1
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Ichiyama-Kobayashi S, Hata K, Wakamori K, Takahata Y, Murakami T, Yamanaka H, Takano H, Yao R, Uzawa N, Nishimura R. Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development. JCI Insight 2024; 9:e175486. [PMID: 38855864 DOI: 10.1172/jci.insight.175486] [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: 09/06/2023] [Accepted: 05/01/2024] [Indexed: 06/11/2024] Open
Abstract
The transcription factor SRY-related HMG box 9 (Sox9) is essential for chondrogenesis. Mutations in and around SOX9 cause campomelic dysplasia (CD) characterized by skeletal malformations. Although the function of Sox9 in this context is well studied, the mechanisms that regulate Sox9 expression in chondrocytes remain to be elucidated. Here, we have used genome-wide profiling to identify 2 Sox9 enhancers located in a proximal breakpoint cluster responsible for CD. Enhancer activity of E308 (located 308 kb 5' upstream) and E160 (located 160 kb 5' upstream) correlated with Sox9 expression levels, and both enhancers showed a synergistic effect in vitro. While single deletions in mice had no apparent effect, simultaneous deletion of both E308 and E160 caused a dwarf phenotype, concomitant with a reduction of Sox9 expression in chondrocytes. Moreover, bone morphogenetic protein 2-dependent chondrocyte differentiation of limb bud mesenchymal cells was severely attenuated in E308/E160 deletion mice. Finally, we found that an open chromatin region upstream of the Sox9 gene was reorganized in the E308/E160 deletion mice to partially compensate for the loss of E308 and E160. In conclusion, our findings reveal a mechanism of Sox9 gene regulation in chondrocytes that might aid in our understanding of the pathophysiology of skeletal disorders.
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Affiliation(s)
- Sachi Ichiyama-Kobayashi
- Department of Molecular and Cellular Biochemistry
- Department of Oral and Maxillofacial Oncology and Surgery, and
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry
| | - Kanta Wakamori
- Department of Molecular and Cellular Biochemistry
- Department of Oral and Maxillofacial Oncology and Surgery, and
| | - Yoshifumi Takahata
- Department of Molecular and Cellular Biochemistry
- Genome Editing Research and Development Unit, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | | | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Hiroshi Takano
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Narikazu Uzawa
- Department of Oral and Maxillofacial Oncology and Surgery, and
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2
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Cheng YHH, Bohaczuk SC, Stergachis AB. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum Genet 2024; 143:559-605. [PMID: 38436667 PMCID: PMC11078748 DOI: 10.1007/s00439-023-02639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.
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Affiliation(s)
- Y H Hank Cheng
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C Bohaczuk
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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3
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Wang L, Liu Z, Zhao S, Xu K, Aceves V, Qiu C, Troutwine B, Liu L, Ma S, Niu Y, Wang S, Yuan S, Li X, Zhao L, Liu X, Wu Z, Zhang TJ, Gray RS, Wu N. Variants in the SOX9 transactivation middle domain induce axial skeleton dysplasia and scoliosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.29.23290174. [PMID: 37398377 PMCID: PMC10312849 DOI: 10.1101/2023.05.29.23290174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
SOX9 is an essential transcriptional regulator of cartilage development and homeostasis. In humans, dysregulation of SOX9 is associated with a wide spectrum of skeletal disorders, including campomelic and acampomelic dysplasia, and scoliosis. The mechanism of how SOX9 variants contribute to the spectrum of axial skeletal disorders is not well understood. Here, we report four novel pathogenic variants of SOX9 identified in a large cohort of patients with congenital vertebral malformations. Three of these heterozygous variants are in the HMG and DIM domains, and for the first time, we report a pathogenic variant within the transactivation middle (TAM) domain of SOX9 . Probands with these variants exhibit variable skeletal dysplasia, ranging from isolated vertebral malformation to acampomelic dysplasia. We also generated a Sox9 hypomorphic mutant mouse model bearing a microdeletion within the TAM domain ( Sox9 Asp272del ). We demonstrated that disturbance of the TAM domain with missense mutation or microdeletion results in reduced protein stability but does not affect the transcriptional activity of SOX9. Homozygous Sox9 Asp272del mice exhibited axial skeletal dysplasia including kinked tails, ribcage anomalies, and scoliosis, recapitulating phenotypes observed in human, while heterozygous mutants display a milder phenotype. Analysis of primary chondrocytes and the intervertebral discs in Sox9 Asp272del mutant mice revealed dysregulation of a panel of genes with major contributions of the extracellular matrix, angiogenesis, and ossification-related processes. In summary, our work identified the first pathologic variant of SOX9 within the TAM domain and demonstrated that this variant is associated with reduced SOX9 protein stability. Our finding suggests that reduced SOX9 stability caused by variants in the TAM domain may be responsible for the milder forms of axial skeleton dysplasia in humans.
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4
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Ogawa Y, Terao M, Tsuji-Hosokawa A, Tsuchiya I, Hasegawa M, Takada S. SOX9 and SRY binding sites on mouse mXYSRa/Enh13 enhancer redundantly regulate Sox9 expression to varying degrees. Hum Mol Genet 2023; 32:55-64. [PMID: 35921234 DOI: 10.1093/hmg/ddac184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 01/25/2023] Open
Abstract
Sox9 plays an essential role in mammalian testis formation. It has been reported that gene expression in the testes is regulated by enhancers. Among them, mXYSRa/Enh13-which is located at far upstream of the transcription start site-plays a critical role, wherein its deletion causes complete male-to-female sex reversal in mice. It has been proposed that the binding sites (BSs) of SOX9 and SRY, the latter of which is the sex determining gene on the Y chromosome, are associated with mXYSRa/Enh13. They function as an enhancer, whereby the sequences are evolutionarily conserved and in vivo binding of SOX9 and SRY to mXYSRa/Enh13 has been demonstrated previously. However, their precise in vivo functions have not been examined to date. To this end, this study generated mice with substitutions on the SOX9 and SRY BSs to reveal their in vivo functions. Homozygous mutants of SOX9 and SRY BS were indistinguishable from XY males, whereas double mutants had small testes, suggesting that these functions are redundant and that there is another functional sequence on mXYSRa/Enh13, since mXYSRa/Enh13 deletion mice are XY females. In addition, the majority of hemizygous mice with substitutions in SOX9 BS and SRY BS were female and male, respectively, suggesting that SOX9 BS contributes more to SRY BS for mXYSRa/Enh13 to function. The additive effect of SOX9 and SRY via these BSs was verified using an in vitro assay. In conclusion, SOX9 BS and SRY BS function redundantly in vivo, and at least one more functional sequence should exist in mXYSRa/Enh13.
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Affiliation(s)
- Yuya Ogawa
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan.,Department of NCCHD, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Miho Terao
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Atsumi Tsuji-Hosokawa
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Iku Tsuchiya
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan.,Department of NCCHD, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Midori Hasegawa
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan.,Department of NCCHD, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan.,Department of NCCHD, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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5
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Chen Q, Dai J, Bian Q. Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects. SCIENCE ADVANCES 2022; 8:eabo3648. [PMID: 36417512 PMCID: PMC9683718 DOI: 10.1126/sciadv.abo3648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Aberrations in tissue-specific enhancers underlie many developmental defects. Disrupting a noncoding region distal from the human SOX9 gene causes the Pierre Robin sequence (PRS) characterized by the undersized lower jaw. Such a craniofacial-specific defect has been previously linked to enhancers transiently active in cranial neural crest cells (CNCCs). We demonstrate that the PRS region also strongly regulates Sox9 in CNCC-derived Meckel's cartilage (MC), but not in limb cartilages, even after decommissioning of CNCC enhancers. Such an MC-specific regulatory effect correlates with the MC-specific chromatin contacts between the PRS region and Sox9, highlighting the importance of lineage-dependent chromatin topology in instructing enhancer usage. By integrating the enhancer signatures and chromatin topology, we uncovered >10,000 enhancers that function differentially between MC and limb cartilages and demonstrated their association with human diseases. Our findings provide critical insights for understanding the choreography of gene regulation during development and interpreting the genetic basis of craniofacial pathologies.
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Affiliation(s)
- Qiming Chen
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
| | - Jiewen Dai
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
- Corresponding author. (J.D.); (Q.B.)
| | - Qian Bian
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Corresponding author. (J.D.); (Q.B.)
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6
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Sreenivasan R, Gonen N, Sinclair A. SOX Genes and Their Role in Disorders of Sex Development. Sex Dev 2022; 16:80-91. [PMID: 35760052 DOI: 10.1159/000524453] [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: 04/01/2021] [Accepted: 03/29/2022] [Indexed: 11/19/2022] Open
Abstract
SOX genesare master regulatory genes controlling development and are fundamental to the establishment of sex determination in a multitude of organisms. The discovery of the master sex-determining gene SRY in 1990 was pivotal for the understanding of how testis development is initiated in mammals. With this discovery, an entire family of SOX factors were uncovered that play crucial roles in cell fate decisions during development. The importance of SOX genes in human reproductive development is evident from the various disorders of sex development (DSD) upon loss or overexpression of SOX gene function. Here, we review the roles that SOX genes play in gonad development and their involvement in DSD. We start with an overview of sex determination and differentiation, DSDs, and the SOX gene family and function. We then provide detailed information and discussion on SOX genes that have been implicated in DSDs, both at the gene and regulatory level. These include SRY, SOX9, SOX3, SOX8, and SOX10. This review provides insights on the crucial balance of SOX gene expression levels needed for gonad development and maintenance and how changes in these levels can lead to DSDs.
