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Xu K, Li G, Niu Y, Wu Z, Zhang TJ, Zhang S, Wu N. First copy number variant in trans with single nucleotide variant in CCN6 causing progressive pseudorheumatoid dysplasia revealed by genome sequencing and deep phenotyping in monozygotic twins. Am J Med Genet A 2024; 194:e63801. [PMID: 38958524 DOI: 10.1002/ajmg.a.63801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/21/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024]
Abstract
Biallelic pathogenic variants in CCN6 cause progressive pseudorheumatoid dysplasia (PPD), a rare skeletal dysplasia. The predominant features include noninflammatory progressive joint stiffness and enlargement, which are not unique to this condition. Nearly 100% of the reported variants are single nucleotide variants or small indels, and missing of a second variant has been reported. Genome sequencing (GS) covers various types of variants and deep phenotyping (DP) provides detailed and precise information facilitating genetic data interpretation. The combination of GS and DP improves diagnostic yield, especially in rare and undiagnosed diseases. We identified a novel compound heterozygote involving a disease-causing copy number variant (g.112057664_112064205del) in trans with a single nucleotide variant (c.624dup(p.Cys209MetfsTer21)) in CCN6 in a pair of monozygotic twins, through the methods of GS and DP. The twins had received three nondiagnostic results before. The g.112057664_112064205del variant was missed by all the tests, and the recorded phenotypes were inaccurate or even misleading. The twins were diagnosed with PPD, ending a 13-year diagnostic odyssey. There may be other patients with PPD experiencing underdiagnosis and misdiagnosis due to inadequate genetic testing or phenotyping methods. This case highlights the critical role of GS and DP in facilitating an accurate and timely diagnosis.
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Affiliation(s)
- Kexin Xu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 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
| | - Guozhuang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 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
| | - Yuchen Niu
- Clinical Biobank, Medical Research Center, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - 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, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 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
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shuyang Zhang
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Department of Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 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
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Wen W, Zhao Z, Zheng Z, Zhao S, Zhao H, Cheng X, Du H, Li Z, Wang S, Qiu G, Wu Z, Zhang TJ, Wu N. Rare variant association analyses reveal the significant contribution of carbohydrate metabolic disturbance in severe adolescent idiopathic scoliosis. J Med Genet 2024; 61:666-676. [PMID: 38724173 PMCID: PMC11228217 DOI: 10.1136/jmg-2023-109667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/18/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Adolescent idiopathic scoliosis (AIS), the predominant genetic-influenced scoliosis, results in spinal deformities without vertebral malformations. However, the molecular aetiology of AIS remains unclear. METHODS Using genome/exome sequencing, we studied 368 patients with severe AIS (Cobb angle >40°) and 3794 controls from a Han Chinese cohort. We performed gene-based and pathway-based weighted rare variant association tests to assess the mutational burden of genes and established biological pathways. Differential expression analysis of muscle tissues from 14 patients with AIS and 15 controls was served for validation. RESULTS SLC16A8, a lactate transporter linked to retinal glucose metabolism, was identified as a novel severe AIS-associated gene (p=3.08E-06, false discovery rate=0.009). Most AIS cases with deleterious SLC16A8 variants demonstrated early onset high myopia preceding scoliosis. Pathway-based burden test also revealed a significant enrichment in multiple carbohydrate metabolism pathways, especially galactose metabolism. Patients with deleterious variants in these genes demonstrated a significantly larger spinal curve. Genes related to catabolic processes and nutrient response showed divergent expression between AIS cases and controls, reinforcing our genomic findings. CONCLUSION This study uncovers the pivotal role of genetic variants in carbohydrate metabolism in the development of AIS, unveiling new insights into its aetiology and potential treatment.
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Affiliation(s)
- Wen Wen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, Beijing, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, Beijing, Beijing, China
| | - Zhifa Zheng
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, Beijing, Beijing, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Baylor College of Medicine Department of Molecular and Human Genetics, Houston, Texas, USA
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Feinberg School of Medicine, Northwestern University; Chicago, Chicago, Illinois, USA
| | - Xi Cheng
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, Beijing, China
| | - Huakang Du
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, Beijing, China
| | - Ziquan Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, Beijing, Beijing, China
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, Beijing, Beijing, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, Beijing, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, Beijing, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, Beijing, Beijing, China
- Wenzhou Medical University, Wenzhou, Zhejiang, China
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Liu Y, Fan X, Qian K, Wu C, Zhang L, Yuan L, Man Z, Wu S, Li P, Wang X, Li W, Zhang Y, Sun S, Yu C. Deciphering the pathogenic role of rare RAF1 heterozygous missense mutation in the late-presenting DDH. Front Genet 2024; 15:1375736. [PMID: 38952713 PMCID: PMC11215071 DOI: 10.3389/fgene.2024.1375736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/17/2024] [Indexed: 07/03/2024] Open
Abstract
Background Developmental Dysplasia of the Hip (DDH) is a skeletal disorder where late-presenting forms often escape early diagnosis, leading to limb and pain in adults. The genetic basis of DDH is not fully understood despite known genetic predispositions. Methods We employed Whole Genome Sequencing (WGS) to explore the genetic factors in late-presenting DDH in two unrelated families, supported by phenotypic analyses and in vitro validation. Results In both cases, a novel de novo heterozygous missense mutation in RAF1 (c.193A>G [p.Lys65Glu]) was identified. This mutation impacted RAF1 protein structure and function, altering downstream signaling in the Ras/ERK pathway, as demonstrated by bioinformatics, molecular dynamics simulations, and in vitro validations. Conclusion This study contributes to our understanding of the genetic factors involved in DDH by identifying a novel mutation in RAF1. The identification of the RAF1 mutation suggests a possible involvement of the Ras/ERK pathway in the pathogenesis of late-presenting DDH, indicating its potential role in skeletal development.
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Affiliation(s)
- Yuzhao Liu
- Department of Joint Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xuesong Fan
- Shandong Mental Health Center, Shandong University, Jinan, China
| | - Kun Qian
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Changshun Wu
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Laibo Zhang
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Lin Yuan
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Zhentao Man
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Shuai Wu
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Ping Li
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Xianquan Wang
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Wei Li
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yuanqing Zhang
- Shandong Mental Health Center, Shandong University, Jinan, China
| | - Shui Sun
- Department of Joint Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Orthopaedic Research Laboratory, Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Chenxi Yu
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Digital Health Laboratory, Queen Mary Hospital, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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Feng X, Ye Y, Zhang J, Zhang Y, Zhao S, Mak JCW, Otomo N, Zhao Z, Niu Y, Yonezawa Y, Li G, Lin M, Li X, Cheung PWH, Xu K, Takeda K, Wang S, Xie J, Kotani T, Choi VNT, Song YQ, Yang Y, Luk KDK, Lee KS, Li Z, Li PS, Leung CYH, Lin X, Wang X, Qiu G, Watanabe K, Wu Z, Posey JE, Ikegawa S, Lupski JR, Cheung JPY, Zhang TJ, Gao B, Wu N. Core planar cell polarity genes VANGL1 and VANGL2 in predisposition to congenital vertebral malformations. Proc Natl Acad Sci U S A 2024; 121:e2310283121. [PMID: 38669183 PMCID: PMC11067467 DOI: 10.1073/pnas.2310283121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital scoliosis (CS), affecting approximately 0.5 to 1 in 1,000 live births, is commonly caused by congenital vertebral malformations (CVMs) arising from aberrant somitogenesis or somite differentiation. While Wnt/ß-catenin signaling has been implicated in somite development, the function of Wnt/planar cell polarity (Wnt/PCP) signaling in this process remains unclear. Here, we investigated the role of Vangl1 and Vangl2 in vertebral development and found that their deletion causes vertebral anomalies resembling human CVMs. Analysis of exome sequencing data from multiethnic CS patients revealed a number of rare and deleterious variants in VANGL1 and VANGL2, many of which exhibited loss-of-function and dominant-negative effects. Zebrafish models confirmed the pathogenicity of these variants. Furthermore, we found that Vangl1 knock-in (p.R258H) mice exhibited vertebral malformations in a Vangl gene dose- and environment-dependent manner. Our findings highlight critical roles for PCP signaling in vertebral development and predisposition to CVMs in CS patients, providing insights into the molecular mechanisms underlying this disorder.
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Affiliation(s)
- Xin Feng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing100730, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yongyu Ye
- Department of Orthopedic Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou510080, China
| | - Jianan Zhang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yuanqiang Zhang
- Department of Orthopaedic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan250012, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Judith C. W. Mak
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Nao Otomo
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo108-8639, Japan
| | - Zhengye Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
| | - Yoshiro Yonezawa
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo108-8639, Japan
| | - Guozhuang Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Mao Lin
- Department of Orthopedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou310003, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
| | - Prudence Wing Hang Cheung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kexin Xu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Kazuki Takeda
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo108-8639, Japan
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
| | - Junjie Xie
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Toshiaki Kotani
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Vanessa N. T. Choi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - You-Qiang Song
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen518009, China
| | - Yang Yang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Keith Dip Kei Luk
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kin Shing Lee
- Center for Comparative Medicine Research, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ziquan Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Pik Shan Li
- Center for Comparative Medicine Research, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Connie Y. H. Leung
- Center for Comparative Medicine Research, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiaochen Lin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiaolu Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | | | - Kota Watanabe
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
| | | | - Zhihong Wu
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston77030, TX
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo108-8639, Japan
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston77030, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston77030, TX
- Texas Children’s Hospital, Houston77030, TX
- Department of Pediatrics, Baylor College of Medicine, Houston77030, TX
| | - Jason Pui Yin Cheung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen518009, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Bo Gao
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen518009, China
- Centre for Translational Stem Cell Biology, Hong Kong Special Administrative Region, China
- Key Laboratory of Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
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5
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Huang Y, Qiu Y, Ding L, Ren S, Jiang Y, Luo J, Huang J, Yin X, Fu S, Zhao J, Hu K, Liao J. Somatic mutations in four novel genes contribute to homologous recombination deficiency in breast cancer: a real-world clinical tumor sequencing study. J Pathol Clin Res 2024; 10:e12367. [PMID: 38504382 PMCID: PMC10951049 DOI: 10.1002/2056-4538.12367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/31/2024] [Accepted: 02/13/2024] [Indexed: 03/21/2024]
Abstract
Breast cancers involving mutations in homologous recombination (HR) genes, most commonly BRCA1 and BRCA2 (BRCA1/2), respond well to PARP inhibitors and platinum-based chemotherapy. However, except for these specific HR genes, it is not clear which other mutations contribute to homologous recombination defects (HRD). Here, we performed next-generation sequencing of tumor tissues and matched blood samples from 119 breast cancer patients using the OncoScreen Plus panel. Genomic mutation characteristics and HRD scores were analyzed. In the HR genes, we found that BRCA1/2 and PLAB2 mutations were related to HRD. HRD was also detected in a subset of patients without germline or somatic mutations in BRCA1/2, PLAB2, or other HR-related genes. Notably, LRP1B, NOTCH3, GATA2, and CARD11 (abbreviated as LNGC) mutations were associated with high HRD scores in breast cancer patients. Furthermore, functional experiments demonstrated that silencing CARD11 and GATA2 impairs HR repair efficiency and enhances the sensitivity of tumor cells to olaparib treatment. In summary, in the absence of mutations in the HR genes, the sensitivity of tumor cells to PARP inhibitors and platinum-based chemotherapy may be enhanced in a subset of breast cancer patients with LNGC somatic mutations.
