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Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N. Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality. Cell Rep 2024; 43:113907. [PMID: 38461417 PMCID: PMC11005513 DOI: 10.1016/j.celrep.2024.113907] [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: 05/10/2023] [Revised: 12/29/2023] [Accepted: 02/19/2024] [Indexed: 03/12/2024] Open
Abstract
Adolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is sexually dimorphic, with increased incidence in females. A genome-wide association study identified a female-specific AIS susceptibility locus near the PAX1 gene. Here, we use mouse enhancer assays, three mouse enhancer knockouts, and subsequent phenotypic analyses to characterize this region. Using mouse enhancer assays, we characterize a sequence, PEC7, which overlaps the AIS-associated variant, and find it to be active in the tail tip and intervertebral disc. Removal of PEC7 or Xe1, a known sclerotome enhancer nearby, or deletion of both sequences lead to a kinky tail phenotype only in the Xe1 and combined (Xe1+PEC7) knockouts, with only the latter showing a female sex dimorphic phenotype. Extensive phenotypic characterization of these mouse lines implicates several differentially expressed genes and estrogen signaling in the sex dimorphic bias. In summary, our work functionally characterizes an AIS-associated locus and dissects the mechanism for its sexual dimorphism.
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Affiliation(s)
- Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rory R Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mai Nobuhara
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Murray
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Xin Ruan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jonathan J Rios
- Center for Translational Research, Scottish Rite for Children, Dallas, TX 75390, USA; Department of Orthopedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carol A Wise
- Center for Translational Research, Scottish Rite for Children, Dallas, TX 75390, USA; Department of Orthopedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA.
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Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng RR, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, Gurnett CA, Gerdhem P, Ikegawa S, Rios JJ, Ahituv N, Wise CA. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis. eLife 2024; 12:RP89762. [PMID: 38277211 PMCID: PMC10945706 DOI: 10.7554/elife.89762] [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] [Indexed: 01/27/2024] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is a common and progressive spinal deformity in children that exhibits striking sexual dimorphism, with girls at more than fivefold greater risk of severe disease compared to boys. Despite its medical impact, the molecular mechanisms that drive AIS are largely unknown. We previously defined a female-specific AIS genetic risk locus in an enhancer near the PAX1 gene. Here, we sought to define the roles of PAX1 and newly identified AIS-associated genes in the developmental mechanism of AIS. In a genetic study of 10,519 individuals with AIS and 93,238 unaffected controls, significant association was identified with a variant in COL11A1 encoding collagen (α1) XI (rs3753841; NM_080629.2_c.4004C>T; p.(Pro1335Leu); p=7.07E-11, OR = 1.118). Using CRISPR mutagenesis we generated Pax1 knockout mice (Pax1-/-). In postnatal spines we found that PAX1 and collagen (α1) XI protein both localize within the intervertebral disc-vertebral junction region encompassing the growth plate, with less collagen (α1) XI detected in Pax1-/- spines compared to wild-type. By genetic targeting we found that wild-type Col11a1 expression in costal chondrocytes suppresses expression of Pax1 and of Mmp3, encoding the matrix metalloproteinase 3 enzyme implicated in matrix remodeling. However, the latter suppression was abrogated in the presence of the AIS-associated COL11A1P1335L mutant. Further, we found that either knockdown of the estrogen receptor gene Esr2 or tamoxifen treatment significantly altered Col11a1 and Mmp3 expression in chondrocytes. We propose a new molecular model of AIS pathogenesis wherein genetic variation and estrogen signaling increase disease susceptibility by altering a PAX1-COL11a1-MMP3 signaling axis in spinal chondrocytes.
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Affiliation(s)
- Hao Yu
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
| | - Anas M Khanshour
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
| | - Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California, San FranciscoSan FranciscoUnited States
| | - Nao Otomo
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical SciencesTokyoJapan
| | - Yoshinao Koike
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical SciencesTokyoJapan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Elisabet Einarsdottir
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of TechnologySolnaSweden
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong KongHong Kong SARChina
| | - Lilian Antunes
- Department of Neurology, Washington University in St. LouisSt. LouisUnited States
| | - Yared H Kidane
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
| | - Reuel Cornelia
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
| | - Rory R Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California, San FranciscoSan FranciscoUnited States
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California, San FranciscoSan FranciscoUnited States
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Jimin Pei
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Bret M Evers
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Ophthalmology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jason Pui Yin Cheung
- Department of Orthopaedics and Traumatology LKS Faculty of Medicine, The University of Hong KongHong Kong SARChina
| | - John A Herring
- Department of Orthopedic Surgery, Scottish Rite for ChildrenDallasUnited States
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical CenterDallasUnited States
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - You-qiang Song
- School of Biomedical Sciences, The University of Hong KongHong Kong SARChina
| | - Christina A Gurnett
- Department of Neurology, Washington University in St. LouisSt. LouisUnited States
| | - Paul Gerdhem
- Department of Surgical Sciences, Uppsala UniversityUppsalaSweden
- Department of Orthopaedics and Hand Surgery, Uppsala University HospitalUppsalaSweden
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, Stockholm, Uppsala UniversityUppsalaSweden
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical SciencesTokyoJapan
| | - Jonathan J Rios
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical CenterDallasUnited States
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California, San FranciscoSan FranciscoUnited States
| | - Carol A Wise
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical CenterDallasUnited States
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
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3
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Wang X, Yue M, Cheung JPY, Cheung PWH, Fan Y, Wu M, Wang X, Zhao S, Khanshour AM, Rios JJ, Chen Z, Wang X, Tu W, Chan D, Yuan Q, Qin D, Qiu G, Wu Z, Zhang TJ, Ikegawa S, Wu N, Wise CA, Hu Y, Luk KDK, Song YQ, Gao B. Impaired glycine neurotransmission causes adolescent idiopathic scoliosis. J Clin Invest 2024; 134:e168783. [PMID: 37962965 PMCID: PMC10786698 DOI: 10.1172/jci168783] [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: 01/12/2023] [Accepted: 11/08/2023] [Indexed: 11/16/2023] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common form of spinal deformity, affecting millions of adolescents worldwide, but it lacks a defined theory of etiopathogenesis. Because of this, treatment of AIS is limited to bracing and/or invasive surgery after onset. Preonset diagnosis or preventive treatment remains unavailable. Here, we performed a genetic analysis of a large multicenter AIS cohort and identified disease-causing and predisposing variants of SLC6A9 in multigeneration families, trios, and sporadic patients. Variants of SLC6A9, which encodes glycine transporter 1 (GLYT1), reduced glycine-uptake activity in cells, leading to increased extracellular glycine levels and aberrant glycinergic neurotransmission. Slc6a9 mutant zebrafish exhibited discoordination of spinal neural activities and pronounced lateral spinal curvature, a phenotype resembling human patients. The penetrance and severity of curvature were sensitive to the dosage of functional glyt1. Administration of a glycine receptor antagonist or a clinically used glycine neutralizer (sodium benzoate) partially rescued the phenotype. Our results indicate a neuropathic origin for "idiopathic" scoliosis, involving the dysfunction of synaptic neurotransmission and central pattern generators (CPGs), potentially a common cause of AIS. Our work further suggests avenues for early diagnosis and intervention of AIS in preadolescents.
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Affiliation(s)
- Xiaolu Wang
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
- School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Shatin, Hong Kong, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Ming Yue
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Jason Pui Yin Cheung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Orthopaedics and Traumatology, University of Hong Kong–Shenzhen Hospital, Shenzhen, China
| | - Prudence Wing Hang Cheung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yanhui Fan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Meicheng Wu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xiaojun Wang
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Sen Zhao
- Department of Orthopaedic Surgery, Department of Medical Research Center, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital (PUMCH) and Chinese Academy of Medical Sciences, Beijing, China
| | - Anas M. Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children (SRC), Dallas, Texas, USA
| | - Jonathan J. Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children (SRC), Dallas, Texas, USA
- Eugene McDermott Center for Human Growth and Development, Departments of Orthopaedic Surgery and Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zheyi Chen
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xiwei Wang
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Wenwei Tu
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Danny Chan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Qiuju Yuan
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Tai Po, Hong Kong, China
| | - Dajiang Qin
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Tai Po, Hong Kong, China
| | - Guixing Qiu
- Department of Orthopaedic Surgery, Department of Medical Research Center, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital (PUMCH) and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Department of Orthopaedic Surgery, Department of Medical Research Center, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital (PUMCH) and Chinese Academy of Medical Sciences, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopaedic Surgery, Department of Medical Research Center, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital (PUMCH) and Chinese Academy of Medical Sciences, Beijing, China
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Nan Wu
- Department of Orthopaedic Surgery, Department of Medical Research Center, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital (PUMCH) and Chinese Academy of Medical Sciences, Beijing, China
| | - Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children (SRC), Dallas, Texas, USA
- Eugene McDermott Center for Human Growth and Development, Departments of Orthopaedic Surgery and Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yong Hu
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Orthopaedics and Traumatology, University of Hong Kong–Shenzhen Hospital, Shenzhen, China
| | - Keith Dip Kei Luk
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - You-Qiang Song
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Medicine, University of Hong Kong–Shenzhen Hospital, Shenzhen, China
- State Key Laboratory of Brain and Cognitive Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Bo Gao
- School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Shatin, Hong Kong, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Orthopaedics and Traumatology, University of Hong Kong–Shenzhen Hospital, Shenzhen, China
- Centre for Translational Stem Cell Biology, Tai Po, Hong Kong, China
- Key Laboratory of Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Shatin, Hong Kong, China
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4
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Rios JJ, Li Y, Paria N, Bohlender RJ, Huff C, Rosenfeld JA, Liu P, Bi W, Haga K, Fukuda M, Vashisth S, Kaur K, Chahrour MH, Bober MB, Duker AL, Ladha FA, Hanchard NA, Atala K, Khanshour AM, Smith L, Wise CA, Delgado MR. RAB1A haploinsufficiency phenocopies the 2p14-p15 microdeletion and is associated with impaired neuronal differentiation. Am J Hum Genet 2023; 110:2103-2111. [PMID: 37924809 PMCID: PMC10722380 DOI: 10.1016/j.ajhg.2023.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/03/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/06/2023] Open
Abstract
Hereditary spastic parapareses (HSPs) are clinically heterogeneous motor neuron diseases with variable age of onset and severity. Although variants in dozens of genes are implicated in HSPs, much of the genetic basis for pediatric-onset HSP remains unexplained. Here, we re-analyzed clinical exome-sequencing data from siblings with HSP of unknown genetic etiology and identified an inherited nonsense mutation (c.523C>T [p.Arg175Ter]) in the highly conserved RAB1A. The mutation is predicted to produce a truncated protein with an intact RAB GTPase domain but without two C-terminal cysteine residues required for proper subcellular protein localization. Additional RAB1A mutations, including two frameshift mutations and a mosaic missense mutation (c.83T>C [p.Leu28Pro]), were identified in three individuals with similar neurodevelopmental presentations. In rescue experiments, production of the full-length, but not the truncated, RAB1a rescued Golgi structure and cell proliferation in Rab1-depleted cells. In contrast, the missense-variant RAB1a disrupted Golgi structure despite intact Rab1 expression, suggesting a dominant-negative function of the mosaic missense mutation. Knock-down of RAB1A in cultured human embryonic stem cell-derived neurons resulted in impaired neuronal arborization. Finally, RAB1A is located within the 2p14-p15 microdeletion syndrome locus. The similar clinical presentations of individuals with RAB1A loss-of-function mutations and the 2p14-p15 microdeletion syndrome implicate loss of RAB1A in the pathogenesis of neurodevelopmental manifestations of this microdeletion syndrome. Our study identifies a RAB1A-related neurocognitive disorder with speech and motor delay, demonstrates an essential role for RAB1a in neuronal differentiation, and implicates RAB1A in the etiology of the neurodevelopmental sequelae associated with the 2p14-p15 microdeletion syndrome.
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Affiliation(s)
- Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Departments of Pediatrics University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Yang Li
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Nandina Paria
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Ryan J Bohlender
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chad Huff
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Pengfei Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Weimin Bi
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Kentaro Haga
- Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Mitsunori Fukuda
- Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shayal Vashisth
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kiran Kaur
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria H Chahrour
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Peter O'Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael B Bober
- Nemours Children's Hospital, Wilmington, DE 19803, USA; Thomas Jefferson University, Philadelphia, PA 19144, USA
| | | | - Farah A Ladha
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil A Hanchard
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kristhen Atala
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Linsley Smith
- Department of Neurology, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Departments of Pediatrics University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mauricio R Delgado
- Department of Neurology, Scottish Rite for Children, Dallas, TX 75219, USA; Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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5
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Ghanbari F, Otomo N, Gamache I, Iwami T, Koike Y, Khanshour AM, Ikegawa S, Wise CA, Terao C, Manousaki D. Interrogating Causal Effects of Body Composition and Puberty-Related Risk Factors on Adolescent Idiopathic Scoliosis: A Two-Sample Mendelian Randomization Study. JBMR Plus 2023; 7:e10830. [PMID: 38130750 PMCID: PMC10731118 DOI: 10.1002/jbm4.10830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 12/23/2023] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common form of pediatric musculoskeletal disorder. Observational studies have pointed to several risk factors for AIS, but almost no evidence exists to support their causal association with AIS. Here, we applied Mendelian randomization (MR), known to limit bias from confounding and reverse causation, to investigate causal associations between body composition and puberty-related exposures and AIS risk in Europeans and Asians. For our two-sample MR studies, we used single nucleotide polymorphisms (SNPs) associated with body mass index (BMI), waist-hip ratio, lean mass, childhood obesity, bone mineral density (BMD), 25-hydroxyvitamin D (25OHD), age at menarche, and pubertal growth in large European genome-wide association studies (GWAS), and with adult osteoporosis risk and age of menarche in Biobank Japan. We extracted estimates of the aforementioned SNPs on AIS risk from the European or Asian subsets of the largest multiancestry AIS GWAS (N = 7956 cases/88,459 controls). The results of our inverse variance-weighted (IVW) MR estimates suggest no causal association between the aforementioned risk factors and risk of AIS. Pleiotropy-sensitive MR methods yielded similar results. However, restricting our analysis to European females with AIS, we observed a causal association between estimated BMD and the risk of AIS (IVW odds ratio for AIS = 0.1, 95% confidence interval 0.01 to 0.7, p = 0.02 per SD increase in estimated BMD), but this association was no longer significant after adjusting for BMI, body fat mass, and 25OHD and remained significant after adjusting for age at menarche in multivariable MR. In conclusion, we demonstrated a protective causal effect of BMD on AIS risk in females of European ancestry, but this effect was modified by BMI, body fat mass, and 25OHD levels. Future MR studies using larger AIS GWAS are needed to investigate small effects of the aforementioned exposures on AIS. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Faegheh Ghanbari
- Research Center of the Sainte‐Justine University HospitalUniversity of MontrealMontrealQuebecCanada
| | - Nao Otomo
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical Sciences, RIKENYokohamaJapan
- Department of Orthopedic SurgeryKeio University School of MedicineTokyoJapan
| | - Isabel Gamache
- Research Center of the Sainte‐Justine University HospitalUniversity of MontrealMontrealQuebecCanada
| | - Takuro Iwami
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical Sciences, RIKENYokohamaJapan
- Department of Orthopedic SurgeryKeio University School of MedicineTokyoJapan
| | - Yoshinao Koike
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical Sciences, RIKENYokohamaJapan
- Department of Orthopedic SurgeryHokkaido University Graduate School of MedicineSapporoJapan
| | - Anas M. Khanshour
- Scottish Rite for Children Center for Pediatric Bone Biology and Translational ResearchDallasTexasUSA
| | - Shiro Ikegawa
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical Sciences, RIKENYokohamaJapan
| | - Carol A. Wise
- Scottish Rite for Children Center for Pediatric Bone Biology and Translational ResearchDallasTexasUSA
- McDermott Center for Human Growth & DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Chikashi Terao
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical Sciences, RIKENYokohamaJapan
| | - Despoina Manousaki
- Research Center of the Sainte‐Justine University HospitalUniversity of MontrealMontrealQuebecCanada
- Department of PediatricsUniversity of MontrealMontrealCanada
- Department of Biochemistry and Molecular MedicineUniversity of MontrealMontrealQuebecCanada
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6
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Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng R, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, Gurnett CA, Gerdhem P, Ikegawa S, Rios JJ, Ahituv N, Wise CA. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis. bioRxiv 2023:2023.05.26.542293. [PMID: 37292598 PMCID: PMC10245954 DOI: 10.1101/2023.05.26.542293] [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: 06/10/2023]
Abstract
Adolescent idiopathic scoliosis (AIS) is a common and progressive spinal deformity in children that exhibits striking sexual dimorphism, with girls at more than five-fold greater risk of severe disease compared to boys. Despite its medical impact, the molecular mechanisms that drive AIS are largely unknown. We previously defined a female-specific AIS genetic risk locus in an enhancer near the PAX1 gene. Here we sought to define the roles of PAX1 and newly-identified AIS-associated genes in the developmental mechanism of AIS. In a genetic study of 10,519 individuals with AIS and 93,238 unaffected controls, significant association was identified with a variant in COL11A1 encoding collagen (α1) XI (rs3753841; NM_080629.2_c.4004C>T; p.(Pro1335Leu); P=7.07e-11, OR=1.118). Using CRISPR mutagenesis we generated Pax1 knockout mice (Pax1-/-). In postnatal spines we found that PAX1 and collagen (α1) XI protein both localize within the intervertebral disc (IVD)-vertebral junction region encompassing the growth plate, with less collagen (α1) XI detected in Pax1-/- spines compared to wildtype. By genetic targeting we found that wildtype Col11a1 expression in costal chondrocytes suppresses expression of Pax1 and of Mmp3, encoding the matrix metalloproteinase 3 enzyme implicated in matrix remodeling. However, this suppression was abrogated in the presence of the AIS-associated COL11A1P1335L mutant. Further, we found that either knockdown of the estrogen receptor gene Esr2, or tamoxifen treatment, significantly altered Col11a1 and Mmp3 expression in chondrocytes. We propose a new molecular model of AIS pathogenesis wherein genetic variation and estrogen signaling increase disease susceptibility by altering a Pax1-Col11a1-Mmp3 signaling axis in spinal chondrocytes.
