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Venema WJ, Hiddingh S, van Loosdregt J, Bowes J, Balliu B, de Boer JH, Ossewaarde-van Norel J, Thompson SD, Langefeld CD, de Ligt A, van der Veken LT, Krijger PHL, de Laat W, Kuiper JJW. A cis-regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs. Cell Genom 2024; 4:100460. [PMID: 38190099 PMCID: PMC10794781 DOI: 10.1016/j.xgen.2023.100460] [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] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 01/09/2024]
Abstract
Single-nucleotide polymorphisms (SNPs) near the ERAP2 gene are associated with various autoimmune conditions, as well as protection against lethal infections. Due to high linkage disequilibrium, numerous trait-associated SNPs are correlated with ERAP2 expression; however, their functional mechanisms remain unidentified. We show by reciprocal allelic replacement that ERAP2 expression is directly controlled by the splice region variant rs2248374. However, disease-associated variants in the downstream LNPEP gene promoter are independently associated with ERAP2 expression. Allele-specific conformation capture assays revealed long-range chromatin contacts between the gene promoters of LNPEP and ERAP2 and showed that interactions were stronger in patients carrying the alleles that increase susceptibility to autoimmune diseases. Replacing the SNPs in the LNPEP promoter by reference sequences lowered ERAP2 expression. These findings show that multiple SNPs act in concert to regulate ERAP2 expression and that disease-associated variants can convert a gene promoter region into a potent enhancer of a distal gene.
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Affiliation(s)
- Wouter J Venema
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jorg van Loosdregt
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Brunilda Balliu
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | - Susan D Thompson
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Aafke de Ligt
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, 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
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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2
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Andriessen MVE, Legger GE, Bredius RGM, van Gijn ME, Hak AE, Muller PCEH, Kamphuis S, Klouwer FCC, Kuijpers TW, Leavis HL, Nierkens S, Rutgers A, van der Veken LT, van Well GTJ, Mulders-Manders CM, van Montfrans JM. Clinical Symptoms, Laboratory Parameters and Long-Term Follow-up in a National DADA2 Cohort. J Clin Immunol 2023; 43:1581-1596. [PMID: 37277582 PMCID: PMC10499949 DOI: 10.1007/s10875-023-01521-8] [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: 02/03/2023] [Accepted: 05/13/2023] [Indexed: 06/07/2023]
Abstract
Deficiency of adenosine deaminase-2 (DADA2) is an autosomal recessive autoinflammatory disease with an extremely variable disease presentation. This paper provides a comprehensive overview of the Dutch DADA2 cohort. We performed a retrospective cohort study in 29 ADA2-deficient patients from 23 families with a median age at inclusion of 26 years. All patients had biallelic pathogenic variants in the ADA2 gene. The most common clinical findings included cutaneous involvement (79.3%), (hepato)splenomegaly (70.8%) and recurrent infections (58.6%). Stroke was observed in 41.4% of the patients. The main laboratory abnormalities were hypogammaglobulinemia and various cytopenias. Patients presented most often with a mixed phenotype involving vasculopathy, immunodeficiency and hematologic manifestations (62.1%). In this cohort, malignancies were reported in eight patients (27.6%), of whom five presented with a hematologic malignancy and two with a basal cell carcinoma. Four patients developed hemophagocytic lymphohistiocytosis (HLH) or an HLH-like episode, of whom three passed away during or shortly after the occurrence of HLH. TNF-inhibitors (TNFi) were effective in treating vasculopathy-associated symptoms and preventing stroke, but were hardly effective in the treatment of hematologic manifestations. Three patients underwent hematopoietic cell transplantation and two of them are doing well with complete resolution of DADA2-related symptoms. The overall mortality in this cohort was 17.2%. In conclusion, this cohort describes the clinical, genetic and laboratory findings of 29 Dutch DADA2 patients. We describe the occurrence of HLH as a life-threatening disease complication and report a relatively high incidence of malignancies and mortality.
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Affiliation(s)
- Marie Valérie E Andriessen
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht University, PO Box 85050, 3508 GA, Utrecht, the Netherlands
| | - G Elizabeth Legger
- Department of Pediatric Rheumatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Robbert G M Bredius
- Department of Pediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, the Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - A Elisabeth Hak
- Departments of Internal Medicine and Rheumatology and Clinical Immunology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Petra C E Hissink Muller
- Department of Pediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, the Netherlands
| | - Sylvia Kamphuis
- Department of Pediatric Rheumatology, Sophia Children's Hospital, Erasmus MC University Centre, Rotterdam, the Netherlands
| | - Femke C C Klouwer
- Department of Neurology and Pediatric Neurology, Location AMC, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Helen L Leavis
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Stefan Nierkens
- Center for Translational Immunology, University Medical Center Utrecht & Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Abraham Rutgers
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, 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
| | - Gijs T J van Well
- Department of Pediatrics: Division of Pediatric Infectious Diseases, Immunology and Rheumatology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Catharina M Mulders-Manders
- Department of Internal Medicine, Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht University, PO Box 85050, 3508 GA, Utrecht, the Netherlands.
