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Erkens RGA, Calis JJA, Verwoerd A, De Roock S, Ter Haar NM, Den Engelsman G, Van der Veken LT, Ernst RF, Van Deutekom HWM, Pickering A, Scholman RC, Jansen MHA, Swart JF, Sinha R, Roth J, Schulert GS, Grom AA, Van Loosdregt J, Vastert SJ. Recombinant Interleukin-1 Receptor Antagonist Is an Effective First-Line Treatment Strategy in New-Onset Systemic Juvenile Idiopathic Arthritis, Irrespective of HLA-DRB1 Background and IL1RN Variants. Arthritis Rheumatol 2024; 76:119-129. [PMID: 37471469 DOI: 10.1002/art.42656] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/07/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023]
Abstract
OBJECTIVE Human leukocyte antigen (HLA)-DRB1*15:01 has been recently associated with interstitial lung disease (LD), eosinophilia, and drug reactions in systemic juvenile idiopathic arthritis (sJIA). Additionally, genetic variants in IL1RN have been linked to poor response to anakinra. We sought to reproduce these findings in a prospective cohort study of patients with new-onset sJIA treated with anakinra as first-line therapy. METHODS HLA and IL1RN risk alleles were identified via whole-genome sequencing. Treatment responses and complications were compared between carriers versus noncarriers. RESULTS Seventeen of 65 patients (26%) carried HLA-DRB1*15:01, comparable with the general population, and there was enrichment for HLA-DRB1*11:01, a known risk locus for sJIA. The rates of clinical inactive disease (CID) at 6 months, 1 year, and 2 years were generally high, irrespective of HLA-DRB1 or IL1RN variants, but significantly lower in carriers of an HLA-DRB1*11:01 allele. One patient, an HLA-DRB1*15:01 carrier, developed sJIA-LD. Of the three patients with severe drug reactions to biologics, one carried HLA-DRB1*15:01. The prevalence of eosinophilia did not significantly differ between HLA-DRB1*15:01 carriers and noncarriers at disease onset (6.2% vs 14.9%, P = 0.67) nor after the start of anakinra (35.3% vs 37.5% in the first 2 years of disease). CONCLUSION We observed high rates of CID using anakinra as first-line treatment irrespective of HLA-DRB1 or IL1RN variants. Only one of the 17 HLA-DRB1*15:01 carriers developed sJIA-LD, and of the three patients with drug reactions to biologics, only one carried HLA-DRB1*15:01. Although thorough monitoring for the development of drug hypersensitivity and refractory disease courses in sJIA, including sJIA-LD, remains important, our data support the early start of biologic therapy in patients with new-onset sJIA irrespective of HLA-DRB1 background or IL1RN variants.
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Affiliation(s)
- Remco G A Erkens
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Jorg J A Calis
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Anouk Verwoerd
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Sytze De Roock
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Nienke M Ter Haar
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Gerda Den Engelsman
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Lars T Van der Veken
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Robert F Ernst
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | | | | | - Rianne C Scholman
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Marc H A Jansen
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Joost F Swart
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Rashmi Sinha
- Systemic Juvenile Idiopathic Arthritis Foundation, Cincinnati, Ohio
| | | | - Grant S Schulert
- Cincinnati Children's Hospital and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Alexei A Grom
- Cincinnati Children's Hospital and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jorg Van Loosdregt
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
| | - Sebastiaan J Vastert
- University Medical Center Utrecht and University of Utrecht, Utrecht, The Netherlands
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van der Voorn SM, van Drie E, Proost V, Dimitrova K, Ernst RF, James CA, Tichnell C, Murray B, Calkins H, Saguner AM, Duru F, Ellinor PT, Bezzina CR, Jurgens SJ, van Tintelen JP, van Veen TAB. Lack of Evidence for the Role of the p.(Ser96Ala) Polymorphism in Histidine-Rich Calcium Binding Protein as a Secondary Hit in Cardiomyopathies. Int J Mol Sci 2023; 24:15931. [PMID: 37958923 PMCID: PMC10648441 DOI: 10.3390/ijms242115931] [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: 09/20/2023] [Revised: 10/17/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Inherited forms of arrhythmogenic and dilated cardiomyopathy (ACM and DCM) are characterized by variable disease expression and age-related penetrance. Calcium (Ca2+) is crucially important for proper cardiac function, and dysregulation of Ca2+ homeostasis seems to underly cardiomyopathy etiology. A polymorphism, c.286T>G p.