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Affiliation(s)
- Hao Yu
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Nao Otomo
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, JP
| | - Yoshinao Koike
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, JP
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, JP
| | - Elisabet Einarsdottir
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, SE
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, CN
| | - Lilian Antunes
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Reuel Cornelia
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Rory Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, CN
| | - Jimin Pei
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bret M Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jason Pui Yin Cheung
- Department of Orthopaedics and Traumatology LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, CN
| | - John A Herring
- Department of Orthopedic Surgery, Scottish Rite for Children, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, JP
| | - You-Qiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, CN
| | - Christina A Gurnett
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Paul Gerdhem
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, Stockholm, Uppsala University, Uppsala, SE
- Department of Surgical Sciences, Uppsala University and
- Department of Orthopaedics and Hand Surgery, Uppsala University Hospital, Uppsala, SE
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, JP
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Moore HG, Patibandla SD, McClung AM, Grauer JN, Sucato DJ, Wise CA, Johnson ME, Rathjen KE, McIntosh AL, Ramo BA, Brooks JT. Do Children With Medicaid Insurance Have Increased Revision Rates 5 Years After Posterior Spinal Fusions? J Pediatr Orthop 2023; 43:615-619. [PMID: 37694695 DOI: 10.1097/bpo.0000000000002504] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
BACKGROUND Socioeconomic disparities in musculoskeletal care are increasingly recognized, however, no studies to date have investigated the role of the insurance carrier on outcomes after posterior spinal fusion (PSF) with segmental spinal instrumentation for adolescent idiopathic scoliosis (AIS). METHODS A US insurance dataset was queried using the PearlDiver Mariner software for all patients aged 10 to 18 undergoing PSF for a primary diagnosis of AIS between 2010 and 2020. Age, sex, geographic region, number of levels fused, and baseline medical comorbidities were queried. Complications occurring within 90 days of the index surgery were queried using the International Classification of Diseases, Ninth Revision (ICD-9) and International Classification of Diseases, 10th Revision (ICD-10) codes. Revision surgery was also queried up to 5 years after the index PSF. Categorical variables were compared using the Fisher χ 2 tests and continuous variables were compared using independent t tests. All-cause revision within 5 years was compared using the Kaplan-Meier analysis and a log-rank test. Significance was set at P -value <0.05. RESULTS A total of 10,794 patients were identified with 9006 (83.4%) patients with private insurance and 1788 (16.6%) patients insured by Medicaid. The mean follow-up in the database was 5.36±3 years for patients with private insurance and 4.78±2.9 years for patients with Medicaid insurance ( P <0.001). Children with AIS and Medicaid insurance had a significantly higher prevalence of asthma, hypertension, and obesity. A larger percentage of children with Medicaid insurance (41.3%) underwent a ≥13-level PSF compared with privately insured children (34.5%) ( P <0.001). Medicaid patients did not experience higher odds of postoperative complications; in addition, revision surgeries occurred in 1.1% and 1.8% of patients with private insurance and Medicaid insurance, respectively at 5 years postoperatively ( P =0.223). CONCLUSION Despite worse baseline comorbidities and longer fusion constructs, AIS patients insured with Medicaid did not have higher rates of complications or revisions at 5-year follow-up versus privately insured patients. LEVEL OF EVIDENCE Level III-retrospective cohort study.
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Jolly A, Du H, Borel C, Chen N, Zhao S, Grochowski CM, Duan R, Fatih JM, Dawood M, Salvi S, Jhangiani SN, Muzny DM, Koch A, Rouskas K, Glentis S, Deligeoroglou E, Bacopoulou F, Wise CA, Dietrich JE, Van den Veyver IB, Dimas AS, Brucker S, Sutton VR, Gibbs RA, Antonarakis SE, Wu N, Coban-Akdemir ZH, Zhu L, Posey JE, Lupski JR. Rare variant enrichment analysis supports GREB1L as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. HGG Adv 2023; 4:100188. [PMID: 37124138 PMCID: PMC10130500 DOI: 10.1016/j.xhgg.2023.100188] [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: 11/02/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only WNT4 (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was used to further reproduce GREB1L findings in diverse genetic backgrounds. Proband and OMIM phenotypes annotated using the Human Phenotype Ontology were analyzed to quantitatively delineate the phenotypic spectrum associated with GREB1L variant alleles found in our MRKH cohort and those previously published. This study reports 18 novel GREB1L variant alleles, 16 within a multiethnic MRKH cohort and two within a congenital scoliosis cohort. Cohort-wide analyses for a burden of rare variants within a single gene identified likely damaging variants in GREB1L (MIM: 617782), a known disease gene for renal hypoplasia and uterine abnormalities (MIM: 617805), in 16 of 590 MRKH probands. GREB1L variant alleles, including a CNV null allele, were found in 8 MRKH type 1 probands and 8 MRKH type II probands. This study used quantitative phenotypic analyses in a worldwide multiethnic cohort to identify and strengthen the association of GREB1L to isolated uterine agenesis (MRKH type I) and syndromic MRKH type II.
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Affiliation(s)
- Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | | | - Na Chen
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - André Koch
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Efthymios Deligeoroglou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Flora Bacopoulou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jennifer E. Dietrich
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Ignatia B. Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Antigone S. Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Sara Brucker
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Stylianos E. Antonarakis
- University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, 1205 Geneva, Switzerland
- Medigenome, the Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zeynep H. Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Lan Zhu
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
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9
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Otomo N, Khanshour AM, Koido M, Takeda K, Momozawa Y, Kubo M, Kamatani Y, Herring JA, Ogura Y, Takahashi Y, Minami S, Uno K, Kawakami N, Ito M, Sato T, Watanabe K, Kaito T, Yanagida H, Taneichi H, Harimaya K, Taniguchi Y, Shigematsu H, Iida T, Demura S, Sugawara R, Fujita N, Yagi M, Okada E, Hosogane N, Kono K, Nakamura M, Chiba K, Kotani T, Sakuma T, Akazawa T, Suzuki T, Nishida K, Kakutani K, Tsuji T, Sudo H, Iwata A, Inami S, Wise CA, Kochi Y, Matsumoto M, Ikegawa S, Watanabe K, Terao C. Evidence of causality of low body mass index on risk of adolescent idiopathic scoliosis: a Mendelian randomization study. Front Endocrinol (Lausanne) 2023; 14:1089414. [PMID: 37415668 PMCID: PMC10319580 DOI: 10.3389/fendo.2023.1089414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction Adolescent idiopathic scoliosis (AIS) is a disorder with a three-dimensional spinal deformity and is a common disease affecting 1-5% of adolescents. AIS is also known as a complex disease involved in environmental and genetic factors. A relation between AIS and body mass index (BMI) has been epidemiologically and genetically suggested. However, the causal relationship between AIS and BMI remains to be elucidated. Material and methods Mendelian randomization (MR) analysis was performed using summary statistics from genome-wide association studies (GWASs) of AIS (Japanese cohort, 5,327 cases, 73,884 controls; US cohort: 1,468 cases, 20,158 controls) and BMI (Biobank Japan: 173430 individual; meta-analysis of genetic investigation of anthropometric traits and UK Biobank: 806334 individuals; European Children cohort: 39620 individuals; Population Architecture using Genomics and Epidemiology: 49335 individuals). In MR analyses evaluating the effect of BMI on AIS, the association between BMI and AIS summary statistics was evaluated using the inverse-variance weighted (IVW) method, weighted median method, and Egger regression (MR-Egger) methods in Japanese. Results Significant causality of genetically decreased BMI on risk of AIS was estimated: IVW method (Estimate (beta) [SE] = -0.56 [0.16], p = 1.8 × 10-3), weighted median method (beta = -0.56 [0.18], p = 8.5 × 10-3) and MR-Egger method (beta = -1.50 [0.43], p = 4.7 × 10-3), respectively. Consistent results were also observed when using the US AIS summary statistic in three MR methods; however, no significant causality was observed when evaluating the effect of AIS on BMI. Conclusions Our Mendelian randomization analysis using large studies of AIS and GWAS for BMI summary statistics revealed that genetic variants contributing to low BMI have a causal effect on the onset of AIS. This result was consistent with those of epidemiological studies and would contribute to the early detection of AIS.
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Affiliation(s)
- Nao Otomo
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Anas M. Khanshour
- Center for Translational Research, Scottish Rite for Children, Dallas, TX, United States
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuki Takeda
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Science, The University of Tokyo, Tokyo, Japan
| | - John A. Herring
- Department of Orthopaedic Surgery , Scottish Rite for Children, Dallas, TX, United States
- Department of Orthopaedic Surgery and Pediatric, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yoji Ogura
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yohei Takahashi
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Shohei Minami
- Department of Orthopaedic Surgery, Seirei Sakura Citizen Hospital, Sakura, Japan
| | - Koki Uno
- Department of Orthopaedic Surgery, National Hospital Organization, Kobe Medical Center, Kobe, Japan
| | - Noriaki Kawakami
- Department of Orthopaedic Surgery, Meijo Hospital, Nagoya, Japan
| | - Manabu Ito
- Department of Orthopaedic Surgery, National Hospital Organization, Hokkaido Medical Center, Sapporo, Japan
| | - Tatsuya Sato
- Department of Orthopaedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Kei Watanabe
- Department of Orthopaedic Surgery, Niigata University Medical and Dental General Hospital, Niigata, Japan
| | - Takashi Kaito
- Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Haruhisa Yanagida
- Department of Orthopaedic and Spine Surgery, Fukuoka Children’s Hospital, Fukuoka, Japan
| | - Hiroshi Taneichi
- Department of Orthopaedic Surgery, Dokkyo Medical University School of Medicine, Mibu, Japan
| | - Katsumi Harimaya
- Department of Orthopaedic Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yuki Taniguchi
- Department of Orthopaedic Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Shigematsu
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Japan
| | - Takahiro Iida
- Department of Orthopaedic Surgery, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
- Department of Orthopaedic Surgery, Teine Keijinkai Hospital, Sapporo, Japan
| | - Satoru Demura
- Department of Orthopaedic Surgery Graduated School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Ryo Sugawara
- Department of Orthopaedic Surgery, Jichi Medical University, Shimotsuke, Japan
| | - Nobuyuki Fujita
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
- Department of Orthopaedic Surgery, Fujita Health University, Toyoake, Japan
| | - Mitsuru Yagi
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
- Department of Orthopaedic Surgery, International University of Health and Welfare School of Medicine, Narita, Japan
| | - Eijiro Okada
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Naobumi Hosogane
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
- Department of Orthopaedic Surgery, National Defense Medical College, Tokorozawa, Japan
| | - Katsuki Kono
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
- Department of Orthopaedic Surgery, Kono Orthopaedic Clinic, Tokyo, Japan
| | - Masaya Nakamura
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kazuhiro Chiba
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
- Department of Orthopaedic Surgery, Fujita Health University, Toyoake, Japan
| | - Toshiaki Kotani
- Department of Orthopaedic Surgery, Seirei Sakura Citizen Hospital, Sakura, Japan
| | - Tsuyoshi Sakuma
- Department of Orthopaedic Surgery, Seirei Sakura Citizen Hospital, Sakura, Japan
| | - Tsutomu Akazawa
- Department of Orthopaedic Surgery, Seirei Sakura Citizen Hospital, Sakura, Japan
| | - Teppei Suzuki
- Department of Orthopaedic Surgery, National Hospital Organization, Kobe Medical Center, Kobe, Japan
| | - Kotaro Nishida
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kenichiro Kakutani
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Taichi Tsuji
- Department of Orthopaedic Surgery, Meijo Hospital, Nagoya, Japan
| | - Hideki Sudo
- Department of Advanced Medicine for Spine and Spinal Cord Disorders, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Akira Iwata
- Department of Preventive and Therapeutic Research for Metastatic Bone Tumor, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Satoshi Inami
- Department of Orthopaedic Surgery, Dokkyo Medical University School of Medicine, Mibu, Japan
| | - Carol A. Wise
- Center for Translational Research, Scottish Rite for Children, Dallas, TX, United States
- Department of Orthopaedic Surgery and Pediatric, University of Texas Southwestern Medical Center, Dallas, TX, United States
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental and University, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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10
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Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N. Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality. bioRxiv 2023:2023.04.12.536497. [PMID: 37090618 PMCID: PMC10120660 DOI: 10.1101/2023.04.12.536497] [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: 04/25/2023]
Abstract
Adolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is sexually dimorphic, with increased incidence in females. A GWAS identified a female-specific AIS susceptibility locus near the PAX1 gene. Here, we used mouse enhancer assays, three mouse enhancer knockouts and subsequent phenotypic analyses to characterize this region. Using mouse enhancer assays, we characterized a sequence, PEC7, that overlaps the AIS-associated variant, and found it to be active in the tail tip and intervertebral disc. Removal of PEC7 or Xe1, a known sclerotome enhancer nearby, and deletion of both sequences led to a kinky phenotype only in the Xe1 and combined (Xe1+PEC7) knockouts, with only the latter showing a female sex dimorphic phenotype. Extensive phenotypic characterization of these mouse lines implicated several differentially expressed genes and estrogen signaling in the sex dimorphic bias. In summary, our work functionally characterizes an AIS-associated locus and dissects the mechanism for its sexual dimorphism.