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3
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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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4
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Elsink K, Huibers MMH, Hollink IHIM, Simons A, Zonneveld-Huijssoon E, van der Veken LT, Leavis HL, Henriet SSV, van Deuren M, van de Veerdonk FL, Potjewijd J, Berghuis D, Dalm VASH, Vermont CL, van de Ven AAJM, Lambeck AJA, Abbott KM, van Hagen PM, de Bree GJ, Kuijpers TW, Frederix GWJ, van Gijn ME, van Montfrans JM. Implementation of Early Next-Generation Sequencing for Inborn Errors of Immunity: A Prospective Observational Cohort Study of Diagnostic Yield and Clinical Implications in Dutch Genome Diagnostic Centers. Front Immunol 2022; 12:780134. [PMID: 34992599 PMCID: PMC8724043 DOI: 10.3389/fimmu.2021.780134] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/01/2021] [Indexed: 01/07/2023] Open
Abstract
Objective Inborn errors of immunity (IEI) are a heterogeneous group of disorders, affecting different components of the immune system. Over 450 IEI related genes have been identified, with new genes continually being recognized. This makes the early application of next-generation sequencing (NGS) as a diagnostic method in the evaluation of IEI a promising development. We aimed to provide an overview of the diagnostic yield and time to diagnosis in a cohort of patients suspected of IEI and evaluated by an NGS based IEI panel early in the diagnostic trajectory in a multicenter setting in the Netherlands. Study Design We performed a prospective observational cohort study. We collected data of 165 patients with a clinical suspicion of IEI without prior NGS based panel evaluation that were referred for early NGS using a uniform IEI gene panel. The diagnostic yield was assessed in terms of definitive genetic diagnoses, inconclusive diagnoses and patients without abnormalities in the IEI gene panel. We also assessed time to diagnosis and clinical implications. Results For children, the median time from first consultation to diagnosis was 119 days versus 124 days for adult patients (U=2323; p=0.644). The median turn-around time (TAT) of genetic testing was 56 days in pediatric patients and 60 days in adult patients (U=1892; p=0.191). A definitive molecular diagnosis was made in 25/65 (24.6%) of pediatric patients and 9/100 (9%) of adults. Most diagnosed disorders were identified in the categories of immune dysregulation (n=10/25; 40%), antibody deficiencies (n=5/25; 20%), and phagocyte diseases (n=5/25; 20%). Inconclusive outcomes were found in 76/165 (46.1%) patients. Within the patient group with a genetic diagnosis, a change in disease management occurred in 76% of patients. Conclusion In this cohort, the highest yields of NGS based evaluation for IEI early in the diagnostic trajectory were found in pediatric patients, and in the disease categories immune dysregulation and phagocyte diseases. In cases where a definitive diagnosis was made, this led to important disease management implications in a large majority of patients. More research is needed to establish a uniform diagnostic pathway for cases with inconclusive diagnoses, including variants of unknown significance.
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Affiliation(s)
- Kim Elsink
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Manon M H Huibers
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Iris H I M Hollink
- Department of Clinical Genetics, Erasmus Medical Center, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Annet Simons
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, Radboud University, Nijmegen, Netherlands.,Radboud Institute for Oncology, Radboud University Medical Center, Radboud University, Nijmegen, Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Stefanie S V Henriet
- Department of Pediatric Infectious Diseases and Immunology, Amalia's Children Hospital, Radboud University Nijmegen Medical Centre, Radboud University, Nijmegen, Netherlands
| | - Marcel van Deuren
- Department of Internal Medicine, Radboud University Medical Center, Radboud Center for Infectious Diseases, Nijmegen, Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Center, Radboud Center for Infectious Diseases, Nijmegen, Netherlands
| | - Judith Potjewijd
- Department of Nephrology and Clinical Immunology, Maastricht University Medical Center, Maastricht University, Maastricht, Netherlands
| | - Dagmar Berghuis
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden University, Leiden, Netherlands
| | - Virgil A S H Dalm
- Department of Internal Medicine, Division of Allergy & Clinical Immunology; Department of Immunology, Erasmus University Medical Center Rotterdam, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Clementien L Vermont
- Department of Pediatric Infectious Diseases, Immunology and Rheumatology, Sophia Children's Hospital, Erasmus Medical Center, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Annick A J M van de Ven
- Department of Internal Medicine and Allergology, Rheumatology and Clinical Immunology, University Medical Center Groningen, Groningen, Netherlands
| | - Annechien J A Lambeck
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Kristin M Abbott
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - P Martin van Hagen
- Department of Internal Medicine, Division of Allergy & Clinical Immunology; Department of Immunology, Erasmus University Medical Center Rotterdam, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Mariëlle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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5
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van der Made CI, Potjewijd J, Hoogstins A, Willems HPJ, Kwakernaak AJ, de Sevaux RGL, van Daele PLA, Simons A, Heijstek M, Beck DB, Netea MG, van Paassen P, Elizabeth Hak A, van der Veken LT, van Gijn ME, Hoischen A, van de Veerdonk FL, Leavis HL, Rutgers A. Adult-onset autoinflammation caused by somatic mutations in UBA1: A Dutch case series of patients with VEXAS. J Allergy Clin Immunol 2021; 149:432-439.e4. [PMID: 34048852 DOI: 10.1016/j.jaci.2021.05.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [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: 03/25/2021] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND A novel autoinflammatory syndrome was recently described in male patients who harbored somatic mutations in the X-chromosomal UBA1 gene. These patients were characterized by adult-onset, treatment-refractory inflammation with fever, cytopenia, dysplastic bone marrow, vacuoles in myeloid and erythroid progenitor cells, cutaneous and pulmonary inflammation, chondritis, and vasculitis, which is abbreviated as VEXAS. OBJECTIVE This study aimed to (retrospectively) diagnose VEXAS in patients who had previously been registered as having unclassified autoinflammation. We furthermore aimed to describe clinical experiences with this multifaceted, complex disease. METHODS A systematic reanalysis of whole-exome sequencing data from a cohort of undiagnosed patients with autoinflammation from academic hospitals in The Netherlands was performed. When no sequencing data were available, targeted Sanger sequencing was applied in cases with high clinical suspicion of VEXAS. RESULTS A total of 12 male patients who carried mutations in UBA1 were identified. These patients presented with adult-onset (mean age 67 years, range 47-79 years) autoinflammation with systemic symptoms, elevated inflammatory parameters, and multiorgan involvement, most typically involving the skin and bone marrow. Novel features of VEXAS included interstitial nephritis, cardiac involvement, stroke, and intestinal perforation related to treatment with tocilizumab. Although many types of treatment were initiated, most patients became treatment-refractory, with a high mortality rate of 50%. CONCLUSION VEXAS should be considered in the differential diagnosis of males with adult-onset autoinflammation characterized by systemic symptoms and multiorgan involvement. Early diagnosis can prevent unnecessary diagnostic procedures and provide better prognostic information and more suitable treatment options, including stem cell transplantation.
