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Mannucci I, Dang NDP, Huber H, Murry JB, Abramson J, Althoff T, Banka S, Baynam G, Bearden D, Beleza-Meireles A, Benke PJ, Berland S, Bierhals T, Bilan F, Bindoff LA, Braathen GJ, Busk ØL, Chenbhanich J, Denecke J, Escobar LF, Estes C, Fleischer J, Groepper D, Haaxma CA, Hempel M, Holler-Managan Y, Houge G, Jackson A, Kellogg L, Keren B, Kiraly-Borri C, Kraus C, Kubisch C, Le Guyader G, Ljungblad UW, Brenman LM, Martinez-Agosto JA, Might M, Miller DT, Minks KQ, Moghaddam B, Nava C, Nelson SF, Parant JM, Prescott T, Rajabi F, Randrianaivo H, Reiter SF, Schuurs-Hoeijmakers J, Shieh PB, Slavotinek A, Smithson S, Stegmann APA, Tomczak K, Tveten K, Wang J, Whitlock JH, Zweier C, McWalter K, Juusola J, Quintero-Rivera F, Fischer U, Yeo NC, Kreienkamp HJ, Lessel D. Genotype-phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders. Genome Med 2021; 13:90. [PMID: 34020708 PMCID: PMC8140440 DOI: 10.1186/s13073-021-00900-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/28/2021] [Indexed: 12/27/2022] Open
Abstract
Background We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. Results We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. Conclusions Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00900-3.
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Affiliation(s)
- Ilaria Mannucci
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Nghi D P Dang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Hannes Huber
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Jaclyn B Murry
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeff Abramson
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Thorsten Althoff
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gareth Baynam
- Faculty of Medicine and Health Sciences, University of Western Australia, Perth, WA, Australia.,Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, Australia.,Telethon Kids Institute, Perth, Australia
| | - David Bearden
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | - Ana Beleza-Meireles
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Frederic Bilan
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Laurence A Bindoff
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | - Øyvind L Busk
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jirat Chenbhanich
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246, Hamburg, Germany
| | - Luis F Escobar
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Caroline Estes
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Julie Fleischer
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Yolanda Holler-Managan
- Division of Neurology, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Boris Keren
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Gwenael Le Guyader
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Ulf W Ljungblad
- Department of Pediatrics, Vestfold Hospital, 3116, Tønsberg, Norway
| | | | - Julian A Martinez-Agosto
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Semel Institute of Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pediatrics, Division of Medical Genetics at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew Might
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kelly Q Minks
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | | | - Caroline Nava
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA.,Center for Duchenne Muscular Dystrophy, University of California Los Angeles, Los Angeles, CA, USA
| | - John M Parant
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Hanitra Randrianaivo
- UF de Génétique Médicale, GHSR, CHU de La Réunion, Saint Pierre, La Réunion, France
| | - Simone F Reiter
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | | | - Perry B Shieh
- Department of Neurology at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah Smithson
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kinga Tomczak
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Jordan H Whitlock
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.,Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | | | | | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA.
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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9
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Rissone A, Weinacht KG, la Marca G, Bishop K, Giocaliere E, Jagadeesh J, Felgentreff K, Dobbs K, Al-Herz W, Jones M, Chandrasekharappa S, Kirby M, Wincovitch S, Simon KL, Itan Y, DeVine A, Schlaeger T, Schambach A, Sood R, Notarangelo LD, Candotti F. Reticular dysgenesis-associated AK2 protects hematopoietic stem and progenitor cell development from oxidative stress. ACTA ACUST UNITED AC 2015; 212:1185-202. [PMID: 26150473 PMCID: PMC4516804 DOI: 10.1084/jem.20141286] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 06/01/2015] [Indexed: 12/23/2022]
Abstract
Rissone et al. demonstrate that adenylate kinase AK2, an enzyme mutated in reticular dysgenesis (RD) in humans, prevents oxidative stress during hematopoiesis. Using a zebrafish model, as well as induced pluripotent stem cells derived from an RD patient, they find that AK2 deficiency affects hematopoietic stem and progenitor development with increased oxidative stress. Antioxidant treatment rescues the hematopoietic phenotypes. Adenylate kinases (AKs) are phosphotransferases that regulate the cellular adenine nucleotide composition and play a critical role in the energy homeostasis of all tissues. The AK2 isoenzyme is expressed in the mitochondrial intermembrane space and is mutated in reticular dysgenesis (RD), a rare form of severe combined immunodeficiency (SCID) in humans. RD is characterized by a maturation arrest in the myeloid and lymphoid lineages, leading to early onset, recurrent, and overwhelming infections. To gain insight into the pathophysiology of RD, we studied the effects of AK2 deficiency using the zebrafish model and induced pluripotent stem cells (iPSCs) derived from fibroblasts of an RD patient. In zebrafish, Ak2 deficiency affected hematopoietic stem and progenitor cell (HSPC) development with increased oxidative stress and apoptosis. AK2-deficient iPSCs recapitulated the characteristic myeloid maturation arrest at the promyelocyte stage and demonstrated an increased AMP/ADP ratio, indicative of an energy-depleted adenine nucleotide profile. Antioxidant treatment rescued the hematopoietic phenotypes in vivo in ak2 mutant zebrafish and restored differentiation of AK2-deficient iPSCs into mature granulocytes. Our results link hematopoietic cell fate in AK2 deficiency to cellular energy depletion and increased oxidative stress. This points to the potential use of antioxidants as a supportive therapeutic modality for patients with RD.
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Affiliation(s)
- Alberto Rissone
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Katja Gabriele Weinacht
- Division of Hematology/Oncology and Division of Immunology, Boston Children's Hospital, Boston, MA 02115 Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Giancarlo la Marca
- Department of Neurosciences, Psychology, Pharmacology, and Child Health, University of Florence, 51039 Florence, Italy Meyer Children's University Hospital, 50141 Florence, Italy
| | - Kevin Bishop
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | | | - Jayashree Jagadeesh
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Kerstin Felgentreff
- Division of Hematology/Oncology and Division of Immunology, Boston Children's Hospital, Boston, MA 02115
| | - Kerry Dobbs
- Division of Hematology/Oncology and Division of Immunology, Boston Children's Hospital, Boston, MA 02115
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, 13110 Kuwait City, Kuwait Allergy and Clinical Immunology Unit, Pediatric Department, Al-Sabah Hospital, 70459 Kuwait City, Kuwait
| | - Marypat Jones
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Settara Chandrasekharappa
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Martha Kirby
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Stephen Wincovitch
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Karen Lyn Simon
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Disease, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Alex DeVine
- Division of Hematology/Oncology and Division of Immunology, Boston Children's Hospital, Boston, MA 02115
| | - Thorsten Schlaeger
- Division of Hematology/Oncology and Division of Immunology, Boston Children's Hospital, Boston, MA 02115
| | - Axel Schambach
- Division of Hematology/Oncology and Division of Immunology, Boston Children's Hospital, Boston, MA 02115 Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Raman Sood
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Luigi D Notarangelo
- Division of Hematology/Oncology and Division of Immunology, Boston Children's Hospital, Boston, MA 02115 Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
| | - Fabio Candotti
- Disorders of Immunity Section, Genetics and Molecular Biology Branch; Zebrafish Core and Oncogenesis and Development Section, Translational and Functional Genomics Branch; Genomics Core, Cancer Genetics and Comparative Genomics Branch; Division of Intramural Research Flow Cytometry Core; and Cytogenetics and Microscopy Core, Genetic Disease Research Branch; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 Division of Immunology and Allergy, University Hospital of Lausanne, 1011 Lausanne, Switzerland
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