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Affiliation(s)
- Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rory R. Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mai Nobuhara
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Murray
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Xin Ruan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jonathan J. Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
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11
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Paria N, Khalid A, Shen B, Lemoine B, Chan J, Kidane YH, Oxendine I, Cornelia R, Wise CA, Rios JJ. Molecular Dissection of Somatic Skeletal Disease in Neurofibromatosis Type 1. J Bone Miner Res 2023; 38:288-299. [PMID: 36459048 PMCID: PMC9898201 DOI: 10.1002/jbmr.4755] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/11/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a tumor predisposition syndrome caused by heterozygous NF1 gene mutations. Patients with NF1 present with pleiotropic somatic secondary manifestations, including development of bone pseudarthrosis after fracture. Somatic NF1 gene mutations were reproducibly identified in patient-derived pseudarthrosis specimens, suggesting a local mosaic cell population including somatic pathologic cells. The somatic cellular pathogenesis of NF1 pseudarthroses remains unclear, though defects in osteogenesis have been posited. Here, we applied time-series single-cell RNA-sequencing (scRNA-seq) to patient-matched control and pseudarthrosis-derived primary bone stromal cells (BSCs). We show that osteogenic specification to an osteoblast progenitor cell population was evident for control bone-derived cells and haploinsufficient pseudarthrosis-derived cells. Similar results were observed for somatic patient fracture-derived NF1-/- cells; however, expression of genetic pathways associated with skeletal mineralization were significantly reduced in NF1-/- cells compared with fracture-derived NF1+/- cells. In mice, we show that Nf1 expressed in bone marrow osteoprogenitors is required for the maintenance of the adult skeleton. Results from our study implicate impaired Clec11a-Itga11-Wnt signaling in the pathogenesis of NF1-associated skeletal disease. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Nandina Paria
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Aysha Khalid
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Bo Shen
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ben Lemoine
- Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Jinyan Chan
- Baylor Scott & White Research Institute, Dallas, TX, USA.,Institute of Biomedical Studies, Baylor University, Waco, TX, USA
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Ila Oxendine
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Reuel Cornelia
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX, USA
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12
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Rios JJ, Denton K, Russell J, Kozlitina J, Ferreira CR, Lewanda AF, Mayfield JE, Moresco E, Ludwig S, Tang M, Li X, Lyon S, Khanshour A, Paria N, Khalid A, Li Y, Xie X, Feng JQ, Xu Q, Lu Y, Hammer RE, Wise CA, Beutler B. Germline Saturation Mutagenesis Induces Skeletal Phenotypes in Mice. J Bone Miner Res 2021; 36:1548-1565. [PMID: 33905568 PMCID: PMC8862308 DOI: 10.1002/jbmr.4323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/07/2021] [Accepted: 04/21/2021] [Indexed: 12/28/2022]
Abstract
Proper embryonic and postnatal skeletal development require coordination of myriad complex molecular mechanisms. Disruption of these processes, through genetic mutation, contributes to variation in skeletal development. We developed a high-throughput N-ethyl-N-nitrosourea (ENU)-induced saturation mutagenesis skeletal screening approach in mice to identify genes required for proper skeletal development. Here, we report initial results from live-animal X-ray and dual-energy X-ray absorptiometry (DXA) imaging of 27,607 G3 mice from 806 pedigrees, testing the effects of 32,198 coding/splicing mutations in 13,020 genes. A total of 39.7% of all autosomal genes were severely damaged or destroyed by mutations tested twice or more in the homozygous state. Results from our study demonstrate the feasibility of in vivo mutagenesis to identify mouse models of skeletal disease. Furthermore, our study demonstrates how ENU mutagenesis provides opportunities to create and characterize putative hypomorphic mutations in developmentally essential genes. Finally, we present a viable mouse model and case report of recessive skeletal disease caused by mutations in FAM20B. Results from this study, including engineered mouse models, are made publicly available via the online Mutagenetix database. © 2021 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kristin Denton
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Jamie Russell
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Julia Kozlitina
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Carlos R Ferreira
- Skeletal Genomics Unit, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy F Lewanda
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Joshua E Mayfield
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Eva Moresco
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sara Ludwig
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Miao Tang
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xiaohong Li
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Stephen Lyon
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Anas Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Nandina Paria
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Aysha Khalid
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Yang Li
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Xudong Xie
- Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| | - Jian Q Feng
- Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| | - Qian Xu
- Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| | - Yongbo Lu
- Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| | - Robert E Hammer
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bruce Beutler
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
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13
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Xu D, Lyon S, Bu CH, Hildebrand S, Choi JH, Zhong X, Liu A, Turer EE, Zhang Z, Russell J, Ludwig S, Mahrt E, Nair-Gill E, Shi H, Wang Y, Zhang D, Yue T, Wang KW, SoRelle JA, Su L, Misawa T, McAlpine W, Sun L, Wang J, Zhan X, Choi M, Farokhnia R, Sakla A, Schneider S, Coco H, Coolbaugh G, Hayse B, Mazal S, Medler D, Nguyen B, Rodriguez E, Wadley A, Tang M, Li X, Anderton P, Keller K, Press A, Scott L, Quan J, Cooper S, Collie T, Qin B, Cardin J, Simpson R, Tadesse M, Sun Q, Wise CA, Rios JJ, Moresco EMY, Beutler B. Thousands of induced germline mutations affecting immune cells identified by automated meiotic mapping coupled with machine learning. Proc Natl Acad Sci U S A 2021; 118:e2106786118. [PMID: 34260399 PMCID: PMC8285956 DOI: 10.1073/pnas.2106786118] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Forward genetic studies use meiotic mapping to adduce evidence that a particular mutation, normally induced by a germline mutagen, is causative of a particular phenotype. Particularly in small pedigrees, cosegregation of multiple mutations, occasional unawareness of mutations, and paucity of homozygotes may lead to erroneous declarations of cause and effect. We sought to improve the identification of mutations causing immune phenotypes in mice by creating Candidate Explorer (CE), a machine-learning software program that integrates 67 features of genetic mapping data into a single numeric score, mathematically convertible to the probability of verification of any putative mutation-phenotype association. At this time, CE has evaluated putative mutation-phenotype associations arising from screening damaging mutations in ∼55% of mouse genes for effects on flow cytometry measurements of immune cells in the blood. CE has therefore identified more than half of genes within which mutations can be causative of flow cytometric phenovariation in Mus musculus The majority of these genes were not previously known to support immune function or homeostasis. Mouse geneticists will find CE data informative in identifying causative mutations within quantitative trait loci, while clinical geneticists may use CE to help connect causative variants with rare heritable diseases of immunity, even in the absence of linkage information. CE displays integrated mutation, phenotype, and linkage data, and is freely available for query online.
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Affiliation(s)
- Darui Xu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Stephen Lyon
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Chun Hui Bu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aijie Liu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Emre E Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Elena Mahrt
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Evan Nair-Gill
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hexin Shi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ying Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Duanwu Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Tao Yue
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kuan-Wen Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jeffrey A SoRelle
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lijing Su
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Takuma Misawa
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - William McAlpine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lei Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mihwa Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Roxana Farokhnia
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Andrew Sakla
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sara Schneider
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hannah Coco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Gabrielle Coolbaugh
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Braden Hayse
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sara Mazal
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Dawson Medler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Brandon Nguyen
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Edward Rodriguez
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Andrew Wadley
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Priscilla Anderton
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Katie Keller
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Amanda Press
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sydney Cooper
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Tiffany Collie
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Baifang Qin
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jennifer Cardin
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Rochelle Simpson
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Meron Tadesse
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Qihua Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219
- McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219
- McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390;
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14
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Rios JJ, Denton K, Yu H, Manickam K, Garner S, Russell J, Ludwig S, Rosenfeld JA, Liu P, Munch J, Sucato DJ, Beutler B, Wise CA. Saturation mutagenesis defines novel mouse models of severe spine deformity. Dis Model Mech 2021; 14:269194. [PMID: 34142127 PMCID: PMC8246263 DOI: 10.1242/dmm.048901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Embryonic formation and patterning of the vertebrate spinal column requires coordination of many molecular cues. After birth, the integrity of the spine is impacted by developmental abnormalities of the skeletal, muscular and nervous systems, which may result in deformities, such as kyphosis and scoliosis. We sought to identify novel genetic mouse models of severe spine deformity by implementing in vivo skeletal radiography as part of a high-throughput saturation mutagenesis screen. We report selected examples of genetic mouse models following radiographic screening of 54,497 mice from 1275 pedigrees. An estimated 30.44% of autosomal genes harbored predicted damaging alleles examined twice or more in the homozygous state. Of the 1275 pedigrees screened, 7.4% presented with severe spine deformity developing in multiple mice, and of these, meiotic mapping implicated N-ethyl-N-nitrosourea alleles in 21% of pedigrees. Our study provides proof of concept that saturation mutagenesis is capable of discovering novel mouse models of human disease, including conditions with skeletal, neural and neuromuscular pathologies. Furthermore, we report a mouse model of skeletal disease, including severe spine deformity, caused by recessive mutation in Scube3. By integrating results with a human clinical exome database, we identified a patient with undiagnosed skeletal disease who harbored recessive mutations in SCUBE3, and we demonstrated that disease-associated mutations are associated with reduced transactivation of Smad signaling in vitro. All radiographic results and mouse models are made publicly available through the Mutagenetix online database with the goal of advancing understanding of spine development and discovering novel mouse models of human disease. Summary: We report selected mouse models of spine deformity following mutagenesis across 30% of autosomal genes, results of which are made publicly available to advance understanding of spine development and disease.
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Affiliation(s)
- Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA.,Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Orthopaedic Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kristin Denton
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Hao Yu
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Kandamurugu Manickam
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Shannon Garner
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Baylor Genetics, Houston, TX 77021, USA
| | - Pengfei Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Baylor Genetics, Houston, TX 77021, USA
| | - Jake Munch
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Daniel J Sucato
- Department of Orthopaedics, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA.,Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Orthopaedic Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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15
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Makki N, Zhao J, Liu Z, Eckalbar WL, Ushiki A, Khanshour AM, Wu J, Rios J, Gray RS, Wise CA, Ahituv N. Genomic characterization of the adolescent idiopathic scoliosis-associated transcriptome and regulome. Hum Mol Genet 2020; 29:3606-3615. [PMID: 33179741 PMCID: PMC7823110 DOI: 10.1093/hmg/ddaa242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 08/24/2020] [Accepted: 10/12/2020] [Indexed: 12/27/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is the most common pediatric musculoskeletal disorder, affecting ~3% of the population worldwide. However, its genetic bases and tissues of origin remain largely unknown. Several genome-wide association studies (GWAS) have implicated nucleotide variants in non-coding sequences that control genes with important roles in cartilage, muscle, bone, connective tissue and intervertebral disks (IVDs) as drivers of AIS susceptibility. Here, we set out to define the expression of AIS-associated genes and active regulatory elements by performing RNA-seq and chromatin immunoprecipitation-sequencing against H3 lysine 27 acetylation in these tissues in mouse and human. Our study highlights genetic pathways involving AIS-associated loci that regulate chondrogenesis, IVD development and connective tissue maintenance and homeostasis. In addition, we identify thousands of putative AIS-associated regulatory elements which may orchestrate tissue-specific expression in musculoskeletal tissues of the spine. Quantification of enhancer activity of several candidate regulatory elements from our study identifies three functional enhancers carrying AIS-associated GWAS SNPs at the ADGRG6 and BNC2 loci. Our findings provide a novel genome-wide catalog of AIS-relevant genes and regulatory elements and aid in the identification of novel targets for AIS causality and treatment.
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Affiliation(s)
- Nadja Makki
- Department of Anatomy and Cell Biology, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Zhaoyang Liu
- Department of Pediatrics and Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, TX, USA
| | - Walter L Eckalbar
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Joe Wu
- Health Science Center Libraries, University of Florida, Gainesville, FL, USA
| | - Jonathan Rios
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth and Development and Departments of Orthopaedic Surgery and Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ryan S Gray
- Department of Pediatrics and Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, TX, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth and Development and Departments of Orthopaedic Surgery and Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, 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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16
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Patel C, Khanshour AM, Wilkes D, Rios JJ, Sheff KW, Nassi L, Wise CA. Novel homozygous variant in WISP3 in a family with unrecognized progressive pseudorheumatoid dysplasia. Clin Case Rep 2020; 8:1452-1457. [PMID: 32884773 PMCID: PMC7455413 DOI: 10.1002/ccr3.2884] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/19/2020] [Accepted: 03/29/2020] [Indexed: 11/18/2022] Open
Abstract
We present the use of whole-genome sequencing to correctly diagnose progressive pseudorheumatoid dysplasia in patients with atypical clinical and radiologic findings and prior diagnosis of juvenile idiopathic arthritis.
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Affiliation(s)
- Chandreshkumar Patel
- Scottish Rite for Children Center for Pediatric Bone Biology and Translational ResearchTexas Scottish Rite Hospital for ChildrenDallasTXUSA
| | - Anas M. Khanshour
- Scottish Rite for Children Center for Pediatric Bone Biology and Translational ResearchTexas Scottish Rite Hospital for ChildrenDallasTXUSA
| | - David Wilkes
- Radiology DepartmentTexas Scottish Rite Hospital for ChildrenDallasTXUSA
| | - Jonathan J. Rios
- Scottish Rite for Children Center for Pediatric Bone Biology and Translational ResearchTexas Scottish Rite Hospital for ChildrenDallasTXUSA
- McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PediatricsUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Orthopaedic SurgeryUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Kelly W. Sheff
- North Texas Genome CenterUniversity of Texas at ArlingtonArlingtonTXUSA
| | - Lorien Nassi
- Department of PediatricsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Carol A. Wise
- Scottish Rite for Children Center for Pediatric Bone Biology and Translational ResearchTexas Scottish Rite Hospital for ChildrenDallasTXUSA
- McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PediatricsUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Orthopaedic SurgeryUniversity of Texas Southwestern Medical CenterDallasTXUSA
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17
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Zhao S, Zhang Y, Chen W, Li W, Wang S, Wang L, Zhao Y, Lin M, Ye Y, Lin J, Zheng Y, Liu J, Zhao H, Yan Z, Yang Y, Huang Y, Lin G, Chen Z, Zhang Z, Liu S, Jin L, Wang Z, Chen J, Niu Y, Li X, Wu Y, Wang Y, Du R, Gao N, Zhao H, Yang Y, Liu Y, Tian Y, Li W, Zhao Y, Liu J, Yu B, Zhang N, Yu K, Yang X, Li S, Xu Y, Hu J, Liu Z, Shen J, Zhang S, Su J, Khanshour AM, Kidane YH, Ramo B, Rios JJ, Liu P, Sutton VR, Posey JE, Wu Z, Qiu G, Wise CA, Zhang F, Lupski JR, Zhang J, Wu N. Diagnostic yield and clinical impact of exome sequencing in early-onset scoliosis (EOS). J Med Genet 2020; 58:41-47. [PMID: 32381727 DOI: 10.1136/jmedgenet-2019-106823] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 12/29/2019] [Revised: 02/17/2020] [Accepted: 03/13/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Early-onset scoliosis (EOS), defined by an onset age of scoliosis less than 10 years, conveys significant health risk to affected children. Identification of the molecular aetiology underlying patients with EOS could provide valuable information for both clinical management and prenatal screening. METHODS In this study, we consecutively recruited a cohort of 447 Chinese patients with operative EOS. We performed exome sequencing (ES) screening on these individuals and their available family members (totaling 670 subjects). Another cohort of 13 patients with idiopathic early-onset scoliosis (IEOS) from the USA who underwent ES was also recruited. RESULTS After ES data processing and variant interpretation, we detected molecular diagnostic variants in 92 out of 447 (20.6%) Chinese patients with EOS, including 8 patients with molecular confirmation of their clinical diagnosis and 84 patients with molecular diagnoses of previously unrecognised diseases underlying scoliosis. One out of 13 patients with IEOS from the US cohort was molecularly diagnosed. The age at presentation, the number of organ systems involved and the Cobb angle were the three top features predictive of a molecular diagnosis. CONCLUSION ES enabled the molecular diagnosis/classification of patients with EOS. Specific clinical features/feature pairs are able to indicate the likelihood of gaining a molecular diagnosis through ES.