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Affiliation(s)
- Caspar I van der Made
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Judith Potjewijd
- Department of Internal Medicine, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Annemiek Hoogstins
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Huub P J Willems
- Department of Internal Medicine, Maxima Medisch Centrum, Eindhoven, The Netherlands
| | - Arjan J Kwakernaak
- Department of Internal Medicine and Department of Rheumatology and Clinical Immunology, Amsterdam University Medical Center, location AMC/Meibergdreef, Amsterdam, The Netherlands
| | - Ruud G L de Sevaux
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul L A van Daele
- Department of Internal Medicine and Department of Immunology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marloes Heijstek
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Md
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pieter van Paassen
- Department of Internal Medicine, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - A Elizabeth Hak
- Department of Internal Medicine and Department of Rheumatology and Clinical Immunology, Amsterdam University Medical Center, location AMC/Meibergdreef, Amsterdam, 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
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Hoischen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Abraham Rutgers
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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6
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Venema WJ, Hiddingh S, de Boer JH, Claas FHJ, Mulder A, den Hollander AI, Stratikos E, Sarkizova S, van der Veken LT, Janssen GMC, van Veelen PA, Kuiper JJW. ERAP2 Increases the Abundance of a Peptide Submotif Highly Selective for the Birdshot Uveitis-Associated HLA-A29. Front Immunol 2021; 12:634441. [PMID: 33717175 PMCID: PMC7950316 DOI: 10.3389/fimmu.2021.634441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
Birdshot Uveitis (BU) is a blinding inflammatory eye condition that only affects HLA-A29-positive individuals. Genetic association studies linked ERAP2 with BU, an aminopeptidase which trims peptides before their presentation by HLA class I at the cell surface, which suggests that ERAP2-dependent peptide presentation by HLA-A29 drives the pathogenesis of BU. However, it remains poorly understood whether the effects of ERAP2 on the HLA-A29 peptidome are distinct from its effect on other HLA allotypes. To address this, we focused on the effects of ERAP2 on the immunopeptidome in patient-derived antigen presenting cells. Using complementary HLA-A29-based and pan-class I immunopurifications, isotope-labeled naturally processed and presented HLA-bound peptides were sequenced by mass spectrometry. We show that the effects of ERAP2 on the N-terminus of ligands of HLA-A29 are shared across endogenous HLA allotypes, but discover and replicate that one peptide motif generated in the presence of ERAP2 is specifically bound by HLA-A29. This motif can be found in the amino acid sequence of putative autoantigens. We further show evidence for internal sequence specificity for ERAP2 imprinted in the immunopeptidome. These results reveal that ERAP2 can generate an HLA-A29-specific antigen repertoire, which supports that antigen presentation is a key disease pathway in BU.
