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Darbellay F, Ramisch A, Lopez-Delisle L, Kosicki M, Rauseo A, Jouini Z, Visel A, Andrey G. Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development. Nat Commun 2024; 15:4820. [PMID: 38844479 PMCID: PMC11156918 DOI: 10.1038/s41467-024-49203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Chondrocyte differentiation controls skeleton development and stature. Here we provide a comprehensive map of chondrocyte-specific enhancers and show that they provide a mechanistic framework through which non-coding genetic variants can influence skeletal development and human stature. Working with fetal chondrocytes isolated from mice bearing a Col2a1 fluorescent regulatory sensor, we identify 780 genes and 2'704 putative enhancers specifically active in chondrocytes using a combination of RNA-seq, ATAC-seq and H3K27ac ChIP-seq. Most of these enhancers (74%) show pan-chondrogenic activity, with smaller populations being restricted to limb (18%) or trunk (8%) chondrocytes only. Notably, genetic variations overlapping these enhancers better explain height differences than those overlapping non-chondrogenic enhancers. Finally, targeted deletions of identified enhancers at the Fgfr3, Col2a1, Hhip and, Nkx3-2 loci confirm their role in regulating cognate genes. This enhancer map provides a framework for understanding how genes and non-coding variations influence bone development and diseases.
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Affiliation(s)
- Fabrice Darbellay
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
| | - Anna Ramisch
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
| | - Antonella Rauseo
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland
| | - Zahra Jouini
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, CA, 95343, USA
| | - Guillaume Andrey
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland.
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland.
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Xiong J, Wang X, Fan C, Yan J, Zhu J, Cai T. Hemifacial microsomia is linked to a rare homozygous variant V162I in FRK and validated in zebrafish. Oral Dis 2023; 29:3472-3480. [PMID: 36070195 DOI: 10.1111/odi.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVES Hemifacial microsomia (HFM) is a common birth defect involving the first and second branchial arch derivatives. Although several chromosomal abnormalities and causal gene variants have been identified, genetic etiologies in a majority of cases with HFM remain unknown. This study aimed to identify genetic mutations in affected individuals with HFM. METHODS Whole-exome sequencing and bioinformatics analysis were performed for 16 affected individuals and their family members. Sanger sequencing was applied for confirmation of selected mutations. Zebrafish embryos were used for in situ hybridization of candidate gene, microinjection with antisense morpholino, and cartilage staining. RESULTS A homozygous missense mutation (c.484G > A; p.V162I) in the FRK gene was identified in an 18-year-old girl with HFM and dental abnormalities. Heterozygous mutation of this mutation was identified in her parents, who are first cousins in a consanguineous family. FRK is highly expressed in the Meckel's cartilage during embryonic development in mouse and zebrafish. Knockdown of frk in zebrafish showed a lower length and width ratio of Meckel's cartilage, abnormal mandibular jaw joint, and disorganized ceratobranchial cartilage and bone. CONCLUSIONS We identified a recessive variant in the FRK gene as a novel candidate gene for a patient with HFM and mandibular hypoplasia and revealed its effects on craniofacial and embryonic development in zebrafish.
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Affiliation(s)
- Jianjun Xiong
- Experimental Medicine Section, NIDCR, Bethesda, Maryland, USA
- College of Basic Medical Science, Jiujiang University, Jiujiang, China
- Beijing Angel Gene Medical Technology Co., Ltd., Beijing, China
| | - Xi Wang
- Department of Stomatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunxin Fan
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jizhou Yan
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jinwen Zhu
- Beijing Angel Gene Medical Technology Co., Ltd., Beijing, China
| | - Tao Cai
- Experimental Medicine Section, NIDCR, Bethesda, Maryland, USA
- Developmental Biology Section, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, Maryland, USA
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Leyhr J, Sanchez S, Dollman KN, Tafforeau P, Haitina T. Enhanced contrast synchrotron X-ray microtomography for describing skeleton-associated soft tissue defects in zebrafish mutants. Front Endocrinol (Lausanne) 2023; 14:1108916. [PMID: 36950679 PMCID: PMC10025580 DOI: 10.3389/fendo.2023.1108916] [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: 11/26/2022] [Accepted: 02/10/2023] [Indexed: 03/08/2023] Open
Abstract
Detailed histological analyses are desirable for zebrafish mutants that are models for human skeletal diseases, but traditional histological techniques are limited to two-dimensional thin sections with orientations highly dependent on careful sample preparation. On the other hand, techniques that provide three-dimensional (3D) datasets including µCT scanning are typically limited to visualizing the bony skeleton and lack histological resolution. We combined diffusible iodine-based contrast enhancement (DICE) and propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SRµCT) to image late larval and juvenile zebrafish, obtaining high-quality 3D virtual histology datasets of the mineralized skeleton and surrounding soft tissues. To demonstrate this technique, we used virtual histological thin sections and 3D segmentation to qualitatively and quantitatively compare wild-type zebrafish and nkx3.2 -/- mutants to characterize novel soft-tissue phenotypes in the muscles and tendons of the jaw and ligaments of the Weberian apparatus, as well as the sinus perilymphaticus associated with the inner ear. We could observe disrupted fiber organization and tendons of the adductor mandibulae and protractor hyoideus muscles associated with the jaws, and show that despite this, the overall muscle volumes appeared unaffected. Ligaments associated with the malformed Weberian ossicles were mostly absent in nkx3.2 -/- mutants, and the sinus perilymphaticus was severely constricted or absent as a result of the fused exoccipital and basioccipital elements. These soft-tissue phenotypes have implications for the physiology of nkx3.2 -/- zebrafish, and demonstrate the promise of DICE-PPC-SRµCT for histopathological investigations of bone-associated soft tissues in small-fish skeletal disease models and developmental studies more broadly.