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Affiliation(s)
- Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yuanqiang Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Weiyu Li
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yanxue Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Mao Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yongyu Ye
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Orthopedic Surgery, First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yu Zheng
- School of Finance, Southwestern University of Finance and Economics, Chengdu, Sichuan, China
| | - Jiaqi Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China.,School of Ophthalmology & Optometry and Eye Hospital, School of BiomedicalEngineering, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zihui Yan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yongxin Yang
- Machine Intelligence Group, University of Edinburgh, Edinburgh, UK
| | - Yingzhao Huang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Guanfeng Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zefu Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zhen Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Sen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Lichao Jin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zhaoyang Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Jingdan Chen
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yipeng Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Na Gao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Hong Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Yang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Tian
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Wenli Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Na Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Keyi Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xu Yang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shugang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuan Xu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianhua Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhe Liu
- Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianxiong Shen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Shuyang Zhang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Cardiology, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, School of BiomedicalEngineering, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA
| | - Brandon Ramo
- Department of Orthopaedic Surgery, Scottish Rite for Children, Dallas, Texas, USA
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | | | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Departments of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
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18
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Wise CA, Sepich D, Ushiki A, Khanshour AM, Kidane YH, Makki N, Gurnett CA, Gray RS, Rios JJ, Ahituv N, Solnica-Krezel L. The cartilage matrisome in adolescent idiopathic scoliosis. Bone Res 2020; 8:13. [PMID: 32195011 PMCID: PMC7062733 DOI: 10.1038/s41413-020-0089-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
The human spinal column is a dynamic, segmented, bony, and cartilaginous structure that protects the neurologic system and simultaneously provides balance and flexibility. Children with developmental disorders that affect the patterning or shape of the spine can be at risk of neurologic and other physiologic dysfunctions. The most common developmental disorder of the spine is scoliosis, a lateral deformity in the shape of the spinal column. Scoliosis may be part of the clinical spectrum that is observed in many developmental disorders, but typically presents as an isolated symptom in otherwise healthy adolescent children. Adolescent idiopathic scoliosis (AIS) has defied understanding in part due to its genetic complexity. Breakthroughs have come from recent genome-wide association studies (GWAS) and next generation sequencing (NGS) of human AIS cohorts, as well as investigations of animal models. These studies have identified genetic associations with determinants of cartilage biogenesis and development of the intervertebral disc (IVD). Current evidence suggests that a fraction of AIS cases may arise from variation in factors involved in the structural integrity and homeostasis of the cartilaginous extracellular matrix (ECM). Here, we review the development of the spine and spinal cartilages, the composition of the cartilage ECM, the so-called "matrisome" and its functions, and the players involved in the genetic architecture of AIS. We also propose a molecular model by which the cartilage matrisome of the IVD contributes to AIS susceptibility.
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Affiliation(s)
- Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219 USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
- Departments of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
- Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
| | - Diane Sepich
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158 USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158 USA
| | - Anas M. Khanshour
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219 USA
| | - Yared H. Kidane
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219 USA
| | - Nadja Makki
- Department of Anatomy and Cell Biology, University of Florida, College of Medicine, Gainesville, FL 32610 USA
| | - Christina A. Gurnett
- Departments of Neurology, Washington University School of Medicine, St Louis, MO 63110 USA
- Pediatrics, Washington University School of Medicine, St Louis, MO 63110 USA
- Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO 63110 USA
| | - Ryan S. Gray
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, TX 78723 USA
| | - Jonathan J. Rios
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219 USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
- Departments of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
- Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158 USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158 USA
| | - Lila Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
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19
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Chen W, Lin J, Wang L, Li X, Zhao S, Liu J, Akdemir ZC, Zhao Y, Du R, Ye Y, Song X, Zhang Y, Yan Z, Yang X, Lin M, Shen J, Wang S, Gao N, Yang Y, Liu Y, Li W, Liu J, Zhang N, Yang X, Xu Y, Zhang J, Delgado MR, Posey JE, Qiu G, Rios JJ, Liu P, Wise CA, Zhang F, Wu Z, Lupski JR, Wu N. Front Cover, Volume 41, Issue 1. Hum Mutat 2019. [DOI: 10.1002/humu.23966] [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: 11/06/2022]
Affiliation(s)
- Weisheng Chen
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Graduate School of Peking Union Medical College Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
| | - Jiachen Lin
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Graduate School of Peking Union Medical College Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
| | - Lianlei Wang
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Graduate School of Peking Union Medical College Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
- Department of Central LaboratoryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Sen Zhao
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
| | - Jiaqi Liu
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
- Department of Breast Surgical OncologyNational Cancer Center/Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Zeynep C. Akdemir
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
| | - Yanxue Zhao
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
| | - Renqian Du
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
| | - Yongyu Ye
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
- Department of Orthopaedic SurgeryFirst Affiliated Hospital of Sun Yat‐sen University Guangzhou China
| | - Xiaofei Song
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
| | - Yuanqiang Zhang
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Graduate School of Peking Union Medical College Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
| | - Zihui Yan
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Graduate School of Peking Union Medical College Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
| | - Xinzhuang Yang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
- Department of Central LaboratoryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Mao Lin
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Graduate School of Peking Union Medical College Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
| | - Jianxiong Shen
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
| | - Shengru Wang
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Na Gao
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Ying Yang
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Ying Liu
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Wenli Li
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Jia Liu
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Na Zhang
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Xu Yang
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Yuan Xu
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Jianguo Zhang
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
| | - Mauricio R. Delgado
- Department of Neurology and NeurotherapeuticsUniversity of Texas Southwestern Medical Center at Dallas Dallas Texas
- Neurology DepartmentTexas Scottish Rite Hospital Dallas Texas
| | - Jennifer E. Posey
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
| | - Guixing Qiu
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences Beijing China
| | - Jonathan J. Rios
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children Dallas Texas
- McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic SurgeryUniversity of Texas Southwestern Medical Center at Dallas Dallas Texas
| | - Pengfei Liu
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
- Baylor Genetics Laboratory Houston Texas
| | - Carol A. Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children Dallas Texas
- McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic SurgeryUniversity of Texas Southwestern Medical Center at Dallas Dallas Texas
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University Shanghai China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
- Department of Central LaboratoryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences Beijing China
| | - James R. Lupski
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
- Department of PediatricsBaylor College of Medicine Houston Texas
- Texas Children's Hospital Houston Texas
- Human Genome Sequencing Center, Baylor College of Medicine Houston Texas
| | - Nan Wu
- Department of Orthopaedic SurgeryPeking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity Beijing China
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences Beijing China
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20
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Chen W, Lin J, Wang L, Li X, Zhao S, Liu J, Akdemir ZC, Zhao Y, Du R, Ye Y, Song X, Zhang Y, Yan Z, Yang X, Lin M, Shen J, Wang S, Gao N, Yang Y, Liu Y, Li W, Liu J, Zhang N, Yang X, Xu Y, Zhang J, Delgado MR, Posey JE, Qiu G, Rios JJ, Liu P, Wise CA, Zhang F, Wu Z, Lupski JR, Wu N. TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease. Hum Mutat 2019; 41:182-195. [PMID: 31471994 DOI: 10.1002/humu.23907] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 03/04/2019] [Revised: 08/20/2019] [Accepted: 08/28/2019] [Indexed: 12/30/2022]
Abstract
Congenital scoliosis (CS) is a birth defect with variable clinical and anatomical manifestations due to spinal malformation. The genetic etiology underlying about 10% of CS cases in the Chinese population is compound inheritance by which the gene dosage is reduced below that of haploinsufficiency. In this genetic model, the trait manifests as a result of the combined effect of a rare variant and common pathogenic variant allele at a locus. From exome sequencing (ES) data of 523 patients in Asia and two patients in Texas, we identified six TBX6 gene-disruptive variants from 11 unrelated CS patients via ES and in vitro functional testing. The in trans mild hypomorphic allele was identified in 10 of the 11 subjects; as anticipated these 10 shared a similar spinal deformity of hemivertebrae. The remaining case has a homozygous variant in TBX6 (c.418C>T) and presents a more severe spinal deformity phenotype. We found decreased transcriptional activity and abnormal cellular localization as the molecular mechanisms for TBX6 missense loss-of-function alleles. Expanding the mutational spectrum of TBX6 pathogenic alleles enabled an increased molecular diagnostic detection rate, provided further evidence for the gene dosage-dependent genetic model underlying CS, and refined clinical classification.
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Affiliation(s)
- Weisheng Chen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jiachen Lin
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Lianlei Wang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sen Zhao
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Jiaqi Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yanxue Zhao
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yongyu Ye
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Orthopaedic Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yuanqiang Zhang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zihui Yan
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Xinzhuang Yang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Mao Lin
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Jianxiong Shen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Shengru Wang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Na Gao
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Yang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Wenli Li
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Na Zhang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xu Yang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuan Xu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianguo Zhang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Mauricio R Delgado
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,Neurology Department, Texas Scottish Rite Hospital, Dallas, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Guixing Qiu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Jonathan J Rios
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics Laboratory, Houston, Texas
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Nan Wu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
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21
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Khanshour AM, Kou I, Fan Y, Einarsdottir E, Makki N, Kidane YH, Kere J, Grauers A, Johnson TA, Paria N, Patel C, Singhania R, Kamiya N, Takeda K, Otomo N, Watanabe K, Luk KDK, Cheung KMC, Herring JA, Rios JJ, Ahituv N, Gerdhem P, Gurnett CA, Song YQ, Ikegawa S, Wise CA. Genome-wide meta-analysis and replication studies in multiple ethnicities identify novel adolescent idiopathic scoliosis susceptibility loci. Hum Mol Genet 2019; 27:3986-3998. [PMID: 30395268 DOI: 10.1093/hmg/ddy306] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common musculoskeletal disorder of childhood development. The genetic architecture of AIS is complex, and the great majority of risk factors are undiscovered. To identify new AIS susceptibility loci, we conducted the first genome-wide meta-analysis of AIS genome-wide association studies, including 7956 cases and 88 459 controls from 3 ancestral groups. Three novel loci that surpassed genome-wide significance were uncovered in intragenic regions of the CDH13 (P-value_rs4513093 = 1.7E-15), ABO (P-value_ rs687621 = 7.3E-10) and SOX6 (P-value_rs1455114 = 2.98E-08) genes. Restricting the analysis to females improved the associations at multiple loci, most notably with variants within CDH13 despite the reduction in sample size. Genome-wide gene-functional enrichment analysis identified significant perturbation of pathways involving cartilage and connective tissue development. Expression of both SOX6 and CDH13 was detected in cartilage chondrocytes and chromatin immunoprecipitation sequencing experiments in that tissue revealed multiple HeK27ac-positive peaks overlapping associated loci. Our results further define the genetic architecture of AIS and highlight the importance of vertebral cartilage development in its pathogenesis.
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Affiliation(s)
- Anas M Khanshour
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Ikuyo Kou
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, University of Helsinki, 00014 University of Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, 00014 University of Helsinki, Finland.,Department of Biosciences & Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Nadja Makki
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yared H Kidane
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Juha Kere
- Folkhälsan Institute of Genetics, University of Helsinki, 00014 University of Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, 00014 University of Helsinki, Finland.,Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK.,Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden
| | - Anna Grauers
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden.,Department of Orthopedics, Sundsvall and Härnösand County Hospital, Sundsvall, Sweden
| | - Todd A Johnson
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Nandina Paria
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Chandreshkumar Patel
- McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Richa Singhania
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | | | - Kazuki Takeda
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Nao Otomo
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Keith D K Luk
- Department of Orthopaedics & Traumatology, The University of Hong Kong, Hong Kong, China
| | - Kenneth M C Cheung
- Department of Orthopaedics & Traumatology, The University of Hong Kong, Hong Kong, China
| | - John A Herring
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan J Rios
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nadav Ahituv
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Gerdhem
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden.,Department of Orthopedics, Karolinska University Hospital, K54 Huddinge, Stockholm, Sweden
| | - Christina A Gurnett
- Department of Neurology, School of Medicine, Washington University, St. Louis, MO, USA
| | - You-Qiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Shiro Ikegawa
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Carol A Wise
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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22
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Sadler B, Haller G, Antunes L, Bledsoe X, Morcuende J, Giampietro P, Raggio C, Miller N, Kidane Y, Wise CA, Amarillo I, Walton N, Seeley M, Johnson D, Jenkins C, Jenkins T, Oetjens M, Tong RS, Druley TE, Dobbs MB, Gurnett CA. Distal chromosome 16p11.2 duplications containing SH2B1 in patients with scoliosis. J Med Genet 2019; 56:427-433. [PMID: 30803986 DOI: 10.1136/jmedgenet-2018-105877] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 11/15/2018] [Revised: 01/18/2019] [Accepted: 01/25/2019] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Adolescent idiopathic scoliosis (AIS) is a common musculoskeletal disorder with strong evidence for a genetic contribution. CNVs play an important role in congenital scoliosis, but their role in idiopathic scoliosis has been largely unexplored. METHODS Exome sequence data from 1197 AIS cases and 1664 in-house controls was analysed using coverage data to identify rare CNVs. CNV calls were filtered to include only highly confident CNVs with >10 average reads per region and mean log-ratio of coverage consistent with single-copy duplication or deletion. The frequency of 55 common recurrent CNVs was determined and correlated with clinical characteristics. RESULTS Distal chromosome 16p11.2 microduplications containing the gene SH2B1 were found in 0.7% of AIS cases (8/1197). We replicated this finding in two additional AIS cohorts (8/1097 and 2/433), resulting in 0.7% (18/2727) of all AIS cases harbouring a chromosome 16p11.2 microduplication, compared with 0.06% of local controls (1/1664) and 0.04% of published controls (8/19584) (p=2.28×10-11, OR=16.15). Furthermore, examination of electronic health records of 92 455 patients from the Geisinger health system showed scoliosis in 30% (20/66) patients with chromosome 16p11.2 microduplications containing SH2B1 compared with 7.6% (10/132) of controls (p=5.6×10-4, OR=3.9). CONCLUSIONS Recurrent distal chromosome 16p11.2 duplications explain nearly 1% of AIS. Distal chromosome 16p11.2 duplications may contribute to scoliosis pathogenesis by directly impairing growth or by altering expression of nearby genes, such as TBX6. Individuals with distal chromosome 16p11.2 microduplications should be screened for scoliosis to facilitate early treatment.
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Affiliation(s)
- Brooke Sadler
- Department of Neurology, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Gabe Haller
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Lilian Antunes
- Department of Neurology, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Xavier Bledsoe
- Department of Neurology, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Jose Morcuende
- Department of Orthopaedic Surgery and Rehabilitation, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, Iowa, USA
| | - Philip Giampietro
- Department of Genetics, St. Christopher's Hospital for Children, Philadelphia, Pennsylvania, USA
| | - Cathleen Raggio
- Orthopedic Surgery, Pediatrics, Hospital for Special Surgery, New York City, New York, USA
| | - Nancy Miller
- Department of Orthopedics, University of Colorado at Denver - Anschutz Medical Campus, Aurora, Colorado, USA
| | - Yared Kidane
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Ina Amarillo
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Nephi Walton
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Mark Seeley
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Darren Johnson
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Conner Jenkins
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Troy Jenkins
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - Matthew Oetjens
- Genomic Medicine, Geisinger Health System, Danville, Pennsylvania, USA
| | - R Spencer Tong
- Department of Pediatrics, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Todd E Druley
- Department of Pediatrics, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Matthew B Dobbs
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, St. Louis, Missouri, USA
| | - Christina A Gurnett
- Department of Neurology, Division of Pediatric Neurology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
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23
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Kou I, Watanabe K, Takahashi Y, Momozawa Y, Khanshour A, Grauers A, Zhou H, Liu G, Fan YH, Takeda K, Ogura Y, Zhou T, Iwasaki Y, Kubo M, Wu Z, Matsumoto M, Einarsdottir E, Kere J, Huang D, Qiu G, Qiu Y, Wise CA, Song YQ, Wu N, Su P, Gerdhem P, Ikegawa S. A multi-ethnic meta-analysis confirms the association of rs6570507 with adolescent idiopathic scoliosis. Sci Rep 2018; 8:11575. [PMID: 30069010 PMCID: PMC6070519 DOI: 10.1038/s41598-018-29011-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 11/06/2017] [Accepted: 06/29/2018] [Indexed: 01/04/2023] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common type of spinal deformity and has a significant genetic background. Genome-wide association studies (GWASs) identified several susceptibility loci associated with AIS. Among them is a locus on chromosome 6q24.1 that we identified by a GWAS in a Japanese cohort. The locus is represented by rs6570507 located within GPR126. To ensure the association of rs6570507 with AIS, we conducted a meta-analysis using eight cohorts from East Asia, Northern Europe and USA. The analysis included a total of 6,873 cases and 38,916 controls and yielded significant association (combined P = 2.95 × 10-20; odds ratio = 1.22), providing convincing evidence of the worldwide association between rs6570507 and AIS susceptibility. In silico analyses strongly suggested that GPR126 is a susceptibility gene at this locus.