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Affiliation(s)
- Rajini Sreenivasan
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Andrew Sinclair
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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7
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Gong L, Wang C, Xie H, Gao J, Li T, Qi S, Wang B, Wang J. Identification of a novel heterozygous SOX9 variant in a Chinese family with congenital heart disease. Mol Genet Genomic Med 2022; 10:e1909. [PMID: 35218327 PMCID: PMC9034670 DOI: 10.1002/mgg3.1909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/25/2022] [Accepted: 02/14/2022] [Indexed: 12/02/2022] Open
Abstract
Background Previous studies of individuals with hereditary or sporadic congenital heart disease (CHD) have provided strong evidence for a genetic basis for CHD. The aim of this study was to identify novel pathogenic genes and variants in a Chinese CHD family. Methods Three generations of a family with CHD were recruited. We performed whole exome sequencing for the affected individuals and the proband's unaffected aunt to investigate the genetic causes of CHD in this family. Heterozygous variants carried by the proband and her maternal grandmother, but not the proband's aunt, were selected. The frequencies of the variants detected were assessed using public databases, and their influences on protein function were predicted using online prediction software. The candidate variant was further confirmed by Sanger sequencing of other members of the family. Results On the basis of the family's pedigree, the mode of inheritance was speculated to be autosomal dominant with incomplete penetrance. We identified a novel heterozygous missense variant in SOX9 in all affected individuals and one asymptomatic family member, suggesting an inheritance pattern with incomplete penetrance. The variant was not found in any public database. In addition, the variant was highly conserved among mammals, and was predicted to be deleterious by online software programs. Conclusions We report for the first time a novel heterozygous missense variant in SOX9 (NM_000346:c.931G>T:p.Gly311Cys) in a Chinese CHD family. Our results provide further evidence supporting a causative role for SOX9 variants in CHD.
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Affiliation(s)
- Li Gong
- Department of Cardiothoracic Surgery, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Chunyan Wang
- Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Haiyang Xie
- Department of Cardiothoracic Surgery, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jun Gao
- Department of Ultrasound imaging, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Tengyan Li
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Shenggui Qi
- Qinghai High Altitude Medical Research Institute, Xining, China
| | - Binbin Wang
- Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Jing Wang
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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8
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Qiao X, Wu L, Tang J, Xiang R, Fan L, Huang H, Chen Y. Case report: A de novo Non-sense SOX9 mutation (p.Q417*) located in transactivation domain is Responsible for Campomelic Dysplasia. Front Pediatr 2022; 10:1089194. [PMID: 36741086 PMCID: PMC9890166 DOI: 10.3389/fped.2022.1089194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Campomelic dysplasia (CD) is an autosomal dominant skeletal dysplasia syndrome characterized by shortness and bowing of lower extremities, and often accompanied by XY sex reversal. Heterozygous pathogenic variants of SOX9 or rearrangement involving the long arm of chromosome 17 are the causes of disease. However, evidence for pathogenesis of SOX9 haploinsufficiency is insufficient. METHODS We enrolled a Chinese family where the fetus was diagnosed with CD. The affected fetus was selected for whole-exome sequencing to identify the pathogenic mutations in this family. RESULTS After data filtering, a novel non-sense SOX9 variant (NM_000346.3; c.1249C > T; p.Q417*) was identified as the pathogenic lesion in the fetus. Further co-segregation analysis using Sanger sequencing confirmed that this novel SOX9 mutation (c.1249C > T; p.Q417*) was a de novo mutation in the affected fetus. This terminated codon mutation identified by bioinformatics was located at an evolutionarily conserved site of SOX9. The bioinformatics-based analysis predicted this variant was pathogenic and affected SOX9 transactivation activity. CONCLUSION CD is a rare condition, which connected with SOX9 tightly. We identified a novel heterozygous SOX9 variant (p.Q417*) in a Chinese CD family. Our study supports the putative reduced transactivation of SOX9 variants in the pathogenicity of CD.
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Affiliation(s)
- Xingxing Qiao
- Department of Cardiology, Second Xiangya Hospital Central South University, Changsha, China
| | - Liping Wu
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China.,Obstetric Inpatient Department, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Jianjun Tang
- Department of Cardiology, Second Xiangya Hospital Central South University, Changsha, China
| | - Rong Xiang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Liangliang Fan
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Hao Huang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Yaqin Chen
- Department of Cardiology, Second Xiangya Hospital Central South University, Changsha, China
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9
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Ojiro R, Watanabe Y, Okano H, Takahashi Y, Takashima K, Tang Q, Ozawa S, Saito F, Akahori Y, Jin M, Yoshida T, Shibutani M. Gene expression profiles of multiple brain regions in rats differ between developmental and postpubertal exposure to valproic acid. J Appl Toxicol 2021; 42:864-882. [PMID: 34779009 DOI: 10.1002/jat.4263] [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: 07/25/2021] [Revised: 10/06/2021] [Accepted: 10/19/2021] [Indexed: 11/05/2022]
Abstract
We have previously reported that the valproic acid (VPA)-induced disruption pattern of hippocampal adult neurogenesis differs between developmental and 28-day postpubertal exposure. In the present study, we performed brain region-specific global gene expression profiling to compare the profiles of VPA-induced neurotoxicity between developmental and postpubertal exposure. Offspring exposed to VPA at 0, 667, and 2000 parts per million (ppm) via maternal drinking water from gestational day 6 until weaning (postnatal day 21) were examined, along with male rats orally administered VPA at 0, 200, and 900 mg/kg body weight for 28 days starting at 5 weeks old. Four brain regions-the hippocampal dentate gyrus, corpus callosum, cerebral cortex, and cerebellar vermis-were subjected to expression microarray analysis. Profiled data suggested a region-specific pattern of effects after developmental VPA exposure, and a common pattern of effects among brain regions after postpubertal VPA exposure. Developmental VPA exposure typically led to the altered expression of genes related to nervous system development (Msx1, Xcl1, Foxj1, Prdm16, C3, and Kif11) in the hippocampus, and those related to nervous system development (Neurod1) and gliogenesis (Notch1 and Sox9) in the corpus callosum. Postpubertal VPA exposure led to the altered expression of genes related to neuronal differentiation and projection (Cd47, Cyr61, Dbi, Adamts1, and Btg2) in multiple brain regions. These findings suggested that neurotoxic patterns of VPA might be different between developmental and postpubertal exposure, which was consistent with our previous study. Of note, the hippocampal dentate gyrus might be a sensitive target of developmental neurotoxicants after puberty.
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Affiliation(s)
- Ryota Ojiro
- Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan.,Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan
| | - Yousuke Watanabe
- Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan
| | - Hiromu Okano
- Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan.,Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan
| | - Yasunori Takahashi
- Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan.,Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan
| | - Kazumi Takashima
- Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan.,Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan
| | - Qian Tang
- Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan.,Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan
| | - Shunsuke Ozawa
- Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan.,Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan
| | - Fumiyo Saito
- Chemicals Assessment and Research Center, Chemicals Evaluation and Research Institute, Japan, Bunkyo-ku, Tokyo, Japan.,Department of Toxicology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
| | - Yumi Akahori
- Chemicals Assessment and Research Center, Chemicals Evaluation and Research Institute, Japan, Bunkyo-ku, Tokyo, Japan
| | - Meilan Jin
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Toshinori Yoshida
- Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan.,Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan
| | - Makoto Shibutani
- Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan.,Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan.,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo, Japan
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10
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Atlas G, Sreenivasan R, Sinclair A. Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development. Sex Dev 2021; 15:392-410. [PMID: 34634785 DOI: 10.1159/000519238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 11/19/2022] Open
Abstract
Disorders of sex development (DSD) are a complex group of conditions with highly variable clinical phenotypes, most often caused by failure of gonadal development. DSD are estimated to occur in around 1.7% of all live births. Whilst the understanding of genes involved in gonad development has increased exponentially, approximately 50% of patients with a DSD remain without a genetic diagnosis, possibly implicating non-coding genomic regions instead. Here, we review how variants in the non-coding genome of DSD patients can be identified using techniques such as array comparative genomic hybridization (CGH) to detect copy number variants (CNVs), and more recently, whole genome sequencing (WGS). Once a CNV in a patient's non-coding genome is identified, putative regulatory elements such as enhancers need to be determined within these vast genomic regions. We will review the available online tools and databases that can be used to refine regions with potential enhancer activity based on chromosomal accessibility, histone modifications, transcription factor binding site analysis, chromatin conformation, and disease association. We will also review the current in vitro and in vivo techniques available to demonstrate the functionality of the identified enhancers. The review concludes with a clinical update on the enhancers linked to DSD.
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Affiliation(s)
- Gabby Atlas
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia, .,Department of Endocrinology and Diabetes, Royal Children's Hospital, Melbourne, Victoria, Australia, .,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia,
| | - Rajini Sreenivasan
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Sinclair
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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11
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Takano T, Ota H, Ohishi H, Hata K, Furukawa R, Nakabayashi K. Adult acampomelic campomelic dysplasia and disorders of sex development due to a reciprocal translocation involving chromosome 17q24.3 upstream of the SOX9 gene. Eur J Med Genet 2021; 64:104332. [PMID: 34481091 DOI: 10.1016/j.ejmg.2021.104332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/06/2021] [Accepted: 08/31/2021] [Indexed: 11/19/2022]
Abstract
Balanced chromosomal rearrangements with a breakpoint located upstream of the sex determining region Y-box 9 (SOX9) gene on chromosome 17q24.3 are associated with skeletal abnormalities, campomelic dysplasia (CMPD), or acampomelic campomelic dysplasia (ACMPD). We report on a female patient with a reciprocal translocation of t (11; 17) (p15.4; q24.3), who was diagnosed with acampomelic campomelic dysplasia. The 34-year-old Japanese patient presented with distinct skeletal abnormalities, profound intellectual disability, and female phenotype despite the presence of Y chromosome and the sex determining region Y (SRY) gene. Her menarche started at 33 years and 4 months after hormone therapy of estrogen therapy followed by estrogen progesterone therapy. By conducting whole genome sequencing followed by Sanger sequencing validation, we determined the precise breakpoint positions of the reciprocal translocation, one of which was located 203 kb upstream of the SOX9 gene. Considering the phenotypic variations previously reported among the CMPD/ACMPD patients with a chromosomal translocation in the vicinity of SOX9, the identified translocation was concluded to be responsible for all major phenotypes observed in the patient.
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Affiliation(s)
- Takako Takano
- Department of Child Health, Tokyo Kasei University, Tokyo, Japan; Department of Pediatrics, Tokyo Metropolitan Tobu Medical Center for Children with Developmental Disabilities, Tokyo, Japan.
| | - Hideomi Ota
- Department of Pediatrics, Tokyo Metropolitan Tobu Medical Center for Children with Developmental Disabilities, Tokyo, Japan
| | - Hajime Ohishi
- Department of Obstetrics and Gynecology, Center Hospital of the National Center for Global Health and Medicine, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Rieko Furukawa
- Department of Pediatric Medical Imaging, Jichi Children's Medical Center, Tochigi, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
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12
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Leypold NA, Speicher MR. Evolutionary conservation in noncoding genomic regions. Trends Genet 2021; 37:903-918. [PMID: 34238591 DOI: 10.1016/j.tig.2021.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/25/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022]
Abstract
Humans may share more genomic commonalities with other species than previously thought. According to current estimates, ~5% of the human genome is functionally constrained, which is a much larger fraction than the ~1.5% occupied by annotated protein-coding genes. Hence, ~3.5% of the human genome comprises likely functional conserved noncoding elements (CNEs) preserved among organisms, whose common ancestors existed throughout hundreds of millions of years of evolution. As whole-genome sequencing emerges as a standard procedure in genetic analyses, interpretation of variations in CNEs, including the elucidation of mechanistic and functional roles, becomes a necessity. Here, we discuss the phenomenon of noncoding conservation via four dimensions (sequence, regulatory conservation, spatiotemporal expression, and structure) and the potential significance of CNEs in phenotype variation and disease.