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Affiliation(s)
- Wouter J Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Arend Mulder
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Efstratios Stratikos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Greece
| | - Siranush Sarkizova
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lars T van der Veken
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
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7
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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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8
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van der Veken LT, Maiburg MC, Groenendaal F, van Gijn ME, Bloem AC, Erpelinck C, Gröschel S, Sanders MA, Delwel R, Bierings MB, Buijs A. Lethal neonatal bone marrow failure syndrome with multiple congenital abnormalities, including limb defects, due to a constitutional deletion of 3' MECOM. Haematologica 2018; 103:e173-e176. [PMID: 29439187 DOI: 10.3324/haematol.2017.185033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Lars T van der Veken
- Department of Genetics, University Medical Center Utrecht, Wilhelmina Children's Hospital, Utrecht University, Rotterdam, the Netherlands
| | - Merel C Maiburg
- Department of Genetics, University Medical Center Utrecht, Wilhelmina Children's Hospital, Utrecht University, Rotterdam, the Netherlands
| | - Floris Groenendaal
- Department of Neonatology, University Medical Center Utrecht, Wilhelmina Children's Hospital, Utrecht University, Rotterdam, the Netherlands
| | - Mariëlle E van Gijn
- Department of Genetics, University Medical Center Utrecht, Wilhelmina Children's Hospital, Utrecht University, Rotterdam, the Netherlands
| | - Andries C Bloem
- Department of Immunology, University Medical Center Utrecht, Wilhelmina Children's Hospital, Utrecht University, Rotterdam, the Netherlands
| | - Claudia Erpelinck
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Stefan Gröschel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mathijs A Sanders
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marc B Bierings
- Department of Pediatric Hematology and stem cell transplantation, University Medical Center Utrecht, Wilhelmina Children's Hospital, Utrecht University, the Netherlands
| | - Arjan Buijs
- Department of Genetics, University Medical Center Utrecht, Wilhelmina Children's Hospital, Utrecht University, Rotterdam, the Netherlands
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9
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Hiemcke-Jiwa LS, Leguit RJ, van der Veken LT, Buijs A, Leeuwis JW, de Boer M, Jiwa NM, Bloem AC, Petersen EJ, de Weger RA, Huibers MMH. Lymphoblastic lymphoma with a triple-hit profile: a rare but distinct and relevant entity. Hum Pathol 2016; 63:171-176. [PMID: 27867103 DOI: 10.1016/j.humpath.2016.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Received: 08/12/2016] [Revised: 10/31/2016] [Accepted: 11/03/2016] [Indexed: 11/24/2022]
Abstract
Follicular lymphoma with progression to a high-grade lymphoma bears a poor prognosis. We describe a case of a 60-year-old man who presented in 2012 with an epidural mass, diagnosed as a diffuse large B-cell lymphoma (DLBCL) with concurrent low-grade follicular lymphoma. Three years later, the patient presented with a cervical mass, diagnosed as a lymphoblastic lymphoma (LBL). Both the DLBCL and LBL contained a "triple hit" with BCL2, BCL6, and cMYC translocations demonstrated by fluorescence in situ hybridization analysis and a complex karyotype by single-nucleotide polymorphism array analysis. Furthermore, the 2 lymphomas were shown to be clonally related by clonality analysis and single-nucleotide polymorphism array analysis. This case report presents a highly unusual case of an LBL with a triple hit, originating from a DLBCL, which has rarely been described in the literature and deserves further exploration.
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Affiliation(s)
- Laura S Hiemcke-Jiwa
- Department of Pathology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands.
| | - Roos J Leguit
- Department of Pathology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Lars T van der Veken
- Department of Genetics, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Arjan Buijs
- Department of Genetics, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Jan Willem Leeuwis
- Department of Pathology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Mirthe de Boer
- Department of Pathology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - N Mehdi Jiwa
- Department of Pathology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Andries C Bloem
- Department of Immunology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Eefke J Petersen
- Department of Hematology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Roel A de Weger
- Department of Pathology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
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10
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Giltay JC, Klijn AJ, de Jong TPVM, Kats P, van Breugel M, Lens S, Vromans M, van der Veken LT, Hochstenbach R. Tetraploid/Diploid Mosaicism in Cultured Genital Skin Fibroblasts: Is It Causally Related to Penoscrotal Hypospadias? Mol Syndromol 2016; 7:153-9. [PMID: 27587991 DOI: 10.1159/000446203] [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] [Accepted: 03/29/2016] [Indexed: 11/19/2022] Open
Abstract
Tetraploid/diploid mosaicism is a rare chromosomal abnormality that is infrequently reported in patients with severe developmental delay, growth retardation, and short life span. Here, we present a 6-year-old patient with severe penoscrotal hypospadias and a coloboma of the left eye but with normal growth, normal psychomotor development, and without dysmorphisms. We considered a local, mosaic sex chromosomal aneuploidy as a possible cause of his genital anomaly and performed karyotyping in cultured fibroblasts from the genital skin, obtained during surgical correction. Tetraploid/diploid (92,XXYY/46,XY) mosaicism was found in 43/57 and 6/26 metaphases in 2 separate cultures, respectively. Buccal smear cells, blood lymphocytes, and cells from urine sediment all showed diploidy. We investigated whether this chromosomal abnormality could be found in other patients with severe hypospadias and karyotyped genital fibroblasts of 6 additional patients but found only low frequencies (<11%) of tetraploid cells, not statistically different from those found in control males with no hypospadias. This is the first time tetraploid mosaicism is found in such a high percentage in a patient without psychomotor retardation, dysmorphisms or growth delay. Although the relationship between this observed mosaicism in cultured cells and the underlying pathogenetic mechanism in penoscrotal hypospadias remains to be determined, our data clearly illustrate the power of cytogenetic techniques in detecting mosaicism compared to next-generation sequencing techniques, in which DNA pooled from multiple cells is used.