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Affiliation(s)
- Ikuyo Kou
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan.
| | - Yohei Takahashi
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anas Khanshour
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Anna Grauers
- Department of Orthopaedics, Sundsvall and Härnösand County Hospital, Sundsvall, Sweden.,Department of Clinical Science, Intervention and Technology (CLINTEC) Karolinska Institutet, Stockholm, Sweden
| | - Hang Zhou
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yan-Hui Fan
- Department of Biochemistry, University of Hong Kong, Hong Kong, China
| | - Kazuki Takeda
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yoji Ogura
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Taifeng Zhou
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Zhihong Wu
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Morio Matsumoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | | | | | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Biosciences and Nutrition, , Karolinska Institutet, Huddinge, Sweden
| | - Juha Kere
- Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Biosciences and Nutrition, , Karolinska Institutet, Huddinge, Sweden.,Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, UK
| | - Dongsheng Huang
- Department of Orthopedics, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Yong Qiu
- Department of Spine Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA.,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA.,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - You-Qiang Song
- Department of Biochemistry, University of Hong Kong, Hong Kong, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Peiqiang Su
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Paul Gerdhem
- Department of Clinical Science, Intervention and Technology (CLINTEC) Karolinska Institutet, Stockholm, Sweden.,Department of Orthopaedics, Karolinska University Hospital, Stockholm, Sweden
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.
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24
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Ogura Y, Takeda K, Kou I, Khanshour A, Grauers A, Zhou H, Liu G, Fan YH, Zhou T, Wu Z, Takahashi Y, Matsumoto M, Einarsdottir E, Kere J, Huang D, Qiu G, Xu L, Qiu Y, Wise CA, Song YQ, Wu N, Su P, Gerdhem P, Watanabe K, Ikegawa S. An international meta-analysis confirms the association of BNC2 with adolescent idiopathic scoliosis. Sci Rep 2018; 8:4730. [PMID: 29549362 PMCID: PMC5856832 DOI: 10.1038/s41598-018-22552-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 06/15/2017] [Accepted: 02/26/2018] [Indexed: 11/18/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is a common spinal deformity with the prevalence of approximately 3%. We previously conducted a genome-wide association study (GWAS) using a Japanese cohort and identified a novel locus on chromosome 9p22.2. However, a replication study using multi-population cohorts has not been conducted. To confirm the association of 9p22.2 locus with AIS in multi-ethnic populations, we conducted international meta-analysis using eight cohorts. In total, we analyzed 8,756 cases and 27,822 controls. The analysis showed a convincing evidence of association between rs3904778 and AIS. Seven out of eight cohorts had significant P value, and remaining one cohort also had the same trend as the seven. The combined P was 3.28 × 10−18 (odds ratio = 1.19, 95% confidence interval = 1.14–1.24). In silico analyses suggested that BNC2 is the AIS susceptibility gene in this locus.
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Affiliation(s)
- Yoji Ogura
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kazuki Takeda
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Ikuyo Kou
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Anas Khanshour
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Anna Grauers
- Department of Orthopaedics, Sundsvall and Härnösand County Hospital, Sundsvall, Sweden.,Department of Clinical Science, Intervention and Technology (CLINTEC) Karolinska Institutet, Stockholm, Sweden
| | - Hang Zhou
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yan-Hui Fan
- Department of Biochemistry, University of Hong Kong, Hong Kong, China
| | - Taifeng Zhou
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zhihong Wu
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Yohei Takahashi
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | | | | | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juha Kere
- Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Dongsheng Huang
- Department of Spine Surgery, The Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Leilei Xu
- Department of Spine Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Yong Qiu
- Department of Spine Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - You-Qiang Song
- Department of Biochemistry, University of Hong Kong, Hong Kong, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Peiqiang Su
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Paul Gerdhem
- Department of Clinical Science, Intervention and Technology (CLINTEC) Karolinska Institutet, Stockholm, Sweden.,Department of Orthopaedics, Karolinska University Hospital, Huddinge, Sweden
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan.
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan.
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25
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Giampietro PF, Pourquie O, Raggio C, Ikegawa S, Turnpenny PD, Gray R, Dunwoodie SL, Gurnett CA, Alman B, Cheung K, Kusumi K, Hadley-Miller N, Wise CA. Summary of the first inaugural joint meeting of the International Consortium for scoliosis genetics and the International Consortium for vertebral anomalies and scoliosis, March 16-18, 2017, Dallas, Texas. Am J Med Genet A 2018; 176:253-256. [PMID: 29159998 PMCID: PMC6525596 DOI: 10.1002/ajmg.a.38550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 10/05/2017] [Revised: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 12/13/2022]
Abstract
Scoliosis represents the most common musculoskeletal disorder in children and affects approximately 3% of the world population. Scoliosis is separated into two major phenotypic classifications: congenital and idiopathic. Idiopathic scoliosis is defined as a curvature of the spine of 10° or greater visualized on plane radiograph and does not have associated vertebral malformations (VM). "Congenital" scoliosis (CS) due to malformations in vertebrae is frequently associated with other birth defects. Recently, significant advances have been made in understanding the genetic basis of both conditions. There is evidence that both conditions are etiologically related. A 2-day conference entitled "Genomic Approaches to Understanding and Treating Scoliosis" was held at Scottish Rite Hospital for Children in Dallas, Texas, to synergize research in this field. This first combined, multidisciplinary conference featured international scoliosis researchers in basic and clinical sciences. A major outcome of the conference advancing scoliosis research was the proposal and subsequent vote in favor of merging the International Consortium for Vertebral Anomalies and Scoliosis (ICVAS) and International Consortium for Scoliosis Genetics (ICSG) into a single entity called International Consortium for Spinal Genetics, Development, and Disease (ICSGDD). The ICSGDD is proposed to meet annually as a forum to synergize multidisciplinary spine deformity research.
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Affiliation(s)
| | | | - Cathy Raggio
- Hospital for Special Surgery, New York, New York
| | - Shiro Ikegawa
- RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | | | | | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | | | | | | | | | | | - Carol A Wise
- Texas Scottish Rite Hospital for Children, Dallas, Texas.,University of Texas Southwestern Medical Center, Dallas, Texas
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26
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McIntosh LA, Marion MC, Sudman M, Comeau ME, Becker ML, Bohnsack JF, Fingerlin TE, Griffin TA, Haas JP, Lovell DJ, Maier LA, Nigrovic PA, Prahalad S, Punaro M, Rosé CD, Wallace CA, Wise CA, Moncrieffe H, Howard TD, Langefeld CD, Thompson SD. Genome-Wide Association Meta-Analysis Reveals Novel Juvenile Idiopathic Arthritis Susceptibility Loci. Arthritis Rheumatol 2017; 69:2222-2232. [PMID: 28719732 DOI: 10.1002/art.40216] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/13/2017] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease and has a strong genomic component. To date, JIA genetic association studies have had limited sample sizes, used heterogeneous patient populations, or included only candidate regions. The aim of this study was to identify new associations between JIA patients with oligoarticular disease and those with IgM rheumatoid factor (RF)-negative polyarticular disease, which are clinically similar and the most prevalent JIA disease subtypes. METHODS Three cohorts comprising 2,751 patients with oligoarticular or RF-negative polyarticular JIA were genotyped using the Affymetrix Genome-Wide SNP Array 6.0 or the Illumina HumanCoreExome-12+ Array. Overall, 15,886 local and out-of-study controls, typed on these platforms or the Illumina HumanOmni2.5, were used for association analyses. High-quality single-nucleotide polymorphisms (SNPs) were used for imputation to 1000 Genomes prior to SNP association analysis. RESULTS Meta-analysis showed evidence of association (P < 1 × 10-6 ) at 9 regions: PRR9_LOR (P = 5.12 × 10-8 ), ILDR1_CD86 (P = 6.73 × 10-8 ), WDFY4 (P = 1.79 × 10-7 ), PTH1R (P = 1.87 × 10-7 ), RNF215 (P = 3.09 × 10-7 ), AHI1_LINC00271 (P = 3.48 × 10-7 ), JAK1 (P = 4.18 × 10-7 ), LINC00951 (P = 5.80 × 10-7 ), and HBP1 (P = 7.29 × 10-7 ). Of these, PRR9_LOR, ILDR1_CD86, RNF215, LINC00951, and HBP1 were shown, for the first time, to be autoimmune disease susceptibility loci. Furthermore, associated SNPs included cis expression quantitative trait loci for WDFY4, CCDC12, MTP18, SF3A1, AHI1, COG5, HBP1, and GPR22. CONCLUSION This study provides evidence of both unique JIA risk loci and risk loci overlapping between JIA and other autoimmune diseases. These newly associated SNPs are shown to influence gene expression, and their bounding regions tie into molecular pathways of immunologic relevance. Thus, they likely represent regions that contribute to the pathology of oligoarticular JIA and RF-negative polyarticular JIA.
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Affiliation(s)
- Laura A McIntosh
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
| | - Miranda C Marion
- Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Marc Sudman
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Mary E Comeau
- Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | | | | | | | | | - J Peter Haas
- German Center for Pediatric and Adolescent Rheumatology, Garmisch-Partenkirchen, Germany
| | - Daniel J Lovell
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
| | - Lisa A Maier
- National Jewish Health and University of Colorado, Denver
| | - Peter A Nigrovic
- Boston Children's Hospital and Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Marilynn Punaro
- Texas Scottish Rite Hospital for Children and UT Southwestern Medical Center, Dallas, Texas
| | | | - Carol A Wallace
- Seattle Children's Hospital and Research Institute, Seattle, Washington
| | - Carol A Wise
- Texas Scottish Rite Hospital for Children, McDermott Center for Human Growth and Development, and UT Southwestern Medical Center, Dallas, Texas
| | - Halima Moncrieffe
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
| | | | | | - Susan D Thompson
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
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27
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Martin CA, Murray JE, Carroll P, Leitch A, MacKenzie KJ, Halachev M, Fetit AE, Keith C, Bicknell LS, Fluteau A, Gautier P, Hall EA, Joss S, Soares G, Silva J, Bober MB, Duker A, Wise CA, Quigley AJ, Phadke SR, Wood AJ, Vagnarelli P, Jackson AP. Corrigendum: Mutations in genes encoding condensins cause microcephaly through decatenation failure at mitosis. Genes Dev 2017; 31:953. [DOI: 10.1101/gad.300871.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Hinks A, Bowes J, Cobb J, Ainsworth HC, Marion MC, Comeau ME, Sudman M, Han B, Becker ML, Bohnsack JF, de Bakker PIW, Haas JP, Hazen M, Lovell DJ, Nigrovic PA, Nordal E, Punnaro M, Rosenberg AM, Rygg M, Smith SL, Wise CA, Videm V, Wedderburn LR, Yarwood A, Yeung RSM, Prahalad S, Langefeld CD, Raychaudhuri S, Thompson SD, Thomson W. Fine-mapping the MHC locus in juvenile idiopathic arthritis (JIA) reveals genetic heterogeneity corresponding to distinct adult inflammatory arthritic diseases. Ann Rheum Dis 2016; 76:765-772. [PMID: 27998952 PMCID: PMC5530326 DOI: 10.1136/annrheumdis-2016-210025] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [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: 06/07/2016] [Revised: 09/12/2016] [Accepted: 11/05/2016] [Indexed: 11/06/2022]
Abstract
Objectives Juvenile idiopathic arthritis (JIA) is a heterogeneous group of diseases, comprising seven categories. Genetic data could potentially be used to help redefine JIA categories and improve the current classification system. The human leucocyte antigen (HLA) region is strongly associated with JIA. Fine-mapping of the region was performed to look for similarities and differences in HLA associations between the JIA categories and define correspondences with adult inflammatory arthritides. Methods Dense genotype data from the HLA region, from the Immunochip array for 5043 JIA cases and 14 390 controls, were used to impute single-nucleotide polymorphisms, HLA classical alleles and amino acids. Bivariate analysis was performed to investigate genetic correlation between the JIA categories. Conditional analysis was used to identify additional effects within the region. Comparison of the findings with those in adult inflammatory arthritic diseases was performed. Results We identified category-specific associations and have demonstrated for the first time that rheumatoid factor (RF)-negative polyarticular JIA and oligoarticular JIA are genetically similar in their HLA associations. We also observe that each JIA category potentially has an adult counterpart. The RF-positive polyarthritis association at HLA-DRB1 amino acid at position 13 mirrors the association in adult seropositive rheumatoid arthritis (RA). Interestingly, the combined oligoarthritis and RF-negative polyarthritis dataset shares the same association with adult seronegative RA. Conclusions The findings suggest the value of using genetic data in helping to classify the categories of this heterogeneous disease. Mapping JIA categories to adult counterparts could enable shared knowledge of disease pathogenesis and aetiology and facilitate transition from paediatric to adult services.
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Affiliation(s)
- A Hinks
- Arthritis Research UK Centre for Genetics and Genomics, Manchester Academic Health Science Centre, University Of Manchester, Manchester, UK
| | - J Bowes
- Arthritis Research UK Centre for Genetics and Genomics, Manchester Academic Health Science Centre, University Of Manchester, Manchester, UK
| | - J Cobb
- Arthritis Research UK Centre for Genetics and Genomics, Manchester Academic Health Science Centre, University Of Manchester, Manchester, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - H C Ainsworth
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - M C Marion
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - M E Comeau
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - M Sudman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - B Han
- Divisions of Genetics and Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA.,Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | | | - M L Becker
- Division of Rheumatology and Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy-Kansas City, Kansas City, Missouri, USA
| | - J F Bohnsack
- Division of Allergy, Immunology and Paediatric Rheumatology, University of Utah, Salt Lake City, Utah, USA
| | - P I W de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - J P Haas
- German Center for Pediatric and Adolescent Rheumatology, Garmisch-Partenkirchen, Germany
| | - M Hazen
- Division of Immunology, Department of Rheumatology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - D J Lovell
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - P A Nigrovic
- Division of Immunology, Department of Rheumatology, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - E Nordal
- Department of Paediatrics, University Hospital of North Norway, and UIT The Arctic University of Norway, Tromsø, Norway
| | - M Punnaro
- Arthritis Clinic Texas Scottish Rite Hospital for Children, Dallas, Texas, USA.,Department of Paediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - A M Rosenberg
- Division of Rheumatology, Department of Paediatrics, University of Saskatchewan, Saskatoon, Canada
| | - M Rygg
- Department of Laboratory Medicine, Children's and Women's Health, NTNU - Norwegian University of Science and Technology, and St. Olavs University Hospital, Trondheim, Norway
| | - S L Smith
- Arthritis Research UK Centre for Genetics and Genomics, Manchester Academic Health Science Centre, University Of Manchester, Manchester, UK
| | - C A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA.,Department of Orthopaedic Surgery, Paediatrics, and McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas, USA
| | - V Videm
- Department of Laboratory Medicine, Children's and Women's Health, NTNU - Norwegian University of Science and Technology, and St. Olavs University Hospital, Trondheim, Norway
| | - L R Wedderburn
- Arthritis Research UK Centre for Adolescent Rheumatology, UCL GOS Institute of Child Health, University College London, London, UK.,NIHR-Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - A Yarwood
- Arthritis Research UK Centre for Genetics and Genomics, Manchester Academic Health Science Centre, University Of Manchester, Manchester, UK
| | - R S M Yeung
- The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - S Prahalad
- Department of Paediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, USA
| | - C D Langefeld
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - S Raychaudhuri
- Arthritis Research UK Centre for Genetics and Genomics, Manchester Academic Health Science Centre, University Of Manchester, Manchester, UK.,Divisions of Genetics and Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA.,Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - S D Thompson
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - W Thomson
- Arthritis Research UK Centre for Genetics and Genomics, Manchester Academic Health Science Centre, University Of Manchester, Manchester, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
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29
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Martin CA, Murray JE, Carroll P, Leitch A, Mackenzie KJ, Halachev M, Fetit AE, Keith C, Bicknell LS, Fluteau A, Gautier P, Hall EA, Joss S, Soares G, Silva J, Bober MB, Duker A, Wise CA, Quigley AJ, Phadke SR, Wood AJ, Vagnarelli P, Jackson AP. Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis. Genes Dev 2016; 30:2158-2172. [PMID: 27737959 PMCID: PMC5088565 DOI: 10.1101/gad.286351.116] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [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: 06/29/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022]
Abstract
Martin et al. report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of condensin complexes, cause microcephaly. Frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis are the consequence of failed sister chromatid disentanglement during chromosome compaction. Compaction of chromosomes is essential for accurate segregation of the genome during mitosis. In vertebrates, two condensin complexes ensure timely chromosome condensation, sister chromatid disentanglement, and maintenance of mitotic chromosome structure. Here, we report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of these complexes, cause microcephaly. In addition, hypomorphic Ncaph2 mice have significantly reduced brain size, with frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis. Such DNA bridges also arise in condensin-deficient patient cells, where they are the consequence of failed sister chromatid disentanglement during chromosome compaction. This results in chromosome segregation errors, leading to micronucleus formation and increased aneuploidy in daughter cells. These findings establish “condensinopathies” as microcephalic disorders, with decatenation failure as an additional disease mechanism for microcephaly, implicating mitotic chromosome condensation as a key process ensuring mammalian cerebral cortex size.