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Affiliation(s)
- Jake Leyhr
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Sophie Sanchez
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- European Synchrotron Radiation Facility, Grenoble, France
| | | | - Paul Tafforeau
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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Chondrocyte Hypertrophy in Osteoarthritis: Mechanistic Studies and Models for the Identification of New Therapeutic Strategies. Cells 2022; 11:cells11244034. [PMID: 36552796 PMCID: PMC9777397 DOI: 10.3390/cells11244034] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/08/2022] [Indexed: 12/16/2022] Open
Abstract
Articular cartilage shows limited self-healing ability owing to its low cellularity and avascularity. Untreated cartilage defects display an increased propensity to degenerate, leading to osteoarthritis (OA). During OA progression, articular chondrocytes are subjected to significant alterations in gene expression and phenotype, including a shift towards a hypertrophic-like state (with the expression of collagen type X, matrix metalloproteinases-13, and alkaline phosphatase) analogous to what eventuates during endochondral ossification. Present OA management strategies focus, however, exclusively on cartilage inflammation and degradation. A better understanding of the hypertrophic chondrocyte phenotype in OA might give new insights into its pathogenesis, suggesting potential disease-modifying therapeutic approaches. Recent developments in the field of cellular/molecular biology and tissue engineering proceeded in the direction of contrasting the onset of this hypertrophic phenotype, but knowledge gaps in the cause-effect of these processes are still present. In this review we will highlight the possible advantages and drawbacks of using this approach as a therapeutic strategy while focusing on the experimental models necessary for a better understanding of the phenomenon. Specifically, we will discuss in brief the cellular signaling pathways associated with the onset of a hypertrophic phenotype in chondrocytes during the progression of OA and will analyze in depth the advantages and disadvantages of various models that have been used to mimic it. Afterwards, we will present the strategies developed and proposed to impede chondrocyte hypertrophy and cartilage matrix mineralization/calcification. Finally, we will examine the future perspectives of OA therapeutic strategies.
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Torticollis in Connection with Spine Phenotype. Diagnostics (Basel) 2022; 12:diagnostics12071672. [PMID: 35885576 PMCID: PMC9322745 DOI: 10.3390/diagnostics12071672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose: Torticollis is not of uncommon occurrence in orthopaedic departments. Various theories and studies concerning the pathogenesis of the deformity have been suggested. We aimed to highlight and discuss the underlying cervical and spine malformation complex in correlation with torticollis via radiographic and tomographic analysis and its connection with a specific syndromic entity. Methods: Torticollis has been recognised in six patients (2 boys and 4 girls with an age range of 14–18 years), in addition to a couple of parents manifested persistent backpain. A variable spine malformation complex was the main reason behind torticollis. In addition, some patients manifested plagiocephaly, facial asymmetry and scoliosis/kyphoscoliosis. In some patients, conventional radiographs were of limited value because of the overlapping anatomical structures. Three-dimensional reconstruction CT scanning was the modality of choice, which enlightens the path for the phenotypic characterisation. Results: A 16-year-old-boy presented with torticollis in correlation with pathologic aberration of the spine cartilaginous stage was analysed via 3DCT scan. Comprehensive clinical and radiological phenotypes were in favour of spondylomegepiphyseal dysplasia. The genotype showed a mutation of the NKX3-2 (BAPX1) gene compatible with the diagnosis of spondylo-meg-epiphyseal-metaphyseal dysplasia. His younger male sibling and parents were heterozygous carriers. In two patients with pseudoachondroplasia syndrome, in which odontoid hypoplasia associated with cervical spine synchondrosis causing life-threatening torticollis, Cartilage oligomeric matrix protein (COMP) gene mutation was identified. MURCS syndrome has been diagnosed in two unrelated girls. Torticollis associated with cervical kyphosis was the major presentation since early childhood. Interestingly, one girl showed omovertebral bones of the lower cervical and upper thoracic spine. Her karyotype manifested a balanced translocation of 46 XX, t (14q; 15q). Conclusion: To detect the underlying etiological diagnosis of torticollis, a skeletal survey was the primary diagnostic tool. Conventional radiographs of the craniocervical junction and spine resulted in confusing readings because of the overlapping anatomical structures. Cranio-cervical malformation complex could have serious neurological deficits, especially for children with indefinite diagnosis of torticollis. The widely used term of congenital muscular torticollis resulted in morbid or mortal consequences. Moreover, some patients received vigorous physical therapy on the bases of muscular torticollis. Sadly speaking, this resulted in grave complications. Understanding the imaging phenotype and the genotype in such patients is the baseline tool for precise and proper management. The value of this paper is to sensitise physicians and orthopaedic surgeons to the necessity of comprehensive clinical and radiological phenotypic characterisations in patients with long term skeletal pathology.