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Affiliation(s)
- Yongsheng Huang
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangzhouPR China
| | - Yuntan Qiu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangzhouPR China
| | - Linxiaoxiao Ding
- Breast Tumor Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Shuwei Ren
- Department of Clinical LaboratoryThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Yuanling Jiang
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Jiahuan Luo
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Jinghua Huang
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Xinke Yin
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Sha Fu
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Jianli Zhao
- Breast Tumor Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangzhouPR China
| | - Jianwei Liao
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
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6
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Zhao S, Zhao H, Zhao L, Cheng X, Zheng Z, Wu M, Wen W, Wang S, Zhou Z, Xie H, Ruan D, Li Q, Liu X, Ou C, Li G, Zhao Z, Chen G, Niu Y, Yin X, Hu Y, Zhang X, Liu P, Qiu G, Liu W, Zhao C, Wu Z, Zhang J, Wu N. Unraveling the genetic architecture of congenital vertebral malformation with reference to the developing spine. Nat Commun 2024; 15:1125. [PMID: 38321032 PMCID: PMC10847475 DOI: 10.1038/s41467-024-45442-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Congenital vertebral malformation, affecting 0.13-0.50 per 1000 live births, has an immense locus heterogeneity and complex genetic architecture. In this study, we analyze exome/genome sequencing data from 873 probands with congenital vertebral malformation and 3794 control individuals. Clinical interpretation identifies Mendelian etiologies in 12.0% of the probands and reveals a muscle-related disease mechanism. Gene-based burden test of ultra-rare variants identifies risk genes with large effect sizes (ITPR2, TBX6, TPO, H6PD, and SEC24B). To further investigate the biological relevance of the genetic association signals, we perform single-nucleus RNAseq on human embryonic spines. The burden test signals are enriched in the notochord at early developmental stages and myoblast/myocytes at late stages, highlighting their critical roles in the developing spine. Our work provides insights into the developmental biology of the human spine and the pathogenesis of spine malformation.
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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, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lina Zhao
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xi Cheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhifa Zheng
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Mengfan Wu
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Wen Wen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zixiang Zhou
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Haibo Xie
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Dengfeng Ruan
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Qing Li
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xinquan Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Chengzhu Ou
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Guilin Chen
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuchen Niu
- State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangjie Yin
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuhong Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaochen Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Chengtian Zhao
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Zhihong Wu
- State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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7
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Frasuńska J, Pollak A, Turczyn P, Kutkowska-Kaźmierczak A, Pepłowski J, Płoski R, Tarnacka B. A Study of Polish Family with Scoliosis and Limb Contractures Expands the MYH3 Disease Spectrum. Genes (Basel) 2024; 15:125. [PMID: 38275606 PMCID: PMC10815230 DOI: 10.3390/genes15010125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/31/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
A disease associated with malfunction of the MYH3 gene is characterised by scoliosis, contractures of the V fingers, knees and elbows, dysplasia of the calf muscles, foot deformity and limb length asymmetry. The aim of this study was to identify the cause of musculoskeletal deformities in a three-generation Polish family by exome sequencing. The segregation of the newly described c.866A>C variant of the MYH3 gene in the family indicates an autosomal dominant model of inheritance. The detected MYH3 variant segregates the disease within the family. The presented results expand the MYH3 disease spectrum and emphasize the clinical diagnostic challenge in syndromes harbouring congenital spine defects and joint contractures.
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Affiliation(s)
- Justyna Frasuńska
- Department of Rehabilitation, Medical University of Warsaw, 02-091 Warsaw, Poland; (J.F.); (B.T.)
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Paweł Turczyn
- Clinic of Early Arthritis, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland;
| | | | - Jakub Pepłowski
- The Rare Diseases Laboratory, Laboratory of Genetics, University Center for Laboratory Medicine, University Clinical Centre of the Medical University of Warsaw, 02-097 Warsaw, Poland;
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Beata Tarnacka
- Department of Rehabilitation, Medical University of Warsaw, 02-091 Warsaw, Poland; (J.F.); (B.T.)
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8
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Rebello D, Wohler E, Erfani V, Li G, Aguilera AN, Santiago-Cornier A, Zhao S, Hwang SW, Steiner RD, Zhang TJ, Gurnett CA, Raggio C, Wu N, Sobreira N, Giampietro PF, Ciruna B. COL11A2 as a candidate gene for vertebral malformations and congenital scoliosis. Hum Mol Genet 2023; 32:2913-2928. [PMID: 37462524 PMCID: PMC10508038 DOI: 10.1093/hmg/ddad117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/08/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Human vertebral malformations (VMs) have an estimated incidence of 1/2000 and are associated with significant health problems including congenital scoliosis (CS) and recurrent organ system malformation syndromes such as VACTERL (vertebral anomalies; anal abnormalities; cardiac abnormalities; tracheo-esophageal fistula; renal anomalies; limb anomalies). The genetic cause for the vast majority of VMs are unknown. In a CS/VM patient cohort, three COL11A2 variants (R130W, R1407L and R1413H) were identified in two patients with cervical VM. A third patient with a T9 hemivertebra and the R130W variant was identified from a separate study. These substitutions are predicted to be damaging to protein function, and R130 and R1407 residues are conserved in zebrafish Col11a2. To determine the role for COL11A2 in vertebral development, CRISPR/Cas9 was used to create a nonsense mutation (col11a2L642*) as well as a full gene locus deletion (col11a2del) in zebrafish. Both col11a2L642*/L642* and col11a2del/del mutant zebrafish exhibit vertebral fusions in the caudal spine, which form due to mineralization across intervertebral segments. To determine the functional consequence of VM-associated variants, we assayed their ability to suppress col11a2del VM phenotypes following transgenic expression within the developing spine. While wildtype col11a2 expression suppresses fusions in col11a2del/+ and col11a2del/del backgrounds, patient missense variant-bearing col11a2 failed to rescue the loss-of-function phenotype in these animals. These results highlight an essential role for COL11A2 in vertebral development and support a pathogenic role for two missense variants in CS.
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Affiliation(s)
- Denise Rebello
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vida Erfani
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Guozhuang Li
- Department of Orthopedic Surgery, Key Laboratory of Big Data for Spinal Deformities, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Alexya N Aguilera
- Department of Pediatrics, University of Illinois-Chicago, Chicago, IL 60612, USA
| | - Alberto Santiago-Cornier
- Genetic Section, San Jorge Children’s and Women’s Hospital, San Juan, Puerto Rico 00912, USA
- Department of Public Health, Ponce Health Sciences University, Ponce, Puerto Rico 00912, USA
| | - Sen Zhao
- Department of Orthopedic Surgery, Key Laboratory of Big Data for Spinal Deformities, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven W Hwang
- Shriners Children’s-Philadelphia, Philadelphia, PA 19140, USA
| | - Robert D Steiner
- Department of Pediatrics, University of Wisconsin, Madison, WI 54449, USA
- Marshfield Clinic Health System, Marshfield, WI 54449, USA
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, Key Laboratory of Big Data for Spinal Deformities, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Christina A Gurnett
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | | | - Nan Wu
- Department of Orthopedic Surgery, Key Laboratory of Big Data for Spinal Deformities, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Philip F Giampietro
- Department of Pediatrics, University of Illinois-Chicago, Chicago, IL 60612, USA
| | - Brian Ciruna
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
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9
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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 ADVANCES 2023; 4:100188. [PMID: 37124138 PMCID: PMC10130500 DOI: 10.1016/j.xhgg.2023.100188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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10
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Wang L, Liu Z, Zhao S, Xu K, Aceves V, Qiu C, Troutwine B, Liu L, Ma S, Niu Y, Wang S, Yuan S, Li X, Zhao L, Liu X, Wu Z, Zhang TJ, Gray RS, Wu N. Variants in the SOX9 transactivation middle domain induce axial skeleton dysplasia and scoliosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.29.23290174. [PMID: 37398377 PMCID: PMC10312849 DOI: 10.1101/2023.05.29.23290174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
SOX9 is an essential transcriptional regulator of cartilage development and homeostasis. In humans, dysregulation of SOX9 is associated with a wide spectrum of skeletal disorders, including campomelic and acampomelic dysplasia, and scoliosis. The mechanism of how SOX9 variants contribute to the spectrum of axial skeletal disorders is not well understood. Here, we report four novel pathogenic variants of SOX9 identified in a large cohort of patients with congenital vertebral malformations. Three of these heterozygous variants are in the HMG and DIM domains, and for the first time, we report a pathogenic variant within the transactivation middle (TAM) domain of SOX9 . Probands with these variants exhibit variable skeletal dysplasia, ranging from isolated vertebral malformation to acampomelic dysplasia. We also generated a Sox9 hypomorphic mutant mouse model bearing a microdeletion within the TAM domain ( Sox9 Asp272del ). We demonstrated that disturbance of the TAM domain with missense mutation or microdeletion results in reduced protein stability but does not affect the transcriptional activity of SOX9. Homozygous Sox9 Asp272del mice exhibited axial skeletal dysplasia including kinked tails, ribcage anomalies, and scoliosis, recapitulating phenotypes observed in human, while heterozygous mutants display a milder phenotype. Analysis of primary chondrocytes and the intervertebral discs in Sox9 Asp272del mutant mice revealed dysregulation of a panel of genes with major contributions of the extracellular matrix, angiogenesis, and ossification-related processes. In summary, our work identified the first pathologic variant of SOX9 within the TAM domain and demonstrated that this variant is associated with reduced SOX9 protein stability. Our finding suggests that reduced SOX9 stability caused by variants in the TAM domain may be responsible for the milder forms of axial skeleton dysplasia in humans.
