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Leng K, Cadwell CR, Devine WP, Tihan T, Qi Z, Singhal NS, Glenn OA, Kamiya S, Wiita AP, Berger AC, Shieh JT, Titus EW, Paredes MF, Upadhyay V. Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy. Neurol Genet 2024; 10:e200142. [PMID: 38586598 PMCID: PMC10997208 DOI: 10.1212/nxg.0000000000200142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/24/2024] [Indexed: 04/09/2024]
Abstract
Objectives Mosaic gain of chromosome 1q (chr1q) has been associated with malformation of cortical development (MCD) and epilepsy. Hyaline protoplasmic astrocytopathy (HPA) is a rare neuropathologic finding seen in cases of epilepsy with MCD. The cell-type specificity of mosaic chr1q gain in the brain and the molecular signatures of HPA are unknown. Methods We present the case of a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and HPA. We performed single-nuclei RNA sequencing (snRNA-seq) of brain tissue from the second resection. Results snRNA-seq showed increased expression of chr1q genes specifically in subsets of neurons and astrocytes. Differentially expressed genes associated with inferred chr1q gain included AKT3 and genes associated with cell adhesion or migration. A subpopulation of astrocytes demonstrated marked enrichment for synapse-associated transcripts, possibly linked to the astrocytic inclusions observed in HPA. Discussion snRNA-seq may be used to infer the cell-type specificity of mosaic chromosomal copy number changes and identify associated gene expression alterations, which in the case of chr1q gain may involve aberrations in cell migration. Future studies using spatial profiling could yield further insights on the molecular signatures of HPA.
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Affiliation(s)
- Kun Leng
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Cathryn R Cadwell
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Walter P Devine
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Tarik Tihan
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Zhongxia Qi
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Nilika S Singhal
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Orit A Glenn
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Sherry Kamiya
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Arun P Wiita
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Amy C Berger
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Joseph T Shieh
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Erron W Titus
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Mercedes F Paredes
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Vaibhav Upadhyay
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
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Leng K, Cadwell CR, Patrick Devine W, Tihan T, Qi Z, Singhal N, Glenn O, Kamiya S, Wiita A, Berger A, Shieh JT, Titus EW, Paredes MF, Upadhyay V. Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy. bioRxiv 2024:2023.10.16.562560. [PMID: 38328093 PMCID: PMC10849466 DOI: 10.1101/2023.10.16.562560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Introduction Mosaic gain of chromosome 1q (chr1q) has been associated with malformation of cortical development (MCD) and epilepsy. Hyaline protoplasmic astrocytopathy (HPA) is a rare neuropathological finding seen in cases of epilepsy with MCD. The cell-type specificity of mosaic chr1q gain in the brain and the molecular signatures of HPA are unknown. Methods We present a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and HPA. We performed single-nuclei RNA-sequencing (snRNA-seq) of brain tissue from the second resection. Results snRNA-seq showed increased expression of chr1q genes specifically in subsets of neurons and astrocytes. Differentially expressed genes associated with inferred chr1q gain included AKT3 and genes associated with cell adhesion or migration. A subpopulation of astrocytes demonstrated marked enrichment for synapse-associated transcripts, possibly linked to the astrocytic inclusions observed in HPA. Discussion snRNA-seq may be used to infer the cell type-specificity of mosaic chromosomal copy number changes and identify associated gene expression alterations, which in the case of chr1q gain may involve aberrations in cell migration. Future studies using spatial profiling could yield further insights on the molecular signatures of HPA.
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Affiliation(s)
- Kun Leng
- Medical Scientist Training Program, University of California, San Francisco
| | - Cathryn R. Cadwell
- Department of Pathology, University of California, San Francisco
- Department of Neurological Surgery, University of California San Francisco
- Weill Institute for Neuroscience, University of California, San Francisco
| | | | - Tarik Tihan
- Department of Pathology, University of California, San Francisco
| | - Zhongxia Qi
- Department of Laboratory Medicine, University of California, San Francisco
| | - Nilika Singhal
- Division of Epilepsy, Department of Neurology, University of California, San Francisco
| | - Orit Glenn
- Department of Radiology and Biomedical Imaging, University of California, San Francisco
| | - Sherry Kamiya
- Department of Pathology, University of California, San Francisco
| | - Arun Wiita
- Department of Laboratory Medicine, University of California, San Francisco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
- Chan Zuckerberg Biohub, San Francisco
| | - Amy Berger
- Department of Medicine, University of California, San Francisco
- Current affiliation: Denali Therapeutics
| | - Joseph T. Shieh
- Medical Genetics, Department of Pediatrics, University of California, San Francisco
| | - Erron W. Titus
- Medical Scientist Training Program, University of California, San Francisco
- Department of Laboratory Medicine, University of California, San Francisco
| | - Mercedes F. Paredes
- Weill Institute for Neuroscience, University of California, San Francisco
- Division of Epilepsy, Department of Neurology, University of California, San Francisco
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Shieh JT, Tintos-Hernandez JA, Murali CN, Penon-Portmann M, Flores-Mendez M, Santana A, Bulos JA, Du K, Dupuis L, Damseh N, Mendoza-Londoño R, Berera C, Lee JC, Phillips JJ, Alves CAPF, Dmochowski IJ, Ortiz-González XR. Heterozygous nonsense variants in the ferritin heavy-chain gene FTH1 cause a neuroferritinopathy. HGG Adv 2023; 4:100236. [PMID: 37660254 PMCID: PMC10510067 DOI: 10.1016/j.xhgg.2023.100236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023] Open
Abstract
Ferritin, the iron-storage protein, is composed of light- and heavy-chain subunits, encoded by FTL and FTH1, respectively. Heterozygous variants in FTL cause hereditary neuroferritinopathy, a type of neurodegeneration with brain iron accumulation (NBIA). Variants in FTH1 have not been previously associated with neurologic disease. We describe the clinical, neuroimaging, and neuropathology findings of five unrelated pediatric patients with de novo heterozygous FTH1 variants. Children presented with developmental delay, epilepsy, and progressive neurologic decline. Nonsense FTH1 variants were identified using whole-exome sequencing, with a recurrent variant (p.Phe171∗) identified in four unrelated individuals. Neuroimaging revealed diffuse volume loss, features of pontocerebellar hypoplasia, and iron accumulation in the basal ganglia. Neuropathology demonstrated widespread ferritin inclusions in the brain. Patient-derived fibroblasts were assayed for ferritin expression, susceptibility to iron accumulation, and oxidative stress. Variant FTH1 mRNA transcripts escape nonsense-mediated decay (NMD), and fibroblasts show elevated ferritin protein levels, markers of oxidative stress, and increased susceptibility to iron accumulation. C-terminal variants in FTH1 truncate ferritin's E helix, altering the 4-fold symmetric pores of the heteropolymer, and likely diminish iron-storage capacity. FTH1 pathogenic variants appear to act by a dominant, toxic gain-of-function mechanism. The data support the conclusion that truncating variants in the last exon of FTH1 cause a disorder in the spectrum of NBIA. Targeted knockdown of mutant FTH1 transcript with antisense oligonucleotides rescues cellular phenotypes and suggests a potential therapeutic strategy for this pediatric neurodegenerative disorder.
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Affiliation(s)
- Joseph T Shieh
- Institute for Human Genetics and Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Jesus A Tintos-Hernandez
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Monica Penon-Portmann
- Institute for Human Genetics and Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Marco Flores-Mendez
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Adrian Santana
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Joshua A Bulos
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kang Du
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lucie Dupuis
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Nadirah Damseh
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londoño
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Camilla Berera
- Institute for Human Genetics and Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Julieann C Lee
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Joanna J Phillips
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - César A P F Alves
- Division of Neuroradiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xilma R Ortiz-González
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Epilepsy Neurogenetics Initiative (ENGIN), The Children's Hospital of Philadelphia and Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Sheppard SE, March ME, Seiler C, Matsuoka LS, Kim SE, Kao C, Rubin AI, Battig MR, Khalek N, Schindewolf E, O'Connor N, Pinto E, Priestley JR, Sanders VR, Niazi R, Ganguly A, Hou C, Slater D, Frieden IJ, Huynh T, Shieh JT, Krantz ID, Guerrero JC, Surrey LF, Biko DM, Laje P, Castelo-Soccio L, Nakano TA, Snyder K, Smith CL, Li D, Dori Y, Hakonarson H. Lymphatic disorders caused by mosaic, activating KRAS variants respond to MEK inhibition. JCI Insight 2023; 8:155888. [PMID: 37154160 DOI: 10.1172/jci.insight.155888] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/17/2023] [Indexed: 05/10/2023] Open
Abstract
Central conducting lymphatic anomaly (CCLA) due to congenital maldevelopment of the lymphatics can result in debilitating and life-threatening disease with limited treatment options. We identified 4 individuals with CCLA, lymphedema, and microcystic lymphatic malformation due to pathogenic, mosaic variants in KRAS. To determine the functional impact of these variants and identify a targeted therapy for these individuals, we used primary human dermal lymphatic endothelial cells (HDLECs) and zebrafish larvae to model the lymphatic dysplasia. Expression of the p.Gly12Asp and p.Gly13Asp variants in HDLECs in a 2‑dimensional (2D) model and 3D organoid model led to increased ERK phosphorylation, demonstrating these variants activate the RAS/MAPK pathway. Expression of activating KRAS variants in the venous and lymphatic endothelium in zebrafish resulted in lymphatic dysplasia and edema similar to the individuals in the study. Treatment with MEK inhibition significantly reduced the phenotypes in both the organoid and the zebrafish model systems. In conclusion, we present the molecular characterization of the observed lymphatic anomalies due to pathogenic, somatic, activating KRAS variants in humans. Our preclinical studies suggest that MEK inhibition should be studied in future clinical trials for CCLA due to activating KRAS pathogenic variants.
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Affiliation(s)
| | | | - Christoph Seiler
- Zebrafish Core, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Adam I Rubin
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Nahla Khalek
- Richard D. Wood Jr. Center for Fetal Diagnosis and Treatment and
| | | | | | - Erin Pinto
- Jill and Mark Fishman Center for Lymphatic Disorders, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | - Rojeen Niazi
- Genetic Diagnostic Laboratory, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arupa Ganguly
- Genetic Diagnostic Laboratory, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | | | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Ian D Krantz
- Division of Human Genetics, and
- Roberts Individualized Medical Genetics Center, Division of Human Genetics
| | | | | | | | | | - Leslie Castelo-Soccio
- Dermatology Section, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Taizo A Nakano
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Kristen Snyder
- Division of Oncology, Cancer Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christopher L Smith
- Jill and Mark Fishman Center for Lymphatic Disorders, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Yoav Dori
- Jill and Mark Fishman Center for Lymphatic Disorders, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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Shieh JT, Tintos-Hernández JA, Murali CN, Penon-Portmann M, Flores-Mendez M, Santana A, Bulos JA, Du K, Dupuis L, Damseh N, Mendoza-Londoño R, Berera C, Lee JC, Phillips JJ, Alves CAPF, Dmochowski IJ, Ortiz-González XR. Heterozygous Nonsense Variants in the Ferritin Heavy Chain Gene FTH1 Cause a Novel Pediatric Neuroferritinopathy. medRxiv 2023:2023.01.30.23285099. [PMID: 36778397 PMCID: PMC9915813 DOI: 10.1101/2023.01.30.23285099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ferritin, the iron storage protein, is composed of light and heavy chain subunits, encoded by FTL and FTH1 , respectively. Heterozygous variants in FTL cause hereditary neuroferritinopathy, a type of neurodegeneration with brain iron accumulation (NBIA). Variants in FTH1 have not been previously associated with neurologic disease. We describe the clinical, neuroimaging, and neuropathology findings of five unrelated pediatric patients with de novo heterozygous FTH1 variants. Children presented with developmental delay, epilepsy, and progressive neurologic decline. Nonsense FTH1 variants were identified using whole exome sequencing, with a recurrent de novo variant (p.F171*) identified in three unrelated individuals. Neuroimaging revealed diffuse volume loss, features of pontocerebellar hypoplasia and iron accumulation in the basal ganglia. Neuropathology demonstrated widespread ferritin inclusions in the brain. Patient-derived fibroblasts were assayed for ferritin expression, susceptibility to iron accumulation, and oxidative stress. Variant FTH1 mRNA transcripts escape nonsense-mediated decay (NMD), and fibroblasts show elevated ferritin protein levels, markers of oxidative stress, and increased susceptibility to iron accumulation. C-terminus variants in FTH1 truncate ferritin's E-helix, altering the four-fold symmetric pores of the heteropolymer and likely diminish iron-storage capacity. FTH1 pathogenic variants appear to act by a dominant, toxic gain-of-function mechanism. The data support the conclusion that truncating variants in the last exon of FTH1 cause a novel disorder in the spectrum of NBIA. Targeted knock-down of mutant FTH1 transcript with antisense oligonucleotides rescues cellular phenotypes and suggests a potential therapeutic strategy for this novel pediatric neurodegenerative disorder.