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He H, Li Z, Lu J, Qiang W, Jiang S, Xu Y, Fu W, Zhai X, Zhou L, Qian M, Du J. Single-cell RNA-seq reveals clonal diversity and prognostic genes of relapsed multiple myeloma. Clin Transl Med 2022; 12:e757. [PMID: 35297204 PMCID: PMC8926895 DOI: 10.1002/ctm2.757] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Multiple myeloma (MM) is a clinically and biologically heterogeneous plasma-cell malignancy. Despite extensive research, disease heterogeneity and relapse remain a big challenge in MM therapeutics. We tried to dissect this disease and identify novel biomarkers for patient stratification and treatment outcome prediction by applying single-cell technology. METHODS We performed single-cell RNA sequencing (scRNA-seq) and variable-diversity-joining regions-targeted sequencing (scVDJ-seq) concurrently on bone marrow samples from a cohort of 18 patients with newly diagnosed MM (NDMM; n = 12) or refractory/relapsed MM (RRMM; n = 6). We analysed the malignant clonotypes using scVDJ-seq data and conducted data integration and cell-type annotation through the CCA algorithm based on gene expression profiling. Furthermore, we identified disease status-specific genes and modules by comparison of NDMM and RRMM datasets and explored the findings in a larger MM cohort from the MMRF CoMMpass study. RESULTS We found that all the myeloma cells in either diagnosed or relapsed samples were dominated by a major clone, with a few subclones in several samples (n = 5). Next, we investigated the universal transcriptional features of myeloma cells and identified eight meta-programs correlated with this disease, especially meta-programs 1 and 8 (M1 and M8), which were the most significant and related to cell cycle and stress response, respectively. Furthermore, we classified the malignant plasma cells into eight clusters and found that the cell numbers in clusters 2/6/7 were exclusively higher in relapsed samples. Besides, we identified several attractive candidates for biomarkers (e.g. SMAD1 and STMN1) associated with disease progression and relapse in our dataset and related to overall survival in the CoMMpass dataset. CONCLUSIONS Our data provide insights into the heterogeneity of MM as well as highlight the relevance of intra-tumour heterogeneity and discover novel biomarkers that might be a potent therapy.
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Affiliation(s)
- Haiyan He
- Department of HematologyMyeloma & Lymphoma CenterChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Zifeng Li
- Institute of Pediatrics and Department of Hematology and OncologyChildren's Hospital of Fudan UniversityNational Children's Medical CenterShanghaiChina
| | - Jing Lu
- Department of HematologyMyeloma & Lymphoma CenterChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Wanting Qiang
- Department of HematologyMyeloma & Lymphoma CenterChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Sihan Jiang
- Department of HematologyMyeloma & Lymphoma CenterChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Yaochen Xu
- Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology)Institutes of Biomedical SciencesFudan UniversityShanghaiChina
| | - Weijun Fu
- Department of HematologyMyeloma & Lymphoma CenterChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Xiaowen Zhai
- Institute of Pediatrics and Department of Hematology and OncologyChildren's Hospital of Fudan UniversityNational Children's Medical CenterShanghaiChina
| | - Lin Zhou
- Department of Laboratory MedicineChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and OncologyChildren's Hospital of Fudan UniversityNational Children's Medical CenterShanghaiChina
| | - Juan Du
- Department of HematologyMyeloma & Lymphoma CenterChangzheng HospitalNaval Medical UniversityShanghaiChina
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Zug R. Developmental disorders caused by haploinsufficiency of transcriptional regulators: a perspective based on cell fate determination. Biol Open 2022; 11:bio058896. [PMID: 35089335 PMCID: PMC8801891 DOI: 10.1242/bio.058896] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many human birth defects and neurodevelopmental disorders are caused by loss-of-function mutations in a single copy of transcription factor (TF) and chromatin regulator genes. Although this dosage sensitivity has long been known, how and why haploinsufficiency (HI) of transcriptional regulators leads to developmental disorders (DDs) is unclear. Here I propose the hypothesis that such DDs result from defects in cell fate determination that are based on disrupted bistability in the underlying gene regulatory network (GRN). Bistability, a crucial systems biology concept to model binary choices such as cell fate decisions, requires both positive feedback and ultrasensitivity, the latter often achieved through TF cooperativity. The hypothesis explains why dosage sensitivity of transcriptional regulators is an inherent property of fate decisions, and why disruption of either positive feedback or cooperativity in the underlying GRN is sufficient to cause disease. I present empirical and theoretical evidence in support of this hypothesis and discuss several issues for which it increases our understanding of disease, such as incomplete penetrance. The proposed framework provides a mechanistic, systems-level explanation of HI of transcriptional regulators, thus unifying existing theories, and offers new insights into outstanding issues of human disease. This article has an associated Future Leader to Watch interview with the author of the paper.
