1
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Salinas-Torres VM, Salinas-Torres RA. Casamassima-Morton-Nance Syndrome and Limb-Body Wall Defect: Presentation of the Second Case and Phenotypic Assessment. Pediatr Dev Pathol 2024:10935266241281797. [PMID: 39324207 DOI: 10.1177/10935266241281797] [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] [Indexed: 09/27/2024]
Abstract
Casamassima-Morton-Nance syndrome (CMNS) is a rare disorder characterized by spondylocostal dysostosis (SCD), anal atresia, and urogenital anomalies. We describe a fetus with CMNS associated with a limb-body wall defect (LBWD), the second such case in the literature. We compare the phenotypic differences with previously reported cases, including those with segmentation anomalies of the axial skeleton, body wall defects, or absent/abnormal genitalia, revealing the consistent presence of SCD in CMNS. However, as expected, a wide phenotypic spectrum emerges, providing useful observations for fetal/neonatal screening relevant to differential diagnoses. Advanced diagnostic methods using imaging and next-generation skeletal dysplasia multi-gene panels are advisable, as they enable timely, actionable, well-informed decisions for parental counseling, potential elective termination of pregnancy, and prenatal and/or postnatal care. Most reported cases do not mention the recurrence of these usually lethal anomalies.
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Affiliation(s)
- Víctor M Salinas-Torres
- Secretaria de Salud Durango, Durango General Hospital, Human Genetics and Genomics Department, Durango, México
| | - Rafael A Salinas-Torres
- Instituto Tecnológico de Tijuana, Systems and Computing Department, Tijuana, Baja California, México
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2
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Auwerx C, Kutalik Z, Reymond A. The pleiotropic spectrum of proximal 16p11.2 CNVs. Am J Hum Genet 2024:S0002-9297(24)00301-X. [PMID: 39332410 DOI: 10.1016/j.ajhg.2024.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/18/2024] [Accepted: 08/21/2024] [Indexed: 09/29/2024] Open
Abstract
Recurrent genomic rearrangements at 16p11.2 BP4-5 represent one of the most common causes of genomic disorders. Originally associated with increased risk for autism spectrum disorder, schizophrenia, and intellectual disability, as well as adiposity and head circumference, these CNVs have since been associated with a plethora of phenotypic alterations, albeit with high variability in expressivity and incomplete penetrance. Here, we comprehensively review the pleiotropy associated with 16p11.2 BP4-5 rearrangements to shine light on its full phenotypic spectrum. Illustrating this phenotypic heterogeneity, we expose many parallels between findings gathered from clinical versus population-based cohorts, which often point to the same physiological systems, and emphasize the role of the CNV beyond neuropsychiatric and anthropometric traits. Revealing the complex and variable clinical manifestations of this CNV is crucial for accurate diagnosis and personalized treatment strategies for carrier individuals. Furthermore, we discuss areas of research that will be key to identifying factors contributing to phenotypic heterogeneity and gaining mechanistic insights into the molecular pathways underlying observed associations, while demonstrating how diversity in affected individuals, cohorts, experimental models, and analytical approaches can catalyze discoveries.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
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3
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Li G, Chen Y, Han X, Li N, Li S. Concurrent of compound heterozygous variant of a novel in-frame deletion and the common hypomorphic haplotype in TBX6 and inherited 17q12 microdeletion in a fetus. BMC Pregnancy Childbirth 2024; 24:456. [PMID: 38951757 PMCID: PMC11218386 DOI: 10.1186/s12884-024-06653-2] [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: 02/19/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND TBX6, a member of the T-box gene family, encodes the transcription factor box 6 that is critical for somite segmentation in vertebrates. It is known that the compound heterozygosity of disruptive variants in trans with a common hypomorphic risk haplotype (T-C-A) in the TBX6 gene contribute to 10% of congenital scoliosis (CS) cases. The deletion of chromosome 17q12 is a rare cytogenetic abnormality, which often leads to renal cysts and diabetes mellitus. However, the affected individuals often exhibit clinical heterogeneity and incomplete penetrance. METHODS We here present a Chinese fetus who was shown to have CS by ultrasound examination at 17 weeks of gestation. Trio whole-exome sequencing (WES) was performed to investigate the underlying genetic defects of the fetus. In vitro functional experiments, including western-blotting and luciferase transactivation assay, were performed to determine the pathogenicity of the novel variant of TBX6. RESULTS WES revealed the fetus harbored a compound heterozygous variant of c.338_340del (p.Ile113del) and the common hypomorphic risk haplotype of the TBX6 gene. In vitro functional study showed the p.Ile113del variant had no impact on TBX6 expression, but almost led to complete loss of its transcriptional activity. In addition, we identified a 1.85 Mb deletion on 17q12 region in the fetus and the mother. Though there is currently no clinical phenotype associated with this copy number variation in the fetus, it can explain multiple renal cysts in the pregnant woman. CONCLUSIONS This study is the first to report a Chinese fetus with a single amino acid deletion variant and a T-C-A haplotype of TBX6. The clinical heterogeneity of 17q12 microdeletion poses significant challenges for prenatal genetic counseling. Our results once again suggest the complexity of prenatal genetic diagnosis.
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Affiliation(s)
- Guoqiang Li
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Yiyao Chen
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Xu Han
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Niu Li
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China.
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China.
- Faculty of Medical Laboratory Science, College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Shuyuan Li
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China.
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China.
- Faculty of Medical Laboratory Science, College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
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4
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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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Herlin MK. Genetics of Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome: advancements and implications. Front Endocrinol (Lausanne) 2024; 15:1368990. [PMID: 38699388 PMCID: PMC11063329 DOI: 10.3389/fendo.2024.1368990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a congenital anomaly characterized by agenesis/aplasia of the uterus and upper part of the vagina in females with normal external genitalia and a normal female karyotype (46,XX). Patients typically present during adolescence with complaints of primary amenorrhea where the diagnosis is established with significant implications including absolute infertility. Most often cases appear isolated with no family history of MRKH syndrome or related anomalies. However, cumulative reports of familial recurrence suggest genetic factors to be involved. Early candidate gene studies had limited success in their search for genetic causes of MRKH syndrome. More recently, genomic investigations using chromosomal microarray and genome-wide sequencing have been successful in detecting promising genetic variants associated with MRKH syndrome, including 17q12 (LHX1, HNF1B) and 16p11.2 (TBX6) deletions and sequence variations in GREB1L and PAX8, pointing towards a heterogeneous etiology with various genes involved. With uterus transplantation as an emerging fertility treatment in MRKH syndrome and increasing evidence for genetic etiologies, the need for genetic counseling concerning the recurrence risk in offspring will likely increase. This review presents the advancements in MRKH syndrome genetics from early familial occurrences and candidate gene searches to current genomic studies. Moreover, the review provides suggestions for future genetic investigations and discusses potential implications for clinical practice.
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Affiliation(s)
- Morten Krogh Herlin
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N, Denmark
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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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Szoszkiewicz A, Bukowska-Olech E, Jamsheer A. Molecular landscape of congenital vertebral malformations: recent discoveries and future directions. Orphanet J Rare Dis 2024; 19:32. [PMID: 38291488 PMCID: PMC10829358 DOI: 10.1186/s13023-024-03040-0] [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: 07/18/2023] [Accepted: 01/19/2024] [Indexed: 02/01/2024] Open
Abstract
Vertebral malformations (VMs) pose a significant global health problem, causing chronic pain and disability. Vertebral defects occur as isolated conditions or within the spectrum of various congenital disorders, such as Klippel-Feil syndrome, congenital scoliosis, spondylocostal dysostosis, sacral agenesis, and neural tube defects. Although both genetic abnormalities and environmental factors can contribute to abnormal vertebral development, our knowledge on molecular mechanisms of numerous VMs is still limited. Furthermore, there is a lack of resource that consolidates the current knowledge in this field. In this pioneering review, we provide a comprehensive analysis of the latest research on the molecular basis of VMs and the association of the VMs-related causative genes with bone developmental signaling pathways. Our study identifies 118 genes linked to VMs, with 98 genes involved in biological pathways crucial for the formation of the vertebral column. Overall, the review summarizes the current knowledge on VM genetics, and provides new insights into potential involvement of biological pathways in VM pathogenesis. We also present an overview of available data regarding the role of epigenetic and environmental factors in VMs. We identify areas where knowledge is lacking, such as precise molecular mechanisms in which specific genes contribute to the development of VMs. Finally, we propose future research avenues that could address knowledge gaps.
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Affiliation(s)
- Anna Szoszkiewicz
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland.
| | - Ewelina Bukowska-Olech
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland.
- Centers for Medical Genetics GENESIS, Dąbrowskiego 77A, 60-529, Poznan, Poland.
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8
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Shapiro F, Wang J, Flynn E, Wu JY. Pudgy mouse rib deformities emanate from abnormal paravertebral longitudinal cartilage/bone accumulations. Biol Open 2024; 13:bio060139. [PMID: 38252118 PMCID: PMC10840853 DOI: 10.1242/bio.060139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/03/2023] [Indexed: 01/23/2024] Open
Abstract
The pudgy (pu/pu) mouse, caused by a recessive mutation in the Notch family Delta like-3 gene (Dll3), has severe rib, vertebral body and intervertebral disc abnormalities. Using whole-mount preparations and serial histologic sections we demonstrate: 1) localized paravertebral longitudinal cartilage/bone accumulations (PVLC/BAs) invariably associated with branched, fused and asymmetrically spaced ribs that emanate from it laterally; 2) abnormal rib formation immediately adjacent to abnormal vertebral body and intervertebral disc formation in asymmetric right/left fashion; and 3) patterns of rib deformation that differ in each mouse. Normal BALB/c embryo and age-matched non-affected pu/+ mice assessments allow for pu/pu comparisons. The Dll3 Notch family gene is involved in normal somitogenesis via the segmentation clock mechanism. Although pathogenesis of rib deformation is initially triggered by the Dll3 gene mutation, these findings of abnormal asymmetric costo-vertebral region structure imply that differing patterns cannot be attributed to this single gene mutation alone. All findings implicate a dual mechanism of malformation: the Dll3 gene mutation leading to subtle timing differences in traveling oscillation waves of the segmentation clock and further subsequent misdirection of tissue formation by altered chemical reaction-diffusion and epigenetic landscape responses. PVLC/BAs appear as primary supramolecular structures underlying severe rib malformation associated both with time-sensitive segmentation clock mutations and subsequent reactions.