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Affiliation(s)
- Jacques C Giltay
- Departments of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Aart J Klijn
- Departments of Pediatric Urology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tom P V M de Jong
- Departments of Pediatric Urology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Peter Kats
- Departments of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjolijn van Breugel
- Departments of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susan Lens
- Departments of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martijn Vromans
- Departments of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lars T van der Veken
- Departments of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ron Hochstenbach
- Departments of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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11
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Monroe GR, Kappen IF, Stokman MF, Terhal PA, van den Boogaard MJH, Savelberg SM, van der Veken LT, van Es RJ, Lens SM, Hengeveld RC, Creton MA, Janssen NG, Mink van der Molen AB, Ebbeling MB, Giles RH, Knoers NV, van Haaften G. Compound heterozygous NEK1 variants in two siblings with oral-facial-digital syndrome type II (Mohr syndrome). Eur J Hum Genet 2016; 24:1752-1760. [PMID: 27530628 DOI: 10.1038/ejhg.2016.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/23/2016] [Accepted: 06/28/2016] [Indexed: 01/01/2023] Open
Abstract
The oral-facial-digital (OFD) syndromes comprise a group of related disorders with a combination of oral, facial and digital anomalies. Variants in several ciliary genes have been associated with subtypes of OFD syndrome, yet in most OFD patients the underlying cause remains unknown. We investigated the molecular basis of disease in two brothers with OFD type II, Mohr syndrome, by performing single-nucleotide polymorphism (SNP)-array analysis on the brothers and their healthy parents to identify homozygous regions and candidate genes. Subsequently, we performed whole-exome sequencing (WES) on the family. Using WES, we identified compound heterozygous variants c.[464G>C];[1226G>A] in NIMA (Never in Mitosis Gene A)-Related Kinase 1 (NEK1). The novel variant c.464G>C disturbs normal splicing in an essential region of the kinase domain. The nonsense variant c.1226G>A, p.(Trp409*), results in nonsense-associated alternative splicing, removing the first coiled-coil domain of NEK1. Candidate variants were confirmed with Sanger sequencing and alternative splicing assessed with cDNA analysis. Immunocytochemistry was used to assess cilia number and length. Patient-derived fibroblasts showed severely reduced ciliation compared with control fibroblasts (18.0 vs 48.9%, P<0.0001), but showed no significant difference in cilia length. In conclusion, we identified compound heterozygous deleterious variants in NEK1 in two brothers with Mohr syndrome. Ciliation in patient fibroblasts is drastically reduced, consistent with a ciliary defect pathogenesis. Our results establish NEK1 variants involved in the etiology of a subset of patients with OFD syndrome type II and support the consideration of including (routine) NEK1 analysis in patients suspected of OFD.
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Affiliation(s)
- Glen R Monroe
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Isabelle Fpm Kappen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Plastic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marijn F Stokman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Sanne Mc Savelberg
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lars T van der Veken
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert Jj van Es
- Department of Oral and Maxillofacial Surgery and Special Dental Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susanne M Lens
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rutger C Hengeveld
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marijn A Creton
- Department of Oral and Maxillofacial Surgery and Special Dental Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nard G Janssen
- Department of Oral and Maxillofacial Surgery and Special Dental Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Michelle B Ebbeling
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rachel H Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Regenerative Medicine Center-Hubrecht Institute, Utrecht, The Netherlands
| | - Nine V Knoers
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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12
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de Pagter MS, van Roosmalen MJ, Baas AF, Renkens I, Duran KJ, van Binsbergen E, Tavakoli-Yaraki M, Hochstenbach R, van der Veken LT, Cuppen E, Kloosterman WP. Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring. Am J Hum Genet 2015; 96:651-6. [PMID: 25799107 DOI: 10.1016/j.ajhg.2015.02.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/05/2015] [Indexed: 01/14/2023] Open
Abstract
Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. The chromothripsis in the mothers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across three to five chromosomes. Two mothers did not show any phenotypic abnormalities, although 3-13 protein-coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy-number changes in two children. This resulted in gene-dosage changes, which are probably responsible for the severe congenital phenotypes of these two children. In contrast, the third child, who has a severe congenital disease, harbored all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy-number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein-coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy individuals affects reproduction and is expected to substantially increase the risk of miscarriages, abortions, and severe congenital disease.
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Affiliation(s)
- Mirjam S de Pagter
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands
| | - Markus J van Roosmalen
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands
| | - Annette F Baas
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands
| | - Ivo Renkens
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands
| | - Karen J Duran
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands
| | - Ellen van Binsbergen
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands
| | - Masoumeh Tavakoli-Yaraki
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands
| | - Ron Hochstenbach
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands
| | - Lars T van der Veken
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands
| | - Edwin Cuppen
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands; Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht 3584 CT, the Netherlands
| | - Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands.
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13
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van Heesch S, Simonis M, van Roosmalen MJ, Pillalamarri V, Brand H, Kuijk EW, de Luca KL, Lansu N, Braat AK, Menelaou A, Hao W, Korving J, Snijder S, van der Veken LT, Hochstenbach R, Knegt AC, Duran K, Renkens I, Alekozai N, Jager M, Vergult S, Menten B, de Bruijn E, Boymans S, Ippel E, van Binsbergen E, Talkowski ME, Lichtenbelt K, Cuppen E, Kloosterman WP. Genomic and functional overlap between somatic and germline chromosomal rearrangements. Cell Rep 2014; 9:2001-10. [PMID: 25497101 DOI: 10.1016/j.celrep.2014.11.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 10/20/2014] [Accepted: 11/15/2014] [Indexed: 12/17/2022] Open
Abstract
Genomic rearrangements are a common cause of human congenital abnormalities. However, their origin and consequences are poorly understood. We performed molecular analysis of two patients with congenital disease who carried de novo genomic rearrangements. We found that the rearrangements in both patients hit genes that are recurrently rearranged in cancer (ETV1, FOXP1, and microRNA cluster C19MC) and drive formation of fusion genes similar to those described in cancer. Subsequent analysis of a large set of 552 de novo germline genomic rearrangements underlying congenital disorders revealed enrichment for genes rearranged in cancer and overlap with somatic cancer breakpoints. Breakpoints of common (inherited) germline structural variations also overlap with cancer breakpoints but are depleted for cancer genes. We propose that the same genomic positions are prone to genomic rearrangements in germline and soma but that timing and context of breakage determines whether developmental defects or cancer are promoted.