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Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, 22362 Lund, Sweden
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Waldmann L, Leyhr J, Zhang H, Öhman-Mägi C, Allalou A, Haitina T. The broad role of Nkx3.2 in the development of the zebrafish axial skeleton. PLoS One 2021; 16:e0255953. [PMID: 34411150 PMCID: PMC8376051 DOI: 10.1371/journal.pone.0255953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
The transcription factor Nkx3.2 (Bapx1) is an important chondrocyte maturation inhibitor. Previous Nkx3.2 knockdown and overexpression studies in non-mammalian gnathostomes have focused on its role in primary jaw joint development, while the function of this gene in broader skeletal development is not fully described. We generated a mutant allele of nkx3.2 in zebrafish with CRISPR/Cas9 and applied a range of techniques to characterize skeletal phenotypes at developmental stages from larva to adult, revealing loss of the jaw joint, fusions in bones of the occiput, morphological changes in the Weberian apparatus, and the loss or deformation of bony elements derived from basiventral cartilages of the vertebrae. Axial phenotypes are reminiscent of Nkx3.2 knockout in mammals, suggesting that the function of this gene in axial skeletal development is ancestral to osteichthyans. Our results highlight the broad role of nkx3.2 in zebrafish skeletal development and its context-specific functions in different skeletal elements.
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Affiliation(s)
- Laura Waldmann
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Jake Leyhr
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Hanqing Zhang
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory BioImage Informatics Facility, Uppsala, Sweden
| | - Caroline Öhman-Mägi
- Department of Materials Science and Engineering, Uppsala University, Uppsala, Sweden
| | - Amin Allalou
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory BioImage Informatics Facility, Uppsala, Sweden
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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Smeeton J, Natarajan N, Naveen Kumar A, Miyashita T, Baddam P, Fabian P, Graf D, Crump JG. Zebrafish model for spondylo-megaepiphyseal-metaphyseal dysplasia reveals post-embryonic roles of Nkx3.2 in the skeleton. Development 2021; 148:dev193409. [PMID: 33462117 PMCID: PMC7860120 DOI: 10.1242/dev.193409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/31/2020] [Indexed: 01/10/2023]
Abstract
The regulated expansion of chondrocytes within growth plates and joints ensures proper skeletal development through adulthood. Mutations in the transcription factor NKX3.2 underlie spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD), which is characterized by skeletal defects including scoliosis, large epiphyses, wide growth plates and supernumerary distal limb joints. Whereas nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants display embryonic lethal jaw joint fusions and skeletal reductions, respectively, they lack the skeletal overgrowth seen in SMMD patients. Here, we report adult viable nkx3.2 mutant zebrafish displaying cartilage overgrowth in place of a missing jaw joint, as well as severe dysmorphologies of the facial skeleton, skullcap and spine. In contrast, cartilage overgrowth and scoliosis are absent in rare viable nkx3.2 knockdown animals that lack jaw joints, supporting post-embryonic roles for Nkx3.2. Single-cell RNA-sequencing and in vivo validation reveal increased proliferation and upregulation of stress-induced pathways, including prostaglandin synthases, in mutant chondrocytes. By generating a zebrafish model for the skeletal overgrowth defects of SMMD, we reveal post-embryonic roles for Nkx3.2 in dampening proliferation and buffering the stress response in joint-associated chondrocytes.