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Affiliation(s)
- Joseph T Shieh
- Institute for Human Genetics and Department of Pediatrics, University of California San Francisco, CA, 94143
- These authors contributed equally to this work
| | - Jesus A Tintos-Hernández
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104
- These authors contributed equally to this work
| | - Chaya N. Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Monica Penon-Portmann
- Institute for Human Genetics and Department of Pediatrics, University of California San Francisco, CA, 94143
| | - Marco Flores-Mendez
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Adrian Santana
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Joshua A. Bulos
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Kang Du
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Lucie Dupuis
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Nadirah Damseh
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Roberto Mendoza-Londoño
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Camilla Berera
- Institute for Human Genetics and Department of Pediatrics, University of California San Francisco, CA, 94143
| | - Julieann C Lee
- Division of Neuropathology, Department of Pathology, University of California San Francisco, CA, 94143
| | - Joanna J Phillips
- Division of Neuropathology, Department of Pathology, University of California San Francisco, CA, 94143
- Department of Neurological Surgery, University of California San Francisco, CA, 94143
| | - César A P F Alves
- Division of Neuroradiology, Department of Pediatrics, The Children’s Hospital of Philadelphia
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Xilma R Ortiz-González
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104
- Epilepsy Neurogenetics Initiative (ENGIN), The Children’s Hospital of Philadelphia and Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
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6
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Penon-Portmann M, Westbury SK, Li L, Pluthero FG, Liu RJY, Yao HHY, Geng RSQ, Warner N, Muise AM, Lotz-Esquivel S, Howell-Ramirez M, Saborío-Chacon P, Fernández-Rojas S, Saborio-Rocafort M, Jiménez-Hernández M, Wang-Zuniga C, Cartín-Sánchez W, Shieh JT, Badilla-Porras R, Kahr WHA. Platelet VPS16B is dependent on VPS33B expression, as determined in two siblings with arthrogryposis, renal dysfunction, and cholestasis syndrome. J Thromb Haemost 2022; 20:1712-1719. [PMID: 35325493 DOI: 10.1111/jth.15711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/28/2022] [Accepted: 03/15/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Platelet α-granule biogenesis in precursor megakaryocytes is critically dependent on VPS33B and VPS16B, as demonstrated by the platelet α-granule deficiency seen in the rare multisystem disorder arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome associated with biallelic pathogenic variants in VPS33B and VIPAS39 (encoding VPS16B). VPS33B and VPS16B are ubiquitously expressed proteins that are known to interact and play key roles in protein sorting and trafficking between subcellular locations. However, there remain significant gaps in our knowledge of the nature of these interactions in primary cells from patients with ARC syndrome. OBJECTIVES To use primary cells from patients with ARC syndrome to better understand the interactions and roles of VPS33B and VPS16B in platelets and precursor megakaryocytes. PATIENTS/METHODS The proband and his male sibling were clinically suspected to have ARC syndrome. Confirmatory genetic testing and platelet phenotyping, including electron microscopy and protein expression analysis, was performed with consent in a research setting. RESULTS We describe the first case of ARC syndrome identified in Costa Rica, associated with a novel homozygous nonsense VPS33B variant that is linked with loss of expression of both VPS33B and VPS16B in platelets. CONCLUSION These results indicate that stable expression of VPS16B in platelets, their precursor megakaryocytes, and other cells is dependent on VPS33B. We suggest that systematic evaluation of primary cells from patients with a range of VPS33B and VIPAS39 variants would help to elucidate the interactions and functions of these proteins.
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Affiliation(s)
- Monica Penon-Portmann
- Servicio de Genética Médica y Metabolismo, Departamento de Pediatría, Hospital Nacional de Niños, "Dr. Carlos Sáenz Herrera", Caja Costarricense de Seguro Social (CCSS) & Sistema de Estudios de Posgrado, Universidad de Costa Rica, San José, Costa Rica
- Department of Pediatrics & Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Sarah K Westbury
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Program in Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ling Li
- Program in Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fred G Pluthero
- Program in Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Richard J Y Liu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Helen H Y Yao
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ryan S Q Geng
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Neil Warner
- SickKids Inflammatory Bowel Disease Center, Hospital for Sick Children, Research Institute, Toronto, Ontario, Canada
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center, Hospital for Sick Children, Research Institute, Toronto, Ontario, Canada
- Departments of Paediatrics and Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Cell Biology Program, Hospital for Sick Children, Research Institute, Toronto, Ontario, Canada
| | - Stephanie Lotz-Esquivel
- Servicio de Genética Médica y Metabolismo, Departamento de Pediatría, Hospital Nacional de Niños, "Dr. Carlos Sáenz Herrera", Caja Costarricense de Seguro Social (CCSS) & Sistema de Estudios de Posgrado, Universidad de Costa Rica, San José, Costa Rica
- Clínica Multidisciplinaria de Enfermedades Raras y Huérfanas, Departamento de Medicina Interna, Hospital San Juan de Dios, Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Marianela Howell-Ramirez
- Servicio de Nefrología, Departamento de Pediatría, Hospital Nacional de Niños, "Dr. Carlos Sáenz Herrera", Caja Costarricense de Seguro Social & Sistema de Estudios de Posgrado, Universidad de Costa Rica, San José, Costa Rica
| | - Pablo Saborío-Chacon
- Servicio de Nefrología, Departamento de Pediatría, Hospital Nacional de Niños, "Dr. Carlos Sáenz Herrera", Caja Costarricense de Seguro Social & Sistema de Estudios de Posgrado, Universidad de Costa Rica, San José, Costa Rica
| | - Sara Fernández-Rojas
- Servicio de Nefrología, Departamento de Pediatría, Hospital Nacional de Niños, "Dr. Carlos Sáenz Herrera", Caja Costarricense de Seguro Social & Sistema de Estudios de Posgrado, Universidad de Costa Rica, San José, Costa Rica
| | - Manuel Saborio-Rocafort
- Servicio de Genética Médica y Metabolismo, Departamento de Pediatría, Hospital Nacional de Niños, "Dr. Carlos Sáenz Herrera", Caja Costarricense de Seguro Social (CCSS) & Sistema de Estudios de Posgrado, Universidad de Costa Rica, San José, Costa Rica
- Programa Nacional de Tamizaje Neonatal, Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Mildred Jiménez-Hernández
- Programa Nacional de Tamizaje Neonatal, Caja Costarricense de Seguro Social, San José, Costa Rica
- Laboratorio Nacional de Tamizaje Neonatal y Alto Riesgo, Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Carolina Wang-Zuniga
- Servicio de Dermatología, Departamento de Pediatría, Hospital Nacional de Niños, "Dr. Carlos Sáenz Herrera", Caja Costarricense de Seguro Social & Sistema de Estudios de Posgrado, Universidad de Costa Rica, San José, Costa Rica
| | - Walter Cartín-Sánchez
- Laboratorio de Estudios Especializados e Investigación, Hospital Nacional de Niños, "Dr. Carlos Sáenz Herrera", Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Joseph T Shieh
- Department of Pediatrics & Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Ramses Badilla-Porras
- Servicio de Genética Médica y Metabolismo, Departamento de Pediatría, Hospital Nacional de Niños, "Dr. Carlos Sáenz Herrera", Caja Costarricense de Seguro Social (CCSS) & Sistema de Estudios de Posgrado, Universidad de Costa Rica, San José, Costa Rica
- Laboratorio Nacional de Tamizaje Neonatal y Alto Riesgo, Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Walter H A Kahr
- Departments of Paediatrics and Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Cell Biology Program, Hospital for Sick Children, Research Institute, Toronto, Ontario, Canada
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7
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Blair DR, Hoffmann TJ, Shieh JT. Common genetic variation associated with Mendelian disease severity revealed through cryptic phenotype analysis. Nat Commun 2022; 13:3675. [PMID: 35760791 PMCID: PMC9237040 DOI: 10.1038/s41467-022-31030-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
Clinical heterogeneity is common in Mendelian disease, but small sample sizes make it difficult to identify specific contributing factors. However, if a disease represents the severely affected extreme of a spectrum of phenotypic variation, then modifier effects may be apparent within a larger subset of the population. Analyses that take advantage of this full spectrum could have substantially increased power. To test this, we developed cryptic phenotype analysis, a model-based approach that infers quantitative traits that capture disease-related phenotypic variability using qualitative symptom data. By applying this approach to 50 Mendelian diseases in two cohorts, we identify traits that reliably quantify disease severity. We then conduct genome-wide association analyses for five of the inferred cryptic phenotypes, uncovering common variation that is predictive of Mendelian disease-related diagnoses and outcomes. Overall, this study highlights the utility of computationally-derived phenotypes and biobank-scale cohorts for investigating the complex genetic architecture of Mendelian diseases.
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Affiliation(s)
- David R Blair
- Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA, USA.
| | - Thomas J Hoffmann
- Institute for Human Genetics, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA, USA. .,Institute for Human Genetics, San Francisco, CA, USA.
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8
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Penon-Portmann M, Eldomery MK, Potocki L, Marafi D, Posey JE, Coban-Akdemir Z, Harel T, Grochowski CM, Loucks H, Devine WP, Van Ziffle J, Doherty D, Lupski JR, Shieh JT. De novo heterozygous variants in SLC30A7 are a candidate cause for Joubert syndrome. Am J Med Genet A 2022; 188:2360-2366. [PMID: 35751429 PMCID: PMC9756141 DOI: 10.1002/ajmg.a.62872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 11/08/2022]
Abstract
Joubert syndrome (JS), a well-established ciliopathy, is characterized by the distinctive molar tooth sign on brain MRI, ataxia, and neurodevelopmental features. Other manifestations can include polydactyly, accessory frenula, renal, or liver disease. Here, we report individuals meeting criteria for JS with de novo heterozygous variants in SLC30A7 (Chr1p21.2). The first individual is a female with history of unilateral postaxial polydactyly, classic molar tooth sign on MRI, macrocephaly, ataxia, ocular motor apraxia, neurodevelopmental delay, and precocious puberty. Exome sequencing detected a de novo heterozygous missense variant in SLC30A7: NM_133496.5: c.407 T > C, (p.Val136Ala). The second individual had bilateral postaxial polydactyly, molar tooth sign, macrocephaly, developmental delay, and an extra oral frenulum. A de novo deletion-insertion variant in SLC30A7, c.490_491delinsAG (p.His164Ser) was found. Both de novo variants affect highly conserved residues. Variants were not identified in known Joubert genes for either case. SLC30A7 has not yet been associated with a human phenotype. The SLC30 family of zinc transporters, like SLC30A7, permit cellular efflux of zinc, and although it is expressed in the brain its functions remain unknown. Published data from proteomic studies support SLC30A7 interaction with TCTN3, another protein associated with JS. The potential involvement of such genes in primary cilia suggest a role in Sonic Hedgehog signaling. SLC30A7 is a candidate JS-associated gene. Future work could be directed toward further characterization of SLC30A7 variants and understanding its function.
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Affiliation(s)
- Monica Penon-Portmann
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Hailey Loucks
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Walter Patrick Devine
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Jessica Van Ziffle
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
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9
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Tong S, Devine WP, Shieh JT. Tumor and Constitutional Sequencing for Neurofibromatosis Type 1. JCO Precis Oncol 2022; 6:e2100540. [PMID: 35584348 PMCID: PMC9200388 DOI: 10.1200/po.21.00540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
NF1 variants in tumors are important to recognize, as multiple mechanisms may give rise to biallelic variants. Both deletions and copy-neutral loss of heterozygosity (LOH) are potential mechanisms of NF1 loss, distinct from point mutations, and additional genes altered may drive different tumor types. This study investigates whether tumors from individuals with neurofibromatosis type 1 (NF1) demonstrate additional gene variants and detects NF1 second hits using paired germline and somatic sequencing. In addition, rare tumor types in NF1 may also be characterized by tumor sequencing. NF1 second hits are primarily copy-neutral LOH and offer opportunity for variant interpretation
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Affiliation(s)
- Schuyler Tong
- Division of Hematology/Oncology, Pediatrics, Benioff Children's Hospital Oakland, University of California San Francisco, San Francisco, CA
| | - W Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA
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10
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Shieh JT, Penon-Portmann M, Wong KHY, Levy-Sakin M, Verghese M, Slavotinek A, Gallagher RC, Mendelsohn BA, Tenney J, Beleford D, Perry H, Chow SK, Sharo AG, Brenner SE, Qi Z, Yu J, Klein OD, Martin D, Kwok PY, Boffelli D. Application of full-genome analysis to diagnose rare monogenic disorders. NPJ Genom Med 2021; 6:77. [PMID: 34556655 PMCID: PMC8460793 DOI: 10.1038/s41525-021-00241-5] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/21/2020] [Indexed: 11/30/2022] Open
Abstract
Current genetic tests for rare diseases provide a diagnosis in only a modest proportion of cases. The Full-Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to detect small variants, structural variants with breakpoint resolution, and phasing. We built a variant prioritization pipeline and tested FGA’s utility for diagnosis of rare diseases in a clinical setting. FGA identified structural variants and small variants with an overall diagnostic yield of 40% (20 of 50 cases) and 35% in exome-negative cases (8 of 23 cases), 4 of these were structural variants. FGA detected and mapped structural variants that are missed by short reads, including non-coding duplication, and phased variants across long distances of more than 180 kb. With the prioritization algorithm, longer DNA technologies could replace multiple tests for monogenic disorders and expand the range of variants detected. Our study suggests that genomes produced from technologies like FGA can improve variant detection and provide higher resolution genome maps for future application.
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Affiliation(s)
- Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA. .,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA.