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Affiliation(s)
- Frederic Shapiro
- Department of Medicine/Endocrinology, Stanford University School of Medicine, Palo Alto CA 94305, USA
- Department of Bioengineering, Northeastern University, Boston MA 02115, USA
| | - Jamie Wang
- Department of Medicine/Endocrinology, Stanford University School of Medicine, Palo Alto CA 94305, USA
| | - Evelyn Flynn
- Orthopaedic Research Laboratory, Boston Children's Hospital, Boston MA 02115, USA
| | - Joy Y. Wu
- Department of Medicine/Endocrinology, Stanford University School of Medicine, Palo Alto CA 94305, USA
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9
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Liu L, Wang J, Liu X, Wang J, Chen L, Zhu H, Mai J, Hu T, Liu S. Prenatal prevalence and postnatal manifestations of 16p11.2 deletions: A new insights into neurodevelopmental disorders based on clinical investigations combined with multi-omics analysis. Clin Chim Acta 2024; 552:117671. [PMID: 37984529 DOI: 10.1016/j.cca.2023.117671] [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: 06/08/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND The 16p11.2 deletion is one of the most common genetic aetiologies of neurodevelopmental disorders (NDDs). The prenatal phenotype of 16p11.2 deletion and the potential mechanism associated with postnatal clinical manifestations were largely unknow. We revealed the developmental trajectories of 16p11.2 deletion from the prenatal to postnatal periods and to identify key signaling pathways and candidate genes contributing to neurodevelopmental abnormalities. METHODS In this 5-y retrospective cohort study, women with singleton pregnancies who underwent amniocentesis for chromosomal abnormalities were included. Test of copy-number variations (CNVs) involved single nucleotide polymorphism-array and CNV-seq was performed to detected 16p11.2 deletion. For infants born carrying the 16p11.2 deletion, neurological and intellectual evaluations using the Chinese version of the Gesell Development Scale. For patients observed to have vertebral malformations, Sanger sequencing for T-C-A haplotype of TBX6 was performed. For those infants with clinical manifestations, whole-exome sequencing was consecutively performed in trios to rule out single-gene diseases, and transcriptomics combined with untargeted metabolomics were performed. RESULTS The prevalence of 16p11.2 deletion was 0.063% (55/86,035) in the prenatal period. Up to 80% (20/25) of the 16p11.2 deletions were proven de novo by parental confirmation. Approximately half of 16p11.2 deletions (28/55) were detected with prenatal abnormal ultrasound findings. Vertebral malformations were identified as the most distinctive structural malformations and were enriched in fetuses with 16p11.2 deletions compared with controls (90.9‰ [5/55] vs. 8.4‰ [72/85,980]; P < 0.001). All 5 fetuses with vertebral malformations were confirmed to have the TBX6 haplotype of T-C-A. Overall, 47.6% (10/21) infants birthed were diagnosed with NDDs of different degrees. Language impairment was the predominant manifestation (7/10; 70.0%), followed by motor delay (5/10; 50%). Multi-omics analysis indicated that MAPK3 was the central hub of the differentially expressed gene (DEG) network. We firstly reported that histidine-associated metabolism may be the core metabolic pathway related to the 16p11.2 deletion. CONCLUSION We demonstrated the prenatal presentation, incomplete penetrance and variable expressivity of the 16p11.2 deletion. We identified vertebral malformations were the most distinctive prenatal phenotypes, and language impairment was the predominant postnatal manifestation. Most of the 16p11.2 deletion was de novo. Meanwhile, we suggested that MAPK3 and histidine-associated metabolism may contribute to neurodevelopmental abnormalities of 16p11.2 deletion.
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Affiliation(s)
- Lan Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Medical College, Tibet University, Lhasa, Tibet 850000, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xijing Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Chen
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongmei Zhu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jingqun Mai
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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10
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Martin G, Canuet M, Rahli M, Schuller A, Enache I, Kessler R, Riou M. Severe pre-capillary pulmonary hypertension associated with kyphoscoliosis: Description of 4 cases. Respir Med Res 2023; 84:101034. [PMID: 37625378 DOI: 10.1016/j.resmer.2023.101034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 08/27/2023]
Affiliation(s)
- Guillaume Martin
- Chest diseases department, Nouvel hôpital civil, University Hospital of Strasbourg, Strasbourg, France
| | - Matthieu Canuet
- Chest diseases department, Nouvel hôpital civil, University Hospital of Strasbourg, Strasbourg, France
| | - Mohamed Rahli
- Chest diseases department, Nouvel hôpital civil, University Hospital of Strasbourg, Strasbourg, France
| | - Armelle Schuller
- Chest diseases department, Nouvel hôpital civil, University Hospital of Strasbourg, Strasbourg, France
| | - Irina Enache
- Department of Physiology and Functional Exploration, Nouvel hôpital civil, University Hospital of Strasbourg, Strasbourg, France; University of Strasbourg, Translational Medicine Federation of Strasbourg (FMTS), CRBS, Team 3072 "Mitochondria, Oxidative Stress and Muscle Protection", 1 rue Eugène Boeckel, CS 60026, 67084 Strasbourg, France
| | - Romain Kessler
- Chest diseases department, Nouvel hôpital civil, University Hospital of Strasbourg, Strasbourg, France; INSERM-UNISTRA, UMR 1260 'Regenerative NanoMedicine', University of Strasbourg, 1 rue Eugène Boeckel, CS 60026, 67084 Strasbourg, France
| | - Marianne Riou
- Chest diseases department, Nouvel hôpital civil, University Hospital of Strasbourg, Strasbourg, France; Department of Physiology and Functional Exploration, Nouvel hôpital civil, University Hospital of Strasbourg, Strasbourg, France; University of Strasbourg, Translational Medicine Federation of Strasbourg (FMTS), CRBS, Team 3072 "Mitochondria, Oxidative Stress and Muscle Protection", 1 rue Eugène Boeckel, CS 60026, 67084 Strasbourg, France.
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11
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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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12
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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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13
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Zheng Y, Shen P, Tong M, Li H, Ren C, Wu F, Li H, Yang H, Cai B, Du W, Zhao X, Yao S, Quan R. WISP2 downregulation inhibits the osteogenic differentiation of BMSCs in congenital scoliosis by regulating Wnt/β-catenin pathway. Biochim Biophys Acta Mol Basis Dis 2023:166783. [PMID: 37302424 DOI: 10.1016/j.bbadis.2023.166783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 05/09/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
OBJECTIVES Bone marrow mesenchymal stem cells (BMSCs) are instrumental in bone development, metabolism, and marrow microenvironment homeostasis. Despite this, the relevant effects and mechanisms of BMSCs on congenital scoliosis (CS) remain undefined. Herein, it becomes our focus to reveal the corresponding effects and mechanisms implicated. METHODS BMSCs from CS patients (hereafter referred as CS-BMSCs) and healthy donors (NC-BMSCs) were observed and identified. Differentially expressed genes in BMSCs were analyzed utilizing scRNA-seq and RNA-seq profiles. The multi-differentiation potential of BMSCs following the transfection or infection was evaluated. The expression levels of factors related to osteogenic differentiation and Wnt/β-catenin pathway were further determined as appropriate. RESULTS A decreased osteogenic differentiation ability was shown in CS-BMSCs. Both the proportion of LEPR+ BMSCs and the expression level of WNT1-inducible-signaling pathway protein 2 (WISP2) were decreased in CS-BMSCs. WISP2 knockdown suppressed the osteogenic differentiation of NC-BMSCs, while WISP2 overexpression facilitated the osteogenesis of CS-BMSCs via acting on the Wnt/β-catenin pathway. CONCLUSIONS Our study collectively indicates WISP2 knockdown blocks the osteogenic differentiation of BMSCs in CS by regulating Wnt/β-catenin signaling, thus providing new insights into the aetiology of CS.
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Affiliation(s)
- Yang Zheng
- Zhejiang Chinese Medical University, Hangzhou, China; Department of Orthopedics Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Panyang Shen
- Department of Orthopedics Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengsha Tong
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Hangchao Li
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Conglin Ren
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Fengqing Wu
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Hanyu Li
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Huan Yang
- Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou, China
| | - Bingbing Cai
- Department of Orthopedics, Xiaoshan Traditional Chinese Medical Hospital, Hangzhou, China
| | - Weibin Du
- Department of Orthopedics, Xiaoshan Traditional Chinese Medical Hospital, Hangzhou, China
| | - Xing Zhao
- Department of Orthopedics Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Shasha Yao
- Department of Orthopedics Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Renfu Quan
- Zhejiang Chinese Medical University, Hangzhou, China; Department of Orthopedics, Xiaoshan Traditional Chinese Medical Hospital, Hangzhou, China; Research Institute of Orthopedics, The Affiliated Jiangnan Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
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14
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Vodopiutz J, Steurer LM, Haufler F, Laccone F, Garczarczyk-Asim D, Hilkenmeier M, Steinbauer P, Janecke AR. Leri-Weill Dyschondrosteosis Caused by a Leaky Homozygous SHOX Splice-Site Variant. Genes (Basel) 2023; 14:genes14040877. [PMID: 37107635 PMCID: PMC10138022 DOI: 10.3390/genes14040877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
SHOX deficiency is a common genetic cause of short stature of variable degree. SHOX haploinsufficiency causes Leri-Weill dyschondrosteosis (LWD) as well as nonspecific short stature. SHOX haploinsufficiency is known to result from heterozygous loss-of-function variants with pseudo-autosomal dominant inheritance, while biallelic SHOX loss-of-function variants cause the more severe skeletal dysplasia, Langer mesomelic dyschondrosteosis (LMD). Here we report for the first time the pseudo-autosomal recessive inheritance of LWD in two siblings caused by a novel homozygous non-canonical, leaky splice-site variant in intron 3 of SHOX: c.544+5G>C. Transcript analyses in patient-derived fibroblasts showed homozygous patients to produce approximately equal amounts of normally spliced mRNA and mRNA with the abnormal retention of intron 3 and containing a premature stop codon (p.Val183Glyfs*31). The aberrant transcript was shown to undergo nonsense-mediated mRNA decay, and thus resulting in SHOX haploinsufficiency in the homozygous patient. Six healthy relatives who are of normal height are heterozygous for this variant and fibroblasts from a heterozygote for the c.544+5G>C variant produced wild-type transcript amounts comparable to healthy control. The unique situation reported here highlights the fact that the dosage of SHOX determines the clinical phenotype rather than the Mendelian inheritance pattern of SHOX variants. This study extends the molecular and inheritance spectrum of SHOX deficiency disorder and highlights the importance of functional testing of SHOX variants of unknown significance in order to allow appropriate counseling and precision medicine for each family individual.