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Affiliation(s)
- Carol-Anne Martin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Jennie E Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paula Carroll
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Andrea Leitch
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Karen J Mackenzie
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Mihail Halachev
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Ahmed E Fetit
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Charlotte Keith
- South East Scotland Cytogenetics Service, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Louise S Bicknell
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.,Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Adeline Fluteau
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Emma A Hall
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Shelagh Joss
- West of Scotland Genetic Service, Southern General Hospital, Glasgow G51 4TF, United Kingdom
| | - Gabriela Soares
- Centro de Genética Médica Doutor Jacinto Magalhães, Centro Hospitalar do Porto, 4099-028 Porto, Portugal
| | - João Silva
- Instituto de Biologia Molecular e Celular (IBMC), 4150 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Michael B Bober
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Angela Duker
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,Department of Pediatrics, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas 75350, USA
| | - Alan J Quigley
- Department of Radiology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, United Kingdom
| | - Shubha R Phadke
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh 226014, India
| | | | - Andrew J Wood
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paola Vagnarelli
- Biosciences, Research Institute for Health and Environment, Brunel University, London UB8 3PH, United Kingdom
| | - Andrew P Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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30
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Raj P, Rai E, Song R, Khan S, Wakeland BE, Viswanathan K, Arana C, Liang C, Zhang B, Dozmorov I, Carr-Johnson F, Mitrovic M, Wiley GB, Kelly JA, Lauwerys BR, Olsen NJ, Cotsapas C, Garcia CK, Wise CA, Harley JB, Nath SK, James JA, Jacob CO, Tsao BP, Pasare C, Karp DR, Li QZ, Gaffney PM, Wakeland EK. Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity. eLife 2016; 5:e12089. [PMID: 26880555 PMCID: PMC4811771 DOI: 10.7554/elife.12089] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [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: 10/05/2015] [Accepted: 02/13/2016] [Indexed: 12/15/2022] Open
Abstract
Targeted sequencing of sixteen SLE risk loci among 1349 Caucasian cases and controls produced a comprehensive dataset of the variations causing susceptibility to systemic lupus erythematosus (SLE). Two independent disease association signals in the HLA-D region identified two regulatory regions containing 3562 polymorphisms that modified thirty-seven transcription factor binding sites. These extensive functional variations are a new and potent facet of HLA polymorphism. Variations modifying the consensus binding motifs of IRF4 and CTCF in the XL9 regulatory complex modified the transcription of HLA-DRB1, HLA-DQA1 and HLA-DQB1 in a chromosome-specific manner, resulting in a 2.5-fold increase in the surface expression of HLA-DR and DQ molecules on dendritic cells with SLE risk genotypes, which increases to over 4-fold after stimulation. Similar analyses of fifteen other SLE risk loci identified 1206 functional variants tightly linked with disease-associated SNPs and demonstrated that common disease alleles contain multiple causal variants modulating multiple immune system genes.
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Affiliation(s)
- Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ekta Rai
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ran Song
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shaheen Khan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Benjamin E Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kasthuribai Viswanathan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carlos Arana
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chaoying Liang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Bo Zhang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ferdicia Carr-Johnson
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Mitja Mitrovic
- Department of Neurology, Yale School of Medicine, New Haven, United States
| | - Graham B Wiley
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Bernard R Lauwerys
- Pole de pathologies rhumatismales, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Bruxelles, Belgium
| | - Nancy J Olsen
- Division of Rheumatology, Department of Medicine, Penn State Medical School, Hershey, United States
| | - Chris Cotsapas
- Department of Neurology, Yale School of Medicine, New Haven, United States
| | - Christine K Garcia
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carol A Wise
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, United States
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, United States
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - John B Harley
- Cincinnati VA Medical Center, Cincinnati, United States
- Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Swapan K Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Chaim O Jacob
- Department of Medicine, University of Southern California, Los Angeles, United States
| | - Betty P Tsao
- Department of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Chandrashekhar Pasare
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - David R Karp
- Rheumatic Diseases Division, Department of Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Quan Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
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Li YR, Li J, Zhao SD, Bradfield JP, Mentch FD, Maggadottir SM, Hou C, Abrams DJ, Chang D, Gao F, Guo Y, Wei Z, Connolly JJ, Cardinale CJ, Bakay M, Glessner JT, Li D, Kao C, Thomas KA, Qiu H, Chiavacci RM, Kim CE, Wang F, Snyder J, Richie MD, Flatø B, Førre Ø, Denson LA, Thompson SD, Becker ML, Guthery SL, Latiano A, Perez E, Resnick E, Russell RK, Wilson DC, Silverberg MS, Annese V, Lie BA, Punaro M, Dubinsky MC, Monos DS, Strisciuglio C, Staiano A, Miele E, Kugathasan S, Ellis JA, Munro JE, Sullivan KE, Wise CA, Chapel H, Cunningham-Rundles C, Grant SFA, Orange JS, Sleiman PMA, Behrens EM, Griffiths AM, Satsangi J, Finkel TH, Keinan A, Prak ETL, Polychronakos C, Baldassano RN, Li H, Keating BJ, Hakonarson H. Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. Nat Med 2015; 21:1018-27. [PMID: 26301688 DOI: 10.1038/nm.3933] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 07/23/2015] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of susceptibility genes, including shared associations across clinically distinct autoimmune diseases. We performed an inverse χ(2) meta-analysis across ten pediatric-age-of-onset autoimmune diseases (pAIDs) in a case-control study including more than 6,035 cases and 10,718 shared population-based controls. We identified 27 genome-wide significant loci associated with one or more pAIDs, mapping to in silico-replicated autoimmune-associated genes (including IL2RA) and new candidate loci with established immunoregulatory functions such as ADGRL2, TENM3, ANKRD30A, ADCY7 and CD40LG. The pAID-associated single-nucleotide polymorphisms (SNPs) were functionally enriched for deoxyribonuclease (DNase)-hypersensitivity sites, expression quantitative trait loci (eQTLs), microRNA (miRNA)-binding sites and coding variants. We also identified biologically correlated, pAID-associated candidate gene sets on the basis of immune cell expression profiling and found evidence of genetic sharing. Network and protein-interaction analyses demonstrated converging roles for the signaling pathways of type 1, 2 and 17 helper T cells (TH1, TH2 and TH17), JAK-STAT, interferon and interleukin in multiple autoimmune diseases.
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Affiliation(s)
- Yun R Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jin Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sihai D Zhao
- Department of Biostatistics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jonathan P Bradfield
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frank D Mentch
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - S Melkorka Maggadottir
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cuiping Hou
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Debra J Abrams
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Diana Chang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.,Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, USA
| | - Feng Gao
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | - Yiran Guo
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - John J Connolly
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christopher J Cardinale
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marina Bakay
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joseph T Glessner
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dong Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Charlly Kao
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kelly A Thomas
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Haijun Qiu
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rosetta M Chiavacci
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cecilia E Kim
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Fengxiang Wang
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - James Snyder
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marylyn D Richie
- Department of Biochemistry and Molecular Biology, Eberly College of Science, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Berit Flatø
- Department of Rheumatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Øystein Førre
- Department of Rheumatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Lee A Denson
- Division of Gastroenterology, The Center for Inflammatory Bowel Disease, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Susan D Thompson
- Divison of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mara L Becker
- Division of Rheumatology, Children's Mercy Hospitals and Clinics, Kansas City, Missouri, USA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah School of Medicine and Primary Children's Medical Center, Salt Lake City, Utah, USA
| | - Anna Latiano
- Division of Gastroenterology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Elena Perez
- Division of Pediatric Allergy and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Elena Resnick
- Institute of Immunology and Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Yorkhill Hospital for Sick Children, Glasgow, Scotland, UK
| | - David C Wilson
- Paediatric Gastroenterology and Nutrition, Royal Hospital for Sick Children, University of Edinburgh, Ediburgh, UK
| | - Mark S Silverberg
- Mount Sinai Hospital IBD Centre, University of Toronto, Toronto, Ontario, Canada
| | - Vito Annese
- Unit of Gastroenterology, Department of Medical and Surgical Specialties, Careggi University Hospital, Florence, Italy
| | - Benedicte A Lie
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Marilynn Punaro
- Department of Rheumatology, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Marla C Dubinsky
- Department of Pediatrics, Pediatric IBD Center, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Dimitri S Monos
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Caterina Strisciuglio
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Annamaria Staiano
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Erasmo Miele
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine and Children's Health Care of Atlanta, Atlanta, Georgia, USA
| | - Justine A Ellis
- Genes, Environment and Complex Disease, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Pediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Jane E Munro
- Pediatric Rheumatology Unit, Royal Children's Hospital, Parkville, Victoria, Australia.,Arthritis and Rheumatology Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Helen Chapel
- Department of Clinical Immunology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Struan F A Grant
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jordan S Orange
- Section of Immunology, Allergy, and Rheumatology, Department of Pediatric Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Patrick M A Sleiman
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward M Behrens
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Rheumatology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Anne M Griffiths
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Jack Satsangi
- Gastrointestinal Unit, Division of Medical Sciences, School of Molecular and Clinical Medicine, University of Edinburgh, Edinburgh, UK
| | - Terri H Finkel
- Department of Pediatrics, Nemours Children's Hospital, Orlando, Florida, USA
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.,Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, USA
| | - Eline T Luning Prak
- Department of Pathology and Lab Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Constantin Polychronakos
- Departments of Pediatrics and Human Genetics, McGill University Health Centre Research Institute, Montréal, Québec, Canada
| | - Robert N Baldassano
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Gastroenterology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hongzhe Li
- Department of Pathology and Lab Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J Keating
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Pulmonary Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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Sharma S, Londono D, Eckalbar WL, Gao X, Zhang D, Mauldin K, Kou I, Takahashi A, Matsumoto M, Kamiya N, Murphy KK, Cornelia R, Herring JA, Burns D, Ahituv N, Ikegawa S, Gordon D, Wise CA. A PAX1 enhancer locus is associated with susceptibility to idiopathic scoliosis in females. Nat Commun 2015; 6:6452. [PMID: 25784220 PMCID: PMC4365504 DOI: 10.1038/ncomms7452] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [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: 08/04/2014] [Accepted: 01/30/2015] [Indexed: 12/12/2022] Open
Abstract
Idiopathic scoliosis (IS) is a common paediatric musculoskeletal disease that displays a strong female bias. By performing a genome-wide association study (GWAS) of 3,102 individuals, we identify significant associations with 20p11.22 SNPs for females (P=6.89 × 10−9) but not males (P=0.71). This association with IS is also found in independent female cohorts from the United States of America and Japan (overall P=2.15 × 10−10, OR=1.30 (rs6137473)). Unexpectedly, the 20p11.22 IS risk alleles were previously associated with protection from early-onset alopecia, another sexually dimorphic condition. The 174-kb associated locus is distal to PAX1, which encodes paired box 1, a transcription factor involved in spine development. We identify a sequence in the associated locus with enhancer activity in zebrafish somitic muscle and spinal cord, an activity that is abolished by IS-associated SNPs. We thus identify a sexually dimorphic IS susceptibility locus, and propose the first functionally defined candidate mutations in an enhancer that may regulate expression in specific spinal cells. Girls are tenfold more likely than boys to require surgical treatment for idiopathic scoliosis, a common paediatric skeletal disorder. Here, Sharma et al. identify the first sexually dimorphic idiopathic scoliosis risk locus, and demonstrate that it may play a role in the regulation of spinal cells.
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Affiliation(s)
- Swarkar Sharma
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Research Department, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA
| | - Douglas Londono
- Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Walter L Eckalbar
- Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, California 94143, USA
| | - Xiaochong Gao
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Research Department, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA
| | - Dongping Zhang
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Research Department, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA
| | - Kristen Mauldin
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Research Department, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA
| | - Ikuyo Kou
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo 108-8639, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama 230-0045, Japan
| | - Morio Matsumoto
- Department of Orthopaedic Surgery, School of Medicine, Keio University, Tokyo 108-8345, Japan
| | - Nobuhiro Kamiya
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Research Department, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA
| | - Karl K Murphy
- Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, California 94143, USA
| | - Reuel Cornelia
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Research Department, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA
| | | | | | - John A Herring
- 1] Department of Orthopaedics, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA [2] Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
| | - Dennis Burns
- Department of Pathology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, California 94143, USA
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo 108-8639, Japan
| | - Derek Gordon
- Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Carol A Wise
- 1] Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Research Department, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA [2] Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA [3] McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA [4] McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
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Paria N, Cho TJ, Choi IH, Kamiya N, Kayembe K, Mao R, Margraf RL, Obermosser G, Oxendine I, Sant DW, Song MH, Stevenson DA, Viskochil DH, Wise CA, Kim HKW, Rios JJ. Neurofibromin deficiency-associated transcriptional dysregulation suggests a novel therapy for tibial pseudoarthrosis in NF1. J Bone Miner Res 2014; 29:2636-42. [PMID: 24932921 PMCID: PMC4268180 DOI: 10.1002/jbmr.2298] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/09/2014] [Accepted: 06/12/2014] [Indexed: 12/25/2022]
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant disease caused by mutations in NF1. Among the earliest manifestations is tibial pseudoarthrosis and persistent nonunion after fracture. To further understand the pathogenesis of pseudoarthrosis and the underlying bone remodeling defect, pseudoarthrosis tissue and cells cultured from surgically resected pseudoarthrosis tissue from NF1 individuals were analyzed using whole-exome and whole-transcriptome sequencing as well as genomewide microarray analysis. Genomewide analysis identified multiple genetic mechanisms resulting in somatic biallelic NF1 inactivation; no other genes with recurring somatic mutations were identified. Gene expression profiling identified dysregulated pathways associated with neurofibromin deficiency, including phosphoinositide 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) signaling pathways. Unlike aggressive NF1-associated malignancies, tibial pseudoarthrosis tissue does not harbor a high frequency of somatic mutations in oncogenes or other tumor-suppressor genes, such as p53. However, gene expression profiling indicates that pseudoarthrosis tissue has a tumor-promoting transcriptional pattern, despite lacking tumorigenic somatic mutations. Significant overexpression of specific cancer-associated genes in pseudoarthrosis highlights a potential for receptor tyrosine kinase inhibitors to target neurofibromin-deficient pseudoarthrosis and promote proper bone remodeling and fracture healing.
