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Shepherdson JL, Hutchison K, Don DW, McGillivray G, Choi TI, Allan CA, Amor DJ, Banka S, Basel DG, Buch LD, Carere DA, Carroll R, Clayton-Smith J, Crawford A, Dunø M, Faivre L, Gilfillan CP, Gold NB, Gripp KW, Hobson E, Holtz AM, Innes AM, Isidor B, Jackson A, Katsonis P, Amel Riazat Kesh L, Küry S, Lecoquierre F, Lockhart P, Maraval J, Matsumoto N, McCarrier J, McCarthy J, Miyake N, Moey LH, Németh AH, Østergaard E, Patel R, Pope K, Posey JE, Schnur RE, Shaw M, Stolerman E, Taylor JP, Wadman E, Wakeling E, White SM, Wong LC, Lupski JR, Lichtarge O, Corbett MA, Gecz J, Nicolet CM, Farnham PJ, Kim CH, Shinawi M. Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt. Am J Hum Genet 2024; 111:487-508. [PMID: 38325380 PMCID: PMC10940019 DOI: 10.1016/j.ajhg.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
Pathogenic variants in multiple genes on the X chromosome have been implicated in syndromic and non-syndromic intellectual disability disorders. ZFX on Xp22.11 encodes a transcription factor that has been linked to diverse processes including oncogenesis and development, but germline variants have not been characterized in association with disease. Here, we present clinical and molecular characterization of 18 individuals with germline ZFX variants. Exome or genome sequencing revealed 11 variants in 18 subjects (14 males and 4 females) from 16 unrelated families. Four missense variants were identified in 11 subjects, with seven truncation variants in the remaining individuals. Clinical findings included developmental delay/intellectual disability, behavioral abnormalities, hypotonia, and congenital anomalies. Overlapping and recurrent facial features were identified in all subjects, including thickening and medial broadening of eyebrows, variations in the shape of the face, external eye abnormalities, smooth and/or long philtrum, and ear abnormalities. Hyperparathyroidism was found in four families with missense variants, and enrichment of different tumor types was observed. In molecular studies, DNA-binding domain variants elicited differential expression of a small set of target genes relative to wild-type ZFX in cultured cells, suggesting a gain or loss of transcriptional activity. Additionally, a zebrafish model of ZFX loss displayed an altered behavioral phenotype, providing additional evidence for the functional significance of ZFX. Our clinical and experimental data support that variants in ZFX are associated with an X-linked intellectual disability syndrome characterized by a recurrent facial gestalt, neurocognitive and behavioral abnormalities, and an increased risk for congenital anomalies and hyperparathyroidism.
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Affiliation(s)
- James L Shepherdson
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA
| | - Katie Hutchison
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - George McGillivray
- Victorian Clinical Genetics Services, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, Daejeon 34134, Korea
| | - Carolyn A Allan
- Hudson Institute of Medical Research, Monash University, and Department of Endocrinology, Monash Health, Melbourne, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, VIC, Australia
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Donald G Basel
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | | | - Renée Carroll
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ali Crawford
- Medical Genomics Research, Illumina Inc, San Diego, CA, USA
| | - Morten Dunø
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Laurence Faivre
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, Dijon, France; INSERM UMR1231, Equipe GAD, Université de Bourgogne-Franche Comté, 21000 Dijon, France
| | - Christopher P Gilfillan
- Eastern Health Clinical School, Monash University, Melbourne, VIC, Australia; Department of Endocrinology, Eastern Health, Box Hill Hospital, Melbourne, VIC, Australia
| | - Nina B Gold
- Harvard Medical School, Boston, MA, USA; Division of Medical Genetics and Metabolism, Massachusetts General Hospital, Boston, MA, USA
| | - Karen W Gripp
- Division of Medical Genetics, Nemours Children's Hospital, Wilmington, DE, USA
| | - Emma Hobson
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Department of Clinical Genetics, Chapel Allerton Hospital, Leeds, UK
| | - Alexander M Holtz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - A Micheil Innes
- Departments of Medical Genetics and Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, 44000 Nantes, France
| | - Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Leila Amel Riazat Kesh
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Department of Clinical Genetics, Chapel Allerton Hospital, Leeds, UK
| | - Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, 44000 Nantes, France
| | - François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Paul Lockhart
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, VIC, Australia
| | - Julien Maraval
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, Dijon, France; INSERM UMR1231, Equipe GAD, Université de Bourgogne-Franche Comté, 21000 Dijon, France
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Julie McCarrier
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Josephine McCarthy
- Department of Endocrinology, Eastern Health, Box Hill Hospital, Melbourne, VIC, Australia
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Lip Hen Moey
- Department of Genetics, Penang General Hospital, George Town, Penang, Malaysia
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rushina Patel
- Medical Genetics, Kaiser Permanente Oakland Medical Center, Oakland, CA, USA
| | - Kate Pope
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Julie P Taylor
- Medical Genomics Research, Illumina Inc, San Diego, CA, USA
| | - Erin Wadman
- Division of Medical Genetics, Nemours Children's Hospital, Wilmington, DE, USA
| | - Emma Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Susan M White
- Victorian Clinical Genetics Services, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, VIC, Australia
| | - Lawrence C Wong
- Medical Genetics, Kaiser Permanente Downey Medical Center, Downey, CA, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Charles M Nicolet
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Korea.