| | - Monica Penon-Portmann
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Karen H Y Wong
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Michelle Verghese
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Anne Slavotinek
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Renata C Gallagher
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Bryce A Mendelsohn
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tenney
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Daniah Beleford
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Hazel Perry
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Stephen K Chow
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Andrew G Sharo
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Zhongxia Qi
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jingwei Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ophir D Klein
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA.,Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
| | - David Martin
- Children's Hospital Oakland Research Institute, Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.,Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
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11
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Biesecker LG, Adam MP, Alkuraya FS, Amemiya AR, Bamshad MJ, Beck AE, Bennett JT, Bird LM, Carey JC, Chung B, Clark RD, Cox TC, Curry C, Dinulos MBP, Dobyns WB, Giampietro PF, Girisha KM, Glass IA, Graham JM, Gripp KW, Haldeman-Englert CR, Hall BD, Innes AM, Kalish JM, Keppler-Noreuil KM, Kosaki K, Kozel BA, Mirzaa GM, Mulvihill JJ, Nowaczyk MJM, Pagon RA, Retterer K, Rope AF, Sanchez-Lara PA, Seaver LH, Shieh JT, Slavotinek AM, Sobering AK, Stevens CA, Stevenson DA, Tan TY, Tan WH, Tsai AC, Weaver DD, Williams MS, Zackai E, Zarate YA. Response to Hamosh et al. Am J Hum Genet 2021; 108:1809-1810. [PMID: 34478656 DOI: 10.1016/j.ajhg.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Margaret P Adam
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | | | - Michael J Bamshad
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Anita E Beck
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA; Seattle Children's Hospital, Seattle, WA 98015, USA
| | - James T Bennett
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute and Division Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego, San Diego 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - John C Carey
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Brian Chung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Queen Mary Hospital, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Robin D Clark
- Loma Linda University School of Medicine, Department of Pediatrics, Division of Medical Genetics, Loma Linda, CA 92354, USA
| | - Timothy C Cox
- Department of Oral and Craniofacial Sciences, School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Cynthia Curry
- Genetic Medicine, Department of Pediatrics, University of California, Fresno, Fresno, CA 93701, USA
| | - Mary Beth Palko Dinulos
- The Geisel School of Medicine at Dartmouth, Department of Pediatrics, Section of Genetics and Child Development, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - William B Dobyns
- Division of Genetics and Metabolism, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Ian A Glass
- Department of Pediatrics and Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - John M Graham
- Cedars-Sinai Medical Center and Harbor-UCLA Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Karen W Gripp
- Division of Medical Genetics, Department of Pediatrics, AI DuPont Hospital for Children/Nemours, Wilmington, DE 19803, USA
| | | | - Bryan D Hall
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Pediatrics and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Kenjiro Kosaki
- Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Beth A Kozel
- Translational Vascular Medicine Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ghayda M Mirzaa
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - John J Mulvihill
- University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Malgorzata J M Nowaczyk
- Molecular Medicine & Pathology and Pediatrics, McMaster University, Hamilton, ON L8S 3K9, Canada
| | - Roberta A Pagon
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA
| | | | - Alan F Rope
- Genome Medical, South San Francisco, CA 94080, USA
| | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center and David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90048, USA
| | - Laurie H Seaver
- Spectrum Health Medical Genetics and Genomics/Helen Devos Children's Hospital, Department of Pediatrics and Human Development, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
| | - Joseph T Shieh
- Institute for Human Genetics and Division of Medical Genetics, Department of Pediatrics Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anne M Slavotinek
- Institute for Human Genetics and Division of Medical Genetics, Department of Pediatrics Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew K Sobering
- Augusta University/University of Georgia Athens, Medical Partnership, Athens, GA 30606, USA
| | - Cathy A Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, TN 37403, USA
| | - David A Stevenson
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Palo Alto, CA 94305, USA
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Wen-Hann Tan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Anne C Tsai
- Section of Genetics, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David D Weaver
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, 975 W. Walnut Street, Indianapolis, IN 46202, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA
| | - Elaine Zackai
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, PA 19104, USA
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
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12
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Alankarage D, Szot JO, Pachter N, Slavotinek A, Selleri L, Shieh JT, Winlaw D, Giannoulatou E, Chapman G, Dunwoodie SL. Functional characterization of a novel PBX1 de novo missense variant identified in a patient with syndromic congenital heart disease. Hum Mol Genet 2021; 29:1068-1082. [PMID: 31625560 DOI: 10.1093/hmg/ddz231] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/13/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
Pre-B cell leukemia factor 1 (PBX1) is an essential developmental transcription factor, mutations in which have recently been associated with CAKUTHED syndrome, characterized by multiple congenital defects including congenital heart disease (CHD). During analysis of a whole-exome-sequenced cohort of heterogeneous CHD patients, we identified a de novo missense variant, PBX1:c.551G>C p.R184P, in a patient with tetralogy of Fallot with absent pulmonary valve and extra-cardiac phenotypes. Functional analysis of this variant by creating a CRISPR-Cas9 gene-edited mouse model revealed multiple congenital anomalies. Congenital heart defects (persistent truncus arteriosus and ventricular septal defect), hypoplastic lungs, hypoplastic/ectopic kidneys, aplastic adrenal glands and spleen, as well as atretic trachea and palate defects were observed in the homozygous mutant embryos at multiple stages of development. We also observed developmental anomalies in a proportion of heterozygous embryos, suggestive of a dominant mode of inheritance. Analysis of gene expression and protein levels revealed that although Pbx1 transcripts are higher in homozygotes, amounts of PBX1 protein are significantly decreased. Here, we have presented the first functional model of a missense PBX1 variant and provided strong evidence that p.R184P is disease-causal. Our findings also expand the phenotypic spectrum associated with pathogenic PBX1 variants in both humans and mice.
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Affiliation(s)
- Dimuthu Alankarage
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia
| | - Justin O Szot
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia
| | - Nick Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Western Australia, 6008 Perth, Australia.,University of Western Australia, School of Paediatrics and Child Health, Western Australia, 6009 Perth, Australia
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, 94158 CA, USA.,Institute of Human Genetics, University of California San Francisco, San Francisco, 94143 CA, USA
| | - Licia Selleri
- Institute of Human Genetics, University of California San Francisco, San Francisco, 94143 CA, USA.,Program in Craniofacial Biology, Department of Orofacial Sciences, University of California San Francisco, San Francisco, 94143 CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, 94143 CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, 94158 CA, USA.,Institute of Human Genetics, University of California San Francisco, San Francisco, 94143 CA, USA
| | - David Winlaw
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Heart Centre for Children, The Children's Hospital at Westmead, New South Wales, 2145 Sydney, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, University of Sydney, New South Wales, 2006 Sydney, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Faculty of Medicine, University of New South Wales, St Vincent's Clinical School, New South Wales, 2010 Sydney, Australia
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Faculty of Medicine, University of New South Wales, St Vincent's Clinical School, New South Wales, 2010 Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Faculty of Medicine, University of New South Wales, St Vincent's Clinical School, New South Wales, 2010 Sydney, Australia
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13
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Gao S, Nelson J, Weinsheimer S, Winkler EA, Rutledge C, Abla AA, Gupta N, Shieh JT, Cooke DL, Hetts SW, Tihan T, Hess CP, Ko N, Walcott BP, McCulloch CE, Lawton MT, Su H, Pawlikowska L, Kim H. Somatic mosaicism in the MAPK pathway in sporadic brain arteriovenous malformation and association with phenotype. J Neurosurg 2021; 136:148-155. [PMID: 34214981 DOI: 10.3171/2020.11.jns202031] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/16/2020] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Sporadic brain arteriovenous malformation (BAVM) is a tangled vascular lesion characterized by direct artery-to-vein connections that can cause life-threatening intracerebral hemorrhage (ICH). Recently, somatic mutations in KRAS have been reported in sporadic BAVM, and mutations in other mitogen-activated protein kinase (MAPK) signaling pathway genes have been identified in other vascular malformations. The objectives of this study were to systematically evaluate somatic mutations in MAPK pathway genes in patients with sporadic BAVM lesions and to evaluate the association of somatic mutations with phenotypes of sporadic BAVM severity. METHODS The authors performed whole-exome sequencing on paired lesion and blood DNA samples from 14 patients with sporadic BAVM, and 295 genes in the MAPK signaling pathway were evaluated to identify genes with somatic mutations in multiple patients with BAVM. Digital droplet polymerase chain reaction was used to validate KRAS G12V and G12D mutations and to assay an additional 56 BAVM samples. RESULTS The authors identified a total of 24 candidate BAVM-associated somatic variants in 11 MAPK pathway genes. The previously identified KRAS G12V and G12D mutations were the only recurrent mutations. Overall, somatic KRAS G12V was present in 14.5% of BAVM lesions and G12D was present in 31.9%. The authors did not detect a significant association between the presence or allelic burden of KRAS mutation and three BAVM phenotypes: lesion size (maximum diameter), age at diagnosis, and age at ICH. CONCLUSIONS The authors confirmed the high prevalence of somatic KRAS mutations in sporadic BAVM lesions and identified several candidate somatic variants in other MAPK pathway genes. These somatic variants may contribute to understanding of the etiology of sporadic BAVM and the clinical characteristics of patients with this condition.
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Affiliation(s)
- Sen Gao
- Departments of1Anesthesia and Perioperative Care.,2Center for Cerebrovascular Research, and
| | - Jeffrey Nelson
- Departments of1Anesthesia and Perioperative Care.,2Center for Cerebrovascular Research, and
| | - Shantel Weinsheimer
- Departments of1Anesthesia and Perioperative Care.,2Center for Cerebrovascular Research, and.,4Institute for Human Genetics, University of California, San Francisco, California
| | | | | | | | | | - Joseph T Shieh
- 4Institute for Human Genetics, University of California, San Francisco, California.,11Pediatrics, and
| | | | | | | | | | | | - Brian P Walcott
- 3Neurological Surgery.,8NorthShore University Health System, Evanston, Illinois; and
| | | | - Michael T Lawton
- 10Department of Neurosurgery, Barrow Neurological Institute, Phoenix, Arizona
| | - Hua Su
- Departments of1Anesthesia and Perioperative Care.,2Center for Cerebrovascular Research, and
| | - Ludmila Pawlikowska
- Departments of1Anesthesia and Perioperative Care.,2Center for Cerebrovascular Research, and.,4Institute for Human Genetics, University of California, San Francisco, California
| | - Helen Kim
- Departments of1Anesthesia and Perioperative Care.,2Center for Cerebrovascular Research, and.,4Institute for Human Genetics, University of California, San Francisco, California
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14
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Cousin MA, Creighton BA, Breau KA, Spillmann RC, Torti E, Dontu S, Tripathi S, Ajit D, Edwards RJ, Afriyie S, Bay JC, Harper KM, Beltran AA, Munoz LJ, Falcon Rodriguez L, Stankewich MC, Person RE, Si Y, Normand EA, Blevins A, May AS, Bier L, Aggarwal V, Mancini GMS, van Slegtenhorst MA, Cremer K, Becker J, Engels H, Aretz S, MacKenzie JJ, Brilstra E, van Gassen KLI, van Jaarsveld RH, Oegema R, Parsons GM, Mark P, Helbig I, McKeown SE, Stratton R, Cogne B, Isidor B, Cacheiro P, Smedley D, Firth HV, Bierhals T, Kloth K, Weiss D, Fairley C, Shieh JT, Kritzer A, Jayakar P, Kurtz-Nelson E, Bernier RA, Wang T, Eichler EE, van de Laar IMBH, McConkie-Rosell A, McDonald MT, Kemppainen J, Lanpher BC, Schultz-Rogers LE, Gunderson LB, Pichurin PN, Yoon G, Zech M, Jech R, Winkelmann J, Beltran AS, Zimmermann MT, Temple B, Moy SS, Klee EW, Tan QKG, Lorenzo DN. Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome. Nat Genet 2021; 53:1006-1021. [PMID: 34211179 PMCID: PMC8273149 DOI: 10.1038/s41588-021-00886-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 05/14/2021] [Indexed: 12/22/2022]
Abstract
SPTBN1 encodes βII-spectrin, the ubiquitously expressed β-spectrin that forms micrometer-scale networks associated with plasma membranes. Mice deficient in neuronal βII-spectrin have defects in cortical organization, developmental delay and behavioral deficiencies. These phenotypes, while less severe, are observed in haploinsufficient animals, suggesting that individuals carrying heterozygous SPTBN1 variants may also show measurable compromise of neural development and function. Here we identify heterozygous SPTBN1 variants in 29 individuals with developmental, language and motor delays; mild to severe intellectual disability; autistic features; seizures; behavioral and movement abnormalities; hypotonia; and variable dysmorphic facial features. We show that these SPTBN1 variants lead to effects that affect βII-spectrin stability, disrupt binding to key molecular partners, and disturb cytoskeleton organization and dynamics. Our studies define SPTBN1 variants as the genetic basis of a neurodevelopmental syndrome, expand the set of spectrinopathies affecting the brain and underscore the critical role of βII-spectrin in the central nervous system.
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Affiliation(s)
- Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
| | - Blake A Creighton
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | | | - Sruthi Dontu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Swarnendu Tripathi
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Deepa Ajit
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Reginald J Edwards
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Simone Afriyie
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julia C Bay
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kathryn M Harper
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alvaro A Beltran
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Human Pluripotent Stem Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lorena J Munoz
- Human Pluripotent Stem Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Liset Falcon Rodriguez
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Yue Si
- GeneDx, Gaithersburg, MD, USA
| | | | | | - Alison S May
- Department of Neurology, Columbia University, New York, NY, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Vimla Aggarwal
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | | | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | | | - Eva Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Paul Mark
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Ingo Helbig
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah E McKeown
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert Stratton
- Genetics, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- Université de Nantes, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- Université de Nantes, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Pilar Cacheiro
- William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Damian Smedley
- William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Helen V Firth
- Department of Clinical Genetics, Cambridge University Hospitals, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Deike Weiss
- Neuropediatrics, Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cecilia Fairley
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Amy Kritzer
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - Evangeline Kurtz-Nelson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Marie T McDonald
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Jennifer Kemppainen
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Lauren B Gunderson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Grace Yoon
- Divisions of Clinical/Metabolic Genetics and Neurology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Adriana S Beltran
- Human Pluripotent Stem Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brenda Temple
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Queenie K-G Tan
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Damaris N Lorenzo
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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15
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Hetts SW, Shieh JT, Ohliger MA, Conrad MB. Hereditary Hemorrhagic Telangiectasia: The Convergence of Genotype, Phenotype, and Imaging in Modern Diagnosis and Management of a Multisystem Disease. Radiology 2021; 300:17-30. [PMID: 33973836 DOI: 10.1148/radiol.2021203487] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant disease that manifests as vascular malformations in the brain, lung, liver, gastrointestinal tract, nasal mucosa, and skin. Diagnosis and management of HHT is guided in large part by imaging studies, making it a condition with which the radiology community needs familiarity. Proper screening and care lead to improved morbidity and mortality in patients with HHT. International guidelines were recently updated and form the basis for a detailed discussion of the role of imaging and image-guided therapy in HHT. © RSNA, 2021 Online supplemental material is available for this article.