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Affiliation(s)
- Nandina Paria
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
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Gao X, Gotway G, Rathjen K, Johnston C, Sparagana S, Wise CA. Genomic Analyses of Patients With Unexplained Early-Onset Scoliosis. Spine Deform 2014; 2:324-332. [PMID: 27927329 PMCID: PMC4228381 DOI: 10.1016/j.jspd.2014.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 03/17/2014] [Accepted: 04/21/2014] [Indexed: 12/20/2022]
Abstract
STUDY DESIGN To test for rare genetic mutations, a cohort of patients with unexplained early-onset scoliosis (EOS) was screened using high-density microarray genotyping. A cohort of patients with adolescent idiopathic scoliosis (AIS) was similarly screened and the results were compared. SUMMARY OF BACKGROUND DATA Patients with scoliosis in infancy or early childhood (EOS) are at high risk for progressive deformity and associated problems including respiratory compromise. Early-onset scoliosis is frequently associated with genetic disorders but many patients present with nonspecific clinical features and without an associated diagnosis. The authors hypothesized that EOS in these patients may be caused by rare genetic mutations detectable by next-generation genomic methods. METHODS The researchers identified 24 patients with unexplained EOS from pediatric orthopedic clinics. They genotyped them, along with 39 connecting family members, using the Illumina OmniExpress-12, version 1.0 beadchip. Resulting genotypes were analyzed for chromosomal changes, specifically copy number variation and absence of heterozygosity. They screened 482 adolescent idiopathic scoliosis (AIS) patients and 744 healthy controls, who were similarly genotyped with the same beadchip, for chromosomal changes identified in the EOS cohort. RESULTS Copy number variation and absence of heterozygosity analyses revealed a genetic diagnosis of chromosome 15q24 microdeletion syndrome in 1 patient and maternal uniparental disomy of chromosome 14 in a second one. Prior genetic testing and clinical evaluations had been negative in both cases. A large novel chromosome 10 deletion was likely causal in a third EOS patient. These mutations identified in the EOS patients were absent in AIS patients and controls, and thus were not associated with AIS or found in asymptomatic individuals. CONCLUSIONS These data underscore the usefulness of updated genetic evaluations including high-density microarray-based genotyping and other next-generation methods in patients with unexplained EOS, even when prior genetic studies were negative. These data also suggest the intriguing possibility that other mutations detectable by whole genome sequencing, as well as epigenetic effects, await discovery in the EOS population.
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Affiliation(s)
- Xiaochong Gao
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children. Dallas, TX
| | - Garrett Gotway
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Karl Rathjen
- Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Charles Johnston
- Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Steven Sparagana
- Department of Neurology, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Carol A. Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX,To whom correspondence should be directed. Telephone: 214-559-7861 Fax: 214-559-7872
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35
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Londono D, Kou I, Johnson TA, Sharma S, Ogura Y, Tsunoda T, Takahashi A, Matsumoto M, Herring JA, Lam TP, Wang X, Tam EMS, Song YQ, Fan YH, Chan D, Cheah KSE, Qiu X, Jiang H, Huang D, Su P, Sham P, Cheung KMC, Luk KDK, Gordon D, Qiu Y, Cheng J, Tang N, Ikegawa S, Wise CA. A meta-analysis identifies adolescent idiopathic scoliosis association withLBX1locus in multiple ethnic groups. J Med Genet 2014; 51:401-6. [DOI: 10.1136/jmedgenet-2013-102067] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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36
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Paria N, Copley LA, Herring JA, Kim HKW, Richards BS, Sucato DJ, Rios JJ, Wise CA. The impact of large-scale genomic methods in orthopaedic disorders: insights from genome-wide association studies. J Bone Joint Surg Am 2014; 96:e38. [PMID: 24599210 DOI: 10.2106/jbjs.m.00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Nandina Paria
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Lawson A Copley
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - John A Herring
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Harry K W Kim
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - B Stephens Richards
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Daniel J Sucato
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Jonathan J Rios
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
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37
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Paria N, Copley LA, Herring JA, Kim HKW, Richards BS, Sucato DJ, Wise CA, Rios JJ. Whole-exome sequencing: discovering genetic causes of orthopaedic disorders. J Bone Joint Surg Am 2013; 95:e1851-8. [PMID: 24306708 DOI: 10.2106/jbjs.l.01620] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Nandina Paria
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., C.A.W., and J.J.R.), Department of Orthopaedics (L.A.C., J.A.H, B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-mail address for J.J. Rios:
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Murray JE, Bicknell LS, Yigit G, Duker AL, van Kogelenberg M, Haghayegh S, Wieczorek D, Kayserili H, Albert MH, Wise CA, Brandon J, Kleefstra T, Warris A, van der Flier M, Bamforth JS, Doonanco K, Adès L, Ma A, Field M, Johnson D, Shackley F, Firth H, Woods CG, Nürnberg P, Gatti RA, Hurles M, Bober MB, Wollnik B, Jackson AP. Extreme growth failure is a common presentation of ligase IV deficiency. Hum Mutat 2013; 35:76-85. [PMID: 24123394 PMCID: PMC3995017 DOI: 10.1002/humu.22461] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 09/24/2013] [Indexed: 12/20/2022]
Abstract
Ligase IV syndrome is a rare differential diagnosis for Nijmegen breakage syndrome owing to a shared predisposition to lympho-reticular malignancies, significant microcephaly, and radiation hypersensitivity. Only 16 cases with mutations in LIG4 have been described to date with phenotypes varying from malignancy in developmentally normal individuals, to severe combined immunodeficiency and early mortality. Here, we report the identification of biallelic truncating LIG4 mutations in 11 patients with microcephalic primordial dwarfism presenting with restricted prenatal growth and extreme postnatal global growth failure (average OFC -10.1 s.d., height -5.1 s.d.). Subsequently, most patients developed thrombocytopenia and leucopenia later in childhood and many were found to have previously unrecognized immunodeficiency following molecular diagnosis. None have yet developed malignancy, though all patients tested had cellular radiosensitivity. A genotype-phenotype correlation was also noted with position of truncating mutations corresponding to disease severity. This work extends the phenotypic spectrum associated with LIG4 mutations, establishing that extreme growth retardation with microcephaly is a common presentation of bilallelic truncating mutations. Such growth failure is therefore sufficient to consider a diagnosis of LIG4 deficiency and early recognition of such cases is important as bone marrow failure, immunodeficiency, and sometimes malignancy are long term sequelae of this disorder.
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Affiliation(s)
- Jennie E Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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Prahalad S, Conneely KN, Jiang Y, Sudman M, Wallace CA, Brown MR, Ponder LA, Rohani-Pichavant M, Zwick ME, Cutler DJ, Angeles-Han ST, Vogler LB, Kennedy C, Rouster-Stevens K, Wise CA, Punaro M, Reed AM, Mellins ED, Bohnsack JF, Glass DN, Thompson SD. Susceptibility to childhood-onset rheumatoid arthritis: investigation of a weighted genetic risk score that integrates cumulative effects of variants at five genetic loci. Arthritis Rheum 2013; 65:1663-7. [PMID: 23450725 PMCID: PMC3683854 DOI: 10.1002/art.37913] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 02/19/2013] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Children with childhood-onset rheumatoid arthritis (RA) include those with rheumatoid factor or anti-citrullinated protein antibody-positive juvenile idiopathic arthritis. To test the hypothesis that adult-onset RA-associated variants are also associated with childhood-onset RA, we investigated RA-associated variants at 5 loci in a cohort of patients with childhood-onset RA. We also assessed the cumulative association of these variants in susceptibility to childhood-onset RA using a weighted genetic risk score (wGRS). METHODS A total of 155 children with childhood-onset RA and 684 healthy controls were genotyped for 5 variants in the PTPN22, TRAF1/C5, STAT4, and TNFAIP3 loci. High-resolution HLA-DRB1 genotypes were available for 149 cases and 373 controls. We tested each locus for association with childhood-onset RA via logistic regression. We also computed a wGRS for each subject, with weights based on the natural log of the published odds ratios (ORs) for the alleles investigated, and used logistic regression to test the wGRS for association with childhood-onset RA. RESULTS Childhood-onset RA was associated with TNFAIP3 rs10499194 (OR 0.60 [95% confidence interval 0.44-0.83]), PTPN22 rs2476601 (OR 1.61 [95% confidence interval 1.11-2.31]), and STAT4 rs7574865 (OR 1.41 [95% confidence interval 1.06-1.87]) variants. The wGRS was significantly different between cases and controls (P < 2 × 10(-16) ). Individuals in the third to fifth quintiles of wGRS had a significantly increased disease risk compared to baseline (individuals in the first quintile). Higher wGRS was associated with increased risk of childhood-onset RA, especially among males. CONCLUSION The magnitude and direction of the association between TNFAIP3, STAT4, and PTPN22 variants and childhood-onset RA are similar to those observed in RA, suggesting that adult-onset RA and childhood-onset RA share common genetic risk factors. Using a wGRS, we have demonstrated the cumulative association of RA-associated variants with susceptibility to childhood-onset RA.
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Affiliation(s)
- Sampath Prahalad
- Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA
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Kou I, Takahashi Y, Johnson TA, Takahashi A, Guo L, Dai J, Qiu X, Sharma S, Takimoto A, Ogura Y, Jiang H, Yan H, Kono K, Kawakami N, Uno K, Ito M, Minami S, Yanagida H, Taneichi H, Hosono N, Tsuji T, Suzuki T, Sudo H, Kotani T, Yonezawa I, Londono D, Gordon D, Herring JA, Watanabe K, Chiba K, Kamatani N, Jiang Q, Hiraki Y, Kubo M, Toyama Y, Tsunoda T, Wise CA, Qiu Y, Shukunami C, Matsumoto M, Ikegawa S. Genetic variants in GPR126 are associated with adolescent idiopathic scoliosis. Nat Genet 2013; 45:676-9. [PMID: 23666238 DOI: 10.1038/ng.2639] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/19/2013] [Indexed: 11/09/2022]
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common pediatric skeletal disease. We previously reported a locus on chromosome 10q24.31 associated with AIS susceptibility in Japanese using a genome-wide association study (GWAS) consisting of 1,033 cases and 1,473 controls. To identify additional AIS-associated loci, we expanded the study by adding X-chromosome SNPs in the GWAS and increasing the size of the replication cohorts. Through a stepwise association study including 1,819 cases and 25,939 controls, we identified a new susceptibility locus on chromosome 6q24.1 in Japanese (P = 2.25 × 10(-10); odds ratio (OR) = 1.28). The most significantly associated SNP, rs6570507, was in GPR126 (encoding G protein-coupled receptor 126). Its association was replicated in Han Chinese and European-ancestry populations (combined P = 1.27 × 10(-14); OR = 1.27). GPR126 was highly expressed in cartilage, and the knockdown of gpr126 in zebrafish caused delayed ossification of the developing spine. Our results should provide insights into the etiology and pathogenesis of AIS.
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Affiliation(s)
- Ikuyo Kou
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
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Geusau A, Mothes-Luksch N, Nahavandi H, Pickl WF, Wise CA, Pourpak Z, Ponweiser E, Eckhart L, Sunder-Plassmann R. Identification of a homozygous PSTPIP1 mutation in a patient with a PAPA-like syndrome responding to canakinumab treatment. JAMA Dermatol 2013; 149:209-15. [PMID: 23426477 DOI: 10.1001/2013.jamadermatol.717] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Pyogenic sterile arthritis, pyoderma gangrenosum, and acne (PAPA) syndrome (OMIM 604416) is a rare autosomal dominant inherited autoinflammatory syndrome characterized by pyogenic sterile arthritis and less frequently accompanied by pyoderma gangrenosum and acne. It is associated with dominant missense mutations in the proline-serine-threonine phosphatase-interacting protein 1 gene (PSTPIP1) located on chromosome 15. The patient was diagnosed as having features of a PAPA-like syndrome in which cutaneous manifestations, such as pyoderma gangrenosum and acne fulminans, predominated. OBSERVATIONS Sequencing of the PSTPIP1 gene was performed in the patient and his extended family. The patient's DNA analysis revealed a homozygous nucleotide exchange c.773G>C in the PSTPIP1 gene, leading to the substitution of glycine 258 by alanine (p.Gly258Ala), a previously reported heterozygous polymorphism. Heterozygous changes were identified in both of the patient's parents and in 7 other family members, all of whom were asymptomatic. The patient was treated with canakinumab, a human anti-interleukin 1β monoclonal antibody, which led to rapid remission of the symptoms. CONCLUSIONS To our knowledge, this is the first reported case of the resolution of dermatological symptoms associated with a PAPA-like syndrome using canakinumab treatment. Further study of the p.Gly258Ala variant is warranted to determine whether this mutation has a role in causing an apparently recessive cutaneous syndrome resembling PAPA syndrome.
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Affiliation(s)
- Alexandra Geusau
- Division of Immunology, Allergy, and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria.
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Londono D, Chen KM, Musolf A, Wang R, Shen T, Brandon J, Herring JA, Wise CA, Zou H, Jin M, Yu L, Finch SJ, Matise TC, Gordon D. A novel method for analyzing genetic association with longitudinal phenotypes. Stat Appl Genet Mol Biol 2013; 12:241-61. [PMID: 23502345 DOI: 10.1515/sagmb-2012-0070] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Knowledge of genes influencing longitudinal patterns may offer information about predicting disease progression. We developed a systematic procedure for testing association between SNP genotypes and longitudinal phenotypes. We evaluated false positive rates and statistical power to localize genes for disease progression. We used genome-wide SNP data from the Framingham Heart Study. With longitudinal data from two real studies unrelated to Framingham, we estimated three trajectory curves from each study. We performed simulations by randomly selecting 500 individuals. In each simulation replicate, we assigned each individual to one of the three trajectory groups based on the underlying hypothesis (null or alternative), and generated corresponding longitudinal data. Individual Bayesian posterior probabilities (BPPs) for belonging to a specific trajectory curve were estimated. These BPPs were treated as a quantitative trait and tested (using the Wald test) for genome-wide association. Empirical false positive rates and power were calculated. Our method maintained the expected false positive rate for all simulation models. Also, our method achieved high empirical power for most simulations. Our work presents a method for disease progression gene mapping. This method is potentially clinically significant as it may allow doctors to predict disease progression based on genotype and determine treatment accordingly.
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Affiliation(s)
- Douglas Londono
- Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Road, Piscataway, NJ 08854, USA
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Rios JJ, Paria N, Burns DK, Israel BA, Cornelia R, Wise CA, Ezaki M. Somatic gain-of-function mutations in PIK3CA in patients with macrodactyly. Hum Mol Genet 2012; 22:444-51. [PMID: 23100325 PMCID: PMC3542862 DOI: 10.1093/hmg/dds440] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Macrodactyly is a discrete congenital anomaly consisting of enlargement of all tissues localized to the terminal portions of a limb, typically within a ‘nerve territory’. The classic terminology for this condition is ‘lipofibromatous hamartoma of nerve’ or Type I macrodactyly. The peripheral nerve, itself, is enlarged both in circumference and in length. It is not related to neurofibromatosis (NF1), nor is it associated with vascular malformations, such as in the recently reported CLOVES syndrome. The specific nerve pathophysiology in this form of macrodactyly has not been well described and a genetic etiology for this specific form of enlargement is unknown. To identify the genetic cause of macrodactyly, we used whole-exome sequencing to identify somatic mutations present in the affected nerve of a single patient. We confirmed a novel mutation in PIK3CA (R115P) present in the patient's affected nerve tissue but not in blood DNA. Sequencing PIK3CA exons identified gain-of-function mutations (E542K, H1047L or H1047R) in the affected tissue of five additional unrelated patients; mutations were absent in blood DNA available from three patients. Immunocytochemistry confirmed AKT activation in cultured cells from the nerve of a macrodactyly patient. Additionally, we found that the most abnormal structure within the involved nerve in a macrodactylous digit is the perineurium, with additional secondary effects on the axon number and size. Thus, isolated congenital macrodactyly is caused by somatic activation of the PI3K/AKT cell-signaling pathway and is genetically and biochemically related to other overgrowth syndromes.
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Affiliation(s)
- Jonathan J Rios
- Sarah M and Charles E Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA.