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Affiliation(s)
- Joanna Smeeton
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY 10032, USA
| | - Natasha Natarajan
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Arati Naveen Kumar
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tetsuto Miyashita
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Pranidhi Baddam
- Department of Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Peter Fabian
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Daniel Graf
- Department of Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2R7, Canada
| | - J. Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Accogli A, Geraldo AF, Piccolo G, Riva A, Scala M, Balagura G, Salpietro V, Madia F, Maghnie M, Zara F, Striano P, Tortora D, Severino M, Capra V. Diagnostic Approach to Macrocephaly in Children. Front Pediatr 2021; 9:794069. [PMID: 35096710 PMCID: PMC8795981 DOI: 10.3389/fped.2021.794069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/02/2021] [Indexed: 01/19/2023] Open
Abstract
Macrocephaly affects up to 5% of the pediatric population and is defined as an abnormally large head with an occipitofrontal circumference (OFC) >2 standard deviations (SD) above the mean for a given age and sex. Taking into account that about 2-3% of the healthy population has an OFC between 2 and 3 SD, macrocephaly is considered as "clinically relevant" when OFC is above 3 SD. This implies the urgent need for a diagnostic workflow to use in the clinical setting to dissect the several causes of increased OFC, from the benign form of familial macrocephaly and the Benign enlargement of subarachnoid spaces (BESS) to many pathological conditions, including genetic disorders. Moreover, macrocephaly should be differentiated by megalencephaly (MEG), which refers exclusively to brain overgrowth, exceeding twice the SD (3SD-"clinically relevant" megalencephaly). While macrocephaly can be isolated and benign or may be the first indication of an underlying congenital, genetic, or acquired disorder, megalencephaly is most likely due to a genetic cause. Apart from the head size evaluation, a detailed family and personal history, neuroimaging, and a careful clinical evaluation are crucial to reach the correct diagnosis. In this review, we seek to underline the clinical aspects of macrocephaly and megalencephaly, emphasizing the main differential diagnosis with a major focus on common genetic disorders. We thus provide a clinico-radiological algorithm to guide pediatricians in the assessment of children with macrocephaly.
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Affiliation(s)
- Andrea Accogli
- Division of Medical Genetics, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Ana Filipa Geraldo
- Diagnostic Neuroradiology Unit, Imaging Department, Centro Hospitalar Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal
| | - Gianluca Piccolo
- Pediatric Neurology and Neuromuscular Diseases Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Antonella Riva
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Ganna Balagura
- Pediatric Neurology and Neuromuscular Diseases Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Vincenzo Salpietro
- Pediatric Neurology and Neuromuscular Diseases Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Francesca Madia
- Pediatric Clinic and Endocrinology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Mohamad Maghnie
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy.,Pediatric Clinic and Endocrinology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy.,Medical Genetics Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Pasquale Striano
- Pediatric Neurology and Neuromuscular Diseases Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Domenico Tortora
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Valeria Capra
- Medical Genetics Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
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Miyashita T, Baddam P, Smeeton J, Oel AP, Natarajan N, Gordon B, Palmer AR, Crump JG, Graf D, Allison WT. nkx3.2 mutant zebrafish accommodate jaw joint loss through a phenocopy of the head shapes of Paleozoic jawless fish. J Exp Biol 2020; 223:jeb216945. [PMID: 32527964 PMCID: PMC10668335 DOI: 10.1242/jeb.216945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
The vertebrate jaw is a versatile feeding apparatus. To function, it requires a joint between the upper and lower jaws, so jaw joint defects are often highly disruptive and difficult to study. To describe the consequences of jaw joint dysfunction, we engineered two independent null alleles of a single jaw joint marker gene, nkx3.2, in zebrafish. These mutations caused zebrafish to become functionally jawless via fusion of the upper and lower jaw cartilages (ankylosis). Despite lacking jaw joints, nkx3.2 mutants survived to adulthood and accommodated this defect by: (a) having a remodeled skull with a fixed open gape, reduced snout and enlarged branchial region; and (b) performing ram feeding in the absence of jaw-generated suction. The late onset and broad extent of phenotypic changes in the mutants suggest that modifications to the skull are induced by functional agnathia, secondarily to nkx3.2 loss of function. Interestingly, nkx3.2 mutants superficially resemble ancient jawless vertebrates (anaspids and furcacaudiid thelodonts) in overall head shape. Because no homology exists in individual skull elements between these taxa, the adult nkx3.2 phenotype is not a reversal but rather a convergence due to similar functional requirements of feeding without moveable jaws. This remarkable analogy strongly suggests that jaw movements themselves dramatically influence the development of jawed vertebrate skulls. Thus, these mutants provide a unique model with which to: (a) investigate adaptive responses to perturbation in skeletal development; (b) re-evaluate evolutionarily inspired interpretations of phenocopies generated by gene knockdowns and knockouts; and (c) gain insight into feeding mechanics of the extinct agnathans.