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Affiliation(s)
- Steven W Hetts
- From the Department of Radiology and Biomedical Imaging (S.W.H., M.O., M.C.), HHT Center of Excellence (S.W.H., J.S., M.O., M.C.), and Department of -Pediatrics (J.S.), University of California San Francisco, 505 Parnassus Ave, L-351, San Francisco, CA 94143-0628
| | - Joseph T Shieh
- From the Department of Radiology and Biomedical Imaging (S.W.H., M.O., M.C.), HHT Center of Excellence (S.W.H., J.S., M.O., M.C.), and Department of -Pediatrics (J.S.), University of California San Francisco, 505 Parnassus Ave, L-351, San Francisco, CA 94143-0628
| | - Michael A Ohliger
- From the Department of Radiology and Biomedical Imaging (S.W.H., M.O., M.C.), HHT Center of Excellence (S.W.H., J.S., M.O., M.C.), and Department of -Pediatrics (J.S.), University of California San Francisco, 505 Parnassus Ave, L-351, San Francisco, CA 94143-0628
| | - Miles B Conrad
- From the Department of Radiology and Biomedical Imaging (S.W.H., M.O., M.C.), HHT Center of Excellence (S.W.H., J.S., M.O., M.C.), and Department of -Pediatrics (J.S.), University of California San Francisco, 505 Parnassus Ave, L-351, San Francisco, CA 94143-0628
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16
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Sheppard SE, Campbell IM, Harr MH, Gold N, Li D, Bjornsson HT, Cohen JS, Fahrner JA, Fatemi A, Harris JR, Nowak C, Stevens CA, Grand K, Au M, Graham JM, Sanchez-Lara PA, Campo MD, Jones MC, Abdul-Rahman O, Alkuraya FS, Bassetti JA, Bergstrom K, Bhoj E, Dugan S, Kaplan JD, Derar N, Gripp KW, Hauser N, Innes AM, Keena B, Kodra N, Miller R, Nelson B, Nowaczyk MJ, Rahbeeni Z, Ben-Shachar S, Shieh JT, Slavotinek A, Sobering AK, Abbott MA, Allain DC, Amlie-Wolf L, Au PYB, Bedoukian E, Beek G, Barry J, Berg J, Bernstein JA, Cytrynbaum C, Chung BHY, Donoghue S, Dorrani N, Eaton A, Flores-Daboub JA, Dubbs H, Felix CA, Fong CT, Fung JLF, Gangaram B, Goldstein A, Greenberg R, Ha TK, Hersh J, Izumi K, Kallish S, Kravets E, Kwok PY, Jobling RK, Knight Johnson AE, Kushner J, Lee BH, Levin B, Lindstrom K, Manickam K, Mardach R, McCormick E, McLeod DR, Mentch FD, Minks K, Muraresku C, Nelson SF, Porazzi P, Pichurin PN, Powell-Hamilton NN, Powis Z, Ritter A, Rogers C, Rohena L, Ronspies C, Schroeder A, Stark Z, Starr L, Stoler J, Suwannarat P, Velinov M, Weksberg R, Wilnai Y, Zadeh N, Zand DJ, Falk MJ, Hakonarson H, Zackai EH, Quintero-Rivera F. Expanding the genotypic and phenotypic spectrum in a diverse cohort of 104 individuals with Wiedemann-Steiner syndrome. Am J Med Genet A 2021; 185:1649-1665. [PMID: 33783954 DOI: 10.1002/ajmg.a.62124] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/19/2022]
Abstract
Wiedemann-Steiner syndrome (WSS) is an autosomal dominant disorder caused by monoallelic variants in KMT2A and characterized by intellectual disability and hypertrichosis. We performed a retrospective, multicenter, observational study of 104 individuals with WSS from five continents to characterize the clinical and molecular spectrum of WSS in diverse populations, to identify physical features that may be more prevalent in White versus Black Indigenous People of Color individuals, to delineate genotype-phenotype correlations, to define developmental milestones, to describe the syndrome through adulthood, and to examine clinicians' differential diagnoses. Sixty-nine of the 82 variants (84%) observed in the study were not previously reported in the literature. Common clinical features identified in the cohort included: developmental delay or intellectual disability (97%), constipation (63.8%), failure to thrive (67.7%), feeding difficulties (66.3%), hypertrichosis cubiti (57%), short stature (57.8%), and vertebral anomalies (46.9%). The median ages at walking and first words were 20 months and 18 months, respectively. Hypotonia was associated with loss of function (LoF) variants, and seizures were associated with non-LoF variants. This study identifies genotype-phenotype correlations as well as race-facial feature associations in an ethnically diverse cohort, and accurately defines developmental trajectories, medical comorbidities, and long-term outcomes in individuals with WSS.
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Affiliation(s)
- Sarah E Sheppard
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian M Campbell
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Margaret H Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nina Gold
- Mass General Hospital for Children, Division of Medical Genetics and Metabolism and Harvard Medical School, Boston, Massachusetts, USA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Iceland
| | - Julie S Cohen
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ali Fatemi
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline R Harris
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Catherine Nowak
- Division of Genetics and Genomics, Boston Children's Hospital, The Feingold Center for Children, Boston, Massachusetts, USA
| | - Cathy A Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, Tennessee, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Miguel Del Campo
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Marilyn C Jones
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Omar Abdul-Rahman
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jennifer A Bassetti
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Katherine Bergstrom
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Elizabeth Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sarah Dugan
- Division of Medical Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Julie D Kaplan
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nada Derar
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Karen W Gripp
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Natalie Hauser
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - A Micheil Innes
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Beth Keena
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Neslida Kodra
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Rebecca Miller
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Beverly Nelson
- Department of Clinical Skills, St. George's University, True Blue, Grenada
| | | | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shay Ben-Shachar
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joseph T Shieh
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Andrew K Sobering
- Department of Biochemistry, St. George's University, True Blue, Grenada
| | - Mary-Alice Abbott
- Medical Genetics, Department of Pediatrics, University of Massachusetts Medical School - Baystate, Springfield, Massachusetts, USA
| | - Dawn C Allain
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Louise Amlie-Wolf
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Ping Yee Billie Au
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Emma Bedoukian
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Geoffrey Beek
- Children's Hospital of Minnesota, Minneapolis, Minnesota, USA
| | - James Barry
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Janet Berg
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Sarah Donoghue
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Naghmeh Dorrani
- Department of Pediatrics, University of California Los Angeles, California, Los Angeles, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA
| | - Alison Eaton
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | | | - Holly Dubbs
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Carolyn A Felix
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Chin-To Fong
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jasmine Lee Fong Fung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Balram Gangaram
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Amy Goldstein
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rotem Greenberg
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Thoa K Ha
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Joseph Hersh
- Weisskopf Child Evaluation Center, Department of Pediatrics, University of Louisville, Louisville, Kentucky, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Staci Kallish
- Division of Translational Medicine and Human Genetics Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elijah Kravets
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Pui-Yan Kwok
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Rebekah K Jobling
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | | | - Jessica Kushner
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Bo Hoon Lee
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Brooke Levin
- MD Anderson Cancer Center at Cooper, Cooper University Health Care, Camden, New Jersey, USA
| | | | - Kandamurugu Manickam
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Rebecca Mardach
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Elizabeth McCormick
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - D Ross McLeod
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - Frank D Mentch
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kelly Minks
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Colleen Muraresku
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA.,Department of Human Genetics, Center for Duchenne Muscular Dystrophy University of California Los Angeles, California, Los Angeles, USA
| | - Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Pavel N Pichurin
- Clinical Genomics Center, University of California Los Angeles, Los Angeles, California, USA
| | - Nina N Powell-Hamilton
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Zoe Powis
- Quest Diagnostics Kalamzoo, Kalamzoo, Michigan, USA
| | - Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Caleb Rogers
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Luis Rohena
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Carey Ronspies
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Audrey Schroeder
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lois Starr
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joan Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Rockville, Maryland, USA
| | - Milen Velinov
- NYS Institute for Basic Research in developmental Disabilities, Staten Island, New York, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Yael Wilnai
- Genetic Institute, Sourasky Medical Center, Te-Aviv, Tel Aviv, Israel
| | - Neda Zadeh
- Genetics Center and CHOC Children's Hospital, Orange, California, USA
| | - Dina J Zand
- Rare Disease Institute, Children's National Medical Center, Washington, District of Columbia, USA
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Fabiola Quintero-Rivera
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, California, Los Angeles, USA
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17
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Chenbhanich J, Hu Y, Hetts S, Cooke D, Dowd C, Devine P, Russell B, Kang SHL, Chang VY, Abla AA, Cornett P, Yeh I, Lee H, Martinez-Agosto JA, Frieden IJ, Shieh JT. Segmental overgrowth and aneurysms due to mosaic PDGFRB p.(Tyr562Cys). Am J Med Genet A 2021; 185:1430-1436. [PMID: 33683022 DOI: 10.1002/ajmg.a.62126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 12/18/2020] [Accepted: 01/14/2021] [Indexed: 01/19/2023]
Abstract
Activating variants in the platelet-derived growth factor receptor β gene (PDGFRB) have been associated with Kosaki overgrowth syndrome, infantile myofibromatosis, and Penttinen premature aging syndrome. A recently described phenotype with fusiform aneurysm has been associated with mosaic PDGFRB c.1685A > G p.(Tyr562Cys) variant. Few reports however have examined the vascular phenotypes and mosaic effects of PDGFRB variants. We describe clinical characteristics of two patients with a recurrent mosaic PDGFRB p.(Tyr562Cys) variant identified via next-generation sequencing-based genetic testing. We observed intracranial fusiform aneurysm in one patient and found an additional eight patients with aneurysms and phenotypes associated with PDGFRB-activating variants through literature search. The conditions caused by PDGFRB-activating variants share overlapping features including overgrowth, premature aged skin, and vascular malformations including aneurysms. Aneurysms are progressive and can result in morbidities and mortalities in the absence of successful intervention. Germline and/or somatic testing for PDGFRB gene should be obtained when PDGFRB activating variant-related phenotypes are present. Whole-body imaging of the arterial tree and echocardiography are recommended after diagnosis. Repeating the imaging study within a 6- to 12-month period after detection is reasonable. Finally, further evaluation for the effectiveness and safety profile of kinase inhibitors in this patient population is warranted.
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Affiliation(s)
- Jirat Chenbhanich
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, California, USA
| | - Yan Hu
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Steven Hetts
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Daniel Cooke
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Christopher Dowd
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Patrick Devine
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, California, USA.,Institute of Human Genetics, University of California, San Francisco, California, USA
| | | | - Bianca Russell
- Department of Pediatrics, Division of Medical Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Sung Hae L Kang
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Vivian Y Chang
- Department of Pediatrics, Division of Pediatric Hematology Oncology, University of California Los Angeles, Los Angeles, California, USA
| | - Adib A Abla
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Patricia Cornett
- Department of Hematology and Oncology, University of California, San Francisco, California, USA
| | - Iwei Yeh
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, California, USA.,Department of Dermatology, University of California, San Francisco, California, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Julian A Martinez-Agosto
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Ilona J Frieden
- Department of Dermatology, University of California, San Francisco, California, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, California, USA.,Institute of Human Genetics, University of California, San Francisco, California, USA
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18
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Adhikari AN, Gallagher RC, Wang Y, Currier RJ, Amatuni G, Bassaganyas L, Chen F, Kundu K, Kvale M, Mooney SD, Nussbaum RL, Randi SS, Sanford J, Shieh JT, Srinivasan R, Sunderam U, Tang H, Vaka D, Zou Y, Koenig BA, Kwok PY, Risch N, Puck JM, Brenner SE. The role of exome sequencing in newborn screening for inborn errors of metabolism. Nat Med 2020; 26:1392-1397. [PMID: 32778825 PMCID: PMC8800147 DOI: 10.1038/s41591-020-0966-5] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/08/2020] [Indexed: 02/07/2023]
Abstract
Public health newborn screening (NBS) programs provide population-scale ascertainment of rare, treatable conditions that require urgent intervention. Tandem mass spectrometry (MS/MS) is currently used to screen newborns for a panel of rare inborn errors of metabolism (IEMs)1-4. The NBSeq project evaluated whole-exome sequencing (WES) as an innovative methodology for NBS. We obtained archived residual dried blood spots and data for nearly all IEM cases from the 4.5 million infants born in California between mid-2005 and 2013 and from some infants who screened positive by MS/MS, but were unaffected upon follow-up testing. WES had an overall sensitivity of 88% and specificity of 98.4%, compared to 99.0% and 99.8%, respectively for MS/MS, although effectiveness varied among individual IEMs. Thus, WES alone was insufficiently sensitive or specific to be a primary screen for most NBS IEMs. However, as a secondary test for infants with abnormal MS/MS screens, WES could reduce false-positive results, facilitate timely case resolution and in some instances even suggest more appropriate or specific diagnosis than that initially obtained. This study represents the largest, to date, sequencing effort of an entire population of IEM-affected cases, allowing unbiased assessment of current capabilities of WES as a tool for population screening.
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Affiliation(s)
- Aashish N Adhikari
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Renata C Gallagher
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Yaqiong Wang
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Robert J Currier
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - George Amatuni
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Laia Bassaganyas
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Flavia Chen
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Bioethics, University of California San Francisco, San Francisco, CA, USA
| | - Kunal Kundu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Robert L Nussbaum
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Invitae, San Francisco, CA, USA
| | - Savanna S Randi
- Department of Molecular, Cellular and Developmental Biology, Center for the Molecular Biology of RNA, UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jeremy Sanford
- Department of Molecular, Cellular and Developmental Biology, Center for the Molecular Biology of RNA, UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | - Uma Sunderam
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Hao Tang
- Genetic Disease Screening Program, California Department of Public Health, Richmond, CA, USA
| | - Dedeepya Vaka
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yangyun Zou
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Barbara A Koenig
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Bioethics, University of California San Francisco, San Francisco, CA, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer M Puck
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
- Division of Allergy, Immunology and Blood and Marrow Transplantation, UCSF Benioff Children's Hospital, San Francisco, CA, USA.
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
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19
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Mak CCY, Doherty D, Lin AE, Vegas N, Cho MT, Viot G, Dimartino C, Weisfeld-Adams JD, Lessel D, Joss S, Li C, Gonzaga-Jauregui C, Zarate YA, Ehmke N, Horn D, Troyer C, Kant SG, Lee Y, Ishak GE, Leung G, Barone Pritchard A, Yang S, Bend EG, Filippini F, Roadhouse C, Lebrun N, Mehaffey MG, Martin PM, Apple B, Millan F, Puk O, Hoffer MJV, Henderson LB, McGowan R, Wentzensen IM, Pei S, Zahir FR, Yu M, Gibson WT, Seman A, Steeves M, Murrell JR, Luettgen S, Francisco E, Strom TM, Amlie-Wolf L, Kaindl AM, Wilson WG, Halbach S, Basel-Salmon L, Lev-El N, Denecke J, Vissers LELM, Radtke K, Chelly J, Zackai E, Friedman JM, Bamshad MJ, Nickerson DA, Reid RR, Devriendt K, Chae JH, Stolerman E, McDougall C, Powis Z, Bienvenu T, Tan TY, Orenstein N, Dobyns WB, Shieh JT, Choi M, Waggoner D, Gripp KW, Parker MJ, Stoler J, Lyonnet S, Cormier-Daire V, Viskochil D, Hoffman TL, Amiel J, Chung BHY, Gordon CT. MN1 C-terminal truncation syndrome is a novel neurodevelopmental and craniofacial disorder with partial rhombencephalosynapsis. Brain 2020; 143:55-68. [PMID: 31834374 DOI: 10.1093/brain/awz379] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/02/2019] [Accepted: 10/15/2019] [Indexed: 11/12/2022] Open
Abstract
MN1 encodes a transcriptional co-regulator without homology to other proteins, previously implicated in acute myeloid leukaemia and development of the palate. Large deletions encompassing MN1 have been reported in individuals with variable neurodevelopmental anomalies and non-specific facial features. We identified a cluster of de novo truncating mutations in MN1 in a cohort of 23 individuals with strikingly similar dysmorphic facial features, especially midface hypoplasia, and intellectual disability with severe expressive language delay. Imaging revealed an atypical form of rhombencephalosynapsis, a distinctive brain malformation characterized by partial or complete loss of the cerebellar vermis with fusion of the cerebellar hemispheres, in 8/10 individuals. Rhombencephalosynapsis has no previously known definitive genetic or environmental causes. Other frequent features included perisylvian polymicrogyria, abnormal posterior clinoid processes and persistent trigeminal artery. MN1 is encoded by only two exons. All mutations, including the recurrent variant p.Arg1295* observed in 8/21 probands, fall in the terminal exon or the extreme 3' region of exon 1, and are therefore predicted to result in escape from nonsense-mediated mRNA decay. This was confirmed in fibroblasts from three individuals. We propose that the condition described here, MN1 C-terminal truncation (MCTT) syndrome, is not due to MN1 haploinsufficiency but rather is the result of dominantly acting C-terminally truncated MN1 protein. Our data show that MN1 plays a critical role in human craniofacial and brain development, and opens the door to understanding the biological mechanisms underlying rhombencephalosynapsis.