(Ser96Ala), in the gene encoding the histidine-rich Ca2+ binding (HRC) protein, relevant for sarcoplasmic reticulum Ca2+ cycling, has previously been associated with a marked increased risk of life-threatening arrhythmias among idiopathic DCM patients. Following this finding, we investigated whether p.(Ser96Ala) affects major cardiac disease manifestations in carriers of the phospholamban (PLN) c.40_42delAGA; p.(Arg14del) pathogenic variant (cohort 1); patients diagnosed with, or predisposed to, ACM (cohort 2); and DCM patients (cohort 3). We found that the allele frequency of the p.(Ser96Ala) polymorphism was similar across the general European-American population (control cohort, 40.3-42.2%) and the different cardiomyopathy cohorts (cohorts 1-3, 40.9-43.9%). Furthermore, the p.(Ser96Ala) polymorphism was not associated with life-threatening arrhythmias or heart failure-related events across various patient cohorts. We therefore conclude that there is a lack of evidence supporting the important role of the HRC p.(Ser96Ala) polymorphism as a modifier in cardiomyopathy, refuting previous findings. Further research is required to identify bona fide genomic predictors for the stratification of cardiomyopathy patients and their risk for life-threatening outcomes.
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Affiliation(s)
- Stephanie M. van der Voorn
- Department of Medical Physiology, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands (K.D.)
| | - Esmée van Drie
- Department of Genetics, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands
- Netherlands Heart Institute, 3511 EP Utrecht, The Netherlands
| | - Virginnio Proost
- Departments of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers Location Academic Medical Center, 1105 AZ Amsterdam, The Netherlands (C.R.B.)
| | - Kristina Dimitrova
- Department of Medical Physiology, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands (K.D.)
| | | | - Robert F. Ernst
- Department of Genetics, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands
| | - Cynthia A. James
- Department of Medicine, Division Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA (C.T.)
| | - Crystal Tichnell
- Department of Medicine, Division Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA (C.T.)
| | - Brittney Murray
- Department of Medicine, Division Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA (C.T.)
| | - Hugh Calkins
- Department of Medicine, Division Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA (C.T.)
| | - Ardan M. Saguner
- Department of Cardiology, University Heart Center Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Firat Duru
- Department of Cardiology, University Heart Center Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
- Center for Integrative Human Physiology (ZIHP), University of Zurich, 8091 Zurich, Switzerland
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Connie R. Bezzina
- Departments of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers Location Academic Medical Center, 1105 AZ Amsterdam, The Netherlands (C.R.B.)
| | - Sean J. Jurgens
- Departments of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers Location Academic Medical Center, 1105 AZ Amsterdam, The Netherlands (C.R.B.)
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J. Peter van Tintelen
- Department of Genetics, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands
- Netherlands Heart Institute, 3511 EP Utrecht, The Netherlands
| | - Toon A. B. van Veen
- Department of Medical Physiology, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands (K.D.)
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3
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Niskanen JE, Ohlsson Å, Ljungvall I, Drögemüller M, Ernst RF, Dooijes D, van Deutekom HWM, van Tintelen JP, Snijders Blok CJB, van Vugt M, van Setten J, Asselbergs FW, Petrič AD, Salonen M, Hundi S, Hörtenhuber M, Kere J, Pyle WG, Donner J, Postma AV, Leeb T, Andersson G, Hytönen MK, Häggström J, Wiberg M, Friederich J, Eberhard J, Harakalova M, van Steenbeek FG, Wess G, Lohi H. Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human. Genome Med 2023; 15:73. [PMID: 37723491 PMCID: PMC10506233 DOI: 10.1186/s13073-023-01221-3] [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: 03/09/2023] [Accepted: 08/17/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis. METHODS We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts. RESULTS Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes. CONCLUSIONS Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.