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Affiliation(s)
- Tetsuto Miyashita
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Pranidhi Baddam
- Department of Dentistry, University of Alberta, Edmonton, AB, Canada T6G 2R3
| | - Joanna Smeeton
- Department of Stem Cell Biology and Regenerative Medicine, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - A Phil Oel
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Natasha Natarajan
- Department of Stem Cell Biology and Regenerative Medicine, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Brogan Gordon
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - A Richard Palmer
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Daniel Graf
- Department of Dentistry, University of Alberta, Edmonton, AB, Canada T6G 2R3
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada T6G 2R7
| | - W Ted Allison
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada T6G 2R7
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12
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Castro JPL, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife 2019; 8:e42014. [PMID: 31169497 PMCID: PMC6606024 DOI: 10.7554/elife.42014] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 05/19/2019] [Indexed: 12/30/2022] Open
Abstract
Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.
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Affiliation(s)
- João PL Castro
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | | | | | | | - Layla Hiramatsu
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - Marek Kučka
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - William H Beluch
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - Ronald Naumann
- Max Planck Institute for Molecular Cell Biology and GeneticsDresdenGermany
| | | | | | - Nicholas H Barton
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
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13
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Baird DA, Evans DS, Kamanu FK, Gregory JS, Saunders FR, Giuraniuc CV, Barr RJ, Aspden RM, Jenkins D, Kiel DP, Orwoll ES, Cummings SR, Lane NE, Mullin BH, Williams FMK, Richards JB, Wilson SG, Spector TD, Faber BG, Lawlor DA, Grundberg E, Ohlsson C, Pettersson‐Kymmer U, Capellini TD, Richard D, Beck TJ, Evans DM, Paternoster L, Karasik D, Tobias JH. Identification of Novel Loci Associated With Hip Shape: A Meta-Analysis of Genomewide Association Studies. J Bone Miner Res 2019; 34:241-251. [PMID: 30320955 PMCID: PMC6375741 DOI: 10.1002/jbmr.3605] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/30/2018] [Accepted: 10/06/2018] [Indexed: 02/05/2023]
Abstract
We aimed to report the first genomewide association study (GWAS) meta-analysis of dual-energy X-ray absorptiometry (DXA)-derived hip shape, which is thought to be related to the risk of both hip osteoarthritis and hip fracture. Ten hip shape modes (HSMs) were derived by statistical shape modeling using SHAPE software, from hip DXA scans in the Avon Longitudinal Study of Parents and Children (ALSPAC; adult females), TwinsUK (mixed sex), Framingham Osteoporosis Study (FOS; mixed), Osteoporotic Fractures in Men study (MrOS), and Study of Osteoporotic Fractures (SOF; females) (total N = 15,934). Associations were adjusted for age, sex, and ancestry. Five genomewide significant (p < 5 × 10-9 , adjusted for 10 independent outcomes) single-nucleotide polymorphisms (SNPs) were associated with HSM1, and three SNPs with HSM2. One SNP, in high linkage disequilibrium with rs2158915 associated with HSM1, was associated with HSM5 at genomewide significance. In a look-up of previous GWASs, three of the identified SNPs were associated with hip osteoarthritis, one with hip fracture, and five with height. Seven SNPs were within 200 kb of genes involved in endochondral bone formation, namely SOX9, PTHrP, RUNX1, NKX3-2, FGFR4, DICER1, and HHIP. The SNP adjacent to DICER1 also showed osteoblast cis-regulatory activity of GSC, in which mutations have previously been reported to cause hip dysplasia. For three of the lead SNPs, SNPs in high LD (r2 > 0.5) were identified, which intersected with open chromatin sites as detected by ATAC-seq performed on embryonic mouse proximal femora. In conclusion, we identified eight SNPs independently associated with hip shape, most of which were associated with height and/or mapped close to endochondral bone formation genes, consistent with a contribution of processes involved in limb growth to hip shape and pathological sequelae. These findings raise the possibility that genetic studies of hip shape might help in understanding potential pathways involved in hip osteoarthritis and hip fracture. © 2018 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Denis A Baird
- Musculoskeletal Research UnitUniversity of BristolBristolUK
| | - Daniel S Evans
- California Pacific Medical Center Research InstituteSan FranciscoCAUSA
| | - Frederick K Kamanu
- Institute for Aging ResearchHebrew SeniorLifeDepartment of MedicineBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMAUSA
| | | | - Fiona R Saunders
- Arthritis and Musculoskeletal MedicineUniversity of AberdeenAberdeenUK
| | | | - Rebecca J Barr