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Affiliation(s)
- Nicole A Leypold
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria.
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, Graz, Austria.
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13
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Nakamichi R, Kurimoto R, Tabata Y, Asahara H. Transcriptional, epigenetic and microRNA regulation of growth plate. Bone 2020; 137:115434. [PMID: 32422296 PMCID: PMC7387102 DOI: 10.1016/j.bone.2020.115434] [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: 04/09/2020] [Revised: 05/13/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
Endochondral ossification is a critical event in bone formation, particularly in long shaft bones. Many cellular differentiation processes work in concert to facilitate the generation of cartilage primordium to formation of trabecular structures, all of which occur within the growth plate. Previous studies have revealed that the growth plate is tightly regulated by various transcription factors, epigenetic systems, and microRNAs. Hence, understanding these mechanisms that regulate the growth plate is crucial to furthering the current understanding on skeletal diseases, and in formulating effective treatment strategies. In this review, we focus on describing the function and mechanisms of the transcription factors, epigenetic systems, and microRNAs known to regulate the growth plate.
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Affiliation(s)
- Ryo Nakamichi
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MBB-102, La Jolla, CA 92037, USA; Department of Orthopaedic Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Ryota Kurimoto
- Department of Systems Biomedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yusuke Tabata
- Department of Orthopaedic Surgery, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan
| | - Hirosi Asahara
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MBB-102, La Jolla, CA 92037, USA; Department of Systems Biomedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
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14
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Tariq A, Hao Q, Sun Q, Singh DK, Jadaliha M, Zhang Y, Chetlangia N, Ma J, Holton SE, Bhargava R, Lal A, Prasanth SG, Prasanth KV. LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells. RNA (NEW YORK, N.Y.) 2020; 26:175-185. [PMID: 31690584 PMCID: PMC6961546 DOI: 10.1261/rna.073254.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/30/2019] [Indexed: 05/08/2023]
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) subtypes with a poor prognosis and high recurrence rate. Recent studies have identified vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type-specific expression of lncRNAs and their potential role in regulating the expression of oncogenic and tumor suppressor genes have made them promising cancer drug targets. By performing a transcriptome screen in an isogenic TNBC/basal subtype BC progression cell line model, we recently reported ∼1800 lncRNAs that display aberrant expression during breast cancer progression. Mechanistic studies on one such nuclear-retained lncRNA, linc02095, reveal that it promotes breast cancer proliferation by facilitating the expression of oncogenic transcription factor, SOX9. Both linc02095 and SOX9 display coregulated expression in BC patients as well in basal subtype BC cell lines. Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase II occupancy at the SOX9 gene body as well as defective SOX9 mRNA export, implying that linc02095 positively regulates SOX9 transcription and mRNA export. Finally, we identify a positive feedback loop in BC cells that controls the expression of both linc02095 and SOX9 Thus, our results unearth tumor-promoting activities of a nuclear lncRNA linc02095 by facilitating the expression of key oncogenic transcription factor in BC.
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Affiliation(s)
- Aamira Tariq
- Department of Biosciences, Comsats Institute of Information Technology, Islamabad 45550, Pakistan
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Sun
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mahdieh Jadaliha
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Sarah E Holton
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Rohit Bhargava
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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15
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Wu N, Liu B, Du H, Zhao S, Li Y, Cheng X, Wang S, Lin J, Zhou J, Qiu G, Wu Z, Zhang J. The Progress of CRISPR/Cas9-Mediated Gene Editing in Generating Mouse/Zebrafish Models of Human Skeletal Diseases. Comput Struct Biotechnol J 2019; 17:954-962. [PMID: 31360334 PMCID: PMC6639410 DOI: 10.1016/j.csbj.2019.06.006] [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: 02/25/2019] [Revised: 05/28/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
Genetic factors play a substantial role in the etiology of skeletal diseases, which involve 1) defects in skeletal development, including intramembranous ossification and endochondral ossification; 2) defects in skeletal metabolism, including late bone growth and bone remodeling; 3) defects in early developmental processes related to skeletal diseases, such as neural crest cell (NCC) and cilia functions; 4) disturbance of the cellular signaling pathways which potentially affect bone growth. Efficient and high-throughput genetic methods have enabled the exploration and verification of disease-causing genes and variants. Animal models including mouse and zebrafish have been extensively used in functional mechanism studies of causal genes and variants. The conventional approaches of generating mutant animal models include spontaneous mutagenesis, random integration, and targeted integration via mouse embryonic stem cells. These approaches are costly and time-consuming. Recent development and application of gene-editing tools, especially the CRISPR/Cas9 system, has significantly accelerated the process of gene-editing in diverse organisms. Here we review both mice and zebrafish models of human skeletal diseases generated by CRISPR/Cas9 system, and their contributions to deciphering the underpins of disease mechanisms.
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Affiliation(s)
- Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Bowen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yaqi Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Xi Cheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, 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, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Junde Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | | | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
- Central Laboratory & Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Central Laboratory & Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Correspondence to: Z. Wu, Central Laboratory & Medical Research Center, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, China.
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
- Correspondence to: J. Zhang, Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Medical Research Center of Orthopedics, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing 100730, China.
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16
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Patel B, Byrne JLB, Phillips A, Hotaling JM, Johnstone EB. When standard genetic testing does not solve the mystery: a rare case of preimplantation genetic diagnosis for campomelic dysplasia in the setting of parental mosaicism. Fertil Steril 2019; 110:732-736. [PMID: 30196970 DOI: 10.1016/j.fertnstert.2018.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 01/10/2023]
Abstract
OBJECTIVE To report a rare case of somatic mosaicism with a germline component of campomelic dysplasia in a woman undergoing in vitro fertilization with preimplantation genetic diagnosis (IVF-PGD). DESIGN Case report. SETTING Clinic. PATIENT(S) A 28-year old G2P0110 and her 34-year old husband had two previous pregnancies complicated by fetal campomelic dysplasia with suspected germline mosaic mutation. The couple, both phenotypically normal, underwent IVF-PGD to reduce their chances of transmission. None of the embryos could initially be determined to be disease free, because all embryos shared either a maternal or a paternal short tandem repeat haplotype with the products of conception from her last pregnancy. INTERVENTION(S) Peripheral-blood cytogenomic single-nucleotide polymorphism (SNP) microarray to identify the carrier of the mutation, and IVF-PGD to identify the disease-free embryo. MAIN OUTCOME MEASURE(S) Disease-free embryo. RESULT(S) Only one of the five euploid embryos was identified as disease free. CONCLUSION(S) A woman with suspected germline mosaicism for campomelic dysplasia was found to be a somatic mosaic with a germline component via a peripheral blood SNP microarray test. This identified her solitary disease-free embryo, which was transferred to her uterus but did not result in a viable pregnancy.
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Affiliation(s)
- Biren Patel
- Obstetrics and Gynecology, University of Utah, Salt Lake City, Utah.
| | - Jan L B Byrne
- Obstetrics and Gynecology, University of Utah, Salt Lake City, Utah
| | - Amber Phillips
- Genetic Counseling, University of Utah, Salt Lake City, Utah
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17
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Yip RK, Chan D, Cheah KS. Mechanistic insights into skeletal development gained from genetic disorders. Curr Top Dev Biol 2019; 133:343-385. [DOI: 10.1016/bs.ctdb.2019.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Ogawa Y, Terao M, Hara S, Tamano M, Okayasu H, Kato T, Takada S. Mapping of a responsible region for sex reversal upstream of Sox9 by production of mice with serial deletion in a genomic locus. Sci Rep 2018; 8:17514. [PMID: 30504911 PMCID: PMC6269501 DOI: 10.1038/s41598-018-35746-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/09/2018] [Indexed: 11/09/2022] Open
Abstract
Sox9 plays critical roles in testis formation. By mapping four familial cases of disorders of sexual development, a 32.5 kb sequence located far upstream of SOX9 was previously identified as being a commonly deleted region and named the XY sex reversal region (XYSR). To narrow down a responsible sequence in XYSR, we generated mutant mice with a series of deletions in XYSR by application of the CRISPR/Cas9 system, using a mixture of sgRNAs targeting several kilobase (kb) intervals in the region. When the whole XYSR corresponding sequence in mice was deleted in XY karyotype individuals, the mutation resulted in female offspring, suggesting that an expression mechanism of SOX9/Sox9 through XYSR is conserved in human and mouse. Male-to-female sex reversal was found in mice with a 4.8 kb deletion. We identified a sequence conserved among humans, mice, and opossum, the deletion of which (783 bp) in mice resulted in male-to-female sex reversal. The sequence includes a recently reported critical gonad enhancer for Sox9. Although it cannot be concluded that the human sequence is responsible for XYSR, it is likely. This method is applicable for fine mapping of responsible sequences for disease-causing deletions especially with regard to rare diseases.
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Affiliation(s)
- Yuya Ogawa
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Miho Terao
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Satoshi Hara
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Moe Tamano
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Haruka Okayasu
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Tomoko Kato
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.,Tokyo Metropolitan Institute of Medical Science, Regenerative Medicine Project, Tokyo, 156-8506, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.
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19
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Kalfa N, Gaspari L, Ollivier M, Philibert P, Bergougnoux A, Paris F, Sultan C. Molecular genetics of hypospadias and cryptorchidism recent developments. Clin Genet 2018; 95:122-131. [PMID: 30084162 DOI: 10.1111/cge.13432] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/14/2022]
Abstract
During the last decade, a tremendous amount of work has been devoted to the study of the molecular genetics of isolated hypospadias and cryptorchidism, two minor forms of disorders of sex development (DSD). Beyond the genes involved in gonadal determination and sex differentiation, including those underlying androgen biosynthesis and signaling, new genes have been identified through genome-wide association study and familial clustering. Even if no single genetic defect can explain the whole spectrum of DSD, these recent studies reinforce the strong role of the genetic background in the occurrence of these defects. The timing of signaling disruption may explain the different phenotypes.