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11
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Wu N, Liu L, Zhang Y, Wang L, Wang S, Zhao S, Li G, Yang Y, Lin G, Shen J, Wu Z, Qiu G, Zhang TJ. Retrospective Analysis of Associated Anomalies in 636 Patients with Operatively Treated Congenital Scoliosis. J Bone Joint Surg Am 2023; 105:537-548. [PMID: 37017616 DOI: 10.2106/jbjs.22.00277] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
BACKGROUND Congenital scoliosis is frequently associated with anomalies in multiple organ systems. However, the prevalence and distribution of associated anomalies remain unclear, and there is a large amount of variation in data among different studies. METHODS Six hundred and thirty-six Chinese patients who had undergone scoliosis correction surgery at Peking Union Medical College Hospital from January 2012 to July 2019 were recruited, as a part of the Deciphering disorders Involving Scoliosis and COmorbidities (DISCO) study. The medical data for each subject were collected and analyzed. RESULTS The mean age (and standard deviation) at the time of presentation for scoliosis was 6.4 ± 6.3 years, and the mean Cobb angle of the major curve was 60.8° ± 26.5°. Intraspinal abnormalities were found in 186 (30.3%) of 614 patients, with diastematomyelia being the most common anomaly (59.1%; 110 of 186). The prevalence of intraspinal abnormalities was remarkably higher in patients with failure of segmentation and mixed deformities than in patients with failure of formation (p < 0.001). Patients with intraspinal anomalies showed more severe deformities, including larger Cobb angles of the major curve (p < 0.001). We also demonstrated that cardiac anomalies were associated with remarkably worse pulmonary function, i.e., lower forced expiratory volume in the first second (FEV1), forced vital capacity (FVC), and peak expiratory flow (PEF). Additionally, we identified associations among different concomitant malformations. We found that patients with musculoskeletal anomalies of types other than intraspinal and maxillofacial were 9.2 times more likely to have additional maxillofacial anomalies. CONCLUSIONS In our cohort, comorbidities associated with congenital scoliosis occurred at a rate of 55%. To our knowledge, our study is the first to show that patients with congenital scoliosis and cardiac anomalies have reduced pulmonary function, as demonstrated by lower FEV1, FVC, and PEF. Moreover, the potential associations among concomitant anomalies revealed the importance of a comprehensive preoperative evaluation scheme. LEVEL OF EVIDENCE Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
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Affiliation(s)
- Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Lian Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Department of Emergency Surgery, Qilu Hospital of Shandong University, Jinan, Shandong Province, People's Republic of China
| | - Yuanqiang Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Department of Orthopedic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong Province, People's Republic of China
| | - Lianlei Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Department of Orthopedic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong Province, People's Republic of China
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China
| | - Guozhuang Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China
| | - Yang Yang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Guanfeng Lin
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Jianxiong Shen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Zhihong Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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12
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Dissection of mendelian predisposition and complex genetic architecture of craniovertebral junction malformation. Hum Genet 2023; 142:89-101. [PMID: 36098810 DOI: 10.1007/s00439-022-02474-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/15/2022] [Indexed: 01/18/2023]
Abstract
The craniovertebral junction (CVJ) is an anatomically complex region of the axial skeleton that provides protection of the brainstem and the upper cervical spinal cord. Structural malformation of the CVJ gives rise to life-threatening neurological deficits, such as quadriplegia and dyspnea. Unfortunately, genetic studies on human subjects with CVJ malformation are limited and the pathogenesis remains largely elusive. In this study, we recruited 93 individuals with CVJ malformation and performed exome sequencing. Manual interpretation of the data identified three pathogenic variants in genes associated with Mendelian diseases, including CSNK2A1, MSX2, and DDX3X. In addition, the contribution of copy number variations (CNVs) to CVJ malformation was investigated and three pathogenic CNVs were identified in three affected individuals. To further dissect the complex mutational architecture of CVJ malformation, we performed a gene-based rare variant association analysis utilizing 4371 in-house exomes as control. Rare variants in LGI4 (carrier rate = 3.26%, p = 3.3 × 10-5) and BEST1 (carrier rate = 5.43%, p = 5.77 × 10-6) were identified to be associated with CVJ malformation. Furthermore, gene set analyses revealed that extracellular matrix- and RHO GTPase-associated biological pathways were found to be involved in the etiology of CVJ malformation. Overall, we comprehensively dissected the genetic underpinnings of CVJ malformation and identified several novel disease-associated genes and biological pathways.
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13
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Li G, Strong A, Wang H, Kim JS, Watson D, Zhao S, Vaccaro C, Hartung E, Hakonarson H, Zhang TJ, Giampietro PF, Wu N. TBX6 as a cause of a combined skeletal-kidney dysplasia syndrome. Am J Med Genet A 2022; 188:3469-3481. [PMID: 36161696 PMCID: PMC10473889 DOI: 10.1002/ajmg.a.62972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/24/2022] [Accepted: 08/06/2022] [Indexed: 01/31/2023]
Abstract
TBX6 encodes transcription-factor box 6, a transcription factor critical to paraxial mesoderm segmentation and somitogenesis during embryonic development. TBX6 haploinsufficiency is believed to drive the skeletal and kidney phenotypes associated with the 16p11.2 deletion syndrome. Heterozygous and biallelic variants in TBX6 are associated with vertebral and rib malformations (TBX6-associated congenital scoliosis) and spondylocostal dysostosis, and heterozygous TBX6 variants are associated with increased risk of genitourinary tract malformations. Combined skeletal and kidney phenotypes in individuals harboring heterozygous or biallelic TBX6 variants are rare. Here, we present seven individuals with vertebral and rib malformations and structural kidney differences associated with heterozygous TBX6 gene deletion in trans with a hypomorphic TBX6 allele or biallelic TBX6 variants. Our case series highlights the association between TBX6 and both skeletal and kidney disease.
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Affiliation(s)
- Guozhuang Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Alanna Strong
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Haojun Wang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ji-Sun Kim
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical Center, New Brunswick, NJ
| | - Deborah Watson
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Courtney Vaccaro
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Erum Hartung
- Division of Nephrology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Hakon Hakonarson
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Philip F. Giampietro
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical Center, New Brunswick, NJ
- Department of Pediatrics, University of Illinois-Chicago, Chicago, IL
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
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14
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Ma C, Chen N, Jolly A, Zhao S, Coban-Akdemir Z, Tian W, Kang J, Ye Y, Wang Y, Koch A, Zhang Y, Qin C, Bonilla X, Borel C, Rall K, Chen Z, Jhangiani S, Niu Y, Li X, Qiu G, Zhang S, Luo G, Wu Z, Bacopoulou F, Deligeoroglou E, Zhang TJ, Rosenberg C, Gibbs RA, Dietrich JE, Dimas AS, Liu P, Antonarakis SE, Brucker SY, Posey JE, Lupski JR, Wu N, Zhu L. Functional characteristics of a broad spectrum of TBX6 variants in Mayer-Rokitansky-Küster-Hauser syndrome. Genet Med 2022; 24:2262-2273. [DOI: 10.1016/j.gim.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
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15
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Lin D, Du H, Zhao S, Liu B, Song H, Wang G, Zhang W, Liang H, Liu P, Liu C, Han W, Li Z, Yang Y, Chen S, Zhao L, Li X, Wu Z, Qiu G, Wu Z, Zhang TJ, Wu N, Wang S, Liu J, Liu S, Zuo Y, Liu G, Yu C, Liu L, Shao J, Zhao S, Yan Z, Zhao H, Niu Y, Li X, Wang H, Ma C, Chen Z, Liu B, Cheng X, Lin J, Du H, Li Y, Song S, Tian W, Xie Z, Zhao Z, Zhao L, Zhao Z, Zheng Z, Huang Y, Sun N, Wu N. Phenotype expansion of variants affecting p38 MAPK signaling in hypospadias patients. Orphanet J Rare Dis 2022; 17:209. [PMID: 35606856 PMCID: PMC9128137 DOI: 10.1186/s13023-022-02334-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hypospadias is a congenital anomaly of the male urogenital system. Genetics factors play an important role in its pathogenesis. To search for potential causal genes/variants for hypospadias, we performed exome sequencing in a pedigree with three patients across two generations and a cohort of 49 sporadic patients with hypospadias. Results A novel BRAF variant (NM_004333.6: c.362C > A) was found to co-segregate with the hypospadias phenotype in the disease pedigree. In cells overexpressing the BRAF mutant, the phosphorylation level of p38 MAPK was significantly increased as compared with the cells overexpressing the wild-type BRAF or RASopathy-related BRAF mutant. This variant further led to a reduced transcription level of the SRY gene, which is essential for the normal development of the male reproductive system. In the cohort of sporadic patients, we identified two additional variants in p38 MAPK signaling-related genes (TRIM67 and DAB2IP) potentially associated with hypospadias. Conclusion Our study expands the phenotypic spectrum of variants affecting p38 MAPK signaling toward the involvement of hypospadias.
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16
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De Salvatore S, Ruzzini L, Longo UG, Marino M, Greco A, Piergentili I, Costici PF, Denaro V. Exploring the association between specific genes and the onset of idiopathic scoliosis: a systematic review. BMC Med Genomics 2022; 15:115. [PMID: 35590413 PMCID: PMC9118580 DOI: 10.1186/s12920-022-01272-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background Idiopathic Scoliosis (IS) is the most common spinal deformity in adolescents, accounting for 80% of all spinal deformities. However, the etiology remains uncertain in most cases, being identified as Adolescent Idiopathic Scoliosis (AIS). IS treatments range from observation and sport to bracing or surgery. Several risk factors including sex and familiarity, have been linked with IS. Although there are still many uncertainties regarding the cause of this pathology, several studies report a greater incidence of the defect in families in which at least one other first degree relative is affected. This study systematically reviews the available literature to identify the most significant genes or variants related to the development and onset of IS. Methods The research question was formulated using a PIOS approach on the following databases: Medline, Embase, Cinahl, Scopus, Web of Science and Google Scholar. The search was performed from July to August 2021, and articles from the inception of the database to August 2021 were searched. Results 24 of the 919 initially identified studies were included in the present review. The 24 included studies observed a total of 16,316 cases and 81,567 controls. All the considered studies stated either the affected gene and/or specific SNPs. CHD7, SH2B1, ESR, CALM1, LBX1, MATN1, CHL1, FBN1 and FBN2 genes were associated with IS development. Conclusions Although association can be found in some candidate genes the field of research regarding genetic association with the onset of IS still requires more information.
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Affiliation(s)
- Sergio De Salvatore
- Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128, Rome, Italy.,Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Via Alvaro del Portillo, 21, 00128, Rome, Italy
| | - Laura Ruzzini
- Department of Orthopedics, Children's Hospital Bambino Gesù, 00165, Palidoro, Rome, Italy
| | - Umile Giuseppe Longo
- Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128, Rome, Italy. .,Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Via Alvaro del Portillo, 21, 00128, Rome, Italy.
| | - Martina Marino
- Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128, Rome, Italy.,Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Via Alvaro del Portillo, 21, 00128, Rome, Italy
| | - Alessandra Greco
- Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128, Rome, Italy.,Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Via Alvaro del Portillo, 21, 00128, Rome, Italy
| | - Ilaria Piergentili
- Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128, Rome, Italy.,Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Via Alvaro del Portillo, 21, 00128, Rome, Italy
| | - Pier Francesco Costici
- Department of Orthopedics, Children's Hospital Bambino Gesù, 00165, Palidoro, Rome, Italy
| | - Vincenzo Denaro
- Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128, Rome, Italy.,Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Via Alvaro del Portillo, 21, 00128, Rome, Italy
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17
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Wang F, Li Y, Zhao S, Chen Z, Xu Z, Wang L, Zhang TJ, Yan J, Cao L, Wang P, Li A, Zhong Y, Wu Z, Qi X, Zhang M, Wu N. The utility of hierarchical genetic testing in paediatric liver disease. Liver Int 2022; 42:1097-1108. [PMID: 35257483 DOI: 10.1111/liv.15235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 02/13/2023]
Abstract
BACKGROUND & AIMS Genetic factors underlie a substantial proportion of paediatric liver diseases. Hereditary liver diseases have considerable genetic heterogeneity and variable clinical manifestations, which bring great challenges to clinical and molecular diagnoses. In this study, we investigated a group of paediatric patients with varying degrees of liver dysfunction using a hierarchical genetic testing strategy. METHODS We first applied a panel encompassing 166 known causal genes of liver disease. We then used exome sequencing (ES) in those patients whose cases remained undiagnosed to identify the genetic aetiology of their symptoms. RESULTS In total, we enrolled 131 unrelated paediatric patients with liver disease of Chinese Han ethnicity. We first applied targeted gene sequencing of 166 genes to all patients and yielded a diagnostic rate of 35.9% (47 of 131). Eighty-four patients who remained undiagnosed after target gene sequencing were subjected to ES. As a result, eight (8/84, 9.5%) of them obtained molecular diagnoses, including four patients suspected of abnormal bilirubin metabolism and four idiopathic cases. Non-typical genetic findings, including digenic inheritance and dual molecular diagnosis, were also identified. Through a comprehensive assessment of novel candidate variants of uncertain disease association, 11 patients of the remaining undiagnosed patients were able to obtain likely molecular diagnoses. CONCLUSIONS Our study presents evidence for the diagnostic utility of sequential genetic testing in a cohort of patients with paediatric liver disease. Our findings expand the understanding of the phenotypic and mutational spectrum underlying this heterogeneous group of diseases.