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Affiliation(s)
- Sebastiaan van Heesch
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Marieke Simonis
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Vamsee Pillalamarri
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Harrison Brand
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ewart W Kuijk
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Kim L de Luca
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Nico Lansu
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - A Koen Braat
- Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Androniki Menelaou
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Wensi Hao
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Simone Snijder
- Department of Clinical Genetics, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Lars T van der Veken
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Ron Hochstenbach
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Alida C Knegt
- Department of Clinical Genetics, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Karen Duran
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Ivo Renkens
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Najla Alekozai
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Myrthe Jager
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Ewart de Bruijn
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Sander Boymans
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Elly Ippel
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Michael E Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Klaske Lichtenbelt
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Edwin Cuppen
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
| | - Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
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14
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Hochstenbach R, Krijtenburg PJ, van der Veken LT, van der Smagt J, Roeleveld-Versteegh A, Visser G, Terhal P. Monosomy 20 Mosaicism Revealed by Extensive Karyotyping in Blood and Skin Cells: Case Report and Review of the Literature. Cytogenet Genome Res 2014; 144:155-62. [DOI: 10.1159/000369606] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2014] [Indexed: 11/19/2022] Open
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15
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van Nunen DPF, van den Boogaard MJH, Don Griot JPW, Rüttermann M, van der Veken LT, Breugem CC. Elevated Infant Mortality Rate among Dutch Oral Cleft Cases: A Retrospective Analysis from 1997 to 2011. Front Surg 2014; 1:48. [PMID: 25593972 PMCID: PMC4286963 DOI: 10.3389/fsurg.2014.00048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 11/19/2014] [Indexed: 12/04/2022] Open
Abstract
Objectives: First, to determine the infant mortality rate (IMR) for Dutch patients with isolated oral clefts (OC) as well as for patients with clefts seen in association with other malformations. Second, to conduct a similar analysis per cleft type: cleft lip with or without cleft palate (CP), CP (including Robin sequence). Third, to examine the underlying causes of death. Material and Methods: A retrospective review of the charts of patients with OC born in the period 1997–2011 and treated in three regional cleft centers in the Netherlands. Results: One thousand five hundred thirty patients with OC were born during the study period and treated in the cleft centers. The overall IMR for all clefts was 2.09%, significantly higher than the general Dutch IMR of 0.45%. In a subanalysis per cleft type, the IMRs were 1.22, 1.38, 2.45, and 3.62% for cleft lip, cleft lip with CP, CP, and Robin sequence, respectively. The mortality rates for isolated OC did not differ significantly from the general Dutch rate. Causes of death were congenital malformations of the heart in 40.6%, airway/lungs in 15.6%, nervous system in 15.6%, infectious disease in 12.5%, and other or unknown in 15.6%. Conclusion: The elevated IMR observed in Dutch patients with OC is almost exclusively caused by associated congenital malformations. After diagnosis of an oral cleft an in-depth medical examination and a consult by the pediatrician and clinical geneticist is imperative to instigate the appropriate medical management.
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Affiliation(s)
- Daan P F van Nunen
- Division of Plastic and Reconstructive Surgery, University Medical Center Utrecht , Utrecht , Netherlands
| | | | - J Peter W Don Griot
- Department of Plastic, Reconstructive and Hand Surgery, Vrije Universiteit University Medical Center Amsterdam , Amsterdam , Netherlands
| | - Mike Rüttermann
- Department of Plastic Surgery, University Medical Center Groningen , Groningen , Netherlands
| | - Lars T van der Veken
- Department of Medical Genetics, University Medical Center Utrecht , Utrecht , Netherlands
| | - Corstiaan C Breugem
- Division of Plastic and Reconstructive Surgery, University Medical Center Utrecht , Utrecht , Netherlands
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16
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Coenen EA, Zwaan CM, Meyer C, Marschalek R, Pieters R, van der Veken LT, Beverloo HB, van den Heuvel-Eibrink MM. KIAA1524: A novel MLL translocation partner in acute myeloid leukemia. Leuk Res 2010; 35:133-5. [PMID: 20943269 DOI: 10.1016/j.leukres.2010.08.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 08/04/2010] [Accepted: 08/22/2010] [Indexed: 10/19/2022]
Abstract
The Mixed Lineage Leukemia gene on chromosome 11q23 is a frequent site of recurrent translocations in acute leukemias. Its promiscuous character is reflected by the more than 60 different translocation partners described in literature. Prompted by karyotype and atypical FISH results, we identified a new translocation partner in infant acute myeloid leukemia, KIAA1524 on 3q13.13, also known as 'Cancerous Inhibitor of Protein phosphatase 2A (CIP2A)'. This gene was recently identified as a proto-oncogene stabilizing MYC protein in gastric carcinoma. KIAA1524 has never been related to hematologic malignancies before, and the current AML case is the first case in which an MLL-KIAA1524 fusion was described.