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Affiliation(s)
- Julia E Niskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Robert F Ernst
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dennis Dooijes
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hanneke W M van Deutekom
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - J Peter van Tintelen
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Christian J B Snijders Blok
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Marion van Vugt
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Jessica van Setten
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | | | - Milla Salonen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Research Programs Unit, Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - W Glen Pyle
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
- IMPART Investigator Team Canada, Dalhousie Medicine, Saint John, NB, Canada
| | - Jonas Donner
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Helsinki, Finland
| | - Alex V Postma
- Department of Human Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Wiberg
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Jana Friederich
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Jenny Eberhard
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Frank G van Steenbeek
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 108, Utrecht, 3584 CM, The Netherlands
| | - Gerhard Wess
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland.
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland.
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland.
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4
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Elsink K, Huibers MMH, Hollink IHIM, van der Veken LT, Ernst RF, Simons A, Zonneveld-Huijssoon E, van der Hout AH, Abbott KM, Hoischen A, Pieterse M, Kuijpers TW, van Montfrans JM, van Gijn ME. National external quality assessment for next-generation sequencing-based diagnostics of primary immunodeficiencies. Eur J Hum Genet 2021; 29:20-28. [PMID: 32733070 PMCID: PMC7852558 DOI: 10.1038/s41431-020-0702-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 01/31/2020] [Revised: 06/10/2020] [Accepted: 07/21/2020] [Indexed: 11/09/2022] Open
Abstract
Dutch genome diagnostic centers (GDC) use next-generation sequencing (NGS)-based diagnostic applications for the diagnosis of primary immunodeficiencies (PIDs). The interpretation of genetic variants in many PIDs is complicated because of the phenotypic and genetic heterogeneity. To analyze uniformity of variant filtering, interpretation, and reporting in NGS-based diagnostics for PID, an external quality assessment was performed. Four main Dutch GDCs participated in the quality assessment. Unannotated variant call format (VCF) files of two PID patient analyses per laboratory were distributed among the four GDCs, analyzed, and interpreted (eight analyses in total). Variants that would be reported to the clinician and/or advised for further investigation were compared between the centers. A survey measuring the experiences of clinical laboratory geneticists was part of the study. Analysis of samples with confirmed diagnoses showed that all centers reported at least the variants classified as likely pathogenic (LP) or pathogenic (P) variants in all samples, except for variants in two genes (PSTPIP1 and BTK). The absence of clinical information complicated correct classification of variants. In this external quality assessment, the final interpretation and conclusions of the genetic analyses were uniform among the four participating genetic centers. Clinical and immunological data provided by a medical specialist are required to be able to draw proper conclusions from genetic data.
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Affiliation(s)
- Kim Elsink
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Manon M H Huibers
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Iris H I M Hollink
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Robert F Ernst
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Annet Simons
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Annemieke H van der Hout
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kristin M Abbott
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics and Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marc Pieterse
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Mariëlle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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5
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Snoek R, van Jaarsveld RH, Nguyen TQ, Peters EDJ, Elferink MG, Ernst RF, Rookmaaker MB, Lilien MR, Spierings E, Goldschmeding R, Knoers NVAM, van der Zwaag B, van Zuilen AD, van Eerde AM. Genetics-first approach improves diagnostics of ESKD patients younger than 50 years. Nephrol Dial Transplant 2020; 37:349-357. [PMID: 33306124 DOI: 10.1093/ndt/gfaa363] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 09/16/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Often only CKD patients with high likelihood of genetic disease are offered genetic testing. Early genetic testing could obviate the need for kidney biopsies, allowing for adequate prognostication and treatment. To test the viability of a 'genetics first' approach for CKD, we performed genetic testing in a group of kidney transplant recipients <50 years, irrespective of cause of transplant. METHODS From a cohort of 273 transplant patients, we selected 110 that were in care in the UMC Utrecht, had DNA available and were without clear-cut non-genetic disease. Forty patients had been diagnosed with a genetic disease prior to enrollment, in 70 patients we performed a whole exome sequencing based 379 gene panel analysis. RESULTS Genetic analysis yielded a diagnosis in 51%. Extrapolated to the 273 patient cohort, who did not all fit the inclusion criteria, the diagnostic yield was still 21%. Retrospectively, in 43% of biopsied patients the kidney biopsy would not have had added diagnostic value if genetic testing had been performed as a first tier diagnostic. CONCLUSIONS Burden of monogenic disease in transplant patients with ESKD of any cause prior to the age of 50 is between 21 and 51%. Early genetic testing can provide a non-invasive diagnostic, impacting prognostication and treatment and obviating the need for an invasive biopsy. We conclude that in patients who one expects to develop ESKD prior to the age of 50, genetic testing should be considered as first mode of diagnostics.