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Affiliation(s)
- Fuchuan Wang
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yaqi Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zhiqiang Xu
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, P. R. China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Jianguo Yan
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lili Cao
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Pu Wang
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Aiqin Li
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanwei Zhong
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhihong Wu
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaolong Qi
- CHESS Center, Institute of Portal Hypertension, The First Hospital of Lanzhou University, Lanzhou, China
| | - Min Zhang
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
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18
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Garg B, Tomar N, Biswas A, Mehta N, Malhotra R. Understanding Musculoskeletal Disorders Through Next-Generation Sequencing. JBJS Rev 2022; 10:01874474-202204000-00001. [PMID: 35383688 DOI: 10.2106/jbjs.rvw.21.00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
» An insight into musculoskeletal disorders through advancements in next-generation sequencing (NGS) promises to maximize benefits and improve outcomes through improved genetic diagnosis. » The primary use of whole exome sequencing (WES) for musculoskeletal disorders is to identify functionally relevant variants. » The current evidence has shown the superiority of NGS over conventional genotyping for identifying novel and rare genetic variants in patients with musculoskeletal disorders, due to its high throughput and low cost. » Genes identified in patients with scoliosis, osteoporosis, osteoarthritis, and osteogenesis imperfecta using NGS technologies are listed for further reference.
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Affiliation(s)
- Bhavuk Garg
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
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19
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Liu L, Sun L, Chen Y, Wang M, Yu C, Huang Y, Zhao S, Du H, Chen S, Fan X, Tian W, Wu Z, Qiu G, Zhang TJ, Wu N. Delineation of dual molecular diagnosis in patients with skeletal deformity. Orphanet J Rare Dis 2022; 17:139. [PMID: 35346302 PMCID: PMC8962553 DOI: 10.1186/s13023-022-02293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Skeletal deformity is characterized by an abnormal anatomical structure of bone and cartilage. In our previous studies, we have found that a substantial proportion of patients with skeletal deformity could be explained by monogenic disorders. More recently, complex phenotypes caused by more than one genetic defect (i.e., dual molecular diagnosis) have also been reported in skeletal deformities and may complicate the diagnostic odyssey of patients. In this study, we report the molecular and phenotypic characteristics of patients with dual molecular diagnosis and variable skeletal deformities. Results From 1108 patients who underwent exome sequencing, we identified eight probands with dual molecular diagnosis and variable skeletal deformities. All eight patients had dual diagnosis consisting of two autosomal dominant diseases. A total of 16 variants in 12 genes were identified, 5 of which were of de novo origin. Patients with dual molecular diagnosis presented blended phenotypes of two genetic diseases. Mendelian disorders occurred more than once include Osteogenesis Imperfecta Type I (COL1A1, MIM:166200), Neurofibromatosis, Type I (NF1, MIM:162200) and Marfan Syndrome (FBN1, MIM:154700). Conclusions This study demonstrated the complicated skeletal phenotypes associated with dual molecular diagnosis. Exome sequencing represents a powerful tool to detect such complex conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02293-x.
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Affiliation(s)
- Lian Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Liying Sun
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Yujun Chen
- The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Muchuan Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Chenxi Yu
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated To Shandong First Medical University, Shandong, 250021, China
| | - Yingzhao Huang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shaoke Chen
- The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Xin Fan
- The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Wen Tian
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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20
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Sun L, Huang Y, Zhao S, Zhong W, Shi J, Guo Y, Zhao J, Xiong G, Yin Y, Chen Z, Zhang N, Zhao Z, Li Q, Chen D, Niu Y, Li X, Qiu G, Wu Z, Zhang TJ, Tian W, Wu N. Identification of Novel FBN2 Variants in a Cohort of Congenital Contractural Arachnodactyly. Front Genet 2022; 13:804202. [PMID: 35360850 PMCID: PMC8960307 DOI: 10.3389/fgene.2022.804202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/08/2022] [Indexed: 11/25/2022] Open
Abstract
Congenital contractural arachnodactyly (CCA) is a rare autosomal dominant disorder of connective tissue characterized by crumpled ears, arachnodactyly, camptodactyly, large joint contracture, and kyphoscoliosis. The nature course of CCA has not been well-described. We aim to decipher the genetic and phenotypic spectrum of CCA. The cohort was enrolled in Beijing Jishuitan Hospital and Peking Union Medical College Hospital, Beijing, China, based on Deciphering disorders Involving Scoliosis and COmorbidities (DISCO) study (http://www.discostudy.org/). Exome sequencing was performed on patients’ blood DNA. A recent published CCA scoring system was validated in our cohort. Seven novel variants and three previously reported FBN2 variants were identified through exome sequencing. Two variants outside of the neonatal region of FBN2 gene were found. The phenotypes were comparable between patients in our cohort and previous literature, with arachnodactyly, camptodactyly and large joints contractures found in almost all patients. All patients eligible for analysis were successfully classified into likely CCA based on the CCA scoring system. Furthermore, we found a double disease-causing heterozygous variant of FBN2 and ANKRD11 in a patient with blended phenotypes consisting of CCA and KBG syndrome. The identification of seven novel variants broadens the mutational and phenotypic spectrum of CCA and may provide implications for genetic counseling and clinical management.
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Affiliation(s)
- Liying Sun
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Yingzhao Huang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
| | - Wenyao Zhong
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Jile Shi
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
| | - Yang Guo
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Junhui Zhao
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Ge Xiong
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Yuehan Yin
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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 Zhang
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Zongxuan Zhao
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Qingyang Li
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Dan Chen
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
| | - 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
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
- *Correspondence: Terry Jianguo Zhang, ; Wen Tian, ; Nan Wu,
| | - Wen Tian
- Department of Hand Surgery, Clinical and Research Center for Congenital Hand Deformities and Rare Diseases, Beijing Jishuitan Hospital, Beijing, China
- *Correspondence: Terry Jianguo Zhang, ; Wen Tian, ; Nan Wu,
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
- *Correspondence: Terry Jianguo Zhang, ; Wen Tian, ; Nan Wu,
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21
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Wang K, Zhao S, Xie Z, Zhang M, Zhao H, Cheng X, Zhang Y, Niu Y, Liu J, Zhang TJ, Zhang Y, Wu Z, Chu J, Yang X, Wu N. Exome-wide Analysis of De Novo and Rare Genetic Variants in Patients With Brain Arteriovenous Malformation. Neurology 2022; 98:e1670-e1678. [PMID: 35228337 DOI: 10.1212/wnl.0000000000200114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/11/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Brain arteriovenous malformation (bAVM) is a congenital disorder and a leading cause of hemorrhagic stroke. Germline genetic variants play an essential role in the pathogenesis of brain arteriovenous malformation. However, the biological relevance of the disease-associated genes identified in previous studies is elusive. In this study, we aim to systematically investigate the contribution of germline variants to bAVM and explore the critical molecular pathways underlying the pathogenesis of bAVM. METHODS Probands with sporadic bAVM were consecutively recruited into this study from November 2015 to November 2018 and underwent exome sequencing. The controls were aggregated from individuals who were not known to have vascular malformation and underwent exome sequencing for clinical or research purposes. The retained control dataset included 4609 individuals, including 251 individuals with parental samples sequenced. We firstly compared de novo variants in cases and controls and performed a pathway enrichment analysis. A gene-based rare variant association analysis was then performed to identify genes whose variants were significantly enriched in cases. RESULTS We collected an exome-sequenced bAVM cohort consisting of 152 trios and 40 singletons. By firstly focusing on de novo variants, we observed a significant mutational burden of de novo likely gene-disrupting variants in cases versus controls. By performing a pathway enrichment analysis of all nonsynonymous de novo variants identified in cases, we found the angiopoietin-like protein 8 (ANGPTL8) regulatory pathway to be significantly enriched in patients with bAVM. Through an exome-wide rare variant association analysis utilizing 4394 in-house exome data as controls, we identified SLC19A3 as a disease-associated gene for bAVM. In addition, we found that the SLC19A3 variants in cases are preferably located at the N' side of the SLC19A3 protein. These findings implicate a phenotypic extension of SLC19A3-related disorders with a domain-specific effect. DISCUSSION This study provides insights into the biological basis of bAVM by identifying novel molecular pathways and candidate genes.