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Affiliation(s)
- Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Angela E Lin
- Medical Genetics, MassGeneral Hospital for Children, Boston, MA, USA
| | - Nancy Vegas
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Géraldine Viot
- Gynécologie Obstétrique, Hôpital Cochin, Hôpitaux Universitaires Paris Centre (HUPC), Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France
| | - Clémantine Dimartino
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - James D Weisfeld-Adams
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado-Denver School of Medicine, Aurora, CO, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shelagh Joss
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow, UK
| | - Chumei Li
- McMaster University Medical Center, Hamilton, Ontario, Canada
| | | | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, USA
| | - Nadja Ehmke
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Caitlin Troyer
- Pediatrics and Medical Genetics, University of Virginia Health System, Charlottesville, VA, USA
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Center, RC Leiden, The Netherlands
| | - Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Gisele E Ishak
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Radiology, University of Washington, Seattle, WA, USA
| | - Gordon Leung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | | | - Eric G Bend
- Greenwood Genetic Center, Greenwood, SC, USA.,PreventionGenetics, Marshfield, WI, USA
| | - Francesca Filippini
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Nicolas Lebrun
- Institut Cochin, INSERM U1016, CNRS UMR, Paris Descartes University, Paris, France
| | | | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin Apple
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado-Denver School of Medicine, Aurora, CO, USA
| | | | - Oliver Puk
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, RC Leiden, The Netherlands
| | | | - Ruth McGowan
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Steven Pei
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Farah R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Mullin Yu
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ann Seman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Marcie Steeves
- Medical Genetics, MassGeneral Hospital for Children, Boston, MA, USA
| | - Jill R Murrell
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sabine Luettgen
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Louise Amlie-Wolf
- Division of Medical Genetics, A I duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Angela M Kaindl
- Charité - Universitätsmedizin Berlin, Institute of Neuroanatomy and Cell Biology, Department of Pediatric Neurology and Center for Chronically Sick Children, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - William G Wilson
- Pediatrics and Medical Genetics, University of Virginia Health System, Charlottesville, VA, USA
| | - Sara Halbach
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel.,Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Noa Lev-El
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, HB Nijmegen, The Netherlands
| | - Kelly Radtke
- Clinical Genomics Department, Ambry Genetics, Aliso Viejo, CA, USA
| | - Jamel Chelly
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Nouvel Hôpital Civil, Strasbourg, France.,Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67000 Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA.,University of Washington Center for Mendelian Genomics, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,University of Washington Center for Mendelian Genomics, Seattle, WA, USA
| | | | - Russell R Reid
- Department of Surgery, Section of Plastic Surgery, University of Chicago, Chicago, IL, USA
| | - Koenraad Devriendt
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Carey McDougall
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zöe Powis
- Clinical Genomics Department, Ambry Genetics, Aliso Viejo, CA, USA
| | - Thierry Bienvenu
- Institut Cochin, INSERM U1016, CNRS UMR, Paris Descartes University, Paris, France.,Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, 75014 Paris, France
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Department of Paediatrics, University of Melbourne, Melbourne, 3052, Australia
| | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - William B Dobyns
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
| | - Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Darrel Waggoner
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Karen W Gripp
- Division of Medical Genetics, A I duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Joan Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Valérie Cormier-Daire
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France.,Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, Institut Imagine, 75015 Paris, France
| | - David Viskochil
- Division of Medical Genetics, University of Utah, Salt Lake City, UT, USA
| | - Trevor L Hoffman
- Southern California Kaiser Permanente Medical Group, Anaheim, CA, USA
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
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20
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Rabin R, Radmanesh A, Glass IA, Dobyns WB, Aldinger KA, Shieh JT, Romoser S, Bombei H, Dowsett L, Trapane P, Bernat JA, Baker J, Mendelsohn NJ, Popp B, Siekmeyer M, Sorge I, Sansbury FH, Watts P, Foulds NC, Burton J, Hoganson G, Hurst JA, Menzies L, Osio D, Kerecuk L, Cobben JM, Jizi K, Jacquemont S, Bélanger SA, Löhner K, Veenstra-Knol HE, Lemmink HH, Keller-Ramey J, Wentzensen IM, Punj S, McWalter K, Lenberg J, Ellsworth KA, Radtke K, Akbarian S, Pappas J. Genotype-phenotype correlation at codon 1740 of SETD2. Am J Med Genet A 2020; 182:2037-2048. [PMID: 32710489 DOI: 10.1002/ajmg.a.61724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/10/2020] [Accepted: 05/08/2020] [Indexed: 11/06/2022]
Abstract
The SET domain containing 2, histone lysine methyltransferase encoded by SETD2 is a dual-function methyltransferase for histones and microtubules and plays an important role for transcriptional regulation, genomic stability, and cytoskeletal functions. Specifically, SETD2 is associated with trimethylation of histone H3 at lysine 36 (H3K36me3) and methylation of α-tubulin at lysine 40. Heterozygous loss of function and missense variants have previously been described with Luscan-Lumish syndrome (LLS), which is characterized by overgrowth, neurodevelopmental features, and absence of overt congenital anomalies. We have identified 15 individuals with de novo variants in codon 1740 of SETD2 whose features differ from those with LLS. Group 1 consists of 12 individuals with heterozygous variant c.5218C>T p.(Arg1740Trp) and Group 2 consists of 3 individuals with heterozygous variant c.5219G>A p.(Arg1740Gln). The phenotype of Group 1 includes microcephaly, profound intellectual disability, congenital anomalies affecting several organ systems, and similar facial features. Individuals in Group 2 had moderate to severe intellectual disability, low normal head circumference, and absence of additional major congenital anomalies. While LLS is likely due to loss of function of SETD2, the clinical features seen in individuals with variants affecting codon 1740 are more severe suggesting an alternative mechanism, such as gain of function, effects on epigenetic regulation, or posttranslational modification of the cytoskeleton. Our report is a prime example of different mutations in the same gene causing diverging phenotypes and the features observed in Group 1 suggest a new clinically recognizable syndrome uniquely associated with the heterozygous variant c.5218C>T p.(Arg1740Trp) in SETD2.
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Affiliation(s)
- Rachel Rabin
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, New York, USA
| | - Alireza Radmanesh
- Division of Pediatric Neuroradiology, Department of Radiology, NYU School of Medicine, New York, New York, USA
| | - Ian A Glass
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, Division of Medical Genetics, University of Washington, Seattle, Washington, USA.,Department of Neurology, University of Washington, Seattle, Washington, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Joseph T Shieh
- Institute for Human Genetics, Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, California, USA
| | - Shelby Romoser
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Hannah Bombei
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Leah Dowsett
- Kapi'olani Medical Specialists and Department of Pediatrics, University of Hawai'i John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Pamela Trapane
- Division of Pediatric Genetics, Department of Pediatrics, University of Florida College of Medicine-Jacksonville, Jacksonville, Florida, USA
| | - John A Bernat
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Janice Baker
- Genomic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | | | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Manuela Siekmeyer
- Department of Pediatrics Hospital for Children and Adolescents, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Ina Sorge
- Department of Pediatric Radiology, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Francis Hugh Sansbury
- All Wales Medical Genomics Service, Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Patrick Watts
- Department of Ophthalmology, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Nicola C Foulds
- Wessex Clinical Genetics Services, Southampton University Hospital NHS Foundation Trust, Southampton, UK
| | - Jennifer Burton
- University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - George Hoganson
- University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - Jane A Hurst
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Lara Menzies
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Deborah Osio
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Larissa Kerecuk
- Renal Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Jan M Cobben
- North West Thames Regional Genetic Services, Northwick Park Hospitals NHS Foundation Trust, London, UK.,Emma Children Hospital, Amsterdam, The Netherlands
| | - Khadijé Jizi
- CHU Sainte-Justine Hospital, Montreal, Quebec, Canada
| | - Sebastien Jacquemont
- CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Stacey A Bélanger
- Development Clinic, CHU Sainte-Justine Hospital, Montreal, Quebec, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Katharina Löhner
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Henny H Lemmink
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | | | | | | | - Jerica Lenberg
- Rady Children's Hospital Institute for Genomic Medicine, San Diego, California, USA
| | | | - Kelly Radtke
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, USA
| | - Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John Pappas
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, New York, USA.,Clinical Genetics, NYU Orthopedic Hospital, New York, New York, USA
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21
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Chang J, Penon-Portmann M, Shieh JT. Optimizing genetics online resources for diverse readers. Genet Med 2020; 22:640-645. [PMID: 31767985 PMCID: PMC7056640 DOI: 10.1038/s41436-019-0695-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/17/2022] Open
Abstract
PURPOSE Clear and accurate genetic information should be available to health-care consumers at an individualized level of comprehension. The objective of this study is to evaluate the complexity of common online resources and to simplify text content using automated text processing tools. METHODS We extracted all text from Genetics Home Reference and MedlinePlus in bulk and analyzed content using natural language processing. We applied custom tools to improve the readability and compared readability before and after text optimization. RESULTS Commonly used educational materials were more complex than the recommended reading level for the general public. Genetic health information entries from Genetics Home Reference (n = 1279) were written at a median 13.0 grade level. MedlinePlus entries, which are not exclusively genetic (n = 1030), had a median grade level of 7.7. When we optimized text for the 59 actionable conditions by prioritizing medical details using a standard structure, the average reading grade level improved. CONCLUSION Factors that increase complexity are long sentences and difficult words. Future strategies to reduce complexity include prioritizing relevant details and using more illustrations. Simplifying and providing standardized online health resources would benefit diverse consumers and promote inclusivity.
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Affiliation(s)
- Jiyoo Chang
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Monica Penon-Portmann
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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22
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Mendelsohn BA, Beleford DT, Abu-El-Haija A, Alsaleh NS, Rahbeeni Z, Martin PM, Rego S, Huang A, Capodanno G, Shieh JT, Van Ziffle J, Risch N, Alkuraya FS, Slavotinek AM. A novel truncating variant in ring finger protein 113A (RNF113A) confirms the association of this gene with X-linked trichothiodystrophy. Am J Med Genet A 2019; 182:513-520. [PMID: 31880405 DOI: 10.1002/ajmg.a.61450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022]
Abstract
We describe an 11-year old boy with severe global developmental delays, failure to thrive and growth retardation, refractory seizures with recurrent status epilepticus, hypogammaglobulinemia, hypergonadotropic hypogonadism, and duodenal strictures. He had facial and skin findings compatible with trichothiodystrophy, including sparse and brittle hair, thin eyebrows, and dry skin. Exome sequencing showed a hemizygous, truncating variant in RNF113A, c.903_910delGCAGACCA, predicting p.(Gln302fs*12), that was inherited from his mother. Although his clinical features overlap closely with features described in the two previously reported male first cousins with RNF113A loss of function mutations, the duodenal strictures seen in this patient have not been reported. Interestingly, the patient's mother had short stature and 100% skewed X-inactivation as seen in other obligate female carriers. A second male with developmental delays, microcephaly, seizures, ambiguous genitalia, and facial anomalies that included sparse and brittle hair, thin eyebrows and dry skin was recently reported to have c.897_898delTG, predicting p.(Cys299*) in RNF113A and we provide additional clinical details for this patient. This report further supports deleterious variants in RNF113A as a cause of a novel trichothiodystrophy syndrome.
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Affiliation(s)
- Bryce A Mendelsohn
- Division of Medical Genetics, University of California, San Francisco, San Francisco, California
| | - Daniah T Beleford
- Division of Medical Genetics, University of California, San Francisco, San Francisco, California
| | - Aya Abu-El-Haija
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts
| | - Norah S Alsaleh
- Division of Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | - Shannon Rego
- Division of Medical Genetics, University of California, San Francisco, San Francisco, California
| | - Alyssa Huang
- Division of Pediatric Endocrinology, University of California, San Francisco, California
| | - Gina Capodanno
- Division of Pediatric Endocrinology, University of California, San Francisco, California
| | - Joseph T Shieh
- Division of Medical Genetics, University of California, San Francisco, San Francisco, California.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | - Jessica Van Ziffle
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | - Neil Risch
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | - Fowzan S Alkuraya
- Division of Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Anne M Slavotinek
- Division of Medical Genetics, University of California, San Francisco, San Francisco, California.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California
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23
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Ha TK, Mardy AH, Beleford D, Spanier A, Wayman BV, Penon-Portmann M, Wiita AP, Shieh JT. X-linked duplication copy number variation in a familial overgrowth condition. Am J Med Genet C Semin Med Genet 2019; 181:644-649. [PMID: 31762227 DOI: 10.1002/ajmg.c.31756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 05/02/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 01/16/2023]
Abstract
We describe an overgrowth condition associated with X-linked copy number variation. Three brothers displayed an overgrowth pattern at birth that continued postnatally. Clinical findings included macrocephaly, distinctive facial features, developmental delay and variable clubfoot. Normal fetal growth was noted until the third trimester by Hadlock standards, revealing a late gestational overgrowth pattern. Microarray analysis in the family showed a maternally inherited 680 kb copy number duplication at Xq26.1-q26.2 in all three brothers. Molecular sequencing for known overgrowth conditions including GPC3, Sotos 1 (NSD1), Malan (NFIX), Perlman (DIS3L2), Weaver (EZH2), Opitz-Kaveggia (MED12) loci were negative. BWS IC1 and IC2 methylation and CDKN1C testing was also negative. Normal IGF1 levels excluded X-linked acrogiantism. The duplicated region Xq26.1-q26.2 contained IGSF1 and at least part of the lncRNA FIRRE. IGSF1, a highly expressed pituitary immunoglobulin superfamily gene, was recently implicated in a genome-wide association study of canine size. IGSF1 variants were associated with large canine breeds compared to smaller breeds. Our findings support the hypothesis that an X-linked variant encompassing the IGSF1 region may be associated with body size. Although IGSF1 loss has been noted in human hypothyroidism, this is the first reported phenotype in a family with copy number duplication in the region. Our findings suggest that prenatal evaluation, cross-species evaluation, Mendelian, and GWAS studies may describe a distinctive familial condition and its corresponding phenotypic features.