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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Omelková M, Fenger CD, Murray M, Hammer TB, Pravata VM, Bartual SG, Czajewski I, Bayat A, Ferenbach AT, Stavridis MP, van Aalten DMF. An O-GlcNAc transferase pathogenic variant linked to intellectual disability affects pluripotent stem cell self-renewal. Dis Model Mech 2023; 16:dmm049132. [PMID: 37334838 DOI: 10.1242/dmm.049132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 04/19/2023] [Indexed: 06/21/2023] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is an essential enzyme that modifies proteins with O-GlcNAc. Inborn OGT genetic variants were recently shown to mediate a novel type of congenital disorder of glycosylation (OGT-CDG), which is characterised by X-linked intellectual disability (XLID) and developmental delay. Here, we report an OGTC921Y variant that co-segregates with XLID and epileptic seizures, and results in loss of catalytic activity. Colonies formed by mouse embryonic stem cells carrying OGTC921Y showed decreased levels of protein O-GlcNAcylation accompanied by decreased levels of Oct4 (encoded by Pou5f1), Sox2 and extracellular alkaline phosphatase (ALP), implying reduced self-renewal capacity. These data establish a link between OGT-CDG and embryonic stem cell self-renewal, providing a foundation for examining the developmental aetiology of this syndrome.
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Affiliation(s)
- Michaela Omelková
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Christina Dühring Fenger
- Department of Epilepsy Genetics, Filadelfia Danish Epilepsy Centre, Dianalund 4293, Denmark
- Amplexa Genetics A/S, Odense 5000, Denmark
| | - Marta Murray
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Trine Bjørg Hammer
- Department of Epilepsy Genetics, Filadelfia Danish Epilepsy Centre, Dianalund 4293, Denmark
| | - Veronica M Pravata
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Sergio Galan Bartual
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - Ignacy Czajewski
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Allan Bayat
- Department of Epilepsy Genetics, Filadelfia Danish Epilepsy Centre, Dianalund 4293, Denmark
| | - Andrew T Ferenbach
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - Marios P Stavridis
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Daan M F van Aalten
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
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Du M, Wu S, Su C, Wang X, Li B, Lin Y, Yuan S, Chen Y, Zhu C, Wei H. Serum Vitamin B12 is a Promising Auxiliary Index for the Diagnosis of Methylmalonic Acidemia in Children: A Single Center Study in China. Clin Chim Acta 2023; 546:117409. [PMID: 37217112 DOI: 10.1016/j.cca.2023.117409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Vitamin B12 (cobalamin, VitB12) is an essential coenzyme of methylmalonyl-CoA mutase and methionine synthase. Variations in VitB12 metabolism, absorption, transport, or intake may cause changes in methylmalonic acidemia (MMA) biomarkers. We aimed to investigate whether serum Vitamin B12 levels could be used in the early detection of MMA. MATERIALS AND METHODS We included 241 children with MMA and 241 healthy matched controls. We measured serum VitB12 levels by an enzyme immunoassay and investigated the relationship between abnormal VitB12 levels and hematologic parameters as potential risk factors for MMA symptoms. RESULTS Compared with controls, the serum levels of VitB12 were increased in the MMA group (p < 0.001). Serum VitB12 distinguished patients with MMA from healthy children (p < 0.001). Serum VitB12 combined with homocysteine and ammonia identified cblC and mut type MMA, respectively (p < 0.001). Homocysteine, folate, ammonia, NLR, and red blood cells contributed to serum VitB12 in cblC type MMA (p < 0.001); homocysteine, ammonia, and red blood cells, contributed in mut type MMA (p < 0.001); and elevated VitB12 was an independent predictor of MMA clinical onset (p < 0.001). CONCLUSION Serum VitB12 can be used as an early diagnostic biomarker for MMA in children.