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Affiliation(s)
- Kun Wang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Sen Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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, Beijing 100730, China
| | - Zhixin Xie
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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, Beijing 100730, China
| | - Mingqi Zhang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Hengqiang Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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, Beijing 100730, China
| | - Xi Cheng
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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, Beijing 100730, China
| | - Yisen Zhang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jian Liu
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Terry Jianguo Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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, Beijing 100730, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Ying Zhang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Junsheng Chu
- Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Xinjian Yang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Nan Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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, Beijing 100730, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
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22
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Liu J, Zhao H, Zheng Y, Dong L, Zhao S, Huang Y, Huang S, Qian T, Zou J, Liu S, Li J, Yan Z, Li Y, Zhang S, Huang X, Wang W, Li Y, Wang J, Ming Y, Li X, Xing Z, Qin L, Zhao Z, Jia Z, Li J, Liu G, Zhang M, Feng K, Wu J, Zhang J, Yang Y, Wu Z, Liu Z, Ying J, Wang X, Su J, Wang X, Wu N. DrABC: deep learning accurately predicts germline pathogenic mutation status in breast cancer patients based on phenotype data. Genome Med 2022; 14:21. [PMID: 35209950 PMCID: PMC8876403 DOI: 10.1186/s13073-022-01027-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
Background Identifying breast cancer patients with DNA repair pathway-related germline pathogenic variants (GPVs) is important for effectively employing systemic treatment strategies and risk-reducing interventions. However, current criteria and risk prediction models for prioritizing genetic testing among breast cancer patients do not meet the demands of clinical practice due to insufficient accuracy. Methods The study population comprised 3041 breast cancer patients enrolled from seven hospitals between October 2017 and 11 August 2019, who underwent germline genetic testing of 50 cancer predisposition genes (CPGs). Associations among GPVs in different CPGs and endophenotypes were evaluated using a case-control analysis. A phenotype-based GPV risk prediction model named DNA-repair Associated Breast Cancer (DrABC) was developed based on hierarchical neural network architecture and validated in an independent multicenter cohort. The predictive performance of DrABC was compared with currently used models including BRCAPRO, BOADICEA, Myriad, PENN II, and the NCCN criteria. Results In total, 332 (11.3%) patients harbored GPVs in CPGs, including 134 (4.6%) in BRCA2, 131 (4.5%) in BRCA1, 33 (1.1%) in PALB2, and 37 (1.3%) in other CPGs. GPVs in CPGs were associated with distinct endophenotypes including the age at diagnosis, cancer history, family cancer history, and pathological characteristics. We developed a DrABC model to predict the risk of GPV carrier status in BRCA1/2 and other important CPGs. In predicting GPVs in BRCA1/2, the performance of DrABC (AUC = 0.79 [95% CI, 0.74–0.85], sensitivity = 82.1%, specificity = 63.1% in the independent validation cohort) was better than that of previous models (AUC range = 0.57–0.70). In predicting GPVs in any CPG, DrABC (AUC = 0.74 [95% CI, 0.69–0.79], sensitivity = 83.8%, specificity = 51.3% in the independent validation cohort) was also superior to previous models in their current versions (AUC range = 0.55–0.65). After training these previous models with the Chinese-specific dataset, DrABC still outperformed all other methods except for BOADICEA, which was the only previous model with the inclusion of pathological features. The DrABC model also showed higher sensitivity and specificity than the NCCN criteria in the multi-center validation cohort (83.8% and 51.3% vs. 78.8% and 31.2%, respectively, in predicting GPVs in any CPG). The DrABC model implementation is available online at http://gifts.bio-data.cn/. Conclusions By considering the distinct endophenotypes associated with different CPGs in breast cancer patients, a phenotype-driven prediction model based on hierarchical neural network architecture was created for identification of hereditary breast cancer. The model achieved superior performance in identifying GPV carriers among Chinese breast cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01027-9.
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Affiliation(s)
- Jiaqi Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, 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, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yu Zheng
- Fintech Innovation Center, Southwestern University of Finance and Economics, Chengdu, 611130, China
| | - Lin Dong
- Department of Pathology, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Sen Zhao
- Department of Orthopedic Surgery, 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, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yukuan Huang
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, 325027, China.,School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Shengkai Huang
- Department of Laboratory Medicine, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tianyi Qian
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiali Zou
- Department of Breast Surgery, Guiyang Maternal and Child Healthcare Hospital, Guiyang, 550001, China
| | - Shu Liu
- Department of Breast Surgery, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jun Li
- Department of Molecular Pathology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Zihui Yan
- Department of Orthopedic Surgery, 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, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yalun Li
- Department of Breast Surgery, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, China
| | - Shuo Zhang
- Department of Breast Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang, 050019, Hebei, China
| | - Xin Huang
- Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Wenyan Wang
- Department of Breast Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Yiqun Li
- Department of Oncology, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jie Wang
- Department of Ultrasound, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yue Ming
- PET-CT Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaoxin Li
- Medical Research Center, Beijing Key Laboratory for Genetic Research of Skeletal Deformity & Key Laboratory of Big Data for Spinal Deformities, All at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zeyu Xing
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ling Qin
- Department of Breast Surgical Oncology, Cancer Hospital of HuanXing, Beijing, 100021, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, 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, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ziqi Jia
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiaxin Li
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Gang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Menglu Zhang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Kexin Feng
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiang Wu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yongxin Yang
- Machine Intelligence Group, University of Edinburgh, Edinburgh, EH8 9YL, UK
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Medical Research Center, Beijing Key Laboratory for Genetic Research of Skeletal Deformity & Key Laboratory of Big Data for Spinal Deformities, All at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianzhong Su
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, 325027, China. .,School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China. .,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China.
| | - Xiang Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Nan Wu
- Department of Orthopedic Surgery, 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, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China. .,State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
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23
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Wang K, Zhang M, Zhao S, Xie Z, Zhang Y, Liu J, Zhang Y, Yang X, Wu N. Mutational spectrum of syndromic genes in sporadic brain arteriovenous malformation. Chin Neurosurg J 2022; 8:4. [PMID: 35209959 PMCID: PMC8867132 DOI: 10.1186/s41016-022-00270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/13/2022] [Indexed: 11/22/2022] Open
Abstract
Background Brain arteriovenous malformations (BAVMs) are abnormal vessels that are apt to rupture, causing life-threatening intracranial hemorrhage (ICH). The estimated prevalence of BAVMs is 0.05% among otherwise healthy individuals. In this study, we aim to investigate the mutational spectrum of syndromic genes in sporadic BAVM. Methods We recruited a cohort of 150 patients with BAVM and performed whole-exome sequencing on their peripheral blood DNA. To explore the mutational spectrum of syndromic genes in sporadic brain arteriovenous malformation, we selected six genes according to the Online Mendelian Inheritance in Man (OMIM) and literature. All variants in the six candidate genes were extracted and underwent filtering for qualifying variants. Results There are a total of four patients with rare variants in hereditary hemorrhagic telangiectasia-related genes. In addition, we identified two patients have the variant of RASA1 gene in our database, which are also rare mutations that are absent from population databases. However, we did not find any patients with GNAQ mutations in our database. Conclusions In conclusion, we demonstrated that variants in syndromic vascular malformations play important roles in the etiology of sporadic BAVM.
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Affiliation(s)
- Kun Wang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Mingqi Zhang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
| | - Zhixin Xie
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
| | - Yisen Zhang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Jian Liu
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Ying Zhang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Xinjian Yang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China.
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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24
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Zhao S, Zhang Y, Hallgrimsdottir S, Zuo Y, Li X, Batkovskyte D, Liu S, Lindelöf H, Wang S, Hammarsjö A, Yang Y, Ye Y, Wang L, Yan Z, Lin J, Yu C, Chen Z, Niu Y, Wang H, Zhao Z, Liu P, Qiu G, Posey JE, Wu Z, Lupski JR, Micule I, Anderlid BM, Voss U, Sulander D, Kuchinskaya E, Nordgren A, Nilsson O, Zhang TJ, Grigelioniene G, Wu N. Expanding the mutation and phenotype spectrum of MYH3-associated skeletal disorders. NPJ Genom Med 2022; 7:11. [PMID: 35169139 PMCID: PMC8847563 DOI: 10.1038/s41525-021-00273-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/15/2021] [Indexed: 01/05/2023] Open
Abstract
Pathogenic variants in MYH3 cause distal arthrogryposis type 2A and type 2B3 as well as contractures, pterygia and spondylocarpotarsal fusion syndromes types 1A and 1B. These disorders are ultra-rare and their natural course and phenotypic variability are not well described. In this study, we summarize the clinical features and genetic findings of 17 patients from 10 unrelated families with vertebral malformations caused by dominant or recessive pathogenic variants in MYH3. Twelve novel pathogenic variants in MYH3 (NM_002470.4) were identified: three of them were de novo or inherited in autosomal dominant way and nine were inherited in autosomal recessive way. The patients had vertebral segmentation anomalies accompanied with variable joint contractures, short stature and dysmorphic facial features. There was a significant phenotypic overlap between dominant and recessive MYH3-associated conditions regarding the degree of short stature as well as the number of vertebral fusions. All monoallelic variants caused significantly decreased SMAD3 phosphorylation, which is consistent with the previously proposed pathogenic mechanism of impaired canonical TGF-β signaling. Most of the biallelic variants were predicted to be protein-truncating, while one missense variant c.4244T>G,p.(Leu1415Arg), which was inherited in an autosomal recessive way, was found to alter the phosphorylation level of p38, suggesting an inhibition of the non-canonical pathway of TGF-β signaling. In conclusion, the identification of 12 novel pathogenic variants and overlapping phenotypes in 17 affected individuals from 10 unrelated families expands the mutation and phenotype spectrum of MYH3-associated skeletal disorders. We show that disturbances of canonical or non-canonical TGF-β signaling pathways are involved in pathogenesis of MYH3-associated skeletal fusion (MASF) syndrome.
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Affiliation(s)
- Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
| | - Yuanqiang Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China.,Department of Orthopaedic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Sigrun Hallgrimsdottir
- Division of Pediatric Endocrinology and Center for Molecular Medicine, Department of Women's and Children's Health, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Yuzhi Zuo
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Sen Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
| | - Hillevi Lindelöf
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Yang Yang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yongyu Ye
- Department of Joint Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China.,Department of Orthopaedic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Zihui Yan
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
| | - Jiachen Lin
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
| | - Chenxi Yu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Huizi Wang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhi Zhao
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Departments of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ieva Micule
- Clinic of Medical Genetics and Prenatal Diagnostics, Children's Clinical University Hospital, Vienibas gatve 45, Riga, LV-1004, Latvia
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrika Voss
- Department of Pediatric Radiology, Karolinska University Hospital, Stockholm, Sweden
| | - Dennis Sulander
- Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Ekaterina Kuchinskaya
- Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ola Nilsson
- Division of Pediatric Endocrinology and Center for Molecular Medicine, Department of Women's and Children's Health, Karolinska Institutet and University Hospital, Stockholm, Sweden.,School of Medical Sciences, Örebro University and Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | | | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China. .,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China.
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden. .,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing, 100730, China. .,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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25
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Chen Z, Zheng Y, Yang Y, Huang Y, Zhao S, Zhao H, Yu C, Dong X, Zhang Y, Wang L, Zhao Z, Wang S, Yang Y, Ming Y, Su J, Qiu G, Wu Z, Zhang TJ, Wu N. PhenoApt leverages clinical expertise to prioritize candidate genes via machine learning. Am J Hum Genet 2022; 109:270-281. [PMID: 35063063 DOI: 10.1016/j.ajhg.2021.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 12/12/2021] [Indexed: 12/17/2022] Open
Abstract
In recent years, exome sequencing (ES) has shown great utility in the diagnoses of Mendelian disorders. However, after rigorous filtering, a typical ES analysis still involves the interpretation of hundreds of variants, which greatly hinders the rapid identification of causative genes. Since the interpretations of ES data require comprehensive clinical analyses, taking clinical expertise into consideration can speed the molecular diagnoses of Mendelian disorders. To leverage clinical expertise to prioritize candidate genes, we developed PhenoApt, a phenotype-driven gene prioritization tool that allows users to assign a customized weight to each phenotype, via a machine-learning algorithm. Using the ability to rank causative genes in top-10 lists as an evaluation metric, baseline analysis demonstrated that PhenoApt outperformed previous phenotype-driven gene prioritization tools by a relative increase of 22.7%-140.0% in three independent, real-world, multi-center cohorts (cohort 1, n = 185; cohort 2, n = 784; and cohort 3, n = 208). Additional trials showed that, by adding weights to clinical indications, which should be explained by the causative gene, PhenoApt performance was improved by a relative increase of 37.3% in cohort 2 (n = 471) and 21.4% in cohort 3 (n = 208). Moreover, PhenoApt could assign an intrinsic weight to each phenotype based on the likelihood of its being a Mendelian trait using term frequency-inverse document frequency techniques. When clinical indications were assigned with intrinsic weights, PhenoApt performance was improved by a relative increase of 23.7% in cohort 2 and 15.5% in cohort 3. For the integration of PhenoApt into clinical practice, we developed a user-friendly website and a command-line tool.