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Affiliation(s)
- Thoa K Ha
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, California
| | - Anne H Mardy
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California
- Alameda Health System, Eastmont Wellness Center, Oakland, California
| | - Daniah Beleford
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Andrew Spanier
- Alameda Health System, Eastmont Wellness Center, Oakland, California
| | - Brette V Wayman
- UCSF Health Center for Clinical Genetics and Genomics, University of California San Francisco, San Francisco, California
| | - Monica Penon-Portmann
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
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24
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Guo H, Li Y, Shen L, Wang T, Jia X, Liu L, Xu T, Ou M, Hoekzema K, Wu H, Gillentine MA, Liu C, Ni H, Peng P, Zhao R, Zhang Y, Phornphutkul C, Stegmann APA, Prada CE, Hopkin RJ, Shieh JT, McWalter K, Monaghan KG, van Hasselt PM, van Gassen K, Bai T, Long M, Han L, Quan Y, Chen M, Zhang Y, Li K, Zhang Q, Tan J, Zhu T, Liu Y, Pang N, Peng J, Scott DA, Lalani SR, Azamian M, Mancini GMS, Adams DJ, Kvarnung M, Lindstrand A, Nordgren A, Pevsner J, Osei-Owusu IA, Romano C, Calabrese G, Galesi O, Gecz J, Haan E, Ranells J, Racobaldo M, Nordenskjold M, Madan-Khetarpal S, Sebastian J, Ball S, Zou X, Zhao J, Hu Z, Xia F, Liu P, Rosenfeld JA, de Vries BBA, Bernier RA, Xu ZQD, Li H, Xie W, Hufnagel RB, Eichler EE, Xia K. Disruptive variants of CSDE1 associate with autism and interfere with neuronal development and synaptic transmission. Sci Adv 2019; 5:eaax2166. [PMID: 31579823 PMCID: PMC6760934 DOI: 10.1126/sciadv.aax2166] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/27/2019] [Indexed: 05/30/2023]
Abstract
RNA binding proteins are key players in posttranscriptional regulation and have been implicated in neurodevelopmental and neuropsychiatric disorders. Here, we report a significant burden of heterozygous, likely gene-disrupting variants in CSDE1 (encoding a highly constrained RNA binding protein) among patients with autism and related neurodevelopmental disabilities. Analysis of 17 patients identifies common phenotypes including autism, intellectual disability, language and motor delay, seizures, macrocephaly, and variable ocular abnormalities. HITS-CLIP revealed that Csde1-binding targets are enriched in autism-associated gene sets, especially FMRP targets, and in neuronal development and synaptic plasticity-related pathways. Csde1 knockdown in primary mouse cortical neurons leads to an overgrowth of the neurites and abnormal dendritic spine morphology/synapse formation and impaired synaptic transmission, whereas mutant and knockdown experiments in Drosophila result in defects in synapse growth and synaptic transmission. Our study defines a new autism-related syndrome and highlights the functional role of CSDE1 in synapse development and synaptic transmission.
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Affiliation(s)
- Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ying Li
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tianyun Wang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangbin Jia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lijuan Liu
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Tao Xu
- Department of Neurobiology, Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Laboratory of Brain Disorders (Ministry of Science and Technology), Beijing Institute of Brain Disorders, Capital Medical University, Beijing, China
| | - Mengzhu Ou
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Huidan Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Madelyn A. Gillentine
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Cenying Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Hailun Ni
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Pengwei Peng
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Rongjuan Zhao
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yu Zhang
- Key Laboratory of Developmental Disorders in Children, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Chanika Phornphutkul
- Division of Human Genetics, Warren Alpert Medical School of Brown University, Hasbro Children's Hospital/Rhode Island Hospital, Providence, RI, USA
| | | | - Carlos E. Prada
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Human Genetics, Cincinnati Children’s Hospital, Cincinnati, OH, USA
| | - Robert J. Hopkin
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Human Genetics, Cincinnati Children’s Hospital, Cincinnati, OH, USA
| | - Joseph T. Shieh
- Institute for Human Genetics and Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Ting Bai
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Min Long
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lin Han
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yingting Quan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Meilin Chen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yaowen Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kuokuo Li
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiumeng Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jieqiong Tan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tengfei Zhu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yaning Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Grazia M. S. Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Darius J. Adams
- Goryeb Children’s Hospital, Atlantic Health System, Morristown, NJ, USA
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, USA
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ikeoluwa A. Osei-Owusu
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, USA
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | | | - Jozef Gecz
- School of Medicine and the Robinson Research Institute, University of Adelaide at the Women’s and Children’s Hospital, Adelaide, South Australia, Australia
| | - Eric Haan
- Adult Genetics Unit, Royal Adelaide Hospital, and School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Judith Ranells
- Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Melissa Racobaldo
- Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Magnus Nordenskjold
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Suneeta Madan-Khetarpal
- Division of Medical Genetics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Division of Medical Genetics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Susie Ball
- Central Washington Genetics Program, Virginia Mason Memorial, Yakima, WA, USA
| | - Xiaobing Zou
- Children Development Behavior Center of the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jingping Zhao
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Bert B. A. de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Zhi-Qing David Xu
- Department of Neurobiology, Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Laboratory of Brain Disorders (Ministry of Science and Technology), Beijing Institute of Brain Disorders, Capital Medical University, Beijing, China
| | - Honghui Li
- Key Laboratory of Developmental Disorders in Children, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Wei Xie
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Robert B. Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Key Laboratory of Medical Information Research, Central South University, Changsha, Hunan, China
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Chinese Academy of Sciences, Shanghai 200030, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan 410078, China
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25
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Galambos C, Mullen MP, Shieh JT, Schwerk N, Kielt MJ, Ullmann N, Boldrini R, Stucin-Gantar I, Haass C, Bansal M, Agrawal PB, Johnson J, Peca D, Surace C, Cutrera R, Pauciulo MW, Nichols WC, Griese M, Ivy D, Abman SH, Austin ED, Danhaive O. Phenotype characterisation of TBX4 mutation and deletion carriers with neonatal and paediatric pulmonary hypertension. Eur Respir J 2019; 54:13993003.01965-2018. [PMID: 31151956 DOI: 10.1183/13993003.01965-2018] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/19/2019] [Indexed: 11/05/2022]
Abstract
Rare variants in the T-box transcription factor 4 gene (TBX4) have recently been recognised as an emerging cause of paediatric pulmonary hypertension (PH). Their pathophysiology and contribution to persistent pulmonary hypertension in neonates (PPHN) are unknown. We sought to define the spectrum of clinical manifestations and histopathology associated with TBX4 variants in neonates and children with PH.We assessed clinical data and lung tissue in 19 children with PH, including PPHN, carrying TBX4 rare variants identified by next-generation sequencing and copy number variation arrays.Variants included six 17q23 deletions encompassing the entire TBX4 locus and neighbouring genes, and 12 likely damaging mutations. 10 infants presented with neonatal hypoxic respiratory failure and PPHN, and were subsequently discharged home. PH was diagnosed later in infancy or childhood. Three children died and two required lung transplantation. Associated anomalies included patent ductus arteriosus, septal defects, foot anomalies and developmental disability, the latter with a higher prevalence in deletion carriers. Histology in seven infants showed abnormal distal lung development and pulmonary hypertensive remodelling.TBX4 mutations and 17q23 deletions underlie a new form of developmental lung disease manifesting with severe, often biphasic PH at birth and/or later in infancy and childhood, often associated with skeletal anomalies, cardiac defects, neurodevelopmental disability and other anomalies.
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Affiliation(s)
- Csaba Galambos
- Dept of Pathology and Laboratory Services, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA.,Contributed equally to this work as joint first authors
| | - Mary P Mullen
- Dept of Cardiology, Boston Children's Hospital and Pediatrics Harvard Medical School, Boston, MA, USA.,Contributed equally to this work as joint first authors
| | - Joseph T Shieh
- Institute for Human Genetics, Medical Genetics, University of California San Francisco, UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Nicolaus Schwerk
- Clinic for Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Matthew J Kielt
- Division of Pediatric Pulmonology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicola Ullmann
- Division of Pediatric Pulmonology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Renata Boldrini
- Dept of Laboratory Medicine, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Cristina Haass
- Division of Neonatology, San Pietro-Fatebenefratelli Hospital, Rome, Italy
| | - Manish Bansal
- Division of Pediatric Cardiology, University of Iowa Children's Hospital, Iowa City, IA, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine and Genetics and Genomics, Harvard School of Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Joyce Johnson
- Dept of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Donatella Peca
- Dept of Laboratory Medicine, Bambino Gesù Children's Hospital, Rome, Italy
| | - Cecilia Surace
- Dept of Laboratory Medicine, Bambino Gesù Children's Hospital, Rome, Italy
| | - Renato Cutrera
- Division of Pediatric Pulmonology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Michael W Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Dept of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William C Nichols
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Dept of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Matthias Griese
- Division of Pediatric Pulmonology, Ludwig-Maximilians-University, Munich, Germany
| | - Dunbar Ivy
- Division of Pediatric Cardiology, Dept of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Steven H Abman
- Division of Pulmonary Medicine, Dept of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Eric D Austin
- Division of Pediatric Pulmonology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Danhaive
- Division of Neonatology, University of California San Francisco Benioff Children's Hospital, San Francisco, CA, USA .,Division of Neonatology, Catholic University of Louvain, Brussels, Belgium
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26
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Ko J, Pomerantz JH, Perry H, Shieh JT, Slavotinek AM, Oberoi S, Klein OD. Case Report of Floating-Harbor Syndrome With Bilateral Cleft Lip. Cleft Palate Craniofac J 2019; 57:132-136. [PMID: 31248274 DOI: 10.1177/1055665619858257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Floating-Harbor syndrome (FHS) is a rare genetic disorder caused by heterozygous mutations in the Snf2-related CREBBP activator protein (SRCAP) gene. The syndrome is characterized by proportional short stature, delayed bone maturation, delayed speech development, and facial dysmorphism. Submucous cleft palate and cleft lip have been reported in FHS, but to our knowledge orofacial clefting in this condition has not been assessed in detail. Here, we report on a case of bilateral cleft lip in a patient with FHS confirmed by exome sequencing.
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Affiliation(s)
- Jaemin Ko
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Jason H Pomerantz
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA.,Division of Plastic and Reconstructive Surgery, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Hazel Perry
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Anne M Slavotinek
- Division of Medical Genetics, Department of Pediatrics, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Snehlata Oberoi
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Ophir D Klein
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA.,Division of Medical Genetics, Department of Pediatrics, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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27
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Beleford DT, Diab M, Qubty WF, Malloy MJ, Long RK, Shieh JT. Schimke immunoosseous dysplasia and management considerations for vascular risks. Am J Med Genet A 2019; 179:1246-1252. [PMID: 31039288 DOI: 10.1002/ajmg.a.61148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/31/2019] [Accepted: 02/22/2019] [Indexed: 11/06/2022]
Abstract
Schimke immunoosseous dysplasia (SIOD) is a multisystemic condition characterized by early arteriosclerosis and progressive renal insufficiency, among other features. Many SIOD patients have severe, migraine-like headaches, transient neurologic attacks, or cerebral ischemic events. Cerebral events could be exacerbated or precipitated by hypertension, and it is unclear how these are related to arteriosclerotic changes as dyslipidemia is also a feature of SIOD. The correlation between hypercholesterolemia and cardiovascular risk in SIOD is unclear. Also, the etiology and management of headaches is not well characterized. Here we report our clinical observations in the management of SIOD in a patient who was diagnosed in school age despite early signs and symptoms. We describe biallelic variants, including a previously unreported c.1931G>A (p.Arg644Gln) variant in SMARCAL1. We specifically investigated whether migraine-like headaches and progressive nephropathy may be related to blood pressure dysregulation. We found a correlation between tighter blood pressure regulation using ambulatory blood pressure monitoring and a subjective decrease in headache symptoms. We discuss blood pressure medication management in SIOD. We also characterize dyslipidemia relative to atherosclerosis risks and provide new management strategies to consider for optimizing care.
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Affiliation(s)
- Daniah T Beleford
- Division of Medical Genetics, Department of Pediatrics, Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Mohammad Diab
- Pediatric Orthopaedics, Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, California
| | - William F Qubty
- Pediatric Headache, Division of Child Neurology, Department of Neurology, University of California San Francisco, San Francisco, California
| | - Mary J Malloy
- Departments of Medicine and Pediatrics, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California
| | - Roger K Long
- Division of Pediatric Endocrinology, Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, Institute for Human Genetics, University of California San Francisco, San Francisco, California.,Institute for Human Genetics and Department of Pediatrics, University of California San Francisco, San Francisco, California
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28
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Kumar A, Zastrow DB, Kravets EJ, Beleford D, Ruzhnikov MRZ, Grove ME, Dries AM, Kohler JN, Waggott DM, Yang Y, Huang Y, Mackenzie KM, Eng CM, Fisher PG, Ashley EA, Teng JM, Stevenson DA, Shieh JT, Wheeler MT, Bernstein JA. Extracutaneous manifestations in phacomatosis cesioflammea and cesiomarmorata: Case series and literature review. Am J Med Genet A 2019; 179:966-977. [PMID: 30920161 DOI: 10.1002/ajmg.a.61134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022]
Abstract
Phacomatosis pigmentovascularis (PPV) comprises a family of rare conditions that feature vascular abnormalities and melanocytic lesions that can be solely cutaneous or multisystem in nature. Recently published work has demonstrated that both vascular and melanocytic abnormalities in PPV of the cesioflammea and cesiomarmorata subtypes can result from identical somatic mosaic activating mutations in the genes GNAQ and GNA11. Here, we present three new cases of PPV with features of the cesioflammea and/or cesiomarmorata subtypes and mosaic mutations in GNAQ or GNA11. To better understand the risk of potentially occult complications faced by such patients we additionally reviewed 176 cases published in the literature. We report the frequency of clinical findings, their patterns of co-occurrence as well as published recommendations for surveillance after diagnosis. Features assessed include: capillary malformation; dermal and ocular melanocytosis; glaucoma; limb asymmetry; venous malformations; and central nervous system (CNS) anomalies, such as ventriculomegaly and calcifications. We found that ocular findings are common in patients with phacomatosis cesioflammea and cesiomarmorata. Facial vascular involvement correlates with a higher risk of seizures (p = .0066). Our genetic results confirm the role of mosaic somatic mutations in GNAQ and GNA11 in phacomatosis cesioflammea and cesiomarmorata. Their clinical and molecular findings place these conditions on a clinical spectrum encompassing other GNAQ and GNA11 related disorders and inform recommendations for their management.