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Affiliation(s)
- Mengmeng Du
- Children's Hospital Affiliated to Zhengzhou University, Department of Endocrinology, Genetics and Metabolism, Henan Children's Hospital, Zhengz- hou Children's Hospital, Zhengzhou, China; Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience, Zhengzhou University, Zhengzhou, China.
| | - Shengnan Wu
- Children's Hospital Affiliated to Zhengzhou University, Department of Endocrinology, Genetics and Metabolism, Henan Children's Hospital, Zhengz- hou Children's Hospital, Zhengzhou, China.
| | - Chang Su
- Department of Endocrinology, Genetic and Metabolism, Beijing Children's Hospital, Capital Medical University, Beijing, China.
| | - Xiaohong Wang
- Children's Hospital Affiliated to Zhengzhou University, Department of Endocrinology, Genetics and Metabolism, Henan Children's Hospital, Zhengz- hou Children's Hospital, Zhengzhou, China.
| | - Bingbing Li
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience, Zhengzhou University, Zhengzhou, China.
| | - Yifan Lin
- Children's Hospital Affiliated to Zhengzhou University, Department of Endocrinology, Genetics and Metabolism, Henan Children's Hospital, Zhengz- hou Children's Hospital, Zhengzhou, China.
| | - Shuxian Yuan
- Children's Hospital Affiliated to Zhengzhou University, Department of Endocrinology, Genetics and Metabolism, Henan Children's Hospital, Zhengz- hou Children's Hospital, Zhengzhou, China.
| | - Yongxing Chen
- Children's Hospital Affiliated to Zhengzhou University, Department of Endocrinology, Genetics and Metabolism, Henan Children's Hospital, Zhengz- hou Children's Hospital, Zhengzhou, China.
| | - Changlian Zhu
- Children's Hospital Affiliated to Zhengzhou University, Department of Endocrinology, Genetics and Metabolism, Henan Children's Hospital, Zhengz- hou Children's Hospital, Zhengzhou, China; Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Sweden.
| | - Haiyan Wei
- Children's Hospital Affiliated to Zhengzhou University, Department of Endocrinology, Genetics and Metabolism, Henan Children's Hospital, Zhengz- hou Children's Hospital, Zhengzhou, China.
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Wang F, Liang L, Ling S, Yu Y, Chen T, Xu F, Gong Z, Han L. Clinical characteristics and genotype analysis of five infants with cblX type of methylmalonic acidemia. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:298-305. [PMID: 36207831 PMCID: PMC9511482 DOI: 10.3724/zdxbyxb-2022-0194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/30/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE To investigate the clinical and genetic characteristics of infants with cobalamin (cbl) X type of methylmalonic acidemia (MMA). METHODS The clinical data of 5 infants with cblX type of MMA diagnosed in Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine and Shanghai Children's Hospital from the year 2016 to 2020 were collected. The levels of blood acylcarnitines were detected by tandem mass spectrometry, the levels of urinary organic acids were detected by gas-chromatography mass spectrometry, the pathogenic genes were detected by whole exon gene sequencing, and the effect of new pathogenic mutations on three-dimensional protein structure was predicted by bioinformatics analysis. RESULTS Five infants with cblX type were diagnosed, including 4 males and 1 female, and the onset age was 0-6 months. The main clinical manifestations of 4 males were intractable epilepsy, mental and motor retardation, metabolic abnormalities presented mild increase of blood homocysteine level. Among them, 3 cases were accompanied by slight increase of urinary methylmalonic acid, and 1 case was accompanied by increase of blood propionylcarnitine (C3) and C3/acetylcarnitine (C2). Gene detection found that 2 cases carried a same hemizygous mutation c.344C>T (p.A115V) of HCFC1 gene, which was the most reported mutation, and the other 2 cases carried novel pathogenic mutations, c.92G>A (p.R31Q) and c.166G>C (p.V56L). These 3 gene mutations located in the Kelch domain of HCFC1 protein. One female infant carried a benign mutation of c.3731G>T (p.R1244L). Her clinical symptoms were mild, and only the urinary methylmalonic acid was slightly increased. CONCLUSIONS The clinical manifestations of children with cblX type of MMA are intractable epilepsy, mental and motor retardation, and other serious neurological symptoms. Their metabolic abnormalities present the increase of blood homocysteine with methylmalonic acid (urinary methylmalonic acid or/and blood C3, C3/C2). The clinical and biochemical phenotypes are separated, so the diagnosis should be in combination with the results of gene testing.
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Affiliation(s)
- Fei Wang
- 1. Department of Endocrinology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Lili Liang
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Shiying Ling
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Yue Yu
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Ting Chen
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Feng Xu
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Zhuwen Gong
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Lianshu Han
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
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