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26
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A genotype-first analysis in a cohort of Mullerian anomaly. J Hum Genet 2022; 67:347-352. [PMID: 35022528 DOI: 10.1038/s10038-021-00996-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/08/2022]
Abstract
Müllerian anomaly (M.A.) is a group of congenital anatomic abnormalities caused by aberrations of the development process of the Müllerian duct. M.A. can either be isolated or be involved in Mendelian syndromes, such as Dandy-Walker syndrome, Holt-Oram syndrome and Bardet-Biedl syndrome, which are often associated with both uterus and kidney malformations. In this study, we applied a genotype-first approach to analyze the whole-exome sequencing data of 492 patients with M.A. Six potential pathogenic variants were found in five genes previously related to female urogenital deformities (PKD1, SON, SALL1, BMPR1B, ITGA8), which are partially overlapping with our patients' phenotypes. We further identified eight incidental findings in seven genes related to Mendelian syndromes without known association with reproductive anomalies (TEK, COL11A1, ANKRD11, LEMD3, DLG5, SPTB, BMP2), which represent potential phenotype expansions of these genes.
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27
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Liu B, Zhao S, Liu L, Du H, Zhao H, Wang S, Niu Y, Li X, Qiu G, Wu Z, Zhang TJ, Wu N. Aberrant interaction between mutated ADAMTSL2 and LTBP4 is associated with adolescent idiopathic scoliosis. Gene 2021; 814:146126. [PMID: 34958866 DOI: 10.1016/j.gene.2021.146126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/01/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022]
Abstract
Adolescent idiopathic scoliosis (AIS) is a complex spinal structure deformity with a prevalence of 1%-3%. Genetic and hereditary factors have been associated with the etiology of AIS. However, previous studies mainly focused on common single nucleotide polymorphisms which confer modest disease risk. Recently, rare variants in FBN1 and other extracellular matrix genes have been implicated in AIS, suggesting a potential overlapping disease etiology between AIS and hereditary connective tissue disorders (HCTD). In this study, we systematically analyzed rare variants in a set of HCTD-related genes in 302 AIS patients using exome sequencing. We firstly focused on pathogenic variants based on a monogenic inheritance and identified nine disease-associated variants in FBN1, COL11A1, COL11A2 and TGFBR2. We then explored the potential interactions between variants in different genes based on the case-control statistics. We identified three ADAMTSL2-LTBP4 variant pairs in three AIS patients and none in controls. Furthermore, we revealed that the variant pairs identified in these genes could affect the interaction between ADAMTSL2 and LTBP4 and upregulate TGF-β signaling pathway in human fibroblasts. Our findings supported that the aberrant interaction between mutated ADAMTSL2 and LTBP4 was associated with AIS.
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Affiliation(s)
- Bowen Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China
| | - Lian Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.
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28
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Su Z, Yang Y, Wang S, Zhao S, Zhao H, Li X, Niu Y, Qiu G, Wu Z, Wu N, Zhang TJ. The Mutational Landscape of PTK7 in Congenital Scoliosis and Adolescent Idiopathic Scoliosis. Genes (Basel) 2021; 12:genes12111791. [PMID: 34828397 PMCID: PMC8619039 DOI: 10.3390/genes12111791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 01/07/2023] Open
Abstract
Depletion of ptk7 is associated with both congenital scoliosis (CS) and adolescent idiopathic scoliosis (AIS) in zebrafish models. However, only one human variant of PTK7 has been reported previously in a patient with AIS. In this study, we systemically investigated the variant landscape of PTK7 in 583 patients with CS and 302 patients with AIS from the Deciphering Disorders Involving Scoliosis and COmorbidities (DISCO) study. We identified a total of four rare variants in CS and four variants in AIS, including one protein truncating variant (c.464_465delAC) in a patient with CS. We then explored the effects of these variants on protein expression and sub-cellular location. We confirmed that the c.464_465delAC variant causes loss-of-function (LoF) of PTK7. In addition, the c.353C>T and c.2290G>A variants identified in two patients with AIS led to reduced protein expression of PTK7 as compared to that of the wild type. In conclusion, LoF and hypomorphic variants are associated with CS and AIS, respectively.
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Affiliation(s)
- Zhe Su
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (Z.S.); (Y.Y.); (S.W.); (S.Z.); (H.Z.); (G.Q.); (N.W.)
- Graduate School, Peking Union Medical College, Beijing 100005, China
| | - Yang Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (Z.S.); (Y.Y.); (S.W.); (S.Z.); (H.Z.); (G.Q.); (N.W.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (X.L.); (Y.N.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Shengru Wang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (Z.S.); (Y.Y.); (S.W.); (S.Z.); (H.Z.); (G.Q.); (N.W.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (X.L.); (Y.N.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Sen Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (Z.S.); (Y.Y.); (S.W.); (S.Z.); (H.Z.); (G.Q.); (N.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Hengqiang Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (Z.S.); (Y.Y.); (S.W.); (S.Z.); (H.Z.); (G.Q.); (N.W.)
- Graduate School, Peking Union Medical College, Beijing 100005, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (X.L.); (Y.N.); (Z.W.)
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (X.L.); (Y.N.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (X.L.); (Y.N.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Guixing Qiu
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (Z.S.); (Y.Y.); (S.W.); (S.Z.); (H.Z.); (G.Q.); (N.W.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (X.L.); (Y.N.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (X.L.); (Y.N.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Nan Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (Z.S.); (Y.Y.); (S.W.); (S.Z.); (H.Z.); (G.Q.); (N.W.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (X.L.); (Y.N.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Terry Jianguo Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (Z.S.); (Y.Y.); (S.W.); (S.Z.); (H.Z.); (G.Q.); (N.W.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (X.L.); (Y.N.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- Correspondence:
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29
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Lin J, Zhao L, Zhao S, Li S, Zhao Z, Chen Z, Zheng Z, Shao J, Niu Y, Li X, Zhang JT, Wu Z, Wu N. Disruptive NADSYN1 Variants Implicated in Congenital Vertebral Malformations. Genes (Basel) 2021; 12:genes12101615. [PMID: 34681008 PMCID: PMC8535205 DOI: 10.3390/genes12101615] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/07/2021] [Accepted: 10/10/2021] [Indexed: 01/04/2023] Open
Abstract
Genetic perturbations in nicotinamide adenine dinucleotide de novo (NAD) synthesis pathway predispose individuals to congenital birth defects. The NADSYN1 encodes the final enzyme in the de novo NAD synthesis pathway and, therefore, plays an important role in NAD metabolism and organ embryogenesis. Biallelic mutations in the NADSYN1 gene have been reported to be causative of congenital organ defects known as VCRL syndrome (Vertebral-Cardiac-Renal-Limb syndrome). Here, we analyzed the genetic variants in NADSYN1 in an exome-sequenced cohort consisting of patients with congenital vertebral malformations (CVMs). A total number of eight variants in NADSYN1, including two truncating variants and six missense variants, were identified in nine unrelated patients. All enrolled patients presented multiple organ defects, with the involvement of either the heart, kidney, limbs, or liver, as well as intraspinal deformities. An in vitro assay using COS-7 cells demonstrated either significantly reduced protein levels or disrupted enzymatic activity of the identified variants. Our findings demonstrated that functional variants in NADSYN1 were involved in the complex genetic etiology of CVMs and provided further evidence for the causative NADSYN1 variants in congenital NAD Deficiency Disorder.
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Affiliation(s)
- Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (J.L.); (S.Z.); (Z.Z.); (Z.C.); (J.S.); (J.T.Z.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (Z.Z.); (Z.W.)
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Lina Zhao
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (J.L.); (S.Z.); (Z.Z.); (Z.C.); (J.S.); (J.T.Z.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (Z.Z.); (Z.W.)
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Shengjie Li
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (J.L.); (S.Z.); (Z.Z.); (Z.C.); (J.S.); (J.T.Z.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (Z.Z.); (Z.W.)
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zefu Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (J.L.); (S.Z.); (Z.Z.); (Z.C.); (J.S.); (J.T.Z.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (Z.Z.); (Z.W.)
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhifa Zheng
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (Z.Z.); (Z.W.)
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jiashen Shao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (J.L.); (S.Z.); (Z.Z.); (Z.C.); (J.S.); (J.T.Z.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (Z.Z.); (Z.W.)
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yuchen Niu
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoxin Li
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jianguo Terry Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (J.L.); (S.Z.); (Z.Z.); (Z.C.); (J.S.); (J.T.Z.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (Z.Z.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (Z.Z.); (Z.W.)
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (L.Z.); (S.L.); (Y.N.); (X.L.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (J.L.); (S.Z.); (Z.Z.); (Z.C.); (J.S.); (J.T.Z.)
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; (Z.Z.); (Z.W.)
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Correspondence:
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30
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Novel FGFR1 Variants Are Associated with Congenital Scoliosis. Genes (Basel) 2021; 12:genes12081126. [PMID: 34440300 PMCID: PMC8393897 DOI: 10.3390/genes12081126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/21/2022] Open
Abstract
FGFR1 encodes a transmembrane cytokine receptor, which is involved in the early development of the human embryo and plays an important role in gastrulation, organ specification and patterning of various tissues. Pathogenic FGFR1 variants have been associated with Kallmann syndrome and hypogonadotropic hypogonadism. In our congenital scoliosis (CS) patient series of 424 sporadic CS patients under the framework of the Deciphering disorders Involving Scoliosis and COmorbidities (DISCO) study, we identified four unrelated patients harboring FGFR1 variants, including one frameshift and three missense variants. These variants were predicted to be deleterious by in silico prediction and conservation analysis. Signaling activities and expression levels of the mutated protein were evaluated in vitro and compared to that of the wild type (WT) FGFR1. As a result, the overall protein expressions of c.2334dupC, c.2339T>C and c.1261A>G were reduced to 43.9%, 63.4% and 77.4%, respectively. By the reporter gene assay, we observed significantly reduced activity for c.2334dupC, c.2339T>C and c.1261A>G, indicating the diminished FGFR1 signaling pathway. In conclusion, FGFR1 variants identified in our patients led to only mild disruption to protein function, caused milder skeletal and cardiac phenotypes than those reported previously.