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Affiliation(s)
- Eva A Coenen
- Department of Pediatric Oncology and Hematology, Sophia Children's Hospital, Rotterdam, The Netherlands
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17
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van der Veken LT, Dieleman MM, Douben H, van de Brug JC, van de Graaf R, Hoogeboom AJM, Poddighe PJ, de Klein A. Low grade mosaic for a complex supernumerary ring chromosome 18 in an adult patient with multiple congenital anomalies. Mol Cytogenet 2010; 3:13. [PMID: 20618949 PMCID: PMC2909946 DOI: 10.1186/1755-8166-3-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [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: 04/07/2010] [Accepted: 07/09/2010] [Indexed: 11/12/2022] Open
Abstract
Background Several cases have been reported of patients with a ring chromosome 18 replacing one of the normal chromosomes 18. Less common are patients with a supernumerary ring chromosomes 18. High resolution whole genome examination in patients with multiple congenital abnormalities might reveal cytogenetic abnormalities of an unexpected complexity. Results We report a 24 years old male patient with lower spinal anomalies, hypospadia, bifid scrotum, cryptorchism, anal atresia, kidney stones, urethra anomalies, radial dysplasia, and a hypoplastic thumb. Some of the anomalies overlap with the VACTERL association. Chromosome analysis of cultured peripheral blood lymphocytes revealed an additional ring chromosome in 13% of the metaphases. Both parents had a normal karyotype, demonstrating the de novo origin of this ring chromosome. FISH analysis using whole chromosome paints showed that the additional chromosomal material was derived from chromosome 18. Chromosome analysis of cultured fibroblasts revealed only one cell with the supernumerary ring chromosome in the 400 analyzed. To characterize the ring chromosome in more detail peripheral blood derived DNA was analyzed using SNP-arrays. The array results indicated a 5 Mb gain of the pericentromeric region of chromosome 18q10-q11.2. FISH analysis using BAC-probes located in the region indicated the presence of 6 signals on the r(18) chromosome. In addition, microsatellite analysis demonstrated that the unique supernumerary ring chromosome was paternally derived and both normal copies showed biparental disomy. Conclusions We report on an adult patient with multiple congenital abnormalities who had in 13% of his cells a unique supernumerary ring chromosome 18 that was composed of 6 copies of the 5 Mb gene rich region of 18q11.
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Affiliation(s)
- Lars T van der Veken
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
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18
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van der Veken LT, Coccoris M, Swart E, Falkenburg JHF, Schumacher TN, Heemskerk MHM. Alpha beta T cell receptor transfer to gamma delta T cells generates functional effector cells without mixed TCR dimers in vivo. J Immunol 2009; 182:164-70. [PMID: 19109147 DOI: 10.4049/jimmunol.182.1.164] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The successful application of T cell-based immunotherapeutic applications depends on the availability of large numbers of T cells with the desired Ag specificity and phenotypic characteristics. Engineering of TCR-transferred T lymphocytes is an attractive strategy to obtain sufficient T cells with an Ag specificity of choice. However, the introduction of additional TCR chains into T cells leads to the generation of T cells with unknown specificity, due to the formation of mixed dimers between the endogenous and introduced TCR chains. The formation of such potentially autoaggressive T cells may be prevented by using gammadelta T cells as recipient cells, but the in vivo activity of such TCR-engineered gammadelta T cells has not been established. In the present study, we have investigated the in vivo functionality of TCR-transduced gammadelta T cells, in particular their Ag specific proliferative capacity, Ag specific reactivity, in vivo persistence, and their capacity to mount recall responses. The results demonstrate that alphabeta TCR engineering of gammadelta T cells forms a feasible strategy to generate Ag-specific effector T cells that do not express mixed TCR dimers. In view of increasing concerns on the potential autoimmune consequences of mixed TCR dimer formation, the testing of alphabeta TCR engineered gammadelta T cells in clinical trials seems warranted.
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Affiliation(s)
- Lars T van der Veken
- Laboratory of Experimental Hematology, Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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19
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van der Veken LT, Diez Campelo M, van der Hoorn MAWG, Hagedoorn RS, van Egmond HME, van Bergen J, Willemze R, Falkenburg JHF, Heemskerk MHM. Functional Analysis of Killer Ig-Like Receptor-Expressing Cytomegalovirus-Specific CD8+T Cells. J Immunol 2008; 182:92-101. [DOI: 10.4049/jimmunol.182.1.92] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Laurin D, Spierings E, van der Veken LT, Hamrouni A, Falkenburg JHF, Souillet G, Vermeulen C, Farre A, Galambrun C, Rigal D, Bertrand Y, Goulmy E, Eljaafari A. Minor histocompatibility antigen DDX3Y induces HLA-DQ5-restricted T cell responses with limited TCR-Vbeta usage both in vivo and in vitro. Biol Blood Marrow Transplant 2007; 12:1114-24. [PMID: 17085304 DOI: 10.1016/j.bbmt.2006.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2006] [Accepted: 07/20/2006] [Indexed: 11/24/2022]
Abstract
In vitro stimulation of human female T cells with male HLA-identical dendritic cells resulted in the generation of HLA-DQB1*0501/0502-restricted minor histocompatibility H-Y antigen-specific CD4(+) T cell clones. Two clones generated from different HLA-identical pairs were analyzed. Use of HLA-DQ5-expressing female Epstein-Barr virus transformed B lymphoblastoid cell lines transfected with various H-Y genes and loaded with overlapping peptides demonstrated that both T cell clones are specific for a peptide encoded by DDX3Y. Previously, an HLA-DQ5-restricted T cell clone specific for the same peptide was isolated from a patient with graft-versus-host disease. Thus, we compared the T cell receptor (TCR) rearrangements of the 2 in vitro generated T cell clones and the ex vivo isolated T cell clone. All 3 clones shared the same TCRBV5-4* gene segment and 2 of 3 clones also used similar TCR-Valpha segments. Our results suggest that T cells recognizing the HLA-DQ5/DDX3Y T cell epitope might be characterized by a relatively limited TCR-beta repertoire. The differences in the junctional TCR-beta region had no effect on the antigen specificity, but altered the capacity of the TCR to distinguish the HLA-DQ5/DDX3Y complex from its allelic counterpart. The results also demonstrate that in vitro stimulation of T cells with allogeneic HLA-identical dendritic cells may facilitate the characterization of in vivo, potentially relevant HLA class II-restricted minor H epitopes.