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Affiliation(s)
- Nicolas Kalfa
- Département de Chirurgie et Urologie Pédiatrique, Hôpital Lapeyronie, CHU de Montpellier et Université Montpellier, Montpellier, France.,National Reference Center of Genital Development CRMR DEV-GEN Constitutif, Institut Universitaire de Recherche Clinique, Departement de Génétique, Université de Montpellier, Montpellier, France
| | - Laura Gaspari
- National Reference Center of Genital Development CRMR DEV-GEN Constitutif, Institut Universitaire de Recherche Clinique, Departement de Génétique, Université de Montpellier, Montpellier, France.,Unité d'Endocrinologie et Gynécologie Pédiatriques, Service de Pédiatrie, CHU de Montpellier, Hôpital Arnaud de Villeneuve et Université Montpellier, Montpellier, France
| | - Margot Ollivier
- Département de Chirurgie et Urologie Pédiatrique, Hôpital Lapeyronie, CHU de Montpellier et Université Montpellier, Montpellier, France.,National Reference Center of Genital Development CRMR DEV-GEN Constitutif, Institut Universitaire de Recherche Clinique, Departement de Génétique, Université de Montpellier, Montpellier, France
| | - Pascal Philibert
- National Reference Center of Genital Development CRMR DEV-GEN Constitutif, Institut Universitaire de Recherche Clinique, Departement de Génétique, Université de Montpellier, Montpellier, France.,Unité d'Endocrinologie et Gynécologie Pédiatriques, Service de Pédiatrie, CHU de Montpellier, Hôpital Arnaud de Villeneuve et Université Montpellier, Montpellier, France
| | - Anne Bergougnoux
- National Reference Center of Genital Development CRMR DEV-GEN Constitutif, Institut Universitaire de Recherche Clinique, Departement de Génétique, Université de Montpellier, Montpellier, France
| | - Francoise Paris
- National Reference Center of Genital Development CRMR DEV-GEN Constitutif, Institut Universitaire de Recherche Clinique, Departement de Génétique, Université de Montpellier, Montpellier, France.,Unité d'Endocrinologie et Gynécologie Pédiatriques, Service de Pédiatrie, CHU de Montpellier, Hôpital Arnaud de Villeneuve et Université Montpellier, Montpellier, France
| | - Charles Sultan
- National Reference Center of Genital Development CRMR DEV-GEN Constitutif, Institut Universitaire de Recherche Clinique, Departement de Génétique, Université de Montpellier, Montpellier, France.,Unité d'Endocrinologie et Gynécologie Pédiatriques, Service de Pédiatrie, CHU de Montpellier, Hôpital Arnaud de Villeneuve et Université Montpellier, Montpellier, France
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20
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Bertolini F, Schiavo G, Tinarelli S, Santoro L, Utzeri VJ, Dall'Olio S, Nanni Costa L, Gallo M, Fontanesi L. Exploiting phenotype diversity in a local animal genetic resource: Identification of a single nucleotide polymorphism associated with the tail shape phenotype in the autochthonous Casertana pig breed. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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Mochizuki Y, Chiba T, Kataoka K, Yamashita S, Sato T, Kato T, Takahashi K, Miyamoto T, Kitazawa M, Hatta T, Natsume T, Takai S, Asahara H. Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression. Dev Cell 2018; 46:794-806.e6. [PMID: 30146478 PMCID: PMC6324936 DOI: 10.1016/j.devcel.2018.07.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 04/23/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022]
Abstract
SRY-box 9 (SOX9) is a master transcription factor that regulates cartilage development. SOX9 haploinsufficiency resulting from breakpoints in a ∼1-Mb region upstream of SOX9 was reported in acampomelic campomelic dysplasia (ACD) patients, suggesting that essential enhancer regions of SOX9 for cartilage development are located in this long non-coding sequence. However, the cis-acting enhancer region regulating cartilage-specific SOX9 expression remains to be identified. To identify distant cartilage Sox9 enhancers, we utilized the combination of multiple CRISPR/Cas9 technologies including enrichment of the promoter-enhancer complex followed by next-generation sequencing and mass spectrometry (MS), SIN3A-dCas9-mediated epigenetic silencing, and generation of enhancer deletion mice. As a result, we could identify a critical far-upstream cis-element and Stat3 as a trans-acting factor, regulating cartilage-specific Sox9 expression and subsequent skeletal development. Our strategy could facilitate definitive ACD diagnosis and should be useful to reveal the detailed chromatin conformation and regulation.
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Affiliation(s)
- Yusuke Mochizuki
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Department of Orthopaedic Surgery, Nippon Medical School, Tokyo 113-0022, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kensuke Kataoka
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Satoshi Yamashita
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tempei Sato
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tomomi Kato
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kenji Takahashi
- Department of Orthopaedic Surgery, Nippon Medical School, Tokyo 113-0022, Japan
| | - Takeshi Miyamoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Masashi Kitazawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Shinro Takai
- Department of Orthopaedic Surgery, Nippon Medical School, Tokyo 113-0022, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Department of Molecular and Experimental Medicine, The Scripps Research Institute, San Diego, CA 92037, USA.
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Cha S, Lim JE, Park AY, Do JH, Lee SW, Shin C, Cho NH, Kang JO, Nam JM, Kim JS, Woo KM, Lee SH, Kim JY, Oh B. Identification of five novel genetic loci related to facial morphology by genome-wide association studies. BMC Genomics 2018; 19:481. [PMID: 29921221 PMCID: PMC6008943 DOI: 10.1186/s12864-018-4865-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 06/12/2018] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Face morphology is strongly determined by genetic factors. However, only a small number of genes related to face morphology have been identified to date. Here, we performed a two-stage genome-wide association study (GWAS) of 85 face morphological traits in 7569 Koreans (5643 in the discovery set and 1926 in the replication set). RESULTS In this study, we analyzed 85 facial traits, including facial angles. After discovery GWAS, 128 single nucleotide polymorphisms (SNPs) showing an association of P < 5 × 10- 6 were selected to determine the replication of the associations, and meta-analysis of discovery GWAS and the replication analysis resulted in five genome-wide significant loci. The OSR1-WDR35 [rs7567283, G allele, beta (se) = -0.536 (0.096), P = 2.75 × 10- 8] locus was associated with the facial frontal contour; the HOXD1-MTX2 [rs970797, A allele, beta (se) = 0.015 (0.003), P = 3.97 × 10- 9] and WDR27 [rs3736712, C allele, beta (se) = 0.293 (0.048), P = 8.44 × 10- 10] loci were associated with eye shape; and the SOX9 [rs2193054, C allele, beta (se) (ln-transformed) = -0.007 (0.001), P = 6.17 × 10- 17] and DHX35 [rs2206437, A allele, beta (se) = -0.283 (0.047), P = 1.61 × 10- 9] loci were associated with nose shape. WDR35 and SOX9 were related to known craniofacial malformations, i.e., cranioectodermal dysplasia 2 and campomelic dysplasia, respectively. In addition, we found three independent association signals in the SOX9 locus, and six known loci for nose size and shape were replicated in this study population. Interestingly, four SNPs within these five face morphology-related loci showed discrepancies in allele frequencies among ethnic groups. CONCLUSIONS We identified five novel face morphology loci that were associated with facial frontal contour, nose shape, and eye shape. Our findings provide useful genetic information for the determination of face morphology.
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Affiliation(s)
- Seongwon Cha
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - Ji Eun Lim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Ah Yeon Park
- Mibyeong Research Center, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - Jun-Hyeong Do
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - Si Woo Lee
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - Chol Shin
- Division of Pulmonary Sleep and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital and Institute of Human Genomic Study, Korea University Ansan Hospital, Ansan, 15355, Republic of Korea
| | - Nam Han Cho
- Department of Preventive Medicine, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Ji-One Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jeong Min Nam
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jong-Sik Kim
- DNA Forensic Division, Supreme Prosecutors' Office, Seoul, 06590, Republic of Korea
| | - Kwang-Man Woo
- DNA Forensic Division, Supreme Prosecutors' Office, Seoul, 06590, Republic of Korea
| | - Seung-Hwan Lee
- DNA Forensic Division, Supreme Prosecutors' Office, Seoul, 06590, Republic of Korea
| | - Jong Yeol Kim
- KM Fundamental Research Division, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - Bermseok Oh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea.
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Antwi P, Hong CS, Duran D, Jin SC, Dong W, DiLuna M, Kahle KT. A novel association of campomelic dysplasia and hydrocephalus with an unbalanced chromosomal translocation upstream of SOX9. Cold Spring Harb Mol Case Stud 2018; 4:a002766. [PMID: 29695406 PMCID: PMC5983176 DOI: 10.1101/mcs.a002766] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/26/2018] [Indexed: 11/29/2022] Open
Abstract
Campomelic dysplasia is a rare skeletal dysplasia characterized by Pierre Robin sequence, craniofacial dysmorphism, shortening and angulation of long bones, tracheobronchomalacia, and occasionally sex reversal. The disease is due to mutations in SOX9 or chromosomal rearrangements involving the long arm of Chromosome 17 harboring the SOX9 locus. SOX9, a transcription factor, is indispensible in establishing and maintaining neural stem cells in the central nervous system. We present a patient with angulation of long bones and external female genitalia on prenatal ultrasound who was subsequently found to harbor the chromosomal abnormality 46, XY, t(6;17) (p21.1;q24.3) on prenatal genetic testing. Comparative genomic hybridization revealed deletions at 6p21.1 and 17q24.3, the latter being 2.3 Mb upstream of SOX9 Whole-exome sequencing did not identify pathogenic variants in SOX9, suggesting that the 17q24.3 deletion represents a translocation breakpoint farther upstream of SOX9 than previously identified. At 2 mo of age the patient developed progressive communicating ventriculomegaly and thinning of the cortical mantle without clinical signs of increased intracranial pressure. This case suggests ventriculomegaly in some cases represents not a primary impairment of cerebrospinal fluid dynamics, but an epiphenomenon driven by a genetic dysregulation of neural progenitor cell fate.