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Affiliation(s)
- Julia Vodopiutz
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Pulmonology, Allergology and Endocrinology, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
- Vienna Bone and Growth Center, 1130 Vienna, Austria
| | - Lisa-Maria Steurer
- Vienna Bone and Growth Center, 1130 Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Florentina Haufler
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Pulmonology, Allergology and Endocrinology, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Franco Laccone
- Institute of Medical Genetics, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Matthias Hilkenmeier
- Department of Pediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Philipp Steinbauer
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Andreas R Janecke
- Department of Pediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Division of Human Genetics, Medical University of Innsbruck, 6020 Innsbruck, Austria
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15
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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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16
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Liu N, Li H, Li M, Gao Y, Yan H. Prenatally diagnosed 16p11.2 copy number variations by SNP Array: A retrospective case series. Clin Chim Acta 2023; 538:15-21. [PMID: 36374846 DOI: 10.1016/j.cca.2022.10.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVE The 16p11.2 copy number variations (CNVs) are increasingly recognized as one of the most frequent genomic disorders, with a broad spectrum of phenotypes. The fetal phenotype associated with 16p11.2 CNVs is poorly described. The current study presents prenatal series of 16p11.2 CNVs and provides a better understanding of this submicroscopic imbalance in prenatal diagnosis. METHOD Retrospective case series were extracted from a single tertiary referral center performing prenatal single nucleotide polymorphism (SNP) array from April 2017 to December 2021. The maternal demographics, indication for amniocentesis, ultrasound findings, SNP array results, inheritance of the CNVs, and pregnancy outcomes were studied. RESULTS We indentified 30 fetuses carrying 16p11.2 CNVs, representing 0.35% (30/8578) of prenatal SNP array results. The series included 17 fetuses with a proximal deletion, 7 with a distal deletion, 4 with a proximal duplication, and 2 with a distal duplication. Prenatal ultrasound anomalies were reported in 80% of these cases. The most common presentation was vertebralanomalies (9/30). Other features noted in more than one fetus were increased nuchal translucency/nuchal fold (NT/NF) (5/30), absent/hypoplastic nasal bone (3/30), polyhydramnios (3/30), ventricular septal defect (VSD) (2/30), unilateral mild ventriculomegaly (2/30), fetal growth restriction (FGR) (2/30), right aortic arch (2/30). All the 9 vertebralanomalies were present in fetuses harboring proximal deletion (9/17). Familial transmission was confirmed in 44% of cases (11/25) and termination of pregnancy was requested in 62.1% (18/29) of cases. CONCLUSION The 16p11.2 CNVs can have variable prenatal phenotypes and these CNVs are frequently inherited from parents with a milder or normal phenotype. Our results underline that vertebral deformities were frequent in cases of 16p11.2 proximal deletion, and further demonstrate the incomplete penetrance of the CNVs.
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Affiliation(s)
- Nian Liu
- Department of Health Toxicology, MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Prenatal Diagnostic Center, Genetic Lab, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Li
- Prenatal Diagnostic Center, Genetic Lab, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Manman Li
- Prenatal Diagnostic Center, Genetic Lab, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanduo Gao
- Department of Ultrasound, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Yan
- Department of Health Toxicology, MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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17
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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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18
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Umair M, Younus M, Shafiq S, Nayab A, Alfadhel M. Clinical genetics of spondylocostal dysostosis: A mini review. Front Genet 2022; 13:996364. [PMID: 36506336 PMCID: PMC9732429 DOI: 10.3389/fgene.2022.996364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/31/2022] [Indexed: 11/26/2022] Open
Abstract
Spondylocostal dysostosis is a genetic defect associated with severe rib and vertebrae malformations. In recent years, extensive clinical and molecular diagnosis advancements enabled us to identify disease-causing variants in different genes for such severe conditions. The identification of novel candidate genes enabled us to understand the developmental biology and molecular and cellular mechanisms involved in the etiology of these rare diseases. Here, we discuss the clinical and molecular targets associated with spondylocostal dysostosis, including clinical evaluation, genes, and pathways involved. This review might help us understand the basics of such a severe disorder, which might help in proper clinical characterization and help in future therapeutic strategies.
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Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, Ministry of National Guard Health Affairs (MNGH), King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia,*Correspondence: Muhammad Umair, ,
| | - Muhammad Younus
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada
| | - Anam Nayab
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, Pakistan
| | - Majid Alfadhel
- Medical Genomics Research Department, Ministry of National Guard Health Affairs (MNGH), King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia,Genetics and Precision Medicine Department, King Abdullah Specialized Children Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
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19
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Duan R, Hijazi H, Gulec EY, Eker HK, Costa SR, Sahin Y, Ocak Z, Isikay S, Ozalp O, Bozdogan S, Aslan H, Elcioglu N, Bertola DR, Gezdirici A, Du H, Fatih JM, Grochowski CM, Akay G, Jhangiani SN, Karaca E, Gu S, Coban-Akdemir Z, Posey JE, Bayram Y, Sutton VR, Carvalho CM, Pehlivan D, Gibbs RA, Lupski JR. Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability. HGG ADVANCES 2022; 3:100132. [PMID: 36035248 PMCID: PMC9403727 DOI: 10.1016/j.xhgg.2022.100132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022] Open
Abstract
Genetic heterogeneity, reduced penetrance, and variable expressivity, the latter including asymmetric body axis plane presentations, have all been described in families with congenital limb malformations (CLMs). Interfamilial and intrafamilial heterogeneity highlight the complexity of the underlying genetic pathogenesis of these developmental anomalies. Family-based genomics by exome sequencing (ES) and rare variant analyses combined with whole-genome array-based comparative genomic hybridization were implemented to investigate 18 families with limb birth defects. Eleven of 18 (61%) families revealed explanatory variants, including 7 single-nucleotide variant alleles and 3 copy number variants (CNVs), at previously reported "disease trait associated loci": BHLHA9, GLI3, HOXD cluster, HOXD13, NPR2, and WNT10B. Breakpoint junction analyses for all three CNV alleles revealed mutational signatures consistent with microhomology-mediated break-induced replication, a mechanism facilitated by Alu/Alu-mediated rearrangement. Homozygous duplication of BHLHA9 was observed in one Turkish kindred and represents a novel contributory genetic mechanism to Gollop-Wolfgang Complex (MIM: 228250), where triplication of the locus has been reported in one family from Japan (i.e., 4n = 2n + 2n versus 4n = 3n + 1n allelic configurations). Genes acting on limb patterning are sensitive to a gene dosage effect and are often associated with an allelic series. We extend an allele-specific gene dosage model to potentially assist, in an adjuvant way, interpretations of interconnections among an allelic series, clinical severity, and reduced penetrance of the BHLHA9-related CLM spectrum.
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Affiliation(s)
- Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
| | | | - Silvia R. Costa
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
| | - Yavuz Sahin
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
| | - Zeynep Ocak
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
| | - Débora R. Bertola
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Baylor-Hopkins Center for Mendelian Genomics
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
- Department of Medical Genetics, Konya City Hospital, Konya, Turkey
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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20
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Powel JE, Sham CE, Spiliopoulos M, Ferreira CR, Rosenthal E, Sinkovskaya ES, Brown S, Jelin AC, Al-Kouatly HB. Genetics of non-isolated hemivertebra: A systematic review of fetal, neonatal, and infant cases. Clin Genet 2022; 102:262-287. [PMID: 35802600 PMCID: PMC9830455 DOI: 10.1111/cge.14188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 01/12/2023]
Abstract
Hemivertebra is a congenital vertebral malformation caused by unilateral failure of formation during embryogenesis that may be associated with additional abnormalities. A systematic review was conducted to investigate genetic etiologies of non-isolated hemivertebra identified in the fetal, neonatal, and infant periods using PubMed, Cochrane database, Ovid Medline, and ClinicalTrials.gov from inception through May 2022 (PROSPERO ID CRD42021229576). The Human Phenotype Ontology database was accessed May 2022. Studies were deemed eligible for inclusion if they addressed non-isolated hemivertebra or genetic causes of non-isolated hemivertebra identified in the fetal, neonatal, or infant periods. Cases diagnosed clinically without molecular confirmation were included. Systematic review identified 23 cases of non-isolated hemivertebra with karyotypic abnormalities, 2 cases due to microdeletions, 59 cases attributed to single gene disorders, 18 syndromic cases without known genetic etiology, and 14 cases without a known syndromic association. The Human Phenotype Ontology search identified 49 genes associated with hemivertebra. Non-isolated hemivertebra is associated with a diverse spectrum of cytogenetic abnormalities and single gene disorders. Genetic syndromes were notably common. Frequently affected organ systems include musculoskeletal, cardiovascular, central nervous system, genitourinary, gastrointestinal, and facial dysmorphisms. When non-isolated hemivertebra is identified on prenatal ultrasound, the fetus must be assessed for associated anomalies and genetic counseling is recommended.
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Affiliation(s)
- Jennifer E. Powel
- Division of Maternal Fetal Medicine, Department of Obstetrics Gynecology, & Women’s Health, Saint Louis University School of Medicine, Saint Louis, Missouri, USA
| | - Catherine E. Sham
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Michail Spiliopoulos
- Division of Maternal Fetal Medicine, Department of Obstetrics & Gynecology, University of Miami, Miami, Florida, USA
| | - Carlos R. Ferreira
- Section on Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Emily Rosenthal
- Division of Maternal Fetal Medicine, Department of Obstetrics & Gynecology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
| | - Elena S. Sinkovskaya
- Division of Maternal Fetal Medicine, Department of Obstetrics & Gynecology, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Shannon Brown
- Division of Maternal Fetal Medicine, Department of Obstetrics & Gynecology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
| | - Angie C. Jelin
- Division of Maternal Fetal Medicine, Department of Gynecology and Obstetrics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Huda B. Al-Kouatly
- Division of Maternal Fetal Medicine, Department of Obstetrics & Gynecology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
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21
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Yuan B, Schulze KV, Assia Batzir N, Sinson J, Dai H, Zhu W, Bocanegra F, Fong CT, Holder J, Nguyen J, Schaaf CP, Yang Y, Bi W, Eng C, Shaw C, Lupski JR, Liu P. Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits. Genome Med 2022; 14:113. [PMID: 36180924 PMCID: PMC9526336 DOI: 10.1186/s13073-022-01113-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND In medical genetics, discovery and characterization of disease trait contributory genes and alleles depends on genetic reasoning, study design, and patient ascertainment; we suggest a segmental haploid genetics approach to enhance gene discovery and molecular diagnostics. METHODS We constructed a genome-wide map for nonallelic homologous recombination (NAHR)-mediated recurrent genomic deletions and used this map to estimate population frequencies of NAHR deletions based on large-scale population cohorts and region-specific studies. We calculated recessive disease carrier burden using high-quality pathogenic or likely pathogenic variants from ClinVar and gnomAD. We developed a NIRD (NAHR deletion Impact to Recessive Disease) score for recessive disorders by quantifying the contribution of NAHR deletion to the overall allele load that enumerated all pairwise combinations of disease-causing alleles; we used a Punnett square approach based on an assumption of random mating. Literature mining was conducted to identify all reported patients with defects in a gene with a high NIRD score; meta-analysis was performed on these patients to estimate the representation of NAHR deletions in recessive traits from contemporary human genomics studies. Retrospective analyses of extant clinical exome sequencing (cES) were performed for novel rare recessive disease trait gene and allele discovery from individuals with NAHR deletions. RESULTS We present novel genomic insights regarding the genome-wide impact of NAHR recurrent segmental variants on recessive disease burden; we demonstrate the utility of NAHR recurrent deletions to enhance discovery in the challenging context of autosomal recessive (AR) traits and biallelic variation. Computational results demonstrate new mutations mediated by NAHR, involving recurrent deletions at 30 genomic regions, likely drive recessive disease burden for over 74% of loci within these segmental deletions or at least 2% of loci genome-wide. Meta-analyses on 170 literature-reported patients implicate that NAHR deletions are depleted from the ascertained pool of AR trait alleles. Exome reanalysis of personal genomes from subjects harboring recurrent deletions uncovered new disease-contributing variants in genes including COX10, ERCC6, PRRT2, and OTUD7A. CONCLUSIONS Our results demonstrate that genomic sequencing of personal genomes with NAHR deletions could dramatically improve allele and gene discovery and enhance clinical molecular diagnosis. Moreover, results suggest NAHR events could potentially enable human haploid genetic screens as an approach to experimental inquiry into disease biology.