- Arthritis and Musculoskeletal MedicineUniversity of AberdeenAberdeenUK
- MEMO ResearchUniversity of DundeeDundeeUK
| | - Richard M Aspden
- Arthritis and Musculoskeletal MedicineUniversity of AberdeenAberdeenUK
| | | | - Douglas P Kiel
- Institute for Aging ResearchHebrew SeniorLifeDepartment of MedicineBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMAUSA
- Broad Institute of MIT and HarvardBostonMAUSA
| | - Eric S Orwoll
- School of MedicineOregon Health and Science UniversityPortlandORUSA
| | - Steven R Cummings
- California Pacific Medical Center Research InstituteSan FranciscoCAUSA
| | - Nancy E Lane
- University of California at DavisSacramentoCAUSA
| | - Benjamin H Mullin
- Department of Endocrinology and DiabetesSir Charles Gairdner HospitalNedlandsAustralia
- School of Biomedical SciencesUniversity of Western AustraliaPerthAustralia
| | - Frances MK Williams
- Department of Twin Research and Genetic EpidemiologyKing's College LondonLondonUK
| | - J Brent Richards
- Department of Twin Research and Genetic EpidemiologyKing's College LondonLondonUK
- Departments of Medicine, Human Genetics, Epidemiology, and BiostatisticsJewish General HospitalMcGill UniversityMontrealCanada
| | - Scott G Wilson
- Department of Endocrinology and DiabetesSir Charles Gairdner HospitalNedlandsAustralia
- School of Biomedical SciencesUniversity of Western AustraliaPerthAustralia
- Department of Twin Research and Genetic EpidemiologyKing's College LondonLondonUK
| | - Tim D Spector
- Department of Twin Research and Genetic EpidemiologyKing's College LondonLondonUK
| | | | | | - Elin Grundberg
- Department of Human GeneticsMcGill UniversityMontrealCanada
| | - Claes Ohlsson
- Centre for Bone and Arthritis ResearchInstitute of MedicineUniversity of GothenburgGothenburgSweden
| | | | - Terence D Capellini
- Broad Institute of MIT and HarvardBostonMAUSA
- Human Evolutionary BiologyHarvard UniversityBostonMAUSA
| | | | | | - David M Evans
- MRC Integrative Epidemiology UnitUniversity of BristolBristolUK
- University of Queensland Diamantina InstituteTranslational Research InstituteBrisbaneAustralia
| | | | - David Karasik
- Institute for Aging ResearchHebrew SeniorLifeDepartment of MedicineBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMAUSA
- Azrieli Faculty of MedicineBar Ilan UniversitySafedIsrael
| | - Jonathan H Tobias
- Musculoskeletal Research UnitUniversity of BristolBristolUK
- MRC Integrative Epidemiology UnitUniversity of BristolBristolUK
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14
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Lukas P, Olsson L. Bapx1
is required for jaw joint development in amphibians. Evol Dev 2018; 20:192-206. [DOI: 10.1111/ede.12267] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Paul Lukas
- Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst‐Haeckel‐Haus und BiologiedidaktikFriedrich‐Schiller‐Universität JenaJenaGermany
| | - Lennart Olsson
- Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst‐Haeckel‐Haus und BiologiedidaktikFriedrich‐Schiller‐Universität JenaJenaGermany
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15
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Simsek-Kiper PO, Kosukcu C, Akgun-Dogan O, Gocmen R, Utine GE, Soyer T, Korkmaz-Toygar A, Nishimura G, Alikasifoglu M, Boduroglu K. A novel NKX3-2 mutation associated with perinatal lethal phenotype of spondylo-megaepiphyseal-metaphyseal dysplasia in a neonate. Eur J Med Genet 2018; 62:21-26. [PMID: 29704686 DOI: 10.1016/j.ejmg.2018.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 04/11/2018] [Accepted: 04/22/2018] [Indexed: 11/19/2022]
Abstract
Spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD) is an autosomal recessive skeletal dysplasia, characterized by disproportionate short stature with a short and stiff neck and trunk. SMMD is caused by inactivating mutations in NKX3-2, which encodes a homeobox-containing protein. Because of the rarity of the disorder, the diagnostic feature has not been fully established yet. We describe an affected newborn with dysmorphic facial features and severe short trunk. The patient required immediate intubation at the delivery room and duodenal atresia was detected during his course in neonatal intensive care unit. Skeletal survey revealed total absence of the ossification of the vertebral bodies, pubis, and ischia. Mainly the femora was short and broad with mild flaring of the metaphyses. The downward sloping or tented appearance of the ribs was distinctive. A diagnosis of SMMD was made on clinical and radiological grounds. Molecular analysis revealed homozygosity for a novel mutation, c.507-508delCA (p.Gly171Cysfs*55) in exon 2 of NKX3-2. The patient was operated on postnatal day 7 for duodenal atresia. In the post-operative period he developed sepsis and respiratory failure and he died on postnatal day 14. Although no neuroradiologic imaging could be performed, the findings of clubfoot, neuromuscular respiratory insufficiency requiring invasive mechanical ventilation and downward sloping or tented appearance of the ribs were suggestive of very early cervical cord compression leading to perinatal mortality. To our knowledge this patient yet represents one of the most severe postnatal phenotypes of SMMD.