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Affiliation(s)
- David Laurin
- Cell Therapy Department, Etablissement Français du Sang Région Rhône-Alpes, Rhône, France
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21
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Heemskerk MHM, Hagedoorn RS, van der Hoorn MAWG, van der Veken LT, Hoogeboom M, Kester MGD, Willemze R, Falkenburg JHF. Efficiency of T-cell receptor expression in dual-specific T cells is controlled by the intrinsic qualities of the TCR chains within the TCR-CD3 complex. Blood 2006; 109:235-43. [PMID: 16968899 DOI: 10.1182/blood-2006-03-013318] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Genetic engineering of T lymphocytes is an attractive strategy to specifically redirect T-cell immunity toward viral infections and malignancies. We previously demonstrated redirected antileukemic reactivity of cytomegalovirus (CMV)–specific T cells by transfer of minor histocompatibility antigen HA-2–specific T-cell receptors (TCRs). HA-2–TCR-transferred CMV-specific T cells were potent effectors against HA-2–expressing leukemic cells, as well as CMV-expressing cells. Functional activity of these T cells correlated with TCR cell-surface expression. In the present study we analyzed which properties of transferred and endogenous TCRs are crucial for efficient cell-surface expression. We demonstrate that expression of the introduced TCR is not a random process but is determined by characteristics of both the introduced and the endogenously expressed TCR. The efficiency of TCR cell-surface expression is controlled by the intrinsic quality of the TCR complex. In addition, we demonstrate that chimeric TCRs can be formed and that efficiency of TCR expression is independent of whether TCRs are retrovirally introduced or naturally expressed. In conclusion, introduced, endogenous, and chimeric TCRs compete for cell-surface expression in favor of the TCR-CD3 complex with best-pairing properties.
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MESH Headings
- Amino Acid Sequence
- Antigen Presentation
- Cells, Cultured/immunology
- Cytomegalovirus/immunology
- Cytotoxicity, Immunologic
- Flow Cytometry
- Genes, Reporter
- Genes, T-Cell Receptor alpha
- Genes, T-Cell Receptor beta
- Genetic Vectors/genetics
- HLA-A2 Antigen/immunology
- HLA-B7 Antigen/immunology
- HLA-DQ Antigens/immunology
- Humans
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/immunology
- Ligands
- Molecular Sequence Data
- Moloney murine leukemia virus/genetics
- Promoter Regions, Genetic
- Protein Binding
- Receptor-CD3 Complex, Antigen, T-Cell/genetics
- Receptor-CD3 Complex, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Recombinant Fusion Proteins/immunology
- Retroviridae/genetics
- T-Cell Antigen Receptor Specificity
- T-Lymphocytes, Cytotoxic/immunology
- Transduction, Genetic
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Affiliation(s)
- Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, C2-R, PO Box 9600, 2300 RC Leiden, The Netherlands.
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22
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van der Veken LT, Hagedoorn RS, van Loenen MM, Willemze R, Falkenburg JHF, Heemskerk MHM. Alphabeta T-cell receptor engineered gammadelta T cells mediate effective antileukemic reactivity. Cancer Res 2006; 66:3331-7. [PMID: 16540688 DOI: 10.1158/0008-5472.can-05-4190] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Retroviral transfer of T-cell receptors (TCR) to peripheral blood-derived T cells generates large numbers of T cells with the same antigen specificity, potentially useful for adoptive immunotherapy. One drawback of this procedure is the formation of mixed TCR dimers with unknown specificities due to pairing of endogenous and introduced TCR chains. We investigated whether gammadelta T cells can be an alternative effector population for TCR gene transfer because the gammadeltaTCR is not able to form dimers with the alphabetaTCR. Peripheral blood-derived gammadelta T cells were transduced with human leukocyte antigen (HLA) class I- or HLA class II-restricted minor histocompatibility antigen (mHag) or virus-specific TCRs. Because most gammadelta T cells do not express CD4 and CD8, we subsequently transferred these coreceptors. The TCR-transduced gammadelta T cells exerted high levels of antigen-specific cytotoxicity and produced IFN-gamma and IL-4, particularly in the presence of the relevant coreceptor. gammadelta T cells transferred with a TCR specific for the hematopoiesis-specific mHag HA-2 in combination with CD8 displayed high antileukemic reactivity against HA-2-expressing leukemic cells. These data show that transfer of alphabetaTCRs to gammadelta T cells generated potent effector cells for immunotherapy of leukemia, without the expression of potentially hazardous mixed TCR dimers.
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MESH Headings
- CD3 Complex/biosynthesis
- CD3 Complex/genetics
- CD3 Complex/immunology
- Gene Transfer Techniques
- Genetic Engineering
- HLA-A2 Antigen/immunology
- HLA-B7 Antigen/immunology
- Humans
- Immunotherapy, Adoptive/methods
- Leukemia/immunology
- Leukemia/therapy
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/biosynthesis
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Retroviridae/genetics
- T-Lymphocytes/immunology
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Affiliation(s)
- Lars T van der Veken
- Laboratory of Experimental Hematology, Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
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