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Affiliation(s)
- Bo Yuan
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Katharina V. Schulze
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Nurit Assia Batzir
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Jefferson Sinson
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Hongzheng Dai
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Wenmiao Zhu
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | | | - Chin-To Fong
- grid.412750.50000 0004 1936 9166Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - Jimmy Holder
- grid.39382.330000 0001 2160 926XDepartment of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Joanne Nguyen
- grid.267308.80000 0000 9206 2401Department of Pediatrics, University of Texas Health Science Center, Houston, TX USA
| | - Christian P. Schaaf
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.7700.00000 0001 2190 4373Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Yaping Yang
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Weimin Bi
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Christine Eng
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Chad Shaw
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.21940.3e0000 0004 1936 8278Department of Statistics, Rice University, Houston, TX USA
| | - James R. Lupski
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDepartment of Pediatrics, Baylor College of Medicine, Houston, TX USA ,grid.416975.80000 0001 2200 2638Texas Children’s Hospital, Houston, TX USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Baylor Genetics, Houston, TX, USA.
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22
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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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23
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Zhang W, Yao Z, Guo R, Li H, Zhao S, Li W, Zhang X, Hao C. Molecular identification of T-box transcription factor 6 and prognostic assessment in patients with congenital scoliosis: A single-center study. Front Med (Lausanne) 2022; 9:941468. [PMID: 36035411 PMCID: PMC9403053 DOI: 10.3389/fmed.2022.941468] [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: 05/11/2022] [Accepted: 07/14/2022] [Indexed: 11/24/2022] Open
Abstract
Background Congenital scoliosis (CS) is characterized by vertebral malformations. The precise etiology of CS is not fully defined. A compound inheritance of TBX6 was identified in 10% of patients with CS in Han Chinese and formed a distinguishable subtype named TBX6-associated congenital scoliosis (TACS). Methods To investigate the variants and risk haplotype of TBX6, we recruited 121 patients with CS at Beijing Children’s Hospital. We collected the clinical characteristics and surgical treatment options and followed their postoperative prognoses. Results Eight patients (6.6%) were molecularly diagnosed with TACS and carried the previously defined pathogenic TBX6 compound heterozygous variants. All the eight patients with TACS had the typical TACS clinical feature of hemivertebrae in the lower part of the spine. These patients received posterior hemivertebra resection combined with segmental fusion. Follow-ups revealed satisfactory correction without postoperative complications. Conclusion We observed a 6.6% prevalence of TACS in our CS cohort. Follow-ups further highlighted that surgical treatment of hemivertebra resection combined with segmental fusion performed well with prognosis for patients with TACS. This could provide valuable information for CS individuals with compound heterozygosity in TBX6.
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Affiliation(s)
- Wenyan Zhang
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- Ministry of Education of the People’s Republic of China (MOE) Key Laboratory of Major Diseases in Children, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Ziming Yao
- Department of Orthopedics, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Ruolan Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- Ministry of Education of the People’s Republic of China (MOE) Key Laboratory of Major Diseases in Children, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children’s Hospital, Zhengzhou Hospital of Beijing Children’s Hospital, Zhengzhou, China
| | - Haichong Li
- Department of Orthopedics, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Shuang Zhao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- Ministry of Education of the People’s Republic of China (MOE) Key Laboratory of Major Diseases in Children, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- Ministry of Education of the People’s Republic of China (MOE) Key Laboratory of Major Diseases in Children, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children’s Hospital, Zhengzhou Hospital of Beijing Children’s Hospital, Zhengzhou, China
| | - Xuejun Zhang
- Department of Orthopedics, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- *Correspondence: Xuejun Zhang,
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- Ministry of Education of the People’s Republic of China (MOE) Key Laboratory of Major Diseases in Children, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children’s Hospital, Zhengzhou Hospital of Beijing Children’s Hospital, Zhengzhou, China
- Chanjuan Hao,
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24
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Liang N, Zhang Q, He B. Depth Vision-Based Assessment of Bone Marrow Mesenchymal Stem Cell Differentiation Capacity in Patients with Congenital Scoliosis. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:4890008. [PMID: 35449851 PMCID: PMC9018193 DOI: 10.1155/2022/4890008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022]
Abstract
Congenital scoliosis (CS) is a lateral curvature of one or more segments of the spine due to spinal dysplasia during fetal life. CS is clinically defined as a curvature of the spine >10° due to structural abnormalities of the vertebrae during the embryonic period. Its etiology is unknown, but recent studies suggest that it may be closely related to genetic factors, environmental factors, and developmental abnormalities. The induction methods and modern applications of bone marrow MSCs provide a reference for in-depth human research on the induction of differentiation of bone marrow MSCs into osteoblasts. In this paper, by reviewing and organizing the literature on bone marrow MSCs, we summarized and analyzed the biological properties and preparation of bone marrow MSCs, the methods of inducing osteoblasts, the applications in tissue engineering bone, the problems faced, and the future research directions and proposed a method to assess the differentiation ability of bone marrow MSCs in patients with congenital scoliosis based on depth visual characteristics and the change of the method. The method reveals and evaluates the multidirectional differentiation potential of bone marrow MSCs, which can be induced to differentiate into osteoblasts in vitro and can be used to construct bone tissue engineering scaffolds in vitro using tissue engineering techniques. Based on the properties of bone marrow MSCs, their application in congenital scoliosis patients for trauma repair, cell replacement therapy, hematopoietic support, and gene therapy is quite promising. It is necessary to carry out research on the mechanism of osteogenic differentiation of bone marrow MSCs to provide guidance and reference value for their induced differentiation into osteoblasts.
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Affiliation(s)
- Ning Liang
- The Third Affiliated Hospital of Zunyi Medical University (Zunyi First People's Hospital), Zunyi, Guizhou 563000, China
| | - Qiwen Zhang
- The Third Affiliated Hospital of Zunyi Medical University (Zunyi First People's Hospital), Zunyi, Guizhou 563000, China
| | - Bin He
- The Third Affiliated Hospital of Zunyi Medical University (Zunyi First People's Hospital), Zunyi, Guizhou 563000, China
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25
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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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26
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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: 6] [Impact Index Per Article: 3.0] [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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27
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Lupski JR. Clan genomics: From OMIM phenotypic traits to genes and biology. Am J Med Genet A 2021; 185:3294-3313. [PMID: 34405553 PMCID: PMC8530976 DOI: 10.1002/ajmg.a.62434] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 12/20/2022]
Abstract
Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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28
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Vysotskiy M, Zhong X, Miller-Fleming TW, Zhou D, Cox NJ, Weiss LA. Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes. Genome Med 2021; 13:172. [PMID: 34715901 PMCID: PMC8557010 DOI: 10.1186/s13073-021-00972-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 09/16/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Deletions and duplications of the multigenic 16p11.2 and 22q11.2 copy number variant (CNV) regions are associated with brain-related disorders including schizophrenia, intellectual disability, obesity, bipolar disorder, and autism spectrum disorder (ASD). The contribution of individual CNV genes to each of these identified phenotypes is unknown, as well as the contribution of these CNV genes to other potentially subtler health implications for carriers. Hypothesizing that DNA copy number exerts most effects via impacts on RNA expression, we attempted a novel in silico fine-mapping approach in non-CNV carriers using both GWAS and biobank data. METHODS We first asked whether gene expression level in any individual gene in the CNV region alters risk for a known CNV-associated behavioral phenotype(s). Using transcriptomic imputation, we performed association testing for CNV genes within large genotyped cohorts for schizophrenia, IQ, BMI, bipolar disorder, and ASD. Second, we used a biobank containing electronic health data to compare the medical phenome of CNV carriers to controls within 700,000 individuals in order to investigate the full spectrum of health effects of the CNVs. Third, we used genotypes for over 48,000 individuals within the biobank to perform phenome-wide association studies between imputed expressions of individual 16p11.2 and 22q11.2 genes and over 1500 health traits. RESULTS Using large genotyped cohorts, we found individual genes within 16p11.2 associated with schizophrenia (TMEM219, INO80E, YPEL3), BMI (TMEM219, SPN, TAOK2, INO80E), and IQ (SPN), using conditional analysis to identify upregulation of INO80E as the driver of schizophrenia, and downregulation of SPN and INO80E as increasing BMI. We identified both novel and previously observed over-represented traits within the electronic health records of 16p11.2 and 22q11.2 CNV carriers. In the phenome-wide association study, we found seventeen significant gene-trait pairs, including psychosis (NPIPB11, SLX1B) and mood disorders (SCARF2), and overall enrichment of mental traits. CONCLUSIONS Our results demonstrate how integration of genetic and clinical data aids in understanding CNV gene function and implicates pleiotropy and multigenicity in CNV biology.
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Affiliation(s)
- Mikhail Vysotskiy
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, 513 Parnassus Ave., Health Sciences East 9th floor HSE901E, San Francisco, CA, 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, USA
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Xue Zhong
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Dan Zhou
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Lauren A Weiss
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, 513 Parnassus Ave., Health Sciences East 9th floor HSE901E, San Francisco, CA, 94143, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA.
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, USA.
