of the Dutch founder mutations, and the consequences for genetic counselling and testing. (Neth Heart J 2010;18:248-54.).
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Affiliation(s)
- I Christiaans
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, the Netherlands These authors contributed equally
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47
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van de Meerakker JBA, van Engelen K, Mathijssen IB, Lekanne dit Deprez RH, Lam J, Wilde AAM, Baars MJH, Mannens MMAM, Mulder BJM, Moorman AFM, Postma AV. A novel autosomal dominant condition consisting of congenital heart defects and low atrial rhythm maps to chromosome 9q. Eur J Hum Genet 2011; 19:820-6. [PMID: 21386876 DOI: 10.1038/ejhg.2011.33] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Congenital heart defects (CHDs) occur mostly sporadic, but familial CHD cases have been reported. Mutations in several genes, including NKX2.5, GATA4 and NOTCH1, were identified in families and patients with CHD, but the mechanisms underlying CHD are largely unknown. We performed genome-wide linkage analysis in a large four-generation family with autosomal dominant CHD (including atrial septal defect type I and II, tetralogy of Fallot and persistent left superior vena cava) and low atrial rhythm, a unique phenotype that has not been described before. We obtained phenotypic information including electrocardiography, echocardiography and DNA of 23 family members. Genome-wide linkage analysis on 12 affected, 5 unaffected individuals and 1 obligate carrier demonstrated significant linkage only to chromosome 9q21-33 with a multipoint maximum LOD score of 4.1 at marker D9S1690, between markers D9S167 and D9S1682. This 48-cM critical interval corresponds to 39 Mb and contains 402 genes. Sequence analysis of nine candidate genes in this region (INVS, TMOD1, TGFBR1, KLF4, IPPK, BARX1, PTCH1, MEGF9 and S1PR3) revealed no mutations, nor were genomic imbalances detected using array comparative genomic hybridization. In conclusion, we describe a large family with CHD and low atrial rhythm with a significant LOD score to chromosome 9q. The phenotype is representative of a mild form of left atrial isomerism or a developmental defect of the sinus node and surrounding tissue. Because the mechanisms underlying CHD are largely unknown, this study represents an important step towards the discovery of genes implied in cardiogenesis.
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Affiliation(s)
- Judith B A van de Meerakker
- Heart Failure Research Centre, Department of Anatomy and Embryology, Academic Medical Centre, Amsterdam, The Netherlands
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Biegstraaten M, van Schaik IN, Aerts JMFG, Langeveld M, Mannens MMAM, Bour LJ, Sidransky E, Tayebi N, Fitzgibbon E, Hollak CEM. A monozygotic twin pair with highly discordant Gaucher phenotypes. Blood Cells Mol Dis 2010; 46:39-41. [PMID: 21056933 DOI: 10.1016/j.bcmd.2010.10.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 10/10/2010] [Indexed: 01/08/2023]
Abstract
We describe monozygotic twin sisters, born to consanguineous Moroccan parents, who are highly discordant for the manifestations of Gaucher disease. Both carry Gaucher genotype N188S/N188S. One has severe visceral involvement, epilepsy, and a cerebellar syndrome. Her twin does not manifest any symptoms or signs of Gaucher disease but suffers from type 1 diabetes mellitus. The concurrence of a mild Gaucher mutation with a severe phenotype, as well as the occurrence of highly discordant phenotypes in a pair of monozygotic twins, is discussed.
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Affiliation(s)
- M Biegstraaten
- Department of Neurology, Academic Medical Centre, Amsterdam, The Netherlands
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van Kuilenburg ABP, Meijer J, Mul ANPM, Meinsma R, Schmid V, Dobritzsch D, Hennekam RCM, Mannens MMAM, Kiechle M, Etienne-Grimaldi MC, Klümpen HJ, Maring JG, Derleyn VA, Maartense E, Milano G, Vijzelaar R, Gross E. Intragenic deletions and a deep intronic mutation affecting pre-mRNA splicing in the dihydropyrimidine dehydrogenase gene as novel mechanisms causing 5-fluorouracil toxicity. Hum Genet 2010; 128:529-38. [PMID: 20803296 PMCID: PMC2955237 DOI: 10.1007/s00439-010-0879-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 08/17/2010] [Indexed: 02/06/2023]
Abstract
Dihydropyrimidine dehydrogenase (DPD) is the initial enzyme acting in the catabolism of the widely used antineoplastic agent 5-fluorouracil (5FU). DPD deficiency is known to cause a potentially lethal toxicity following administration of 5FU. Here, we report novel genetic mechanisms underlying DPD deficiency in patients presenting with grade III/IV 5FU-associated toxicity. In one patient a genomic DPYD deletion of exons 21–23 was observed. In five patients a deep intronic mutation c.1129–5923C>G was identified creating a cryptic splice donor site. As a consequence, a 44 bp fragment corresponding to nucleotides c.1129–5967 to c.1129–5924 of intron 10 was inserted in the mature DPD mRNA. The deleterious c.1129–5923C>G mutation proved to be in cis with three intronic polymorphisms (c.483 + 18G>A, c.959–51T>G, c.680 + 139G>A) and the synonymous mutation c.1236G>A of a previously identified haplotype. Retrospective analysis of 203 cancer patients showed that the c.1129–5923C>G mutation was significantly enriched in patients with severe 5FU-associated toxicity (9.1%) compared to patients without toxicity (2.2%). In addition, a high prevalence was observed for the c.1129–5923C>G mutation in the normal Dutch (2.6%) and German (3.3%) population. Our study demonstrates that a genomic deletion affecting DPYD and a deep intronic mutation affecting pre-mRNA splicing can cause severe 5FU-associated toxicity. We conclude that screening for DPD deficiency should include a search for genomic rearrangements and aberrant splicing.
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Affiliation(s)
- André B P van Kuilenburg
- Department of Clinical Chemistry, Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands.
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50
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Alders M, Hogan BM, Gjini E, Salehi F, Al-Gazali L, Hennekam EA, Holmberg EE, Mannens MMAM, Mulder MF, Offerhaus GJA, Prescott TE, Schroor EJ, Verheij JBGM, Witte M, Zwijnenburg PJ, Vikkula M, Schulte-Merker S, Hennekam RC. Mutations in CCBE1 cause generalized lymph vessel dysplasia in humans. Nat Genet 2010; 41:1272-4. [PMID: 19935664 DOI: 10.1038/ng.484] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 10/13/2009] [Indexed: 11/09/2022]
Abstract
Lymphedema, lymphangiectasias, mental retardation and unusual facial characteristics define the autosomal recessive Hennekam syndrome. Homozygosity mapping identified a critical chromosomal region containing CCBE1, the human ortholog of a gene essential for lymphangiogenesis in zebrafish. Homozygous and compound heterozygous mutations in seven subjects paired with functional analysis in a zebrafish model identify CCBE1 as one of few genes causing primary generalized lymph-vessel dysplasia in humans.
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Affiliation(s)
- Marielle Alders
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
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