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Affiliation(s)
- Rozemarijn Snoek
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | | | - Tri Q Nguyen
- Department of Pathology, University Medical Center Utrecht, The Netherlands
| | - Edith D J Peters
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | - Martin G Elferink
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | - Robert F Ernst
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | | | - Marc R Lilien
- Department of Pediatric Nephrology, University Medical Center Utrecht, The Netherlands
| | - Eric Spierings
- Department of Immunology, University Medical Center Utrecht, The Netherlands
| | - Roel Goldschmeding
- Department of Pathology, University Medical Center Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Genetics, University Medical Center Groningen, The Netherlands
| | - Bert van der Zwaag
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | - Arjan D van Zuilen
- Department of Nephrology, University Medical Center Utrecht, The Netherlands
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6
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de Lange IM, Mulder F, van 't Slot R, Sonsma ACM, van Kempen MJA, Nijman IJ, Ernst RF, Knoers NVAM, Brilstra EH, Koeleman BPC. Modifier genes in SCN1A-related epilepsy syndromes. Mol Genet Genomic Med 2020; 8:e1103. [PMID: 32032478 PMCID: PMC7196470 DOI: 10.1002/mgg3.1103] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 11/19/2018] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/24/2022] Open
Abstract
Background SCN1A is one of the most important epilepsy‐related genes, with pathogenic variants leading to a range of phenotypes with varying disease severity. Different modifying factors have been hypothesized to influence SCN1A‐related phenotypes. We investigate the presence of rare and more common variants in epilepsy‐related genes as potential modifiers of SCN1A‐related disease severity. Methods 87 patients with SCN1A‐related epilepsy were investigated. Whole‐exome sequencing was performed by the Beijing Genomics Institute (BGI). Functional variants in 422 genes associated with epilepsy and/or neuronal excitability were investigated. Differences in proportions of variants between the epilepsy genes and four control gene sets were calculated, and compared to the proportions of variants in the same genes in the ExAC database. Results Statistically significant excesses of variants in epilepsy genes were observed in the complete cohort and in the combined group of mildly and severely affected patients, particularly for variants with minor allele frequencies of <0.05. Patients with extreme phenotypes showed much greater excesses of epilepsy gene variants than patients with intermediate phenotypes. Conclusion Our results indicate that relatively common variants in epilepsy genes, which would not necessarily be classified as pathogenic, may play a large role in modulating SCN1A phenotypes. They may modify the phenotypes of both severely and mildly affected patients. Our results may be a first step toward meaningful testing of modifier gene variants in regular diagnostics for individual patients, to provide a better estimation of disease severity for newly diagnosed patients.
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Affiliation(s)
- Iris M de Lange
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Flip Mulder
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ruben van 't Slot
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anja C M Sonsma
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjan J A van Kempen
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Isaac J Nijman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert F Ernst
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Eva H Brilstra
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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de Lange IM, Koudijs MJ, van ‘t Slot R, Sonsma ACM, Mulder F, Carbo EC, van Kempen MJA, Nijman IJ, Ernst RF, Savelberg SMC, Knoers NVAM, Brilstra EH, Koeleman BPC. Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing. J Med Genet 2018; 56:75-80. [DOI: 10.1136/jmedgenet-2018-105672] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/24/2018] [Accepted: 09/30/2018] [Indexed: 01/08/2023]
Abstract
BackgroundDravet syndrome is a severe genetic encephalopathy, caused by pathogenic variants in SCN1A. Low-grade parental mosaicism occurs in a substantial proportion of families (7%–13%) and has important implications for recurrence risks. However, parental mosaicism can remain undetected by methods regularly used in diagnostics. In this study, we use single-molecule molecular inversion probes (smMIP), a technique with high sensitivity for detecting low-grade mosaic variants and high cost-effectiveness, to investigate the incidence of parental mosaicism of SCN1A variants in a cohort of 90 families and assess the feasibility of this technique.MethodsDeep sequencing of SCN1A was performed using smMIPs. False positive rates for each of the proband’s pathogenic variants were determined in 145 unrelated samples. If parents showed corresponding variant alleles at a significantly higher rate than the established noise ratio, mosaicism was confirmed by droplet digital PCR (ddPCR).ResultsSequence coverage of at least 100× at the location of the corresponding pathogenic variant was reached for 80 parent couples. The variant ratio was significantly higher than the established noise ratio in eight parent couples, of which four (5%) were regarded as true mosaics, based on ddPCR results. The false positive rate of smMIP analysis without ddPCR was therefore 50%. Three of these variants had previously been considered de novo in the proband by Sanger sequencing.ConclusionsmMIP technology combined withnext generation sequencing (NGS) performs better than Sanger sequencing in the detection of parental mosaicism. Because parental mosaicism has important implications for genetic counselling and recurrence risks, we stress the importance of implementing high-sensitivity NGS-based assays in standard diagnostics.