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31
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Liu J, Wang X, Dong L, Huang X, Zhao H, Li J, Huang S, Yuan P, Wang W, Wang J, Xing Z, Jia Z, Ming Y, Li X, Qin L, Liu G, Wu J, Li Y, Zhang M, Feng K, Ying J, Wang X. The Distinct Performances of Ultrasound, Mammograms, and MRI in Detecting Breast Cancer in Patients With Germline Pathogenic Variants in Cancer Predisposition Genes. Front Oncol 2021; 11:710156. [PMID: 34336698 PMCID: PMC8316045 DOI: 10.3389/fonc.2021.710156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
A proportion of up to 10% of breast cancer resulted from hereditary germline pathogenic variants (GPVs) in cancer predisposition genes (CPGs), which been demonstrated distinct clinical features and imaging manifestations. However, the performance of imaging modalities for breast cancer surveillance in CPG mutation-carriers is still unclear, especially in Asian women. A population of 3002 breast cancer patients who received germline genetic testing of CPGs was enrolled from three hospitals in China. In total, 343 (11.6%) patients were found to harbor GPVs in CPGs, including 137 (4.6%) in BRCA1 and 135 (4.6%) in BRCA2. We compared the performances of ultrasound, mammograms, MRI, and the combining strategies in CPG mutation carriers and non-carriers. As a result, the ultrasound showed a higher detection rate compared with mammograms regardless of the mutation status. However, its detection rate was lower in CPG mutation carriers than in non-carriers (93.2% vs 98.0%, P=2.1×10-4), especially in the BRCA1 mutation carriers (90.9% vs 98.0%, P=2.0×10-4). MRI presented the highest sensitivity (98.5%) and the lowest underestimation rate (14.5%) in CPG mutation carriers among ultrasound, mammograms, and their combination. Supplemental ultrasound or mammograms would add no significant value to MRI for detecting breast cancer (P>0.05). In multivariate logistic regression analysis, the family or personal cancer history could not replace the mutation status as the impact factor for the false-negative result and underestimation. In summary, clinicians and radiologists should be aware of the atypical imaging presentation of breast cancer in patients with GPVs in CPGs.
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Affiliation(s)
- Jiaqi Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Dong
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Huang
- Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Key Laboratory of Big Data for Spinal Deformities, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jiaxin Li
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengkai Huang
- Department of Laboratory Medicine, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Pei Yuan
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenyan Wang
- Department of Breast Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jie Wang
- Department of Ultrasound, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zeyu Xing
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ziqi Jia
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Ming
- PET-CT Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Li
- Department of Radiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ling Qin
- Department of Breast Surgical Oncology, Cancer Hospital of HuanXing, Beijing, China
| | - Gang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Wu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yiqun Li
- Department of Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Menglu Zhang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kexin Feng
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiang Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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32
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Sun L, Huang Y, Zhao S, Zhao J, Yan Z, Guo Y, Lin M, Zhong W, Yin Y, Chen Z, Zhang N, Zhang Y, Zhao Z, Li Q, Wang L, Dong X, Li Y, Li X, Qiu G, Zhang TJ, Wu Z, Tian W, Wu N. Deciphering the mutational signature of congenital limb malformations. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:961-970. [PMID: 34094714 PMCID: PMC8141661 DOI: 10.1016/j.omtn.2021.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/13/2021] [Indexed: 12/20/2022]
Abstract
Congenital limb malformations (CLMs) affect 1 in 500 live births. However, the value of exome sequencing (ES) for CLM is lacking. The purpose of this study was to decipher the mutational signature of CLM on an exome level. We enrolled a cohort of 66 unrelated probands (including 47 families) with CLM requiring surgical correction. ES was performed for all patients and available parental samples. A definite molecular diagnosis was achieved in 21 out of 66 (32%) patients. We identified 19 pathogenic or likely pathogenic single-nucleotide variants and three copy number variants, of which 11 variants were novel. We identified four variants of uncertain significance. Additionally, we identified RPL9 and UBA2 as novel candidate genes for CLM. By comparing the detailed phenotypic features, we expand the phenotypic spectrum of diastrophic dysplasia and chromosome 6q terminal deletion syndrome. We also found that the diagnostic rate was significantly higher in patients with a family history of CLM (p = 0.012) or more than one limb affected (p = 0.034). Our study expands our understanding of the mutational and phenotypic spectrum of CLM and provides novel insights into the genetic basis of these syndromes.
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Affiliation(s)
- Liying Sun
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Yingzhao Huang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Junhui Zhao
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Zihui Yan
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yang Guo
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Mao Lin
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Wenyao Zhong
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Yuehan Yin
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Nan Zhang
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Yuanqiang Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zongxuan Zhao
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Qingyang Li
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiying Dong
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yaqi Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Wen Tian
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
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33
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Gui B, Yu C, Li X, Zhao S, Zhao H, Yan Z, Cheng X, Lin J, Zheng H, Shao J, Zhao Z, Zhao L, Niu Y, Zhao Z, Wang H, Xie B, Wei X, Gui C, Li C, Chen S, Wang Y, Song Y, Gong C, Zhang TJ, Fan X, Wu Z, Chen Y, Wu N. Heterozygous Recurrent Mutations Inducing Dysfunction of ROR2 Gene in Patients With Short Stature. Front Cell Dev Biol 2021; 9:661747. [PMID: 33937263 PMCID: PMC8080376 DOI: 10.3389/fcell.2021.661747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/12/2021] [Indexed: 11/22/2022] Open
Abstract
PURPOSE ROR2, a member of the ROR family, is essential for skeletal development as a receptor of Wnt5a. The present study aims to investigate the mutational spectrum of ROR2 in children with short stature and to identify the underlying molecular mechanisms. METHODS We retrospectively analyzed clinical phenotype and whole-exome sequencing (WES) data of 426 patients with short stature through mutation screening of ROR2. We subsequently examined the changes in protein expression and subcellular location in ROR2 caused by the mutations. The mRNA expression of downstream signaling molecules of the Wnt5a-ROR2 pathway was also examined. RESULTS We identified 12 mutations in ROR2 in 21 patients, including 10 missense, one nonsense, and one frameshift. Among all missense variants, four recurrent missense variants [c.1675G > A(p.Gly559Ser), c.2212C > T(p.Arg738Cys), c.1930G > A(p.Asp644Asn), c.2117G > A(p.Arg706Gln)] were analyzed by experiments in vitro. The c.1675G > A mutation significantly altered the expression and the cellular localization of the ROR2 protein. The c.1675G > A mutation also caused a significantly decreased expression of c-Jun. In contrast, other missense variants did not confer any disruptive effect on the biological functions of ROR2. CONCLUSION We expanded the mutational spectrum of ROR2 in patients with short stature. Functional experiments potentially revealed a novel molecular mechanism that the c.1675G > A mutation in ROR2 might affect the expression of downstream Wnt5a-ROR2 pathway gene by disturbing the subcellular localization and expression of the protein.
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Affiliation(s)
- Baoheng Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
| | - Chenxi Yu
- 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
| | - Xiaoxin Li
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - 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
| | - 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
| | - 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
| | - Xi Cheng
- 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
| | - 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
| | - Haiyang Zheng
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
| | - Jiashen Shao
- 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
| | - Zhengye 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
| | - Lina Zhao
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuchen Niu
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhi Zhao
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Huizi Wang
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bobo Xie
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
| | - Xianda Wei
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chunrong Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chuan Li
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shaoke Chen
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yi Wang
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Yanning Song
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Chunxiu Gong
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Terry 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
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Fan
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yujun Chen
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 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
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
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34
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Fan X, Zhao S, Yu C, Wu D, Yan Z, Fan L, Song Y, Wang Y, Li C, Ming Y, Gui B, Niu Y, Li X, Yang X, Luo S, Zhang Q, Zhao X, Pan H, Li M, Xia W, Qiu G, Liu P, Zhang S, Zhang J, Wu Z, Lupski JR, Posey JE, Chen S, Gong C, Wu N. Exome sequencing reveals genetic architecture in patients with isolated or syndromic short stature. J Genet Genomics 2021; 48:396-402. [PMID: 34006472 DOI: 10.1016/j.jgg.2021.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/08/2021] [Accepted: 02/20/2021] [Indexed: 12/12/2022]
Abstract
Short stature is among the most common endocrinological disease phenotypes of childhood and may occur as an isolated finding or in conjunction with other clinical manifestations. Although the diagnostic utility of clinical genetic testing in short stature has been implicated, the genetic architecture and the utility of genomic studies such as exome sequencing (ES) in a sizable cohort of patients with short stature have not been investigated systematically. In this study, we recruited 561 individuals with short stature from two centers in China during a 4-year period. We performed ES for all patients and available parents. All patients were retrospectively divided into two groups: an isolated short stature group (group I, n = 257) and an apparently syndromic short stature group (group II, n = 304). Causal variants were identified in 135 of 561 (24.1%) patients. In group I, 29 of 257 (11.3%) of the patients were solved by variants in 24 genes. In group II, 106 of 304 (34.9%) patients were solved by variants in 57 genes. Genes involved in fundamental cellular process played an important role in the genetic architecture of syndromic short stature. Distinct genetic architectures and pathophysiological processes underlie isolated and syndromic short stature.
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Affiliation(s)
- Xin Fan
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi 530003, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China
| | - Chenxi Yu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China
| | - Di Wu
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Zihui Yan
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China
| | - Lijun Fan
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yanning Song
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yi Wang
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Chuan Li
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, Guangxi 530003, China; Laboratory of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, Guangxi 530003, China
| | - Yue Ming
- PET-CT Center, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Baoheng Gui
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi 530003, China
| | - Yuchen Niu
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoxin Li
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xinzhuang Yang
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Shiyu Luo
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Qiang Zhang
- Laboratory of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, Guangxi 530003, China
| | - Xiuli Zhao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Hui Pan
- Department of Endocrine and Metabolism, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Mei Li
- Department of Endocrine and Metabolism, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Weibo Xia
- Department of Endocrine and Metabolism, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Pengfei Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Baylor Genetics, Houston, TX 77021, USA
| | - Shuyang Zhang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shaoke Chen
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi 530003, China
| | - Chunxiu Gong
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China.
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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35
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Liu B, Zhao S, Yan Z, Zhao L, Lin J, Wang S, Niu Y, Li X, Qiu G, Zhang TJ, Wu Z, Wu N. Variants Affecting the C-Terminal of CSF1R Cause Congenital Vertebral Malformation Through a Gain-of-Function Mechanism. Front Cell Dev Biol 2021; 9:641133. [PMID: 33816491 PMCID: PMC8017210 DOI: 10.3389/fcell.2021.641133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/10/2021] [Indexed: 11/13/2022] Open
Abstract
CSF1R encodes the colony-stimulating factor 1 receptor which regulates the proliferation, differentiation, and biological activity of monocyte/macrophage lineages. Pathogenic variants in CSF1R could lead to autosomal dominant adult-onset leukoencephalopathy with axonal spheroids and pigmented glia or autosomal recessive skeletal dysplasia. In this study, we identified three heterozygous deleterious rare variants in CSF1R from a congenital vertebral malformation (CVM) cohort. All of the three variants are located within the carboxy-terminal region of CSF1R protein and could lead to an increased stability of the protein. Therefore, we established a zebrafish model overexpressing CSF1R. The zebrafish model exhibits CVM phenotypes such as hemivertebral and vertebral fusion. Furthermore, overexpression of the mutated CSF1R mRNA depleted of the carboxy-terminus led to a higher proportion of zebrafish with vertebral malformations than wild-type CSF1R mRNA did (p = 0.03452), implicating a gain-of-function effect of the C-terminal variant. In conclusion, variants affecting the C-terminal of CSF1R could cause CVM though a potential gain-of-function mechanism.