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Affiliation(s)
- Prince Antwi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Christopher S Hong
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Daniel Duran
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Weilai Dong
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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24
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Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network. BMC Genomics 2017; 18:983. [PMID: 29262782 PMCID: PMC5738906 DOI: 10.1186/s12864-017-4378-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 12/11/2017] [Indexed: 01/05/2023] Open
Abstract
Background Chondrogenesis is the earliest stage of skeletal development and is a highly dynamic process, integrating the activities and functions of transcription factors, cell signaling molecules and extracellular matrix proteins. The molecular mechanisms underlying chondrogenesis have been extensively studied and multiple key regulators of this process have been identified. However, a genome-wide overview of the gene regulatory network in chondrogenesis has not been achieved. Results In this study, employing RNA sequencing, we identified 332 protein coding genes and 34 long non-coding RNA (lncRNA) genes that are highly selectively expressed in human fetal growth plate chondrocytes. Among the protein coding genes, 32 genes were associated with 62 distinct human skeletal disorders and 153 genes were associated with skeletal defects in knockout mice, confirming their essential roles in skeletal formation. These gene products formed a comprehensive physical interaction network and participated in multiple cellular processes regulating skeletal development. The data also revealed 34 transcription factors and 11,334 distal enhancers that were uniquely active in chondrocytes, functioning as transcriptional regulators for the cartilage-selective genes. Conclusions Our findings revealed a complex gene regulatory network controlling skeletal development whereby transcription factors, enhancers and lncRNAs participate in chondrogenesis by transcriptional regulation of key genes. Additionally, the cartilage-selective genes represent candidate genes for unsolved human skeletal disorders. Electronic supplementary material The online version of this article (10.1186/s12864-017-4378-y) contains supplementary material, which is available to authorized users.
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25
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Barter MJ, Gomez R, Hyatt S, Cheung K, Skelton AJ, Xu Y, Clark IM, Young DA. The long non-coding RNA ROCR contributes to SOX9 expression and chondrogenic differentiation of human mesenchymal stem cells. Development 2017; 144:4510-4521. [PMID: 29084806 PMCID: PMC5769619 DOI: 10.1242/dev.152504] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/25/2017] [Indexed: 12/31/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed in a highly tissue-specific manner and function in various aspects of cell biology, often as key regulators of gene expression. In this study, we established a role for lncRNAs in chondrocyte differentiation. Using RNA sequencing we identified a human articular chondrocyte repertoire of lncRNAs from normal hip cartilage donated by neck of femur fracture patients. Of particular interest are lncRNAs upstream of the master chondrocyte transcription factor SOX9 locus. SOX9 is an HMG-box transcription factor that plays an essential role in chondrocyte development by directing the expression of chondrocyte-specific genes. Two of these lncRNAs are upregulated during chondrogenic differentiation of mesenchymal stem cells (MSCs). Depletion of one of these lncRNAs, LOC102723505, which we termed ROCR (regulator of chondrogenesis RNA), by RNA interference disrupted MSC chondrogenesis, concomitant with reduced cartilage-specific gene expression and incomplete matrix component production, indicating an important role in chondrocyte biology. Specifically, SOX9 induction was significantly ablated in the absence of ROCR, and overexpression of SOX9 rescued the differentiation of MSCs into chondrocytes. Our work sheds further light on chondrocyte-specific SOX9 expression and highlights a novel method of chondrocyte gene regulation involving a lncRNA. Summary: This study identified a chondrocyte repertoire of lncRNAs and discovered that ROCR (regulator of chondrogenesis RNA) is important for MSC chondrogenesis and cartilage gene expression by promoting the expression of SOX9.
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Affiliation(s)
- Matt J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Rodolfo Gomez
- Musculoskeletal Pathology Group, Institute IDIS, Travesia choupana s/n, Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706, Spain
| | - Sam Hyatt
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Kat Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Andrew J Skelton
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Yaobo Xu
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Ian M Clark
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
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26
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Baetens D, Mendonça BB, Verdin H, Cools M, De Baere E. Non-coding variation in disorders of sex development. Clin Genet 2017; 91:163-172. [PMID: 27801941 DOI: 10.1111/cge.12911] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/26/2023]
Abstract
Genetic studies in Disorders of Sex Development (DSD), representing a wide spectrum of developmental or functional conditions of the gonad, have mainly been oriented towards the coding genome. Application of genomic technologies, such as whole-exome sequencing, result in a molecular genetic diagnosis in ∼50% of cases with DSD. Many of the genes mutated in DSD encode transcription factors such as SRY, SOX9, NR5A1, and FOXL2, characterized by a strictly regulated spatiotemporal expression. Hence, it can be hypothesized that at least part of the missing genetic variation in DSD can be explained by non-coding mutations in regulatory elements that alter gene expression, either by reduced, mis- or overexpression of their target genes. In addition, structural variations such as translocations, deletions, duplications or inversions can affect the normal chromatin conformation by different mechanisms. Here, we review non-coding defects in human DSD phenotypes and in animal models. The wide variety of non-coding defects found in DSD emphasizes that the regulatory landscape of known and to be discovered DSD genes has to be taken into consideration when investigating the molecular pathogenesis of DSD.
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Affiliation(s)
- D Baetens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - B B Mendonça
- Laboratório de Hormônios e Genética Molecular, LIM/42, Unidade de Adrenal, Disc. de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - H Verdin
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - M Cools
- Department of Pediatrics, Division of Pediatric Endocrinology, Ghent University Hospital and Ghent University, Ghent, Belgium
| | - E De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
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27
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Sreenivasan R, Gordon CT, Benko S, de Iongh R, Bagheri-Fam S, Lyonnet S, Harley V. Altered SOX9 genital tubercle enhancer region in hypospadias. J Steroid Biochem Mol Biol 2017; 170:28-38. [PMID: 27989796 DOI: 10.1016/j.jsbmb.2016.10.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/17/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022]
Abstract
Human mutations in the SOX9 gene or its regulatory region can disrupt testicular development, leading to disorders of sex development (DSDs). Our previous work involving the genomic analysis of isolated DSD patients revealed a 78kb minimal sex determining region (RevSex) far upstream of SOX9 that was duplicated in 46,XX and deleted in 46,XY DSDs. It was postulated that RevSex contains a gonadal enhancer. However, the most highly conserved sub-region within RevSex, called SR4, was neither responsive to sex determining factors in vitro nor active in the gonads of transgenic mice, suggesting that SR4 may not be functioning as a testicular enhancer. Interestingly, SR4 transgenic mice showed reporter activity in the genital tubercle, the primordium of the penis and clitoris, a previously unreported domain of Sox9 expression. SOX9 protein was detected in the genital tubercle, notably in the urethral plate epithelium, preputial glands, ventral surface ectoderm and corpus cavernosa. SR4 may therefore function as a Sox9 genital tubercle enhancer, mutations of which could possibly lead to hypospadias, a birth defect seen in the DSD patients in the RevSex study. SR4 activity and the observed SOX9 expression pattern suggest that SR4 may function as a Sox9 genital tubercle enhancer. However, conditional ablation of Sox9 in the genital tubercle using Shh-Cre/+;Sox9flox/flox mice revealed no genital tubercle abnormalities, possibly due to compensation by similar Sox factors. To conclude, we have identified a novel regulatory enhancer driving Sox9 expression during external genitalia development.
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Affiliation(s)
- Rajini Sreenivasan
- Molecular Genetics and Development, Hudson Institute of Medical Research, Melbourne, Victoria, Australia; Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, Australia; Monash University, Melbourne, Victoria, Australia
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Sabina Benko
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Robb de Iongh
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, Australia
| | - Stefan Bagheri-Fam
- Molecular Genetics and Development, Hudson Institute of Medical Research, Melbourne, Victoria, Australia; Monash University, Melbourne, Victoria, Australia
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Vincent Harley
- Molecular Genetics and Development, Hudson Institute of Medical Research, Melbourne, Victoria, Australia; Monash University, Melbourne, Victoria, Australia.
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Hall MD, Murray CA, Valdez MJ, Perantoni AO. Mesoderm-specific Stat3 deletion affects expression of Sox9 yielding Sox9-dependent phenotypes. PLoS Genet 2017; 13:e1006610. [PMID: 28166224 PMCID: PMC5319801 DOI: 10.1371/journal.pgen.1006610] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 02/21/2017] [Accepted: 01/30/2017] [Indexed: 01/14/2023] Open
Abstract
To date, mutations within the coding region and translocations around the SOX9 gene both constitute the majority of genetic lesions underpinning human campomelic dysplasia (CD). While pathological coding-region mutations typically result in a non-functional SOX9 protein, little is known about what mechanism(s) controls normal SOX9 expression, and subsequently, which signaling pathways may be interrupted by alterations occurring around the SOX9 gene. Here, we report the identification of Stat3 as a key modulator of Sox9 expression in nascent cartilage and developing chondrocytes. Stat3 expression is predominant in tissues of mesodermal origin, and its conditional ablation using mesoderm-specific TCre, in vivo, causes dwarfism and skeletal defects characteristic of CD. Specifically, Stat3 loss results in the expansion of growth plate hypertrophic chondrocytes and deregulation of normal endochondral ossification in all bones examined. Conditional deletion of Stat3 with a Sox9Cre driver produces palate and tracheal irregularities similar to those described in Sox9+/- mice. Furthermore, mesodermal deletion of Stat3 causes global embryonic down regulation of Sox9 expression and function in vivo. Mechanistic experiments ex vivo suggest Stat3 can directly activate the expression of Sox9 by binding to its proximal promoter following activation. These findings illuminate a novel role for Stat3 in chondrocytes during skeletal development through modulation of a critical factor, Sox9. Importantly, they further provide the first evidence for the modulation of a gene product other than Sox9 itself which is capable of modeling pathological aspects of CD and underscore a potentially valuable therapeutic target for patients with the disorder. Campomelic (Greek: “bent limb”) dysplasia is an often-lethal, autosomal-dominant genetic disorder. Typical clinical features include angular long bones, hypoplastic scapulae, cleft palate, clubbed feet, labored breathing and ambiguous external genitalia. To date, the only gene implicated in this disease is SOX9, a critical factor in chondrocyte development. Deleterious mutations within the coding region of SOX9 account for a majority of cases; however, chromosomal breakages or translocations mark a subset of cases, presumably by altering expression of SOX9. We have found that Stat3 loss-of-function mutant mice exhibit features consistent with campomelic dysplasia including dwarfism, bent limbs, cleft palate, laryngotracheomalacia and abnormal growth plate hypertrophic chondrocytes. Importantly, we also demonstrate that ablation of Stat3 from chondroprogenitors reduces the functional level of Sox9 in vivo. Finally, we show that Stat3 may directly regulate Sox9 expression by physically interacting with the promoter in response to stimulation. Taken in total, our findings demonstrate that non-coding region mutations in SOX9, which modulate the accessibility or functionality of Stat-binding elements, may result in decreased physiological levels of SOX9. Our model suggests for the first time, the modulation of a gene other than Sox9 that is capable of recapitulating a large subset of pathologies associated with campomelic dysplasia, which may be exploited for future therapeutic intervention.