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de Lange IM, Koudijs MJ, van 't Slot R, Gunning B, Sonsma ACM, van Gemert LJJM, Mulder F, Carbo EC, van Kempen MJA, Verbeek NE, Nijman IJ, Ernst RF, Savelberg SMC, Knoers NVAM, Brilstra EH, Koeleman BPC. Mosaicism of de novo pathogenic SCN1A
variants in epilepsy is a frequent phenomenon that correlates with variable phenotypes. Epilepsia 2018; 59:690-703. [DOI: 10.1111/epi.14021] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Iris M. de Lange
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Marco J. Koudijs
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Ruben van 't Slot
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | | | - Anja C. M. Sonsma
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | | | - Flip Mulder
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Ellen C. Carbo
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Marjan J. A. van Kempen
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Nienke E. Verbeek
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Isaac J. Nijman
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Robert F. Ernst
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Sanne M. C. Savelberg
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Nine V. A. M. Knoers
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Eva H. Brilstra
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Bobby P. C. Koeleman
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
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van Roon EH, Boot A, Dihal AA, Ernst RF, van Wezel T, Morreau H, Boer JM. BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer. Clin Epigenetics 2013; 5:2. [PMID: 23324568 PMCID: PMC3599401 DOI: 10.1186/1868-7083-5-2] [Citation(s) in RCA: 29] [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] [Received: 10/02/2012] [Accepted: 12/05/2012] [Indexed: 01/19/2023] Open
Abstract
Background Cancer-specific hypermethylation of (promoter) CpG islands is common during the tumorigenesis of colon cancer. Although associations between certain genetic aberrations, such as BRAF mutation and microsatellite instability, and the CpG island methylator phenotype (CIMP), have been found, the mechanisms by which these associations are established are still unclear. We studied genome-wide DNA methylation differences between colorectal tumors carrying a BRAF mutation and BRAF wildtype tumors. Results Using differential methylation hybridization on oligonucleotide microarrays representing 32,171 CpG-rich regions, we identified 1,770 regions with differential methylation between colorectal tumor and paired normal colon. Next, we compared the tumor/normal methylation ratios between different groups of patients. Related to CIMP, we identified 749 differentially methylated regions, of which 86% had a higher tumor/normal methylation ratio in the CIMP-positive group. We identified 758 regions with a BRAF mutation-specific methylation change, of which 96% had a higher tumor/normal methylation ratio in the BRAF mutant group. Among the genes affected by BRAF mutation-specific methylation changes, we found enrichment of several cancer-related pathways, including the PI3 kinase and Wnt signaling pathways. To focus on genes that are silenced in a tumor-specific rather than a lineage-specific manner, we used information on the epigenetic silencing mark H3K27me3 in embryonic stem (ES) cells. Among the genes showing BRAF mutation-specific promoter methylation but no H3K27me3 mark in ES cells were forkhead box (FOX) transcription factors associated with the PI3 kinase pathway, as well as MLH1 and SMO. Repression of FOXD3 gene expression in tumors could be related to its promoter hypermethylation. Conclusions We identified new BRAF mutation-specific methylation changes in colorectal cancer. Epigenetic downregulation of these targets may contribute to mutationally active BRAF-driven tumorigenesis, explaining its association with aberrant DNA methylation.
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Affiliation(s)
- Eddy H van Roon
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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