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de Munnik SA, Otten BJ, Schoots J, Bicknell LS, Aftimos S, Al-Aama JY, van Bever Y, Bober MB, Borm GF, Clayton-Smith J, Deal CL, Edrees AY, Feingold M, Fryer A, van Hagen JM, Hennekam RC, Jansweijer MCE, Johnson D, Kant SG, Opitz JM, Ramadevi AR, Reardon W, Ross A, Sarda P, Schrander-Stumpel CTRM, Sluiter AE, Temple IK, Terhal PA, Toutain A, Wise CA, Wright M, Skidmore DL, Samuels ME, Hoefsloot LH, Knoers NVAM, Brunner HG, Jackson AP, Bongers EMHF. Meier-Gorlin syndrome: growth and secondary sexual development of a microcephalic primordial dwarfism disorder. Am J Med Genet A 2012; 158A:2733-42. [PMID: 23023959 DOI: 10.1002/ajmg.a.35681] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 09/03/2012] [Indexed: 11/09/2022]
Abstract
Meier-Gorlin syndrome (MGS) is a rare autosomal recessive disorder characterized by primordial dwarfism, microtia, and patellar aplasia/hypoplasia. Recently, mutations in the ORC1, ORC4, ORC6, CDT1, and CDC6 genes, encoding components of the pre-replication complex, have been identified. This complex is essential for DNA replication and therefore mutations are expected to impair cell proliferation and consequently could globally reduce growth. However, detailed growth characteristics of MGS patients have not been reported, and so this is addressed here through study of 45 MGS patients, the largest cohort worldwide. Here, we report that growth velocity (length) is impaired in MGS during pregnancy and first year of life, but, thereafter, height increases in paralleled normal reference centiles, resulting in a mean adult height of -4.5 standard deviations (SD). Height is dependent on ethnic background and underlying molecular cause, with ORC1 and ORC4 mutations causing more severe short stature and microcephaly. Growth hormone therapy (n = 9) was generally ineffective, though in two patients with significantly reduced IGF1 levels, growth was substantially improved by GH treatment, with 2SD and 3.8 SD improvement in height. Growth parameters for monitoring growth in future MGS patients are provided and as well we highlight that growth is disproportionately affected in certain structures, with growth related minor genital abnormalities (42%) and mammary hypoplasia (100%) frequently present, in addition to established effects on ears and patellar growth.
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Affiliation(s)
- Sonja A de Munnik
- Department of Human Genetics, Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Thompson SD, Marion MC, Sudman M, Ryan M, Tsoras M, Howard TD, Barnes MG, Ramos PS, Thomson W, Hinks A, Haas JP, Prahalad S, Bohnsack JF, Wise CA, Punaro M, Rosé CD, Pajewski NM, Spigarelli M, Keddache M, Wagner M, Langefeld CD, Glass DN. Genome-wide association analysis of juvenile idiopathic arthritis identifies a new susceptibility locus at chromosomal region 3q13. Arthritis Rheum 2012; 64:2781-91. [PMID: 22354554 PMCID: PMC3366043 DOI: 10.1002/art.34429] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVE In a genome-wide association study of Caucasian patients with juvenile idiopathic arthritis (JIA), we have previously described findings limited to autoimmunity loci shared by JIA and other diseases. The present study was undertaken to identify novel JIA-predisposing loci using genome-wide approaches. METHODS The discovery cohort consisted of Caucasian JIA cases (n = 814) and local controls (n = 658) genotyped on the Affymetrix Genome-Wide SNP 6.0 Array, along with 2,400 out-of-study controls. In a replication study, we genotyped 10 single-nucleotide polymorphisms (SNPs) in 1,744 cases and 7,010 controls from the US and Europe. RESULTS Analysis within the discovery cohort provided evidence of associations at 3q13 within C3orf1 and near CD80 (rs4688011) (odds ratio [OR] 1.37, P = 1.88 × 10(-6) ) and at 10q21 near JMJD1C (rs647989 [OR 1.59, P = 6.1 × 10(-8) ], rs12411988 [OR 1.57, P = 1.16 × 10(-7) ], and rs10995450 [OR 1.31, P = 6.74 × 10(-5) ]). Meta-analysis provided further evidence of association for these 4 SNPs (P = 3.6 × 10(-7) for rs4688011, P = 4.33 × 10(-5) for rs6479891, P = 2.71 × 10(-5) for rs12411988, and P = 5.39 × 10(-5) for rs10995450). Gene expression data on 68 JIA cases and 23 local controls showed cis expression quantitative trait locus associations for C3orf1 SNP rs4688011 (P = 0.024 or P = 0.034, depending on the probe set) and JMJD1C SNPs rs6479891 and rs12411988 (P = 0.01 or P = 0.04, depending on the probe set and P = 0.008, respectively). Using a variance component liability model, it was estimated that common SNP variation accounts for approximately one-third of JIA susceptibility. CONCLUSION Genetic association results and correlated gene expression findings provide evidence of JIA association at 3q13 and suggest novel genes as plausible candidates in disease pathology.
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Affiliation(s)
- Susan D Thompson
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
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Jordan CT, Cao L, Roberson EDO, Duan S, Helms CA, Nair RP, Duffin KC, Stuart PE, Goldgar D, Hayashi G, Olfson EH, Feng BJ, Pullinger CR, Kane JP, Wise CA, Goldbach-Mansky R, Lowes MA, Peddle L, Chandran V, Liao W, Rahman P, Krueger GG, Gladman D, Elder JT, Menter A, Bowcock AM. Rare and common variants in CARD14, encoding an epidermal regulator of NF-kappaB, in psoriasis. Am J Hum Genet 2012; 90:796-808. [PMID: 22521419 PMCID: PMC3376540 DOI: 10.1016/j.ajhg.2012.03.013] [Citation(s) in RCA: 259] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/29/2012] [Accepted: 03/13/2012] [Indexed: 11/26/2022] Open
Abstract
Psoriasis is a common inflammatory disorder of the skin and other organs. We have determined that mutations in CARD14, encoding a nuclear factor of kappa light chain enhancer in B cells (NF-kB) activator within skin epidermis, account for PSORS2. Here, we describe fifteen additional rare missense variants in CARD14, their distribution in seven psoriasis cohorts (>6,000 cases and >4,000 controls), and their effects on NF-kB activation and the transcriptome of keratinocytes. There were more CARD14 rare variants in cases than in controls (burden test p value = 0.0015). Some variants were only seen in a single case, and these included putative pathogenic mutations (c.424G>A [p.Glu142Lys] and c.425A>G [p.Glu142Gly]) and the generalized-pustular-psoriasis mutation, c.413A>C (p.Glu138Ala); these three mutations lie within the coiled-coil domain of CARD14. The c.349G>A (p.Gly117Ser) familial-psoriasis mutation was present at a frequency of 0.0005 in cases of European ancestry. CARD14 variants led to a range of NF-kB activities; in particular, putative pathogenic variants led to levels >2.5× higher than did wild-type CARD14. Two variants (c.511C>A [p.His171Asn] and c.536G>A [p.Arg179His]) required stimulation with tumor necrosis factor alpha (TNF-α) to achieve significant increases in NF-kB levels. Transcriptome profiling of wild-type and variant CARD14 transfectants in keratinocytes differentiated probably pathogenic mutations from neutral variants such as polymorphisms. Over 20 CARD14 polymorphisms were also genotyped, and meta-analysis revealed an association between psoriasis and rs11652075 (c.2458C>T [p.Arg820Trp]; p value = 2.1 × 10(-6)). In the two largest psoriasis cohorts, evidence for association increased when rs11652075 was conditioned on HLA-Cw*0602 (PSORS1). These studies contribute to our understanding of the genetic basis of psoriasis and illustrate the challenges faced in identifying pathogenic variants in common disease.
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Affiliation(s)
- Catherine T Jordan
- Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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Prahalad S, Thompson SD, Conneely KN, Jiang Y, Leong T, Prozonic J, Brown MR, Ponder LA, Angeles-Han ST, Vogler LB, Kennedy C, Wallace CA, Wise CA, Punaro M, Reed A, Park JL, Mellins ED, Zeft AS, Bohnsack JF, Glass DN. Hierarchy of risk of childhood-onset rheumatoid arthritis conferred by HLA-DRB1 alleles encoding the shared epitope. Arthritis Rheum 2012; 64:925-30. [PMID: 21953520 PMCID: PMC3276774 DOI: 10.1002/art.33376] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Associations between shared epitope (SE)-encoding HLA-DRB1 alleles and rheumatoid arthritis (RA) are well established. However, only a limited number of studies have investigated these alleles in patients with childhood-onset RA, which is defined as rheumatoid factor- and/or anti-citrullinated protein antibody-positive juvenile idiopathic arthritis. The aims of this study were to investigate the largest cohort of patients with childhood-onset RA for association with SE alleles and to determine whether there is a hierarchy of risk based on the amino acid sequence of the SE. METHODS High-resolution HLA-DRB1 genotypes were obtained for 204 patients with childhood-onset RA and 373 healthy control subjects. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for different SE-encoding HLA-DRB1 alleles. In addition, genotype ORs were calculated for combinations of SE alleles classified into S(2) , S(3P) , or L alleles, based on amino acid sequences in position 70-74 of the DRβ1 chain, as proposed by Tezenas du Montcel et al. RESULTS We confirmed associations between HLA-DRB1 SE alleles and childhood-onset RA (76% of patients carried 1 or 2 SE alleles compared with 46% of control subjects; OR 3.81, 95% CI 2.4-6.0, P < 1 × 10(-7) ). We also observed associations between individual SE alleles (HLA-DRB1*0101, *0401, *0404, *0405, *0408, and *1001) and childhood-onset RA. Genotype-specific risk estimates suggested a hierarchy of risk, with the highest risk among individuals heterozygous for S(2) /S(3P) (OR 22.3, 95% CI 9.9-50.5, P < 0.0001). CONCLUSION We confirm the association between SE-encoding HLA-DRB1 alleles and susceptibility to childhood-onset RA. The excess risk conferred by carriage of the combination of S(2) and S(3P) risk alleles suggests that children with DRβ1 chains containing the KRAA and QRRAA or RRRAA sequences are especially susceptible to RA.
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Affiliation(s)
- Sampath Prahalad
- Pediatrics and Human Genetics, Emory University, Atlanta, GA 30322, USA.
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Londono D, Buyske S, Finch SJ, Sharma S, Wise CA, Gordon D. TDT-HET: a new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data. BMC Bioinformatics 2012; 13:13. [PMID: 22264315 PMCID: PMC3292499 DOI: 10.1186/1471-2105-13-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [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: 06/17/2011] [Accepted: 01/20/2012] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Locus heterogeneity is one of the most documented phenomena in genetics. To date, relatively little work had been done on the development of methods to address locus heterogeneity in genetic association analysis. Motivated by Zhou and Pan's work, we present a mixture model of linked and unlinked trios and develop a statistical method to estimate the probability that a heterozygous parent transmits the disease allele at a di-allelic locus, and the probability that any trio is in the linked group. The purpose here is the development of a test that extends the classic transmission disequilibrium test (TDT) to one that accounts for locus heterogeneity. RESULTS Our simulations suggest that, for sufficiently large sample size (1000 trios) our method has good power to detect association even the proportion of unlinked trios is high (75%). While the median difference (TDT-HET empirical power - TDT empirical power) is approximately 0 for all MOI, there are parameter settings for which the power difference can be substantial. Our multi-locus simulations suggest that our method has good power to detect association as long as the markers are reasonably well-correlated and the genotype relative risk are larger. Results of both single-locus and multi-locus simulations suggest our method maintains the correct type I error rate.Finally, the TDT-HET statistic shows highly significant p-values for most of the idiopathic scoliosis candidate loci, and for some loci, the estimated proportion of unlinked trios approaches or exceeds 50%, suggesting the presence of locus heterogeneity. CONCLUSIONS We have developed an extension of the TDT statistic (TDT-HET) that allows for locus heterogeneity among coded trios. Benefits of our method include: estimates of parameters in the presence of heterogeneity, and reasonable power even when the proportion of linked trios is small. Also, we have extended multi-locus methods to TDT-HET and have demonstrated that the empirical power may be high to detect linkage. Last, given that we obtain PPBs, we conjecture that the TDT-HET may be a useful method for correctly identifying linked trios. We anticipate that researchers will find this property increasingly useful as they apply next-generation sequencing data in family based studies.
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Affiliation(s)
- Douglas Londono
- Department of Genetics and Human Genetics Institute, Rutgers, The State University of New Jersey, 145 Bevier Road, Piscataway, NJ, 08854 USA
| | - Steven Buyske
- Department of Genetics and Human Genetics Institute, Rutgers, The State University of New Jersey, 145 Bevier Road, Piscataway, NJ, 08854 USA
- Department of Statistics & Biostatistics, Hill Center, Rutgers, The State University of New Jersey, 110 Frelinghuysen Road Piscataway, NJ 08854-8019 USA
| | - Stephen J Finch
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, 11794-3600 USA
| | - Swarkar Sharma
- Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 72519 USA
| | - Carol A Wise
- Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 72519 USA
- Department of Orthopedic Surgery and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 USA
| | - Derek Gordon
- Department of Genetics and Human Genetics Institute, Rutgers, The State University of New Jersey, 145 Bevier Road, Piscataway, NJ, 08854 USA
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McGregor TL, Gurnett CA, Dobbs MB, Wise CA, Morcuende JA, Morgan TM, Menon R, Muglia LJ. Common polymorphisms in human lysyl oxidase genes are not associated with the adolescent idiopathic scoliosis phenotype. BMC Med Genet 2011; 12:92. [PMID: 21740577 PMCID: PMC3154146 DOI: 10.1186/1471-2350-12-92] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/08/2011] [Indexed: 12/13/2022]
Abstract
Background Although adolescent idiopathic scoliosis affects approximately 3% of adolescents, the genetic contributions have proven difficult to identify. Work in model organisms, including zebrafish, chickens, and mice, has implicated the lysyl oxidase family of enzymes in the development of scoliosis. We hypothesized that common polymorphisms in the five human lysyl oxidase genes (LOX, LOXL1, LOXL2, LOXL3, and LOXL4) may be associated with the phenotype of adolescent idiopathic scoliosis. Methods This was a case-control genetic association study. A total of 112 coding and tag SNPs in LOX, LOXL1, LOXL2, LOXL3, and LOXL4 were genotyped in a discovery cohort of 138 cases and 411 controls. Genotypes were tested for association with adolescent idiopathic scoliosis by logistic regression with a two degree of freedom genotypic model and gender as a covariate. Fourteen SNPs with p < 0.1 in the discovery phase were genotyped in an independent replication cohort of 400 cases and 506 controls. Results No evidence for significant association was found between coding or tag SNPs in LOX, LOXL1, LOXL2, LOXL3, and LOXL4 and the phenotype of adolescent idiopathic scoliosis. Conclusions Despite suggestive evidence in model organisms, common variants and known coding SNPs in the five human lysyl oxidase genes do not confer increased genotypic risk for adolescent idiopathic scoliosis. The above methodology does not address rare variants or individually private mutations in these genes, and future research may focus on this area.
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Affiliation(s)
- Tracy L McGregor
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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Edery P, Marcaillou C, Sahbatou M, Labalme A, Chastang J, Touraine R, Tubacher E, Senni F, Bober MB, Nampoothiri S, Jouk PS, Steichen E, Berland S, Toutain A, Wise CA, Sanlaville D, Rousseau F, Clerget-Darpoux F, Leutenegger AL. Association of TALS developmental disorder with defect in minor splicing component U4atac snRNA. Science 2011; 332:240-3. [PMID: 21474761 DOI: 10.1126/science.1202205] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The spliceosome, a ribonucleoprotein complex that includes proteins and small nuclear RNAs (snRNAs), catalyzes RNA splicing through intron excision and exon ligation to produce mature messenger RNAs, which, in turn serve as templates for protein translation. We identified four point mutations in the U4atac snRNA component of the minor spliceosome in patients with brain and bone malformations and unexplained postnatal death [microcephalic osteodysplastic primordial dwarfism type 1 (MOPD 1) or Taybi-Linder syndrome (TALS); Mendelian Inheritance in Man ID no. 210710]. Expression of a subgroup of genes, possibly linked to the disease phenotype, and minor intron splicing were affected in cell lines derived from TALS patients. Our findings demonstrate a crucial role of the minor spliceosome component U4atac snRNA in early human development and postnatal survival.
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Affiliation(s)
- Patrick Edery
- Hospices Civils de Lyon, Service de Cytogénétique Constitutionnelle, Bron, F-69677, France.
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