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Affiliation(s)
- Michael D. Hall
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Caroline A. Murray
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Michael J. Valdez
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Alan O. Perantoni
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
- * E-mail:
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29
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Smyk M, Akdemir KC, Stankiewicz P. SOX9 chromatin folding domains correlate with its real and putative distant cis-regulatory elements. Nucleus 2017; 8:182-187. [PMID: 28085555 DOI: 10.1080/19491034.2017.1279776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Evolutionary conserved transcription factor SOX9, encoded by the dosage sensitive SOX9 gene on chromosome 17q24.3, plays an important role in development of multiple organs, including bones and testes. Heterozygous point mutations and genomic copy-number variant (CNV) deletions involving SOX9 have been reported in patients with campomelic dysplasia (CD), a skeletal malformation syndrome often associated with male-to-female sex reversal. Balanced and unbalanced structural genomic variants with breakpoints mapping up to 1.3 Mb up- and downstream to SOX9 have been described in patients with milder phenotypes, including acampomelic campomelic dysplasia, sex reversal, and Pierre Robin sequence. Based on the localization of breakpoints of genomic rearrangements causing different phenotypes, 5 genomic intervals mapping upstream to SOX9 have been defined. We have analyzed the publically available database of high-throughput chromosome conformation capture (Hi-C) in multiple cell lines in the genomic regions flanking SOX9. Consistent with the literature data, chromatin domain boundaries in the SOX9 locus exhibit conservation across species and remain largely constant across multiple cell types. Interestingly, we have found that chromatin folding domains in the SOX9 locus associate with the genomic intervals harboring real and putative regulatory elements of SOX9, implicating that variation in intra-domain interactions may be critical for dynamic regulation of SOX9 expression in a cell type-specific fashion. We propose that tissue-specific enhancers for other transcription factor genes may similarly utilize chromatin folding sub-domains in gene regulation.
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Affiliation(s)
- Marta Smyk
- a Department of Medical Genetics , Institute of Mother and Child , Warsaw , Poland
| | - Kadir Caner Akdemir
- b Genomic Medicine Department , MD Anderson Cancer Center , Houston , TX , USA
| | - Paweł Stankiewicz
- c Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
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30
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Bashamboo A, McElreavey K. Mechanism of Sex Determination in Humans: Insights from Disorders of Sex Development. Sex Dev 2016; 10:313-325. [DOI: 10.1159/000452637] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2016] [Indexed: 12/13/2022] Open
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31
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Kaissi AA, van Egmond-Fröhlich A, Ryabykh S, Ochirov P, Kenis V, Hofstaetter JG, Grill F, Ganger R, Kircher SG. Spine malformation complex in 3 diverse syndromic entities: Case reports. Medicine (Baltimore) 2016; 95:e5505. [PMID: 27977582 PMCID: PMC5268028 DOI: 10.1097/md.0000000000005505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE Clinical and radiographic phenotypic characterizations were the base line tool of diagnosis in 3 syndromic disorders in which congenital cervico-thoracic kyphosis was the major deformity. PATIENTS CONCERNS Directing maximal care toward the radiographic analysis is not only the axial malformation but also toward the appendicular abnormalities was our main concern. We fully documented the diversity of the spine phenotypic malformation complex via the clinical and radiographic phenotypes. DIAGNOSES We established the diagnosis via phenotypic/genotypic confirmation in 3 diverse syndromic entities namely acampomelic campomelic dysplasia, Larsen syndrome and Morquio syndrome type A (mucopolysaccharidosis type IV A). INTERVENTIONS Surgical interventions have been carried out in the Larsen syndrome and Morquio syndrome type A, resepectively. OUTCOMES The earliest the diagnosis is, the better the results are. The necessity to diagnose children in their first year of life has many folds, firstly the management would be in favor of the child's growth and development and secondly, the prognosis could be clearer to the family and the medical staff as well. Our current paper is to sensitize paediatricians, physicians and orthopedic surgeons regarding the necessity to detect the aetiological understanding in every child who manifests a constellation of malformation complex. LESONS Scoliosis and kyphosis/kyphoscoliosis are not a diagnosis in themselves. Such deformities are mostly a symptom complex correlated to dozens of types of syndromic associations. The rate curve progression and the final severity of congenital spine tilting are related to 3 factors: (a) the type of vertebral malformation present, (b) the patient's phenotype, and
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Affiliation(s)
- Ali Al Kaissi
- Ludwig Boltzmann Institute of Osteology, the Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling, First Medical Department, Hanusch Hospital
- Orthopaedic Hospital of Speising, Paediatric Department
| | | | - Sergey Ryabykh
- Axial Skeleton and Neurosurgery Department, Restorative Traumatology and Orthopaedics, Ilizarov Center, Kurgan, Russia
| | - Polina Ochirov
- Axial Skeleton and Neurosurgery Department, Restorative Traumatology and Orthopaedics, Ilizarov Center, Kurgan, Russia
| | - Vladimir Kenis
- Pediatric Orthopedic Institute n.a. H. Turner, Department of Foot and Ankle Surgery, Neuroorthopaedics and Systemic Disorders, Saint-Petersburg, Russia
| | - Jochen G. Hofstaetter
- Ludwig Boltzmann Institute of Osteology, the Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling, First Medical Department, Hanusch Hospital
| | - Franz Grill
- Ludwig Boltzmann Institute of Osteology, the Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling, First Medical Department, Hanusch Hospital
| | - Rudolf Ganger
- Ludwig Boltzmann Institute of Osteology, the Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling, First Medical Department, Hanusch Hospital
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32
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Ali S, Amina B, Anwar S, Minhas R, Parveen N, Nawaz U, Azam SS, Abbasi AA. Genomic features of human limb specific enhancers. Genomics 2016; 108:143-150. [PMID: 27580967 DOI: 10.1016/j.ygeno.2016.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/08/2016] [Accepted: 08/27/2016] [Indexed: 12/18/2022]
Abstract
To elucidate important cellular and molecular interactions that regulate patterning and skeletal development, vertebrate limbs served as a model organ. A growing body of evidence from detailed studies on a subset of limb regulators like the HOXD cluster or SHH, reveals the importance of enhancers in limb related developmental and disease processes. Exploiting the recent genome-wide availability of functionally confirmed enhancer dataset, this study establishes regulatory interactions for dozens of human limb developmental genes. From these data, it appears that the long-range regulatory interactions are fairly common during limb development. This observation highlights the significance of chromosomal breaks/translocations in human limb deformities. Transcriptional factor (TF) analysis predicts that the differentiation of early nascent limb-bud into future territories entail distinct TF interaction networks. Conclusively, an important motivation for annotating the human limb specific regulatory networks is to pave way for the systematic exploration of their role in disease and evolution.
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Affiliation(s)
- Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Bibi Amina
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Saneela Anwar
- National Center for Bioinformatics, Computational Biology Lab, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Rashid Minhas
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Nazia Parveen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Uzma Nawaz
- Department of Statistics, The Women University, Multan 60000, Pakistan.
| | - Syed Sikandar Azam
- National Center for Bioinformatics, Computational Biology Lab, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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Castori M, Bottillo I, Morlino S, Barone C, Cascone P, Grammatico P, Laino L. Variability in a three-generation family with Pierre Robin sequence, acampomelic campomelic dysplasia, and intellectual disability due to a novel ∼1 Mb deletion upstream of SOX9, and including KCNJ2 and KCNJ16. ACTA ACUST UNITED AC 2015; 106:61-8. [PMID: 26663529 DOI: 10.1002/bdra.23463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Campomelic dysplasia and acampomelic campomelic dysplasia (ACD) are allelic disorders due to heterozygous mutations in or around SOX9. Translocations and deletions involving the SOX9 5' regulatory region are rare causes of these disorders, as well as Pierre Robin sequence (PRS) and 46,XY gonadal dysgenesis. Genotype-phenotype correlations are not straightforward due to the complex epigenetic regulation of SOX9 expression during development. METHODS We report a three-generation pedigree with a novel ∼1 Mb deletion upstream of SOX9 and including KCNJ2 and KCNJ16, and ascertained for dominant transmission of PRS. RESULTS Further characterization of the family identified subtle appendicular anomalies and a variable constellation of axial skeletal features evocative of ACD in several members. Affected males showed learning disability. CONCLUSION The identified deletion was smaller than all other chromosome rearrangements associated with ACD. Comparison with other reported translocations and deletions involving this region allowed further refining of genotype-phenotype correlations and an update of the smallest regions of overlap associated with the different phenotypes. Intrafamilial variability in this pedigree suggests a phenotypic continuity between ACD and PRS in patients carrying mutations in the SOX9 5' regulatory region.
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Affiliation(s)
- Marco Castori
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Irene Bottillo
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Silvia Morlino
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Chiara Barone
- Center for Genetic Counseling and Reproductive Teratology, Maternal and Child Health Department, Garibaldi Nesima Hospital, Catania, Italy
| | - Piero Cascone
- Division of Maxillo-Facial Surgery, Sapienza University, Policlinico Umberto I Hospital, Rome, Italy
| | | | - Paola Grammatico
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Luigi Laino
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
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Bashamboo A, McElreavey K. Human sex-determination and disorders of sex-development (DSD). Semin Cell Dev Biol 2015; 45:77-83. [DOI: 10.1016/j.semcdb.2015.10.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/19/2015] [Accepted: 10/19/2015] [Indexed: 11/28/2022]
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Smyk M, Roeder E, Cheung SW, Szafranski P, Stankiewicz P. A de novo 1.58 Mb deletion, including MAP2K6 and mapping 1.28 Mb upstream to SOX9, identified in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Am J Med Genet A 2015; 167A:1842-50. [PMID: 26059046 DOI: 10.1002/ajmg.a.37057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/23/2015] [Indexed: 12/18/2022]
Abstract
Defects of long-range regulatory elements of dosage-sensitive genes represent an under-recognized mechanism underlying genetic diseases. Haploinsufficiency of SOX9, the gene essential for development of testes and differentiation of chondrocytes, results in campomelic dysplasia, a skeletal malformation syndrome often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.6 Mb up- and downstream to SOX9, and disrupting its distant cis-regulatory elements, have been described in patients with milder forms of campomelic dysplasia, Pierre Robin sequence, and sex reversal. We present an ∼1.58 Mb deletion mapping ∼1.28 Mb upstream to SOX9 that encompasses its putative long-range cis-regulatory element(s) and MAP2K6 in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Low bone mass panel testing using massively parallel sequencing of 23 nuclear genes, including COL1A1 and COL1A2 was negative. Based on the previous mouse model of Map2k6, suggesting that Sox9 is likely a downstream target of the p38 MAPK pathway, and our previous chromosome conformation capture-on-chip (4C) data showing potential interactions between SOX9 promoter and MAP2K6, we hypothesize that deletion of MAP2K6 might have affected SOX9 expression and contributed to our patient's phenotype.