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Affiliation(s)
- Akash Kumar
- Department of Pediatrics, Stanford School of Medicine, Stanford, California
| | - Diane B Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Elijah J Kravets
- Department of Pediatrics, Stanford School of Medicine, Stanford, California
| | - Daniah Beleford
- Institute for Human Genetics and Division of Medical Genetics, Pediatrics, San Francisco, California
| | - Maura R Z Ruzhnikov
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California.,Department of Neurology, Stanford School of Medicine, Stanford, California
| | - Megan E Grove
- Clinical Genomics Program, Stanford Health Care, Stanford, California
| | - Annika M Dries
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Jennefer N Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Daryl M Waggott
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Yaping Yang
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yong Huang
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | | | | | - Christine M Eng
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Paul G Fisher
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California.,Department of Neurology, Stanford School of Medicine, Stanford, California
| | - Euan A Ashley
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California.,Department of Medicine, Stanford University School of Medicine, Stanford, California.,Department of Genetics, Stanford School of Medicine, Stanford, California
| | - Joyce M Teng
- Department of Dermatology, Stanford School of Medicine, Stanford, California
| | - David A Stevenson
- Department of Pediatrics, Stanford School of Medicine, Stanford, California
| | - Joseph T Shieh
- Institute for Human Genetics and Division of Medical Genetics, Pediatrics, San Francisco, California
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California.,Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford School of Medicine, Stanford, California.,Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
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29
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Penon M, Zahed H, Berger V, Su I, Shieh JT. Using exome sequencing to decipher family history in a healthy individual: Comparison of pathogenic and population MTM1 variants. Mol Genet Genomic Med 2018; 6:722-727. [PMID: 30047259 PMCID: PMC6160706 DOI: 10.1002/mgg3.405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/11/2018] [Accepted: 03/13/2018] [Indexed: 12/31/2022] Open
Abstract
Background When a family encounters the loss of a child early in life, extensive genetic testing of the affected neonate is sometimes not performed or not possible. However, the increasing availability of genomic sequencing may allow for direct application to families in cases where there is a condition inherited from parental gene(s). When neonatal testing is not possible, it is feasible to perform family testing as long as there is optimal interpretation of the genomic information. Here, we present an example of a healthy adult woman with a history of recurrent male neonatal losses due to severe respiratory distress who presented to Medical Genetics for evaluation. A family history of additional male neonatal loss was present, suggesting a potential inherited genetic etiology. Methods Although there was no DNA available from the neonates, by performing exome sequencing on the healthy adult woman, we found a missense variant in MTM1 as a potential candidate, which was deemed pathogenic based on multiple criteria including past report. Results By performing an analysis of all known MTM1‐disease associated mutations and control population variation, we can also better infer the effects of missense variations on MTM1, as not all variants are truncating. MTM1‐X‐linked myotubular myopathy is a condition that leads to male perinatal respiratory failure and a high risk for early mortality. Conclusions The application of genetic testing in the healthy population here highlights the broader utility of genomic sequencing in evaluating unexplained recurrent neonatal loss, especially when genetic testing is not available on the affected neonates.
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Affiliation(s)
- Monica Penon
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California
| | - Hengameh Zahed
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California
| | - Victoria Berger
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California.,Department of Obstetrics, Gynecology and Reproductive Science, University of California San Francisco, San Francisco, California
| | - Irene Su
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California
| | - Joseph T Shieh
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California.,Institute for Human Genetics, University of California San Francisco, San Francisco, California
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30
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Lindberg OR, McKinney A, Engler JR, Koshkakaryan G, Gong H, Robinson AE, Ewald AJ, Huillard E, David James C, Molinaro AM, Shieh JT, Phillips JJ. GBM heterogeneity as a function of variable epidermal growth factor receptor variant III activity. Oncotarget 2018; 7:79101-79116. [PMID: 27738329 PMCID: PMC5346701 DOI: 10.18632/oncotarget.12600] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 08/06/2016] [Accepted: 09/29/2016] [Indexed: 11/25/2022] Open
Abstract
Abnormal activation of the epidermal growth factor receptor (EGFR) due to a deletion of exons 2-7 of EGFR (EGFRvIII) is a common alteration in glioblastoma (GBM). While this alteration can drive gliomagenesis, tumors harboring EGFRvIII are heterogeneous. To investigate the role for EGFRvIII activation in tumor phenotype we used a neural progenitor cell-based murine model of GBM driven by EGFR signaling and generated tumor progenitor cells with high and low EGFRvIII activation, pEGFRHi and pEGFRLo. In vivo, ex vivo, and in vitro studies suggested a direct association between EGFRvIII activity and increased tumor cell proliferation, decreased tumor cell adhesion to the extracellular matrix, and altered progenitor cell phenotype. Time-lapse confocal imaging of tumor cells in brain slice cultures demonstrated blood vessel co-option by tumor cells and highlighted differences in invasive pattern. Inhibition of EGFR signaling in pEGFRHi promoted cell differentiation and increased cell-matrix adhesion. Conversely, increased EGFRvIII activation in pEGFRLo reduced cell-matrix adhesion. Our study using a murine model for GBM driven by a single genetic driver, suggests differences in EGFR activation contribute to tumor heterogeneity and aggressiveness.
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Affiliation(s)
- Olle R Lindberg
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, CA, USA
| | - Andrew McKinney
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, CA, USA
| | - Jane R Engler
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, CA, USA
| | - Gayane Koshkakaryan
- Touro University California, College of Osteopathic Medicine, Vallejo, CA, USA
| | - Henry Gong
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, CA, USA
| | - Aaron E Robinson
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, CA, USA
| | - Andrew J Ewald
- Departments of Cell Biology, Oncology, and Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Emmanuelle Huillard
- Université Pierre et Marie Curie (UPMC) UMR-S975, Inserm U1127, CNRS UMR7225, Institut du Cerveau et de la Moelle Epiniere, Paris, France
| | - C David James
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Joseph T Shieh
- Institute for Human Genetics, Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Pathology, Division of Neuropathology, University of California, San Francisco, CA, USA
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31
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Yu Z, Tang PL, Wang J, Bao S, Shieh JT, Leung AW, Zhang Z, Gao F, Wong SY, Hui AL, Gao Y, Dung N, Zhang ZG, Fan Y, Zhou X, Zhang Y, Wong DS, Sham PC, Azhar A, Kwok PY, Tam PP, Lian Q, Cheah KS, Wang B, Song YQ. Mutations in Hnrnpa1 cause congenital heart defects. JCI Insight 2018; 3:98555. [PMID: 29367466 PMCID: PMC5821217 DOI: 10.1172/jci.insight.98555] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/19/2017] [Indexed: 12/21/2022] Open
Abstract
Incomplete penetrance of congenital heart defects (CHDs) was observed in a mouse model. We hypothesized that the contribution of a major genetic locus modulates the manifestation of the CHDs. After genome-wide linkage mapping, fine mapping, and high-throughput targeted sequencing, a recessive frameshift mutation of the heterogeneous nuclear ribonucleoprotein A1 (Hnrnpa1) gene was confirmed (Hnrnpa1ct). Hnrnpa1 was expressed in both the first heart field (FHF) and second heart field (SHF) at the cardiac crescent stage but was only maintained in SHF progenitors after heart tube formation. Hnrnpa1ct/ct homozygous mutants displayed complete CHD penetrance, including truncated and incomplete looped heart tube at E9.5, ventricular septal defect (VSD) and persistent truncus arteriosus (PTA) at E13.5, and VSD and double outlet right ventricle at P0. Impaired development of the dorsal mesocardium and sinoatrial node progenitors was also observed. Loss of Hnrnpa1 expression leads to dysregulation of cardiac transcription networks and multiple signaling pathways, including BMP, FGF, and Notch in the SHF. Finally, two rare heterozygous mutations of HNRNPA1 were detected in human CHDs. These findings suggest a role of Hnrnpa1 in embryonic heart development in mice and humans. Heterogeneous nuclear ribonucleoprotein A1 (Hnrnpa1) is essential for embryonic heart development in both mice and humans.
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Affiliation(s)
- Zhe Yu
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Paul Lf Tang
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Jing Wang
- National Research Institute for Family Planning, Beijing, China
| | - Suying Bao
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Joseph T Shieh
- Institute for Human Genetics and Department of Pediatrics, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Alan Wl Leung
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Zhao Zhang
- Department of Medicine and Ophthalmology
| | - Fei Gao
- Department of Medicine and Ophthalmology
| | - Sandra Yy Wong
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Andy Lc Hui
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Yuan Gao
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Nelson Dung
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Zhi-Gang Zhang
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Yanhui Fan
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | | | - Yalun Zhang
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Dana Sm Wong
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Pak C Sham
- Department of Psychiatry.,Centre for Genome Sciences, and.,State Key Laboratory for Cognitive and Brain Sciences, The University of Hong Kong, Hong Kong, China
| | - Abid Azhar
- Institute of Biotechnology & Genetic Engineering, University of Karachi, Karachi, Pakistan
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Patrick Pl Tam
- Embryology Unit, Children's Medical Research Institute, School of Medical Sciences, University of Sydney, Westmead, New South Wales, Australia
| | | | - Kathryn Se Cheah
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
| | - Binbin Wang
- National Research Institute for Family Planning, Beijing, China
| | - You-Qiang Song
- School of Biomedical Sciences, Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China.,Centre for Genome Sciences, and.,State Key Laboratory for Cognitive and Brain Sciences, The University of Hong Kong, Hong Kong, China.,The University of Hong Kong Shenzhen Institute of Research and Innovation and.,The University of Hong Kong-Southern University of Science and Technology Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China
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32
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Berg JS, Agrawal PB, Bailey DB, Beggs AH, Brenner SE, Brower AM, Cakici JA, Ceyhan-Birsoy O, Chan K, Chen F, Currier RJ, Dukhovny D, Green RC, Harris-Wai J, Holm IA, Iglesias B, Joseph G, Kingsmore SF, Koenig BA, Kwok PY, Lantos J, Leeder SJ, Lewis MA, McGuire AL, Milko LV, Mooney SD, Parad RB, Pereira S, Petrikin J, Powell BC, Powell CM, Puck JM, Rehm HL, Risch N, Roche M, Shieh JT, Veeraraghavan N, Watson MS, Willig L, Yu TW, Urv T, Wise AL. Newborn Sequencing in Genomic Medicine and Public Health. Pediatrics 2017; 139:e20162252. [PMID: 28096516 PMCID: PMC5260149 DOI: 10.1542/peds.2016-2252] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2016] [Indexed: 12/20/2022] Open
Abstract
The rapid development of genomic sequencing technologies has decreased the cost of genetic analysis to the extent that it seems plausible that genome-scale sequencing could have widespread availability in pediatric care. Genomic sequencing provides a powerful diagnostic modality for patients who manifest symptoms of monogenic disease and an opportunity to detect health conditions before their development. However, many technical, clinical, ethical, and societal challenges should be addressed before such technology is widely deployed in pediatric practice. This article provides an overview of the Newborn Sequencing in Genomic Medicine and Public Health Consortium, which is investigating the application of genome-scale sequencing in newborns for both diagnosis and screening.
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Affiliation(s)
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine and
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Alan H Beggs
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Amy M Brower
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Julie A Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | | | - Kee Chan
- Chicago School of Public Health, University of Illinois, Chicago, Illinois
| | | | - Robert J Currier
- Genetic Disease Screening Program, California Department of Public Health, Sacramento, California
| | - Dmitry Dukhovny
- Department of Pediatrics and Division of Neonatology, Oregon Health & Science University, Portland, Oregon
| | | | | | - Ingrid A Holm
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Galen Joseph
- Department of Anthropology, History, and Social Medicine
| | | | | | - Pui-Yan Kwok
- Institute for Human Genetics
- Cardiovascular Research Institute, and Department of Dermatology
| | - John Lantos
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Steven J Leeder
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Megan A Lewis
- RTI International, Research Triangle Park, North Carolina
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas; and
| | | | | | - Richard B Parad
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas; and
| | - Joshua Petrikin
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | | | - Cynthia M Powell
- Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Jennifer M Puck
- Department of Pediatrics, University of California, San Francisco, California
| | | | | | - Myra Roche
- Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Joseph T Shieh
- Institute for Human Genetics
- Department of Pediatrics, Benioff Children's Hospital, and
| | | | - Michael S Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Laurel Willig
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Timothy W Yu
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tiina Urv
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
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33
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Phillips JJ, Gong H, Chen K, Joseph NM, van Ziffle J, Jin LW, Bastian BC, Bollen AW, Perry A, Nicolaides T, Solomon DA, Shieh JT. Activating NRF1-BRAF and ATG7-RAF1 fusions in anaplastic pleomorphic xanthoastrocytoma without BRAF p.V600E mutation. Acta Neuropathol 2016; 132:757-760. [PMID: 27624885 DOI: 10.1007/s00401-016-1616-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 11/25/2022]
Affiliation(s)
- Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, Helen Diller Family Cancer Building, HD492B, San Francisco, CA, 94143, USA.