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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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Lin G, Chai X, Wang S, Yang Y, Shen J, Zhang J. Cross-sectional analysis and trend of vertebral and associated anomalies in Chinese congenital scoliosis population: a retrospective study of one thousand, two hundred and eighty nine surgical cases from 2010 to 2019. INTERNATIONAL ORTHOPAEDICS 2021; 45:2049-2059. [PMID: 34059967 DOI: 10.1007/s00264-021-05061-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/26/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE The objective of this article is to report associated anomaly incidences of a large CS cohort and analyze interrelationships among vertebral anomaly types and associated abnormalities. METHODS We retrospectively searched and extracted medical records of 1289 CS inpatients surgically treated in our institute from January 2010 to December 2019. All patients have taken spine X-ray, CT, MRI, echocardiogram, urogenital ultrasound, and systemic physical examination. We analyzed information on demographics, CS types, and associated anomalies. RESULTS CS type was found to be 49.1% for failure of formation (FF), 19.5% for failure of segmentation (FS), and 31.4% for mixed defects (MD). Intraspinal defects were found in 29.4% patients (16.0% for FF, 45.4% for FS, 40.5% for MD), cardiac in 13.7% (12.3% for FF, 14.3% for FS, 15.6% for MD), genitourinary in 5.8% (4.1% for FF, 6.0% for FS, 8.4% for MD), gastrointestinal in 3.6% (4.7% for FF, 1.6% for FS, 3.0% for MD), and musculoskeletal in 16.4% (10.3% for FF, 19.9% for FS, 23.7% for MD). The intraspinal and musculoskeletal defect incidences were significantly higher in patients with failure of segmentation and mixed defects. We also observed a decreasing trend for intraspinal and musculoskeletal defect incidences as well as a tendency for more failure of formation and less failure of segmentation from 2010 to 2019. CONCLUSIONS The intraspinal and musculoskeletal defect incidences were higher in patients with failure of segmentation and mixed defects. Strong interrelationships were found between intraspinal and musculoskeletal defects and among cardiovascular, genitourinary, and gastrointestinal defects. From 2010 to 2019, the proportion of patients with failure of formation increased significantly, causing a decrease in the intraspinal and musculoskeletal defect incidences over time. Female sex, failure of segmentation, and mixed defects could be considered risk factors for more associated anomalies in CS individuals, which would help surgeons in medical management and prenatal consultation.
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Affiliation(s)
- Guanfeng Lin
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH) Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences (CAMS), 1st Shuaifuyuan Hutong, Beijing, 100730, People's Republic of China
| | - Xiran Chai
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH) Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences (CAMS), 1st Shuaifuyuan Hutong, Beijing, 100730, 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 (PUMCH) Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences (CAMS), 1st Shuaifuyuan Hutong, Beijing, 100730, 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 (PUMCH) Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences (CAMS), 1st Shuaifuyuan Hutong, Beijing, 100730, 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 (PUMCH) Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences (CAMS), 1st Shuaifuyuan Hutong, Beijing, 100730, People's Republic of China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH) Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences (CAMS), 1st Shuaifuyuan Hutong, Beijing, 100730, People's Republic of China.
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31
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Feng X, Cheung JPY, Je JSH, Cheung PWH, Chen S, Yue M, Wang N, Choi VNT, Yang X, Song YQ, Luk KDK, Gao B. Genetic variants of TBX6 and TBXT identified in patients with congenital scoliosis in Southern China. J Orthop Res 2021; 39:971-988. [PMID: 32672867 DOI: 10.1002/jor.24805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/02/2020] [Accepted: 07/09/2020] [Indexed: 02/04/2023]
Abstract
Congenital scoliosis (CS) is a spinal deformity present at birth due to underlying congenital vertebral malformation (CVM) that occurs during embryonic development. Hemivertebrae is the most common anomaly that causes CS. Recently, compound heterozygosity in TBX6 has been identified in Northern Chinese, Japanese, and European CS patient cohorts, which explains about 7%-10% of the affected population. In this report, we recruited 67 CS patients characterized with hemivertebrae in the Southern Chinese population and investigated the TBX6 variant and risk haplotype. We found that two patients with hemivertebrae in the thoracic spine and one patient with hemivertebrae in the lumbar spine carry the previously defined pathogenic TBX6 compound heterozygous variants. In addition, whole exome sequencing of patients with CS and their family members identified a de novo missense mutation (c.G47T: p.R16L) in another member of the T-box family, TBXT. This rare mutation compromised the binding of TBXT to its target sequence, leading to reduced transcriptional activity, and exhibited dominant-negative effect on wild-type TBXT. Our findings further highlight the importance of T-box family genes in the development of congenital scoliosis.
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Affiliation(s)
- Xin Feng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Jason Pui Yin Cheung
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Jimmy S H Je
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Prudence W H Cheung
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Shuxia Chen
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ming Yue
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Ni Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Vanessa N T Choi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Xueyan Yang
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - You-Qiang Song
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Keith D K Luk
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Bo Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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32
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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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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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Chen N, Zhao S, Jolly A, Wang L, Pan H, Yuan J, Chen S, Koch A, Ma C, Tian W, Jia Z, Kang J, Zhao L, Qin C, Fan X, Rall K, Coban-Akdemir Z, Chen Z, Jhangiani S, Liang Z, Niu Y, Li X, Yan Z, Wu Y, Dong S, Song C, Qiu G, Zhang S, Liu P, Posey JE, Zhang F, Luo G, Wu Z, Su J, Zhang J, Chen EY, Rouskas K, Glentis S, Bacopoulou F, Deligeoroglou E, Chrousos G, Lyonnet S, Polak M, Rosenberg C, Dingeldein I, Bonilla X, Borel C, Gibbs RA, Dietrich JE, Dimas AS, Antonarakis SE, Brucker SY, Lupski JR, Wu N, Zhu L. Perturbations of genes essential for Müllerian duct and Wölffian duct development in Mayer-Rokitansky-Küster-Hauser syndrome. Am J Hum Genet 2021; 108:337-345. [PMID: 33434492 DOI: 10.1016/j.ajhg.2020.12.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 12/21/2020] [Indexed: 12/01/2022] Open
Abstract
Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) is associated with congenital absence of the uterus, cervix, and the upper part of the vagina; it is a sex-limited trait. Disrupted development of the Müllerian ducts (MD)/Wölffian ducts (WD) through multifactorial mechanisms has been proposed to underlie MRKHS. In this study, exome sequencing (ES) was performed on a Chinese discovery cohort (442 affected subjects and 941 female control subjects) and a replication MRKHS cohort (150 affected subjects of mixed ethnicity from North America, South America, and Europe). Phenotypic follow-up of the female reproductive system was performed on an additional cohort of PAX8-associated congenital hypothyroidism (CH) (n = 5, Chinese). By analyzing 19 candidate genes essential for MD/WD development, we identified 12 likely gene-disrupting (LGD) variants in 7 genes: PAX8 (n = 4), BMP4 (n = 2), BMP7 (n = 2), TBX6 (n = 1), HOXA10 (n = 1), EMX2 (n = 1), and WNT9B (n = 1), while LGD variants in these genes were not detected in control samples (p = 1.27E-06). Interestingly, a sex-limited penetrance with paternal inheritance was observed in multiple families. One additional PAX8 LGD variant from the replication cohort and two missense variants from both cohorts were revealed to cause loss-of-function of the protein. From the PAX8-associated CH cohort, we identified one individual presenting a syndromic condition characterized by CH and MRKHS (CH-MRKHS). Our study demonstrates the comprehensive utilization of knowledge from developmental biology toward elucidating genetic perturbations, i.e., rare pathogenic alleles involving the same loci, contributing to human birth defects.
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Affiliation(s)
- Na Chen
- Department of Obstetrics and Gynaecology, 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, 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
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; M.D./Ph.D. Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - 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 Orthopedic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Hongxin Pan
- Department of Obstetrics and Gynaecology, The 3rd Affiliated Hospital of Shenzhen University, Luohu hospital, Shenzhen, Guangdong 518000, China
| | - Jian Yuan
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Shaoke Chen
- Department of Pediatrics, the Second Affiliated Hospital of Guangxi Medical University, Guangxi 530003, China
| | - André Koch
- Department of Gynecology and Obstetrics, Research Centre for Women's Health, Tübingen University Hospital, Tübingen 72076, Germany
| | - Congcong Ma
- Department of Obstetrics and Gynaecology, 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
| | - Weijie Tian
- Department of Obstetrics and Gynaecology, 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
| | - Ziqi Jia
- Department of Obstetrics and Gynaecology, 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
| | - Jia Kang
- Department of Obstetrics and Gynaecology, 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
| | - Lina 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
| | - Chenglu Qin
- Department of Obstetrics and Gynaecology, The 3rd Affiliated Hospital of Shenzhen University, Luohu hospital, Shenzhen, Guangdong 518000, China
| | - Xin Fan
- Department of Pediatrics, the Second Affiliated Hospital of Guangxi Medical University, Guangxi 530003, China
| | - Katharina Rall
- Department of Gynecology and Obstetrics, Research Centre for Women's Health, Tübingen University Hospital, Tübingen 72076, Germany
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - 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
| | - Shalini Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ze Liang
- Department of Obstetrics and Gynaecology, 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
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, 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
| | - Yong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Shuangshuang Dong
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai 200011, China
| | - Chengcheng Song
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai 200011, 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
| | - Shuyang Zhang
- Department of Cardiology, 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
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai 200011, China
| | - Guangnan Luo
- Department of Obstetrics and Gynaecology, The 3rd Affiliated Hospital of Shenzhen University, Luohu hospital, Shenzhen, Guangdong 518000, 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, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jianzhong Su
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, 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; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Eugenia Y Chen
- Baylor College of Medicine, Houston, TX 77030, USA; Departments of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA
| | - 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, Thermi, Thessaloniki 57001, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece; Division of Pediatric Hematology/Oncology, First Department of Pediatrics, 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
| | - Efthymios Deligeoroglou
- Division of Pediatric-Adolescent Gynecology and Reconstructive Surgery, 2(nd) Department of Obstetrics and Gynecology, School of Medicine, National and Kapodistrian University of Athens, Aretaieion Hospital, Athens 10679, Greece
| | - George Chrousos
- 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
| | - Stanislas Lyonnet
- Institut Imagine, UMR-1163 INSERM et Universite de Paris, Hospital Universitaire Necker-Enfants Malades, Paris 75015, France
| | - Michel Polak
- Institut Imagine, UMR-1163 INSERM et Universite de Paris, Hospital Universitaire Necker-Enfants Malades, Paris 75015, France
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo 05508-090, Brazil
| | - Irene Dingeldein
- Inselspital FrauenKlinik, University of Bern, Bern 3012, Switzerland
| | - Ximena Bonilla
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1205, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1205, Switzerland
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Seuencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Dietrich
- Departments of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Antigone S Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1205, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva 1205, Switzerland
| | - Sara Y Brucker
- Department of Gynecology and Obstetrics, Research Centre for Women's Health, Tübingen University Hospital, Tübingen 72076, Germany
| | - 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; Human Genome Seuencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - 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; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; 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 100730, China.