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Affiliation(s)
- Bowen Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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 Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
| | - Zihui Yan
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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 of Peking Union Medical College, Beijing, China
| | - Lina Zhao
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jiachen Lin
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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 of Peking Union Medical College, Beijing, China
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical 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 Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
| | | | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, 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
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36
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Liu G, Zhao H, Yan Z, Zhao S, Niu Y, Li X, Wang S, Yang Y, Liu S, Zhang TJ, Wu Z, Wu N. Whole-genome methylation analysis reveals novel epigenetic perturbations of congenital scoliosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:1281-1287. [PMID: 33717649 PMCID: PMC7907230 DOI: 10.1016/j.omtn.2021.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 02/05/2021] [Indexed: 11/24/2022]
Abstract
Congenital scoliosis (CS) is a congenital disease caused by malformations of vertebrae. Recent studies demonstrated that DNA modification could contribute to the pathogenesis of disease. This study aims to identify epigenetic perturbations that may contribute to the pathogenesis of CS. Four CS patients with hemivertebra were enrolled and underwent spine correction operations. DNA was extracted from the hemivertebrae and spinal process collected from the specimen during the hemivertebra resection. Genome-wide DNA methylation profiling was examined at base-pair resolution using whole-genome bisulfite sequencing (WGBS). We identified 343 genes with hyper-differentially methylated regions (DMRs) and 222 genes with hypo-DMRs, respectively. These genes were enriched in the mitogen-activated protein kinase (MAPK) signaling pathway, calcium signaling pathway, and axon guidance in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and were enriched in positive regulation of cell morphogenesis involved in differentiation, regulation of cell morphogenesis involved in differentiation, and regulation of neuron projection development in Biological Process of Gene Ontology (GO-BP) terms. Hyper-DMR-related genes, including IGHG1, IGHM, IGHG3, RNF213, and GSE1, and hypo DMR-related genes, including SORCS2, COL5A1, GRID1, RGS3, and ROBO2, may contribute to the pathogenesis of hemivertebra. The aberrant DNA methylation may be associated with the formation of hemivertebra and congenital scoliosis.
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Affiliation(s)
- Gang Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, 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.,Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, 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, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zihui Yan
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, 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, Beijing 100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yang Yang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Sen Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, 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, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
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37
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Yu C, Xie B, Zhao Z, Zhao S, Liu L, Cheng X, Li X, Cao B, Shao J, Chen J, Zhao H, Yan Z, Su C, Niu Y, Song Y, Wei L, Wang Y, Ren X, Fan L, Zhang B, Li C, Gui B, Zhang Y, Wang L, Chen S, Zhang J, Wu Z, Gong C, Fan X, Wu N. Whole Exome Sequencing Uncovered the Genetic Architecture of Growth Hormone Deficiency Patients. Front Endocrinol (Lausanne) 2021; 12:711991. [PMID: 34589056 PMCID: PMC8475633 DOI: 10.3389/fendo.2021.711991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/09/2021] [Indexed: 02/01/2023] Open
Abstract
PURPOSE Congenital growth hormone deficiency (GHD) is a rare and etiologically heterogeneous disease. We aim to screen disease-causing mutations of GHD in a relatively sizable cohort and discover underlying mechanisms via a candidate gene-based mutational burden analysis. METHODS We retrospectively analyzed 109 short stature patients associated with hormone deficiency. All patients were classified into two groups: Group I (n=45) with definitive GHD and Group II (n=64) with possible GHD. We analyzed correlation consistency between clinical criteria and molecular findings by whole exome sequencing (WES) in two groups. The patients without a molecular diagnosis (n=90) were compared with 942 in-house controls for the mutational burden of rare mutations in 259 genes biologically related with the GH axis. RESULTS In 19 patients with molecular diagnosis, we found 5 possible GHD patients received known molecular diagnosis associated with GHD (NF1 [c.2329T>A, c.7131C>G], GHRHR [c.731G>A], STAT5B [c.1102delC], HRAS [c.187_207dup]). By mutational burden analysis of predicted deleterious variants in 90 patients without molecular diagnosis, we found that POLR3A (p = 0.005), SUFU (p = 0.006), LHX3 (p = 0.021) and CREB3L4 (p = 0.040) represented top genes enriched in GHD patients. CONCLUSION Our study revealed the discrepancies between the laboratory testing and molecular diagnosis of GHD. These differences should be considered when for an accurate diagnosis of GHD. We also identified four candidate genes that might be associated with GHD.
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Affiliation(s)
- Chenxi Yu
- 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 Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Bobo Xie
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
| | - Zhengye 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
| | - 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
| | - Lian 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
| | - Xi Cheng
- 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
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bingyan Cao
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Jiashen Shao
- 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
| | - Jiajia Chen
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, 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
| | - 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
| | - Chang Su
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yanning Song
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Liya Wei
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Yi Wang
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Xiaoya Ren
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Lijun Fan
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Beibei Zhang
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Chuan Li
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
| | - Baoheng Gui
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
| | - Yuanqiang Zhang
- Department of Orthopaedic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lianlei Wang
- Department of Orthopaedic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shaoke Chen
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
| | - 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
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- *Correspondence: Nan Wu, ; Xin Fan, ; Chunxiu Gong, ; Zhihong Wu,
| | - Chunxiu Gong
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
- *Correspondence: Nan Wu, ; Xin Fan, ; Chunxiu Gong, ; Zhihong Wu,
| | - Xin Fan
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Guangxi, China
- Department of Pediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, China
- *Correspondence: Nan Wu, ; Xin Fan, ; Chunxiu Gong, ; Zhihong Wu,
| | - 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
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- *Correspondence: Nan Wu, ; Xin Fan, ; Chunxiu Gong, ; Zhihong Wu,
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Chen Z, Yan Z, Yu C, Liu J, Zhang Y, Zhao S, Lin J, Zhang Y, Wang L, Lin M, Huang Y, Li X, Niu Y, Wang S, Wu Z, Qiu G, Zhang TJ, Wu N. Cost-effectiveness analysis of using the TBX6-associated congenital scoliosis risk score (TACScore) in genetic diagnosis of congenital scoliosis. Orphanet J Rare Dis 2020; 15:250. [PMID: 32933559 PMCID: PMC7493351 DOI: 10.1186/s13023-020-01537-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 09/07/2020] [Indexed: 11/25/2022] Open
Abstract
Background We previously reported a novel clinically distinguishable subtype of congenital scoliosis (CS), namely, TBX6-associated congenital scoliosis (TACS). We further developed the TBX6-associated CS risk score (TACScore), a multivariate phenotype-based model to predict TACS according to the patient’s clinical manifestations. In this study, we aimed to evaluate whether using the TACScore as a screening method prior to performing whole-exome sequencing (WES) is more cost-effective than using WES as the first-line genetic test for CS. Methods We retrospectively collected the molecular data of 416 CS patients in the Deciphering disorders Involving Scoliosis and COmorbidities (DISCO) study. A decision tree was constructed to estimate the cost and the diagnostic time required for the two alternative strategies (TACScore versus WES). Bootstrapping simulations and sensitivity analyses were performed to examine the distributions and robustness of the estimates. The economic evaluation considered both the health care payer and the personal budget perspectives. Results From the health care payer perspective, the strategy of using the TACScore as the primary screening method resulted in an average cost of $1074.2 (95%CI: $1044.8 to $1103.5) and an average diagnostic duration of 38.7d (95%CI: 37.8d to 39.6d) to obtain a molecular diagnosis for each patient. In contrast, the corresponding values were $1169.6 (95%CI: $1166.9 to $1172.2) and 41.4d (95%CI: 41.1d to 41.7d) taking WES as the first-line test (P < 0.001). From the personal budget perspective, patients who were predicted to be positive by the TACScore received a result with an average cost of $715.1 (95%CI: $594.5 to $835.7) and an average diagnostic duration of 30.4d (95%CI: 26.3d to 34.6d). Comparatively, the strategy of WES as the first-line test was estimated to have significantly longer diagnostic time with an average of 44.0d (95%CI: 43.2d to 44.9d), and more expensive with an average of $1193.4 (95%CI: $1185.5 to $1201.3) (P < 0.001). In 100% of the bootstrapping simulations, the TACScore strategy was significantly less costly and more time-saving than WES. The sensitivity analyses revealed that the TACScore strategy remained cost-effective even when the cost per WES decreased to $8.8. Conclusions This retrospective study provides clinicians with economic evidence to integrate the TACScore into clinical practice. The TACScore can be considered a cost-effective tool when it serves as a screening test prior to performing WES.
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Affiliation(s)
- Zefu Chen
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100005, China
| | - Zihui Yan
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100005, China
| | - Chenxi Yu
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100005, China
| | - Jiaqi Liu
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanbin Zhang
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100005, China
| | - Sen Zhao
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
| | - Jiachen Lin
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100005, China
| | - Yuanqiang Zhang
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100005, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100005, China
| | - Mao Lin
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100005, China
| | - Yingzhao Huang
- Department of Orthopedic Surgery, 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, Beijing, 100730, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shengru Wang
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Guixing Qiu
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, 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, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Nan Wu
- Department of Orthopedic Surgery, 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, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Yang Y, Zhao S, Zhang Y, Wang S, Shao J, Liu B, Li Y, Yan Z, Niu Y, Li X, Wang L, Ye Y, Weng X, Wu Z, Zhang J, Wu N. Mutational burden and potential oligogenic model of TBX6-mediated genes in congenital scoliosis. Mol Genet Genomic Med 2020; 8:e1453. [PMID: 32815649 PMCID: PMC7549550 DOI: 10.1002/mgg3.1453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/26/2020] [Accepted: 07/22/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Congenital scoliosis (CS) is a spinal deformity due to vertebral malformations. Although insufficiency of TBX6 dosage contributes to a substantial proportion of CS, the molecular etiology for the majority of CS remains largely unknown. TBX6-mediated genes involved in the process of somitogenesis represent promising candidates. METHODS Individuals affected with CS and without a positive genetic finding were referred to this study. Proband-only exome sequencing (ES) were performed on the recruited individuals, followed by analysis of TBX6-mediated candidate genes, namely MEOX1, MEOX2, MESP2, MYOD1, MYF5, RIPPLY1, and RIPPLY2. RESULTS A total of 584 patients with CS of unknown molecular etiology were recruited. After ES analysis, protein-truncating variants in RIPPLY1 and MYF5 were identified from two individuals, respectively. In addition, we identified five deleterious missense variants (MYOD1, n = 4; RIPPLY2, n = 1) in TBX6-mediated genes. We observed a significant mutational burden of MYOD1 in CS (p = 0.032) compared with the in-house controls (n = 1854). Moreover, a potential oligogenic disease-causing mode was proposed based on the observed mutational co-existence of MYOD1/MEOX1 and MYOD1/RIPPLY1. CONCLUSION Our study characterized the mutational spectrum of TBX6-mediated genes, prioritized core candidate genes/variants, and provided insight into a potential oligogenic disease-causing mode in CS.
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Affiliation(s)
- Yang Yang
- 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 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
| | - 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
| | - Jiashen Shao
- 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
| | - Bowen 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
| | - Yaqi Li
- 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
| | - 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
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical 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 Union Medical College and 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
| | - Yongyu Ye
- Department of Orthopedic Surgery, First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Xisheng Weng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, China
| | | | - 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, 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.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, China
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