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Affiliation(s)
- Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Elizabeth Roeder
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Yao B, Wang Q, Liu CF, Bhattaram P, Li W, Mead TJ, Crish JF, Lefebvre V. The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers. Nucleic Acids Res 2015; 43:5394-408. [PMID: 25940622 PMCID: PMC4477657 DOI: 10.1093/nar/gkv426] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 04/17/2015] [Indexed: 01/18/2023] Open
Abstract
Two decades after the discovery that heterozygous mutations within and around SOX9 cause campomelic dysplasia, a generalized skeleton malformation syndrome, it is well established that SOX9 is a master transcription factor in chondrocytes. In contrast, the mechanisms whereby translocations in the –350/–50-kb region 5′ of SOX9 cause severe disease and whereby SOX9 expression is specified in chondrocytes remain scarcely known. We here screen this upstream region and uncover multiple enhancers that activate Sox9-promoter transgenes in the SOX9 expression domain. Three of them are primarily active in chondrocytes. E250 (located at –250 kb) confines its activity to condensed prechondrocytes, E195 mainly targets proliferating chondrocytes, and E84 is potent in all differentiated chondrocytes. E84 and E195 synergize with E70, previously shown to be active in most Sox9-expressing somatic tissues, including cartilage. While SOX9 protein powerfully activates E70, it does not control E250. It requires its SOX5/SOX6 chondrogenic partners to robustly activate E195 and additional factors to activate E84. Altogether, these results indicate that SOX9 expression in chondrocytes relies on widely spread transcriptional modules whose synergistic and overlapping activities are driven by SOX9, SOX5/SOX6 and other factors. They help elucidate mechanisms underlying campomelic dysplasia and will likely help uncover other disease mechanisms.
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Affiliation(s)
- Baojin Yao
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Qiuqing Wang
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Chia-Feng Liu
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Pallavi Bhattaram
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Wei Li
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Timothy J Mead
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - James F Crish
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Véronique Lefebvre
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
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Gordon CT, Attanasio C, Bhatia S, Benko S, Ansari M, Tan TY, Munnich A, Pennacchio LA, Abadie V, Temple IK, Goldenberg A, van Heyningen V, Amiel J, FitzPatrick D, Kleinjan DA, Visel A, Lyonnet S. Identification of novel craniofacial regulatory domains located far upstream of SOX9 and disrupted in Pierre Robin sequence. Hum Mutat 2015; 35:1011-20. [PMID: 24934569 DOI: 10.1002/humu.22606] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/12/2014] [Indexed: 01/08/2023]
Abstract
Mutations in the coding sequence of SOX9 cause campomelic dysplasia (CD), a disorder of skeletal development associated with 46,XY disorders of sex development (DSDs). Translocations, deletions, and duplications within a ∼2 Mb region upstream of SOX9 can recapitulate the CD-DSD phenotype fully or partially, suggesting the existence of an unusually large cis-regulatory control region. Pierre Robin sequence (PRS) is a craniofacial disorder that is frequently an endophenotype of CD and a locus for isolated PRS at ∼1.2-1.5 Mb upstream of SOX9 has been previously reported. The craniofacial regulatory potential within this locus, and within the greater genomic domain surrounding SOX9, remains poorly defined. We report two novel deletions upstream of SOX9 in families with PRS, allowing refinement of the regions harboring candidate craniofacial regulatory elements. In parallel, ChIP-Seq for p300 binding sites in mouse craniofacial tissue led to the identification of several novel craniofacial enhancers at the SOX9 locus, which were validated in transgenic reporter mice and zebrafish. Notably, some of the functionally validated elements fall within the PRS deletions. These studies suggest that multiple noncoding elements contribute to the craniofacial regulation of SOX9 expression, and that their disruption results in PRS.
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Affiliation(s)
- Christopher T Gordon
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, INSERM U1163, Paris, France
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38
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Kim GJ, Sock E, Buchberger A, Just W, Denzer F, Hoepffner W, German J, Cole T, Mann J, Seguin JH, Zipf W, Costigan C, Schmiady H, Rostásy M, Kramer M, Kaltenbach S, Rösler B, Georg I, Troppmann E, Teichmann AC, Salfelder A, Widholz SA, Wieacker P, Hiort O, Camerino G, Radi O, Wegner M, Arnold HH, Scherer G. Copy number variation of two separate regulatory regions upstream ofSOX9causes isolated 46,XY or 46,XX disorder of sex development. J Med Genet 2015; 52:240-7. [DOI: 10.1136/jmedgenet-2014-102864] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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39
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Atypical breakpoint in a t(6;17) translocation case of acampomelic campomelic dysplasia. Eur J Med Genet 2014; 57:315-8. [DOI: 10.1016/j.ejmg.2014.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/28/2014] [Indexed: 12/29/2022]
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40
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Esplin ED, Li B, Slavotinek A, Novelli A, Battaglia A, Clark R, Curry C, Hudgins L. Nine patients with Xp22.31 microduplication, cognitive deficits, seizures, and talipes anomalies. Am J Med Genet A 2014; 164A:2097-103. [DOI: 10.1002/ajmg.a.36598] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 04/13/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Edward D. Esplin
- Division of Medical Genetics, Department of Pediatrics; Stanford University School of Medicine; Stanford California
| | - Ben Li
- Division of Medical Genetics, Department of Pediatrics; University of California San Francisco; San Francisco California
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics; University of California San Francisco; San Francisco California
| | - Antonio Novelli
- Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza Hospital; San Giovanni Rotondo (FG) Italy
| | - Agatino Battaglia
- The Stella Maris Clinical Research Institute for Child and Adolescent Neurology and Psychiatry; Calambrone (Pisa) Italy
| | - Robin Clark
- Division of Medical Genetics, Department of Pediatrics; Loma Linda University; Loma Linda California
| | - Cynthia Curry
- Division of Medical Genetics, Department of Pediatrics; UCSF Fresno; Fresno California
| | - Louanne Hudgins
- Division of Medical Genetics, Department of Pediatrics; Stanford University School of Medicine; Stanford California
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41
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Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
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Gopakumar H, Superti-Furga A, Unger S, Scherer G, Rajiv PK, Nampoothiri S. Acampomelic form of campomelic dysplasia with SOX9 missense mutation. Indian J Pediatr 2014; 81:98-100. [PMID: 23564514 DOI: 10.1007/s12098-013-1007-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 03/07/2013] [Indexed: 11/27/2022]
Abstract
Campomelic dysplasia is a skeletal dysplasia characterized by flat face, Pierre Robin sequence, shortening and bowing of long bones and club feet. The authors describe a case of "acampomelic" campomelic dysplasia that differs from classical campomelic dysplasia by the absence of bone bowing. This condition is among the most common skeletal dysplasias but is often misdiagnosed in the absence of overt campomelia.
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Affiliation(s)
- Hariharan Gopakumar
- Department of Pediatrics and Neonatology, Amrita Institute of Medical Sciences and Researh Centre, Cochin, Kerala, India
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43
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Smyk M, Szafranski P, Startek M, Gambin A, Stankiewicz P. Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter. Chromosome Res 2013; 21:781-8. [PMID: 24254229 DOI: 10.1007/s10577-013-9386-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/04/2013] [Accepted: 10/08/2013] [Indexed: 12/27/2022]
Abstract
Evolutionarily conserved transcription factor SOX9 is essential for the differentiation of chondrocytes and the development of testes. Heterozygous point mutations and genomic deletions involving SOX9 lead to campomelic dysplasia (CD), a skeletal malformation syndrome often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.6 Mb up- and downstream to SOX9, and likely disrupting its distant cis-regulatory elements, have been described in patients with milder forms of CD. Based on the location of these aberration breakpoints, four clusters upstream of SOX9 have been defined. Interestingly, we found that each of these intervals overlaps a gene encoding long noncoding RNA (lncRNA), suggesting that lncRNAs may contribute to long-range regulation of SOX9 expression. One of the four upstream regions, RevSex (517-595 kb 5' to SOX9), is associated with sex reversal, and was suggested to harbor a testis-specific and sex-determining enhancer. Another sex-determining interval was mapped to a gene desert >1.3 Mb downstream of SOX9. We have performed chromosome conformation capture-on-chip (4C) analysis in Sertoli cells and lymphoblasts to verify the proposed long-range interactions of the SOX9 promoter and to identify potential novel regulatory elements that might be responsible for sex reversal in patients with CD. We identified several novel potentially cis-interacting regions both up- and downstream to SOX9, with some of them overlapping lncRNA genes. Our data point to lncRNAs as likely mediators of some of these regulatory interactions.
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Affiliation(s)
- Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
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44
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Sanchez-Castro M, Gordon CT, Petit F, Nord AS, Callier P, Andrieux J, Guérin P, Pichon O, David A, Abadie V, Bonnet D, Visel A, Pennacchio LA, Amiel J, Lyonnet S, Le Caignec C. Congenital heart defects in patients with deletions upstream of SOX9. Hum Mutat 2013; 34:1628-31. [PMID: 24115316 DOI: 10.1002/humu.22449] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 09/12/2013] [Indexed: 11/12/2022]
Abstract
Heterozygous loss-of-function coding-sequence mutations of the transcription factor SOX9 cause campomelic dysplasia, a rare skeletal dysplasia with congenital bowing of long bones (campomelia), hypoplastic scapulae, a missing pair of ribs, pelvic, and vertebral malformations, clubbed feet, Pierre Robin sequence (PRS), facial dysmorphia, and disorders of sex development. We report here two unrelated families that include patients with isolated PRS, isolated congenital heart defect (CHD), or both anomalies. Patients from both families carried a very similar ∼1 Mb deletion upstream of SOX9. Analysis of ChIP-Seq from mouse cardiac tissue for H3K27ac, a marker of active regulatory elements, led us to identify several putative cardiac enhancers within the deleted region. One of these elements is known to interact with Nkx2.5 and Gata4, two transcription factors responsible for CHDs. Altogether, these data suggest that disruption of cardiac enhancers located upstream of SOX9 may be responsible for CHDs in humans.