| | - Lan Zhu
- Department of Obstetrics and Gynaecology, 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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35
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Li Z, Zhang C, Qiu B, Niu Y, Leng L, Cai S, Tian Y, Zhang TJ, Qiu G, Wu N, Wu Z, Wang Y. Comparative proteomics analysis for identifying the lipid metabolism related pathways in patients with Klippel-Feil syndrome. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:255. [PMID: 33708882 PMCID: PMC7940892 DOI: 10.21037/atm-20-5155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Klippel-Feil syndrome (KFS) represents the rare and complex deformity characterized by congenital defects in the formation or segmentation of the cervical vertebrae. There is a wide gap in understanding the detailed mechanisms of KFS because of its rarity, heterogeneity, small pedigrees, and the broad spectrum of anomalies. Methods We recruited eight patients of Chinese Han ethnicity with KFS, five patients with congenital scoliosis (CS) who presented with congenital fusion of the thoracic or lumbar spine and without known syndrome or cervical deformity, and seven healthy controls. Proteomic analysis by data-independent acquisition (DIA) was performed to identify the differential proteome among the three matched groups and the data were analyzed by bioinformatics tools including Gene Ontology (GO) categories and Ingenuity Pathway Analysis (IPA) database, to explore differentially abundant proteins (DAPs) and canonical pathways involved in the pathogenesis of KFS. Results A total of 49 DAPs were detected between KFS patients and the controls, and moreover, 192 DAPs were identified between patients with KFS and patients with CS. Fifteen DAPs that were common in both comparisons were considered as candidate biomarkers for KFS, including membrane primary amine oxidase, noelin, galectin-3-binding protein, cadherin-5, glyceraldehyde-3-phosphate dehydrogenase, peroxiredoxin-1, CD109 antigen, and eight immunoglobulins. Furthermore, the same significant canonical pathways of LXR/RXR activation and FXR/RXR activation were observed in both comparisons. Seven of DAPs were apolipoproteins related to these pathways that are involved in lipid metabolism. Conclusions This study provides the first proteomic profile for understanding the pathogenesis and identifying predictive biomarkers of KFS. We detected 15 DAPs that were common in both comparisons as candidate predictive biomarkers of KFS. The lipid metabolism-related canonical pathways of LXR/RXR and FXR/RXR activation together with seven differentially abundant apolipoproteins may play significant roles in the etiology of KFS and provide possible pathogenesis correlation between KFS and CS.
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Affiliation(s)
- Ziquan 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
| | - Cong Zhang
- Department of Endocrinology, China-Japan Friendship Hospital, Beijing, China
| | - Bintao Qiu
- 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
| | - 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, China
| | - Ling Leng
- 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
| | - Siyi Cai
- Department of Orthopedic Surgery, 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
| | - Ye Tian
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 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.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,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.,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
| | - Yipeng Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, China
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Lleras-Forero L, Newham E, Teufel S, Kawakami K, Hartmann C, Hammond CL, Knight RD, Schulte-Merker S. Muscle defects due to perturbed somite segmentation contribute to late adult scoliosis. Aging (Albany NY) 2020; 12:18603-18621. [PMID: 32979261 PMCID: PMC7585121 DOI: 10.18632/aging.103856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/14/2020] [Indexed: 01/24/2023]
Abstract
Scoliosis is an abnormal bending of the body axis. Truncated vertebrae or a debilitated ability to control the musculature in the back can cause this condition, but in most cases the causative reason for scoliosis is unknown (idiopathic). Using mutants for somite clock genes with mild defects in the vertebral column, we here show that early defects in somitogenesis are not overcome during development and have long lasting and profound consequences for muscle fiber organization, structure and whole muscle volume. These mutants present only mild alterations in the vertebral column, and muscle shortcomings are uncoupled from skeletal defects. None of the mutants presents an overt musculoskeletal phenotype at larval or early adult stages, presumably due to compensatory growth mechanisms. Scoliosis becomes only apparent during aging. We conclude that adult degenerative scoliosis is due to disturbed crosstalk between vertebrae and muscles during early development, resulting in subsequent adult muscle weakness and bending of the body axis.
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Affiliation(s)
- Laura Lleras-Forero
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU, Münster, Germany,Hubrecht Institute-KNAW and University Medical Center Utrecht, CT, Utrecht, The Netherlands
| | - Elis Newham
- The School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, UK
| | - Stefan Teufel
- Institut für Muskuloskelettale Medizin (IMM), Abteilung Knochen- und Skelettforschung, Universitätsklinikum Münster, Germany
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Christine Hartmann
- Institut für Muskuloskelettale Medizin (IMM), Abteilung Knochen- und Skelettforschung, Universitätsklinikum Münster, Germany
| | - Chrissy L. Hammond
- The School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, UK
| | - Robert D. Knight
- Centre for Craniofacial and Regenerative Biology, King´s College London, London, UK
| | - Stefan Schulte-Merker
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU, Münster, Germany,Hubrecht Institute-KNAW and University Medical Center Utrecht, CT, Utrecht, The Netherlands
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37
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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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38
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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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Wu N, Wang L, Hu J, Zhao S, Liu B, Li Y, Du H, Zhang Y, Li X, Yan Z, Wang S, Wang Y, Zhang J, Wu Z, Disco Deciphering Disorders Involving Scoliosis Comorbidities Study Group, Qiu G. A Recurrent Rare SOX9 Variant (M469V) is Associated with Congenital Vertebral Malformations. Curr Gene Ther 2020; 19:242-247. [PMID: 31549955 DOI: 10.2174/1566523219666190924120307] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVE The genetic variations contributed to a substantial proportion of congenital vertebral malformations (CVM). SOX9 gene, a member of the SOX gene family, has been implicated in CVM. To study the SOX9 mutation in CVM patients is of great significance to explain the pathogenesis of scoliosis (the clinical manifestation of CVM) and to explore the pathogenesis of SOX9-related skeletal deformities. METHODS A total of 50 singleton patients with CVM were included in this study. Exome Sequencing (ES) was performed on all the patients. The recurrent candidate variant of SOX9 gene was validated by Sanger sequencing. Luciferase assay was performed to investigate the functional changes of this variant. RESULTS A recurrent rare heterozygous missense variant in SOX9 gene (NM_000346.3: c.1405A>G, p.M469V) which had not been reported previously was identified in three CVM patients who had the clinical findings of congenital scoliosis without deformities in other systems. This variant was absent from our in-house database and it was predicted to be deleterious (CADD = 24.5). The luciferase assay demonstrated that transactivation capacity of the mutated SOX9 protein was significantly lower than that of the wild-type for the two luciferase reporters (p = 0.0202, p = 0.0082, respectively). CONCLUSION This SOX9 mutation (p.M469V) may contribute to CVM without other systematic deformity, which provides important implications and better understanding of phenotypic variability in SOX9-related skeletal deformities.
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Affiliation(s)
- Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Jianhua Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, 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.,Peking Union Medical College & Chinese Academy of Medical Sciences, 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.,Peking Union Medical College & Chinese Academy of Medical Sciences, 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.,Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Huakang Du
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College & Chinese Academy of Medical Sciences, 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.,Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxin Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 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.,Peking Union Medical College & 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, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Yipeng Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, 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, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | | | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
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40
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Ren X, Yang N, Wu N, Xu X, Chen W, Zhang L, Li Y, Du RQ, Dong S, Zhao S, Chen S, Jiang LP, Wang L, Zhang J, Wu Z, Jin L, Qiu G, Lupski JR, Shi J, Zhang F, Liu P. Increased TBX6 gene dosages induce congenital cervical vertebral malformations in humans and mice. J Med Genet 2020; 57:371-379. [PMID: 31888956 PMCID: PMC9179029 DOI: 10.1136/jmedgenet-2019-106333] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Congenital vertebral malformations (CVMs) manifest with abnormal vertebral morphology. Genetic factors have been implicated in CVM pathogenesis, but the underlying pathogenic mechanisms remain unclear in most subjects. We previously reported that the human 16p11.2 BP4-BP5 deletion and its associated TBX6 dosage reduction caused CVMs. We aim to investigate the reciprocal 16p11.2 BP4-BP5 duplication and its potential genetic contributions to CVMs. METHODS AND RESULTS Patients who were found to carry the 16p11.2 BP4-BP5 duplication by chromosomal microarray analysis were retrospectively analysed for their vertebral phenotypes. The spinal assessments in seven duplication carriers showed that four (57%) presented characteristics of CVMs, supporting the contention that increased TBX6 dosage could induce CVMs. For further in vivo functional investigation in a model organism, we conducted genome editing of the upstream regulatory region of mouse Tbx6 using CRISPR-Cas9 and obtained three mouse mutant alleles (Tbx6up1 to Tbx6up3 ) with elevated expression levels of Tbx6. Luciferase reporter assays showed that the Tbx6up3 allele presented with the 160% expression level of that observed in the reference (+) allele. Therefore, the homozygous Tbx6up3/up3 mice could functionally mimic the TBX6 dosage of heterozygous carriers of 16p11.2 BP4-BP5 duplication (approximately 150%, ie, 3/2 gene dosage of the normal level). Remarkably, 60% of the Tbx6up3/up3 mice manifested with CVMs. Consistent with our observations in humans, the CVMs induced by increased Tbx6 dosage in mice mainly affected the cervical vertebrae. CONCLUSION Our findings in humans and mice consistently support that an increased TBX6 dosage contributes to the risk of developing cervical CVMs.
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Affiliation(s)
- Xiaojun Ren
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Nan Yang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 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, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ximing Xu
- Department of Orthopedic Surgery, Spine Center, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ling Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Yingping Li
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
| | - Ren-Qian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Shuangshuang Dong
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 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, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shuxia Chen
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Ping Jiang
- State key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 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, 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, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong 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, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Li Jin
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Jiangang Shi
- Department of Orthopedic Surgery, Spine Center, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics, Houston, Texas, USA
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41
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Human and mouse studies establish TBX6 in Mendelian CAKUT and as a potential driver of kidney defects associated with the 16p11.2 microdeletion syndrome. Kidney Int 2020; 98:1020-1030. [PMID: 32450157 DOI: 10.1016/j.kint.2020.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/03/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUTs) are the most common cause of chronic kidney disease in children. Human 16p11.2 deletions have been associated with CAKUT, but the responsible molecular mechanism remains to be illuminated. To explore this, we investigated 102 carriers of 16p11.2 deletion from multi-center cohorts, among which we retrospectively ascertained kidney morphologic and functional data from 37 individuals (12 Chinese and 25 Caucasian/Hispanic). Significantly higher CAKUT rates were observed in 16p11.2 deletion carriers (about 25% in Chinese and 16% in Caucasian/Hispanic) than those found in the non-clinically ascertained general populations (about 1/1000 found at autopsy). Furthermore, we identified seven additional individuals with heterozygous loss-of-function variants in TBX6, a gene that maps to the 16p11.2 region. Four of these seven cases showed obvious CAKUT. To further investigate the role of TBX6 in kidney development, we engineered mice with mutated Tbx6 alleles. The Tbx6 heterozygous null (i.e., loss-of-function) mutant (Tbx6+/‒) resulted in 13% solitary kidneys. Remarkably, this incidence increased to 29% in a compound heterozygous model (Tbx6mh/‒) that reduced Tbx6 gene dosage to below haploinsufficiency, by combining the null allele with a novel mild hypomorphic allele (mh). Renal hypoplasia was also frequently observed in these Tbx6-mutated mouse models. Thus, our findings in patients and mice establish TBX6 as a novel gene involved in CAKUT and its gene dosage insufficiency as a potential driver for kidney defects observed in the 16p11.2 microdeletion syndrome.