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
| | - Henry Gong
- Department of Neurological Surgery, University of California San Francisco, Helen Diller Family Cancer Building, HD492B, San Francisco, CA, 94143, USA
| | - Katharine Chen
- Department of Neurological Surgery, University of California San Francisco, Helen Diller Family Cancer Building, HD492B, San Francisco, CA, 94143, USA
| | - Nancy M Joseph
- Clinical Cancer Genomics Laboratory, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Jessica van Ziffle
- Clinical Cancer Genomics Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, CA, USA
- M.I.N.D. (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis Medical Center, Sacramento, CA, USA
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Clinical Cancer Genomics Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Andrew W Bollen
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California San Francisco, Helen Diller Family Cancer Building, HD492B, San Francisco, CA, 94143, USA
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Theodore Nicolaides
- Department of Neurological Surgery, University of California San Francisco, Helen Diller Family Cancer Building, HD492B, San Francisco, CA, 94143, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - David A Solomon
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Clinical Cancer Genomics Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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34
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Peca D, Boldrini R, Johannson J, Shieh JT, Citti A, Petrini S, Salerno T, Cazzato S, Testa R, Messina F, Onofri A, Cenacchi G, Westermark P, Ullmann N, Cogo P, Cutrera R, Danhaive O. Clinical and ultrastructural spectrum of diffuse lung disease associated with surfactant protein C mutations. Eur J Hum Genet 2016; 24:780. [PMID: 27075519 DOI: 10.1038/ejhg.2016.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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35
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Shieh JT. Response to Finsterer and Stöllberger "Explanations for discordance of noncompaction in monozygotic twins". Am J Med Genet A 2015. [PMID: 26198164 DOI: 10.1002/ajmg.a.37200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Joseph T Shieh
- Department of Pediatrics, Institute of Human Genetics, University of California, San Francisco, San Francisco, California
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36
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Bayer ML, Frommelt PC, Blei F, Breur JM, Cordisco MR, Frieden IJ, Goddard DS, Holland KE, Krol AL, Maheshwari M, Metry DW, Morel KD, North PE, Pope E, Shieh JT, Southern JF, Wargon O, Siegel DH, Drolet BA. Congenital cardiac, aortic arch, and vascular bed anomalies in PHACE syndrome (from the International PHACE Syndrome Registry). Am J Cardiol 2013; 112:1948-52. [PMID: 24079520 DOI: 10.1016/j.amjcard.2013.08.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
Abstract
PHACE syndrome represents the association of large infantile hemangiomas of the head and neck with brain, cerebrovascular, cardiac, ocular, and ventral or midline defects. Cardiac and cerebrovascular anomalies are the most common extracutaneous features of PHACE, and they also constitute the greatest source of potential morbidity. Congenital heart disease in PHACE is incompletely described, and this study was conducted to better characterize its features. This study of the International PHACE Syndrome Registry represents the largest central review of clinical, radiologic, and histopathologic data for cardiovascular anomalies in patients with PHACE to date. Sixty-two (41%) of 150 subjects had intracardiac, aortic arch, or brachiocephalic vessel anomalies. Aberrant origin of a subclavian artery was the most common cardiovascular anomaly (present in 31 (21%) of 150 subjects). Coarctation was the second most common anomaly, identified in 28 (19%) of 150 subjects, and can be missed clinically in patients with PHACE because of the frequent association of arch obstruction with aberrant subclavian origin. Twenty-three (37%) of 62 subjects with cardiovascular anomalies required procedural intervention. A greater percentage of hemangiomas were located on the left side of the head and neck in patients with coarctation (46% vs 39%); however, hemangioma distribution did not predict the presence of cardiovascular anomalies overall. In conclusion, PHACE is associated with a high risk of congenital heart disease. Cardiac and aortic arch imaging with detailed assessment of arch patency and brachiocephalic origins is essential for any patient suspected of having PHACE. Longitudinal investigation is needed to determine the long-term outcomes of cardiovascular anomalies in PHACE.
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37
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Cohen CJ, Shieh JT, Pickles RJ, Okegawa T, Hsieh JT, Bergelson JM. The coxsackievirus and adenovirus receptor is a transmembrane component of the tight junction. Proc Natl Acad Sci U S A 2001; 98:15191-6. [PMID: 11734628 PMCID: PMC65005 DOI: 10.1073/pnas.261452898] [Citation(s) in RCA: 492] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The coxsackievirus and adenovirus receptor (CAR) mediates viral attachment and infection, but its physiologic functions have not been described. In nonpolarized cells, CAR localized to homotypic intercellular contacts, mediated homotypic cell aggregation, and recruited the tight junction protein ZO-1 to sites of cell-cell contact. In polarized epithelial cells, CAR and ZO-1 colocalized to tight junctions and could be coprecipitated from cell lysates. CAR expression led to reduced passage of macromolecules and ions across cell monolayers, and soluble CAR inhibited the formation of functional tight junctions. Virus entry into polarized epithelium required disruption of tight junctions. These results indicate that CAR is a component of the tight junction and of the functional barrier to paracellular solute movement. Sequestration of CAR in tight junctions may limit virus infection across epithelial surfaces.
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Affiliation(s)
- C J Cohen
- Division of Immunologic and Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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38
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Abstract
HIV-1 establishes a low-level persistent infection in astrocytes. In this study, we studied the susceptibility of a human astrocyte cell line (SVG-A) to infection with luciferase expressing reporter viruses pseudotyped with envelopes derived from five isolates of HIV-1. SVG-A cells were susceptible to infection by a T-cell tropic isolate and the infection was both CD4 and CXCR4 independent. These data confirm the susceptibility of astrocytes to infection with T-tropic strains of HIV-1 and suggest a novel mechanism by which T-tropic strains of HIV can infect cells.
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Affiliation(s)
- B Schweighardt
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02192, USA
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39
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Albright AV, Shieh JT, O'Connor MJ, González-Scarano F. Characterization of cultured microglia that can be infected by HIV-1. J Neurovirol 2000; 6 Suppl 1:S53-60. [PMID: 10871766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Parenchymal microglia are targets of HIV infection. We, as well as others, have used in vitro microglia culture systems to study the tropism and replication of HIV. Characterization of perivascular and parenchymal microglia surface markers in vivo, in vitro, and ex vivo, has led to the understanding that these cell populations are different, and data from both the HIV and SIV models support the hypothesis that they may play different roles in infection of the CNS. We determined that human adult parenchymal microglia cultured from temporal lobe tissue for use in HIV replication studies, were CD11c+, CD45+, CD68+, CD14- when cultured with standard serum/cytokine-supplemented media. To determine the influence of serum and cytokines on HIV replication in microglia, we designed a new protocol for culturing microglia, and compared the results obtained with this protocol with the standard approach previously described. Microglia cultured in the presence of a 'feeder' layer of glial cells and in the absence of serum and cytokines expressed the same surface markers as pure microglia (>95%) cultured in supplemented media. However, pure microglia cultured in the absence of both serum/cytokines supplements and other glial cells, did not have characteristic microglial morphology and did not support HIV replication to as high a level. Lastly, we determined that unlike monocytes, ex vivo parenchymal microglia were capable of supporting HIV replication.
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Affiliation(s)
- A V Albright
- Department of Neurology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, PA 19104-6146, USA
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40
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Shieh JT, Martín J, Baltuch G, Malim MH, González-Scarano F. Determinants of syncytium formation in microglia by human immunodeficiency virus type 1: role of the V1/V2 domains. J Virol 2000; 74:693-701. [PMID: 10623731 PMCID: PMC111589 DOI: 10.1128/jvi.74.2.693-701.2000] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Microglia are the main reservoir for human immunodeficiency virus type 1 (HIV-1) in the central nervous system (CNS), and multinucleated giant cells, the result of fusion of HIV-1-infected microglia and brain macrophages, are the neuropathologic hallmark of HIV dementia. One potential explanation for the formation of syncytia is viral adaptation for these CD4(+) CNS cells. HIV-1(BORI-15), a virus adapted to growth in microglia by sequential passage in vitro, mediates high levels of fusion and replicates more efficiently in microglia and monocyte-derived-macrophages than its unpassaged parent (J. M. Strizki, A. V. Albright, H. Sheng, M. O'Connor, L. Perrin, and F. Gonzalez-Scarano, J. Virol. 70:7654-7662, 1996). Since the interaction between the viral envelope glycoprotein and CD4 and the chemokine receptor mediates fusion and plays a key role in tropism, we have analyzed the HIV-1(BORI-15) env as a fusogen and in recombinant and pseudotyped viruses. Its syncytium-forming phenotype is not the result of a switch in coreceptor use but rather of the HIV-1(BORI-15) envelope-mediated fusion of CD4(+)CCR5(+) cells with greater efficiency than that of its parental strain, either by itself or in the context of a recombinant virus. Genetic analysis indicated that the syncytium-forming phenotype was due to four discrete amino acid differences in V1/V2, with a single-amino-acid change between the parent and the adapted virus (E153G) responsible for the majority of the effect. Additionally, HIV-1(BORI-15) env-pseudotyped viruses were less sensitive to decreases in the levels of CD4 on transfected 293T cells, leading to the hypothesis that the differences in V1/V2 alter the interaction between this envelope and CD4 or CCR5, or both. In sum, the characterization of the envelope of HIV-1(BORI-15), a highly fusogenic glycoprotein with genetic determinants in V1/V2, may lead to a better understanding of the relationship between HIV replication and syncytium formation in the CNS and of the importance of this region of gp120 in the interaction with CD4 and CCR5.
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Affiliation(s)
- J T Shieh
- Department of Neurology, University of Pennsylvania Medical Center, Philadelphia, Pennsylvania, USA
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41
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Albright AV, Shieh JT, Itoh T, Lee B, Pleasure D, O'Connor MJ, Doms RW, González-Scarano F. Microglia express CCR5, CXCR4, and CCR3, but of these, CCR5 is the principal coreceptor for human immunodeficiency virus type 1 dementia isolates. J Virol 1999; 73:205-13. [PMID: 9847323 PMCID: PMC103824 DOI: 10.1128/jvi.73.1.205-213.1999] [Citation(s) in RCA: 224] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microglia are the main human immunodeficiency virus (HIV) reservoir in the central nervous system and most likely play a major role in the development of HIV dementia (HIVD). To characterize human adult microglial chemokine receptors, we analyzed the expression and calcium signaling of CCR5, CCR3, and CXCR4 and their roles in HIV entry. Microglia expressed higher levels of CCR5 than of either CCR3 or CXCR4. Of these three chemokine receptors, only CCR5 and CXCR4 were able to transduce a signal in microglia in response to their respective ligands, MIP-1beta and SDF-1alpha, as recorded by single-cell calcium flux experiments. We also found that CCR5 is the predominant coreceptor used for infection of human adult microglia by the HIV type 1 dementia isolates HIV-1DS-br, HIV-1RC-br, and HIV-1YU-2, since the anti-CCR5 antibody 2D7 was able to dramatically inhibit microglial infection by both wild-type and single-round luciferase pseudotype reporter viruses. Anti-CCR3 (7B11) and anti-CXCR4 (12G5) antibodies had little or no effect on infection. Last, we found that virus pseudotyped with the DS-br and RC-br envelopes can infect cells transfected with CD4 in conjunction with the G-protein-coupled receptors APJ, CCR8, and GPR15, which have been previously implicated in HIV entry.
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Affiliation(s)
- A V Albright
- Departments of Neurology and Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
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42
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Shieh JT, Albright AV, Sharron M, Gartner S, Strizki J, Doms RW, González-Scarano F. Chemokine receptor utilization by human immunodeficiency virus type 1 isolates that replicate in microglia. J Virol 1998; 72:4243-9. [PMID: 9557714 PMCID: PMC109654 DOI: 10.1128/jvi.72.5.4243-4249.1998] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The role of human immunodeficiency virus (HIV) strain variability remains a key unanswered question in HIV dementia, a condition affecting around 20% of infected individuals. Several groups have shown that viruses within the central nervous system (CNS) of infected patients constitute an independently evolving subset of HIV strains. A potential explanation for the replication and sequestration of viruses within the CNS is the preferential use of certain chemokine receptors present in microglia. To determine the role of specific chemokine coreceptors in infection of adult microglial cells, we obtained a small panel of HIV type 1 brain isolates, as well as other HIV strains that replicate well in cultured microglial cells. These viruses and molecular clones of their envelopes were used in infections, in cell-to-cell fusion assays, and in the construction of pseudotypes. The results demonstrate the predominant use of CCR5, at least among the major coreceptors, with minor use of CCR3 and CXCR4 by some of the isolates or their envelope clones.
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MESH Headings
- Adult
- Brain/pathology
- Brain/virology
- Cells, Cultured
- Cytopathogenic Effect, Viral
- HIV-1/metabolism
- HIV-1/pathogenicity
- HIV-1/physiology
- Humans
- Membrane Fusion
- Microglia/metabolism
- Microglia/virology
- Receptors, CCR3
- Receptors, CCR5/immunology
- Receptors, CCR5/metabolism
- Receptors, CXCR4/immunology
- Receptors, CXCR4/metabolism
- Receptors, Chemokine/immunology
- Receptors, Chemokine/metabolism
- Transfection
- Tumor Cells, Cultured
- Virus Replication
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Affiliation(s)
- J T Shieh
- Department of Neurology, University of Pennsylvania Medical Center, Philadelphia 19104-6146, USA
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43
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Liu MA, Friedman A, Oliff AI, Tai J, Martinez D, Deck RR, Shieh JT, Jenkins TD, Donnelly JJ, Hawe LA. A vaccine carrier derived from Neisseria meningitidis with mitogenic activity for lymphocytes. Proc Natl Acad Sci U S A 1992; 89:4633-7. [PMID: 1533934 PMCID: PMC49137 DOI: 10.1073/pnas.89.10.4633] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Protein carriers vary in their ability to increase the immunogenicity of poorly immunogenic or T-lymphocyte-independent antigens. We examined one such carrier, the outer membrane protein complex derived from Neisseria meningitidis serogroup B strain B11, in an attempt to determine why this outer membrane protein complex was more immunogenic in young infants and in relevant animal models than two other carriers used in conjugates made with Haemophilus influenzae type b polysaccharide, a T-cell-independent antigen. A single protein of the outer membrane protein complex, the class 2 porin protein, was purified and shown to function as a T-helper lymphocyte carrier protein. Unexpectedly, it was also found to have mitogenic activity for lymphocytes that was not due to lipopolysaccharide. This mitogenic activity appears to date to be unique to this carrier protein of the carrier proteins tested and may contribute to the ability of the H. influenzae type b conjugate vaccine made with the outer membrane protein complex to generate IgG anti-polysaccharide antibody responses in mice and infant monkeys and protective immune responses in infants less than 6 months of age.
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Affiliation(s)
- M A Liu
- Department of Cancer Research, Merck Research Laboratories, West Point, PA 19486
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