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Affiliation(s)
- Marta Sanchez-Castro
- INSERM, UMR1087, l'institut du thorax, Nantes, France; Université de Nantes, Nantes, France
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Tan TY, Kilpatrick N, Farlie PG. Developmental and genetic perspectives on Pierre Robin sequence. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:295-305. [PMID: 24127256 DOI: 10.1002/ajmg.c.31374] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Pierre Robin sequence (PRS) is a craniofacial anomaly comprising mandibular hypoplasia, cleft secondary palate and glossoptosis leading to life-threatening obstructive apnea and feeding difficulties during the neonatal period. The respiratory issues require careful management and in severe cases may require extended stays in neonatal intensive care units and surgical intervention such as lengthening the lower jaw or tracheotomy to relieve airway obstruction. These feeding and respiratory complications frequently continue well into childhood, affecting not only growth and development but also impacting on long term educational attainment. The diagnosis of PRS depends on readily recognizable clinical features but the phenotypic similarity of many PRS individuals conceals considerable etiological heterogeneity. Defects in the growth of the mandible sit at the core of PRS and the natural history of PRS can be classified into two major streams: primary defects of mandibular outgrowth and elongation and issues that are external to the mandibular skeleton but that secondarily impact on its growth. These altered developmental trajectories appear to be driven by a range of influences including defects in cartilage growth, neuromuscular function and fetal constraint. Various genetic and cytogenetic associations have been made with PRS and the diversity of these associations highlights the fact that there are numerous ways to arrive at this common phenotypic endpoint.
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46
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Fonseca ACS, Bonaldi A, Bertola DR, Kim CA, Otto PA, Vianna-Morgante AM. The clinical impact of chromosomal rearrangements with breakpoints upstream of the SOX9 gene: two novel de novo balanced translocations associated with acampomelic campomelic dysplasia. BMC MEDICAL GENETICS 2013; 14:50. [PMID: 23648064 PMCID: PMC3658899 DOI: 10.1186/1471-2350-14-50] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 04/23/2013] [Indexed: 12/31/2022]
Abstract
BACKGROUND The association of balanced rearrangements with breakpoints near SOX9 [SRY (sex determining region Y)-box 9] with skeletal abnormalities has been ascribed to the presumptive altering of SOX9 expression by the direct disruption of regulatory elements, their separation from SOX9 or the effect of juxtaposed sequences. CASE PRESENTATION We report on two sporadic apparently balanced translocations, t(7;17)(p13;q24) and t(17;20)(q24.3;q11.2), whose carriers have skeletal abnormalities that led to the diagnosis of acampomelic campomelic dysplasia (ACD; MIM 114290). No pathogenic chromosomal imbalances were detected by a-CGH. The chromosome 17 breakpoints were mapped, respectively, 917-855 kb and 601-585 kb upstream of the SOX9 gene. A distal cluster of balanced rearrangements breakpoints on chromosome 17 associated with SOX9-related skeletal disorders has been mapped to a segment 932-789 kb upstream of SOX9. In this cluster, the breakpoint of the herein described t(17;20) is the most telomeric to SOX9, thus allowing the redefining of the telomeric boundary of the distal breakpoint cluster region related to skeletal disorders to 601-585 kb upstream of SOX9. Although both patients have skeletal abnormalities, the t(7;17) carrier presents with relatively mild clinical features, whereas the t(17;20) was detected in a boy with severe broncheomalacia, depending on mechanical ventilation. Balanced and unbalanced rearrangements associated with disorders of sex determination led to the mapping of a regulatory region of SOX9 function on testicular differentiation to a 517-595 kb interval upstream of SOX9, in addition to TESCO (Testis-specific enhancer of SOX9 core). As the carrier of t(17;20) has an XY sex-chromosome constitution and normal male development for his age, the segment of chromosome 17 distal to the translocation breakpoint should contain the regulatory elements for normal testis development. CONCLUSIONS These two novel translocations illustrate the clinical variability in carriers of balanced translocations with breakpoints near SOX9. The translocation t(17;20) breakpoint provides further evidence for an additional testis-specific SOX9 enhancer 517 to 595 kb upstream of the SOX9 gene.
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Affiliation(s)
- Ana Carolina S Fonseca
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, Brazil
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Position effect on FGF13 associated with X-linked congenital generalized hypertrichosis. Proc Natl Acad Sci U S A 2013; 110:7790-5. [PMID: 23603273 DOI: 10.1073/pnas.1216412110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
X-linked congenital generalized hypertrichosis (Online Mendelian Inheritance in Man 307150) is an extremely rare condition of hair overgrowth on different body sites. We previously reported linkage in a large Mexican family with X-linked congenital generalized hypertrichosis cosegregating with deafness and with dental and palate anomalies to Xq24-27. Using SNP oligonucleotide microarray analysis and whole-genome sequencing, we identified a 389-kb interchromosomal insertion at an extragenic palindrome site at Xq27.1 that completely cosegregates with the disease. Among the genes surrounding the insertion, we found that Fibroblast Growth Factor 13 (FGF13) mRNA levels were significantly reduced in affected individuals, and immunofluorescence staining revealed a striking decrease in FGF13 localization throughout the outer root sheath of affected hair follicles. Taken together, our findings suggest a role for FGF13 in hair follicle growth and in the hair cycle.
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48
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Tonni G, Ventura A, Pattacini P, Bonasoni MP, Baffico AM. p.His165Pro: a novel SOX9 missense mutation of campomelic dysplasia. J Obstet Gynaecol Res 2013; 39:1085-91. [PMID: 23551858 DOI: 10.1111/jog.12032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 11/08/2012] [Indexed: 01/29/2023]
Abstract
Campomelic dysplasia (CD) is a rare skeletal dysplasia caused by mutation in the SOX9 gene located on chromosome 17q24.3-q25.1, which regulates testis and chondrocyte development. Severe bowing of the long bones was seen at second-trimester scan. DNA analysis demonstrated a previously unreported de novo missense mutation in p.His165Pro. Ultrasound-based, molecular biology diagnosis led to early therapeutic termination of pregnancy. Histologic examination of the femoral epyphyseal growth plate confirmed scanty proliferation zone and maturation zone with degenerated chondrocytes.
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Affiliation(s)
- Gabriele Tonni
- Obstetrics and Gynecology, Guastalla Civil Hospital, AUSL Reggio Emilia, Guastalla, Italy.
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49
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Amarillo IE, Dipple KM, Quintero-Rivera F. Familial microdeletion of 17q24.3 upstream of SOX9 is associated with isolated Pierre Robin sequence due to position effect. Am J Med Genet A 2013; 161A:1167-72. [PMID: 23532965 DOI: 10.1002/ajmg.a.35847] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/13/2012] [Indexed: 11/12/2022]
Abstract
Pierre Robin sequence (PRS) is a malformation pattern characterized by the core triad of retrognathia, glossoptosis, and cleft palate that causes difficulty in glossopharyngeal-laryngeal-vagal functions. The etiology of PRS remains largely unknown; previous reports have suggested that it is caused by intrauterine constriction or external conditions such as oligohydramnios, breech position, or abnormal uterine anatomy. Genetic causes include occurrence as a manifestation of many single gene conditions and chromosomal rearrangements. Positional effect on some loci or genes, including SOX9 has also been posited as a cause. Here, we report on an 18-month-old girl born with isolated PRS. Clinical chromosome microarray analysis (CMA) revealed a maternally inherited ~623 kb microdeletion that is -725 kb upstream of 5' SOX9 at chromosome locus 17q24.3. Her mother had cleft palate. This region, although devoid of any genes, is known to have a position effect on SOX9 due to elimination of highly conserved non-coding cis-regulatory elements. This report supports the evidence that deregulation of an intact SOX9 coding region is a cause of or associated with isolated PRS, and provides further evidence that CMA in the clinical setting is a powerful tool in detecting microdeletions in gene "desert" regions that have pathogenic position effect on specific genes.
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Affiliation(s)
- Ina E Amarillo
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90024, USA
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Parveen N, Masood A, Iftikhar N, Minhas BF, Minhas R, Nawaz U, Abbasi AA. Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. BMC Genomics 2013; 14:122. [PMID: 23432897 PMCID: PMC3599049 DOI: 10.1186/1471-2164-14-122] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/19/2013] [Indexed: 12/03/2022] Open
Abstract
Background Human genome is enriched with thousands of conserved non-coding elements (CNEs). Recently, a medium throughput strategy was employed to analyze the ability of human CNEs to drive tissue specific expression during mouse embryogenesis. These data led to the establishment of publicly available genome wide catalog of functionally defined human enhancers. Scattering of enhancers over larger regions in vertebrate genomes seriously impede attempts to pinpoint their precise target genes. Such associations are prerequisite to explore the significance of this in vivo characterized catalog of human enhancers in development, disease and evolution. Results This study is an attempt to systematically identify the target gene-bodies for functionally defined human CNE-enhancers. For the purpose we adopted the orthology/paralogy mapping approach and compared the CNE induced reporter expression with reported endogenous expression pattern of neighboring genes. This procedure pinpointed specific target gene-bodies for the total of 192 human CNE-enhancers. This enables us to gauge the maximum genomic search space for enhancer hunting: 4 Mb of genomic sequence around the gene of interest (2 Mb on either side). Furthermore, we used human-rodent comparison for a set of 159 orthologous enhancer pairs to infer that the central nervous system (CNS) specific gene expression is closely associated with the cooperative interaction among at least eight distinct transcription factors: SOX5, HFH, SOX17, HNF3β, c-FOS, Tal1beta-E47S, MEF and FREAC. Conclusions In conclusion, the systematic wiring of cis-acting sites and their target gene bodies is an important step to unravel the role of in vivo characterized catalog of human enhancers in development, physiology and medicine.
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Affiliation(s)
- Nazia Parveen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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