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42
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Zhao S, Zhang Y, Chen W, Li W, Wang S, Wang L, Zhao Y, Lin M, Ye Y, Lin J, Zheng Y, Liu J, Zhao H, Yan Z, Yang Y, Huang Y, Lin G, Chen Z, Zhang Z, Liu S, Jin L, Wang Z, Chen J, Niu Y, Li X, Wu Y, Wang Y, Du R, Gao N, Zhao H, Yang Y, Liu Y, Tian Y, Li W, Zhao Y, Liu J, Yu B, Zhang N, Yu K, Yang X, Li S, Xu Y, Hu J, Liu Z, Shen J, Zhang S, Su J, Khanshour AM, Kidane YH, Ramo B, Rios JJ, Liu P, Sutton VR, Posey JE, Wu Z, Qiu G, Wise CA, Zhang F, Lupski JR, Zhang J, Wu N. Diagnostic yield and clinical impact of exome sequencing in early-onset scoliosis (EOS). J Med Genet 2020; 58:41-47. [PMID: 32381727 DOI: 10.1136/jmedgenet-2019-106823] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/17/2020] [Accepted: 03/13/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Early-onset scoliosis (EOS), defined by an onset age of scoliosis less than 10 years, conveys significant health risk to affected children. Identification of the molecular aetiology underlying patients with EOS could provide valuable information for both clinical management and prenatal screening. METHODS In this study, we consecutively recruited a cohort of 447 Chinese patients with operative EOS. We performed exome sequencing (ES) screening on these individuals and their available family members (totaling 670 subjects). Another cohort of 13 patients with idiopathic early-onset scoliosis (IEOS) from the USA who underwent ES was also recruited. RESULTS After ES data processing and variant interpretation, we detected molecular diagnostic variants in 92 out of 447 (20.6%) Chinese patients with EOS, including 8 patients with molecular confirmation of their clinical diagnosis and 84 patients with molecular diagnoses of previously unrecognised diseases underlying scoliosis. One out of 13 patients with IEOS from the US cohort was molecularly diagnosed. The age at presentation, the number of organ systems involved and the Cobb angle were the three top features predictive of a molecular diagnosis. CONCLUSION ES enabled the molecular diagnosis/classification of patients with EOS. Specific clinical features/feature pairs are able to indicate the likelihood of gaining a molecular diagnosis through ES.
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Affiliation(s)
- Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yuanqiang Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Weiyu Li
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yanxue Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Mao Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yongyu Ye
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Orthopedic Surgery, First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yu Zheng
- School of Finance, Southwestern University of Finance and Economics, Chengdu, Sichuan, China
| | - Jiaqi Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China.,School of Ophthalmology & Optometry and Eye Hospital, School of BiomedicalEngineering, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zihui Yan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yongxin Yang
- Machine Intelligence Group, University of Edinburgh, Edinburgh, UK
| | - Yingzhao Huang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Guanfeng Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zefu Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zhen Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Sen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Lichao Jin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zhaoyang Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Jingdan Chen
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yipeng Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Na Gao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Hong Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Yang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Tian
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Wenli Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Na Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Keyi Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xu Yang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shugang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuan Xu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianhua Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhe Liu
- Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianxiong Shen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Shuyang Zhang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Cardiology, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, School of BiomedicalEngineering, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA
| | - Brandon Ramo
- Department of Orthopaedic Surgery, Scottish Rite for Children, Dallas, Texas, USA
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | | | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Departments of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
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Al Dhaheri N, Wu N, Zhao S, Wu Z, Blank RD, Zhang J, Raggio C, Halanski M, Shen J, Noonan K, Qiu G, Nemeth B, Sund S, Dunwoodie SL, Chapman G, Glurich I, Steiner RD, Wohler E, Martin R, Sobreira NL, Giampietro PF. KIAA1217: A novel candidate gene associated with isolated and syndromic vertebral malformations. Am J Med Genet A 2020; 182:1664-1672. [PMID: 32369272 DOI: 10.1002/ajmg.a.61607] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/05/2020] [Accepted: 04/05/2020] [Indexed: 12/30/2022]
Abstract
Vertebral malformations (VMs) are caused by alterations in somitogenesis and may occur in association with other congenital anomalies. The genetic etiology of most VMs remains unknown and their identification may facilitate the development of novel therapeutic and prevention strategies. Exome sequencing was performed on both the discovery cohort of nine unrelated probands from the USA with VMs and the replication cohort from China (Deciphering Disorders Involving Scoliosis & COmorbidities study). The discovery cohort was analyzed using the PhenoDB analysis tool. Heterozygous and homozygous, rare and functional variants were selected and evaluated for their ClinVar, HGMD, OMIM, GWAS, mouse model phenotypes, and other annotations to identify the best candidates. Genes with candidate variants in three or more probands were selected. The replication cohort was analyzed by another in-house developed pipeline. We identified rare heterozygous variants in KIAA1217 in four out of nine probands in the discovery cohort and in five out of 35 probands in the replication cohort. Collectively, we identified 11 KIAA1217 rare variants in 10 probands, three of which have not been described in gnomAD and one of which is a nonsense variant. We propose that genetic variations of KIAA1217 may contribute to the etiology of VMs.
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Affiliation(s)
- Noura Al Dhaheri
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, College of Medicine and Health Sciences, UAE University, Al-Ain, UAE
| | - Nan Wu
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Sen Zhao
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | | | - Jianguo Zhang
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Cathy Raggio
- Hospital for Special Surgery, New York, New York, USA
| | | | - Jianxiong Shen
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ken Noonan
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Guixing Qiu
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Blaise Nemeth
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sarah Sund
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,University of New South Wales, Sydney, New South Wales, Australia
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,University of New South Wales, Sydney, New South Wales, Australia
| | - Ingrid Glurich
- Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Robert D Steiner
- University of Wisconsin-Madison, Madison, Wisconsin, USA.,Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Renan Martin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nara Lygia Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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44
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Karolak JA, Gambin T, Honey EM, Slavik T, Popek E, Stankiewicz P. A de novo 2.2 Mb recurrent 17q23.1q23.2 deletion unmasks novel putative regulatory non-coding SNVs associated with lethal lung hypoplasia and pulmonary hypertension: a case report. BMC Med Genomics 2020; 13:34. [PMID: 32143628 PMCID: PMC7060516 DOI: 10.1186/s12920-020-0701-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Application of whole genome sequencing (WGS) enables identification of non-coding variants that play a phenotype-modifying role and are undetectable by exome sequencing. Recently, non-coding regulatory single nucleotide variants (SNVs) have been reported in patients with lethal lung developmental disorders (LLDDs) or congenital scoliosis with recurrent copy-number variant (CNV) deletions at 17q23.1q23.2 or 16p11.2, respectively. CASE PRESENTATION Here, we report a deceased newborn with pulmonary hypertension and pulmonary interstitial emphysema with features suggestive of pulmonary hypoplasia, resulting in respiratory failure and neonatal death soon after birth. Using the array comparative genomic hybridization and WGS, two heterozygous recurrent CNV deletions: ~ 2.2 Mb on 17q23.1q23.2, involving TBX4, and ~ 600 kb on 16p11.2, involving TBX6, that both arose de novo on maternal chromosomes were identified. In the predicted lung-specific enhancer upstream to TBX4, we have detected seven novel putative regulatory non-coding SNVs that were absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. CONCLUSIONS Our findings further support a recently reported model of complex compound inheritance of LLDD in which both non-coding and coding heterozygous TBX4 variants contribute to the lung phenotype. In addition, this is the first report of a patient with combined de novo heterozygous recurrent 17q23.1q23.2 and 16p11.2 CNV deletions.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781, Poznan, Poland
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland
| | - Engela M Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria, South Africa
| | - Tomas Slavik
- Ampath Pathology Laboratories, and Department of Anatomical Pathology, University of Pretoria, Pretoria, South Africa
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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45
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Lin M, Liu Z, Liu G, Zhao S, Li C, Chen W, Coban Akdemir Z, Lin J, Song X, Wang S, Xu Q, Zhao Y, Wang L, Zhang Y, Yan Z, Liu S, Liu J, Chen Y, Zuo Y, Yang X, Sun T, Yang X, Niu Y, Li X, You W, Qiu B, Ding C, Liu P, Zhang S, Carvalho CMB, Posey JE, Qiu G, Lupski JR, Wu Z, Zhang J, Wu N. Genetic and molecular mechanism for distinct clinical phenotypes conveyed by allelic truncating mutations implicated in FBN1. Mol Genet Genomic Med 2020; 8:e1023. [PMID: 31774634 PMCID: PMC6978264 DOI: 10.1002/mgg3.1023] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/21/2019] [Accepted: 10/11/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The molecular and genetic mechanisms by which different single nucleotide variant alleles in specific genes, or at the same genetic locus, cause distinct disease phenotypes often remain unclear. Allelic truncating mutations of FBN1 could cause either classical Marfan syndrome (MFS) or a more complicated phenotype associated with Marfanoid-progeroid-lipodystrophy syndrome (MPLS). METHODS We investigated a small cohort, encompassing two classical MFS and one MPLS subjects from China, whose clinical presentation included scoliosis potentially requiring surgical intervention. Targeted next generation sequencing was performed on all the participants. We analyzed the molecular diagnosis, clinical features, and the potential molecular mechanism involved in the MPLS subject in our cohort. RESULTS We report a novel de novo FBN1 mutation for the first Chinese subject with MPLS, a more complicated fibrillinopathy, and two subjects with more classical MFS. We further predict that the MPLS truncating mutation, and others previously reported, is prone to escape the nonsense-mediated decay (NMD), while MFS mutations are predicted to be subjected to NMD. Also, the MPLS mutation occurs within the glucogenic hormone asprosin domain of FBN1. In vitro experiments showed that the single MPLS mutation p.Glu2759Cysfs*9 appears to perturb proper FBN1 protein aggregation as compared with the classical MFS mutation p.Tyr2596Thrfs*86. Both mutations appear to upregulate SMAD2 phosphorylation in vitro. CONCLUSION We provide direct evidence that a dominant-negative interaction of FBN1 potentially explains the complex MPLS phenotypes through genetic and functional analysis. Our study expands the mutation spectrum of FBN1 and highlights the potential molecular mechanism for MPLS.
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46
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Identification of novel FBN1 variations implicated in congenital scoliosis. J Hum Genet 2019; 65:221-230. [PMID: 31827250 PMCID: PMC6983459 DOI: 10.1038/s10038-019-0698-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/23/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022]
Abstract
Congenital scoliosis (CS) is a form of scoliosis caused by congenital vertebral malformations. Genetic predisposition has been demonstrated in CS. We previously reported that TBX6 loss-of-function causes CS in a compound heterozygous model; however, this model can explain only 10% of CS. Many monogenic and polygenic CS genes remain to be elucidated. In this study, we analyzed exome sequencing (ES) data of 615 Chinese CS from the Deciphering Disorders Involving Scoliosis and COmorbidities (DISCO) project. Cosegregation studies for 103 familial CS identified a novel heterozygous nonsense variant, c.2649G>A (p.Trp883Ter) in FBN1. The association between FBN1 and CS was then analyzed by extracting FBN1 variants from ES data of 574 sporadic CS and 828 controls; 30 novel variants were identified and prioritized for further analyses. A mutational burden test showed that the deleterious FBN1 variants were significantly enriched in CS subjects (OR = 3.9, P = 0.03 by Fisher’s exact test). One missense variant, c.2613A>C (p.Leu871Phe) was recurrent in two unrelated CS subjects, and in vitro functional experiments for the variant suggest that FBN1 may contribute to CS by upregulating the transforming growth factor beta (TGF-β) signaling. Our study expanded the phenotypic spectrum of FBN1, and provided nove insights into the genetic etiology of CS.
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47
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Hansen AW, Murugan M, Li H, Khayat MM, Wang L, Rosenfeld J, Andrews BK, Jhangiani SN, Coban Akdemir ZH, Sedlazeck FJ, Ashley-Koch AE, Liu P, Muzny DM, Davis EE, Katsanis N, Sabo A, Posey JE, Yang Y, Wangler MF, Eng CM, Sutton VR, Lupski JR, Boerwinkle E, Gibbs RA. A Genocentric Approach to Discovery of Mendelian Disorders. Am J Hum Genet 2019; 105:974-986. [PMID: 31668702 PMCID: PMC6849092 DOI: 10.1016/j.ajhg.2019.09.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/27/2019] [Indexed: 12/20/2022] Open
Abstract
The advent of inexpensive, clinical exome sequencing (ES) has led to the accumulation of genetic data from thousands of samples from individuals affected with a wide range of diseases, but for whom the underlying genetic and molecular etiology of their clinical phenotype remains unknown. In many cases, detailed phenotypes are unavailable or poorly recorded and there is little family history to guide study. To accelerate discovery, we integrated ES data from 18,696 individuals referred for suspected Mendelian disease, together with relatives, in an Apache Hadoop data lake (Hadoop Architecture Lake of Exomes [HARLEE]) and implemented a genocentric analysis that rapidly identified 154 genes harboring variants suspected to cause Mendelian disorders. The approach did not rely on case-specific phenotypic classifications but was driven by optimization of gene- and variant-level filter parameters utilizing historical Mendelian disease-gene association discovery data. Variants in 19 of the 154 candidate genes were subsequently reported as causative of a Mendelian trait and additional data support the association of all other candidate genes with disease endpoints.
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Affiliation(s)
- Adam W Hansen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mullai Murugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael M Khayat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liwen Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - B Kim Andrews
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erica E Davis
- Pediatric Genetic and translational Medicine Center (P-GeM), Stanley Manne Children's Research Institute, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nicholas Katsanis
- Pediatric Genetic and translational Medicine Center (P-GeM), Stanley Manne Children's Research Institute, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Aniko Sabo
- Department of Molecular and Human Genetics, Baylor College of Medicine, 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
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; School of Public Health, UTHealth, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
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48
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Chen W, Lin J, Wang L, Li X, Zhao S, Liu J, Akdemir ZC, Zhao Y, Du R, Ye Y, Song X, Zhang Y, Yan Z, Yang X, Lin M, Shen J, Wang S, Gao N, Yang Y, Liu Y, Li W, Liu J, Zhang N, Yang X, Xu Y, Zhang J, Delgado MR, Posey JE, Qiu G, Rios JJ, Liu P, Wise CA, Zhang F, Wu Z, Lupski JR, Wu N. TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease. Hum Mutat 2019; 41:182-195. [PMID: 31471994 DOI: 10.1002/humu.23907] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/20/2019] [Accepted: 08/28/2019] [Indexed: 12/30/2022]
Abstract
Congenital scoliosis (CS) is a birth defect with variable clinical and anatomical manifestations due to spinal malformation. The genetic etiology underlying about 10% of CS cases in the Chinese population is compound inheritance by which the gene dosage is reduced below that of haploinsufficiency. In this genetic model, the trait manifests as a result of the combined effect of a rare variant and common pathogenic variant allele at a locus. From exome sequencing (ES) data of 523 patients in Asia and two patients in Texas, we identified six TBX6 gene-disruptive variants from 11 unrelated CS patients via ES and in vitro functional testing. The in trans mild hypomorphic allele was identified in 10 of the 11 subjects; as anticipated these 10 shared a similar spinal deformity of hemivertebrae. The remaining case has a homozygous variant in TBX6 (c.418C>T) and presents a more severe spinal deformity phenotype. We found decreased transcriptional activity and abnormal cellular localization as the molecular mechanisms for TBX6 missense loss-of-function alleles. Expanding the mutational spectrum of TBX6 pathogenic alleles enabled an increased molecular diagnostic detection rate, provided further evidence for the gene dosage-dependent genetic model underlying CS, and refined clinical classification.
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Affiliation(s)
- Weisheng Chen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jiachen Lin
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Lianlei Wang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sen Zhao
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Jiaqi Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yanxue Zhao
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yongyu Ye
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Orthopaedic Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yuanqiang Zhang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zihui Yan
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Xinzhuang Yang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Mao Lin
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Jianxiong Shen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Shengru Wang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Na Gao
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Yang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Wenli Li
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Na Zhang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xu Yang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuan Xu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianguo Zhang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Mauricio R Delgado
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,Neurology Department, Texas Scottish Rite Hospital, Dallas, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Guixing Qiu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Jonathan J Rios
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics Laboratory, Houston, Texas
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Nan Wu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
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49
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Choy KW, Wang H, Shi M, Chen J, Yang Z, Zhang R, Yan H, Wang Y, Chen S, Chau MHK, Cao Y, Chan OYM, Kwok YK, Zhu Y, Chen M, Leung TY, Dong Z. Prenatal Diagnosis of Fetuses With Increased Nuchal Translucency by Genome Sequencing Analysis. Front Genet 2019; 10:761. [PMID: 31475041 PMCID: PMC6706460 DOI: 10.3389/fgene.2019.00761] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
Background: Increased nuchal translucency (NT) is an important biomarker associated with increased risk of fetal structural anomalies. It is known to be contributed by a wide range of genetic etiologies from single-nucleotide variants to those affecting millions of base pairs. Currently, prenatal diagnosis is routinely performed by karyotyping and chromosomal microarray analysis (CMA); however, both of them have limited resolution. The diversity of the genetic etiologies warrants an integrated assay such as genome sequencing (GS) for comprehensive detection of genomic variants. Herein, we aim to evaluate the feasibility of applying GS in prenatal diagnosis for the fetuses with increased NT. Methods: We retrospectively applied GS (> 30-fold) for fetuses with increased NT (≥3.5 mm) who underwent routine prenatal diagnosis. Detection of single-nucleotide variants, copy number variants, and structural rearrangements was performed simultaneously, and the results were integrated for interpretation in accordance with the guidelines of the American College of Medical Genetics and Genomics. Pathogenic or likely pathogenic (P/LP) variants were selected for validation and parental confirmation, when available. Results: Overall, 50 fetuses were enrolled, including 34 cases with isolated increased NT and 16 cases with other fetal structural malformations. Routine CMA and karyotyping reported eight P/LP CNVs, yielding a diagnostic rate of 16.0% (8/50). In comparison, GS provided a twofold increase in diagnostic yield (32.0%, 16/50), including one mosaic turner syndrome, eight cases with microdeletions/microduplications, and seven cases with P/LP point mutations. Moreover, GS identified two cryptic insertions and two inversions. Follow-up study further demonstrated the potential pathogenicity of an apparently balanced insertion that disrupted an OMIM autosomal dominant disease-causing gene at the insertion site. Conclusions: Our study demonstrates that applying GS in fetuses with increased NT can comprehensively detect and delineate the various genomic variants that are causative to the diseases. Importantly, prenatal diagnosis by GS doubled the diagnostic yield compared with routine protocols. Given a comparable turnaround time and less DNA required, our study provides strong evidence to facilitate GS in prenatal diagnosis, particularly in fetuses with increased NT.
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Affiliation(s)
- Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Huilin Wang
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Mengmeng Shi
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Jingsi Chen
- Department of Obstetrics and Gynecology, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenjun Yang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Rui Zhang
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Huanchen Yan
- Department of Obstetrics and Gynecology, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanfang Wang
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Shaoyun Chen
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ye Cao
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Olivia Y M Chan
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuanfang Zhu
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Min Chen
- Department of Obstetrics and Gynecology, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Zirui Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Department of Obstetrics and Gynecology, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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50
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Abstract
The practice of genomic medicine stands to revolutionize our approach to medical care, and to realize this goal will require discovery of the relationship between rare variation at each of the ~ 20,000 protein-coding genes and their consequent impact on individual health and expression of Mendelian disease. The step-wise evolution of broad-based, genome-wide cytogenetic and molecular genomic testing approaches (karyotyping, chromosomal microarray [CMA], exome sequencing [ES]) has driven much of the rare disease discovery to this point, with genome sequencing representing the newest member of this team. Each step has brought increased sensitivity to interrogate individual genomic variation in an unbiased method that does not require clinical prediction of the locus or loci involved. Notably, each step has also brought unique limitations in variant detection, for example, the low sensitivity of ES for detection of triploidy, and of CMA for detection of copy neutral structural variants. The utility of genome sequencing (GS) as a clinical molecular diagnostic test, and the increased sensitivity afforded by addition of long-read sequencing or other -omics technologies such as RNAseq or metabolomics, are not yet fully explored, though recent work supports improved sensitivity of variant detection, at least in a subset of cases. The utility of GS will also rely upon further elucidation of the complexities of genetic and allelic heterogeneity, multilocus rare variation, and the impact of rare and common variation at a locus, as well as advances in functional annotation of identified variants. Much discovery remains to be done before the potential utility of GS is fully appreciated.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, T603, Houston, TX, 77030, USA.
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