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Affiliation(s)
- Pelin Ozlem Simsek-Kiper
- Division of Pediatric Genetics, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.
| | - Can Kosukcu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey; Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Ozlem Akgun-Dogan
- Division of Pediatric Genetics, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Gulen Eda Utine
- Division of Pediatric Genetics, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Tutku Soyer
- Department of Pediatric Surgery, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ayse Korkmaz-Toygar
- Division of Neonatalogy, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey; Division of Neonatalogy, Department of Pediatrics, Acıbadem University Faculty of Medicine, Istanbul, Turkey
| | - Gen Nishimura
- Department of Radiology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Mehmet Alikasifoglu
- Division of Pediatric Genetics, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey; Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Koray Boduroglu
- Division of Pediatric Genetics, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey; Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
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16
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Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J, Walter K, Iotchkova V, Schwartzentruber J, Huang J, Memari Y, McCarthy S, Crawford AA, Bombieri C, Cocca M, Farmaki AE, Gaunt TR, Jousilahti P, Kooijman MN, Lehne B, Malerba G, Männistö S, Matchan A, Medina-Gomez C, Metrustry SJ, Nag A, Ntalla I, Paternoster L, Rayner NW, Sala C, Scott WR, Shihab HA, Southam L, St Pourcain B, Traglia M, Trajanoska K, Zaza G, Zhang W, Artigas MS, Bansal N, Benn M, Chen Z, Danecek P, Lin WY, Locke A, Luan J, Manning AK, Mulas A, Sidore C, Tybjaerg-Hansen A, Varbo A, Zoledziewska M, Finan C, Hatzikotoulas K, Hendricks AE, Kemp JP, Moayyeri A, Panoutsopoulou K, Szpak M, Wilson SG, Boehnke M, Cucca F, Di Angelantonio E, Langenberg C, Lindgren C, McCarthy MI, Morris AP, Nordestgaard BG, Scott RA, Tobin MD, Wareham NJ, Burton P, Chambers JC, Smith GD, Dedoussis G, Felix JF, Franco OH, Gambaro G, Gasparini P, Hammond CJ, Hofman A, Jaddoe VWV, Kleber M, Kooner JS, Perola M, Relton C, Ring SM, Rivadeneira F, Salomaa V, Spector TD, Stegle O, Toniolo D, Uitterlinden AG, Barroso I, Greenwood CMT, Perry JRB, Walker BR, Butterworth AS, Xue Y, Durbin R, Small KS, Soranzo N, Timpson NJ, Zeggini E. Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits. Am J Hum Genet 2017; 100:865-884. [PMID: 28552196 PMCID: PMC5473732 DOI: 10.1016/j.ajhg.2017.04.014] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/21/2017] [Indexed: 01/05/2023] Open
Abstract
Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of 12 anthropometric traits associated with height, body mass, and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates. Of the 106 signals, 6 are in genomic regions that have not been implicated with related traits before, 28 are independent signals at previously reported regions, and 72 represent previously reported signals for a different anthropometric trait. 71% of signals reside within genes and fine mapping resolves 23 signals to one or two likely causal variants. We confirm genetic overlap between human monogenic and polygenic anthropometric traits and find signal enrichment in cis expression QTLs in relevant tissues. Our results highlight the potential of WGS strategies to enhance biologically relevant discoveries across the frequency spectrum.
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Affiliation(s)
- Ioanna Tachmazidou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Dániel Süveges
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Graham R S Ritchie
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Usher Institute of Population Health Sciences & Informatics, University of Edinburgh, Edinburgh EH16 4UX, UK; MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH16 4UX, UK
| | - Julia Steinberg
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Klaudia Walter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Valentina Iotchkova
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | | | - Jie Huang
- Boston VA Research Institute, Boston, MA 02130, USA
| | - Yasin Memari
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Shane McCarthy
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Andrew A Crawford
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK; BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Cristina Bombieri
- Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona 37134, Italy
| | - Massimiliano Cocca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34100, Italy
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens 17671, Greece
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Pekka Jousilahti
- Department of Health, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Marjolein N Kooijman
- The Generation R Study Group, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Giovanni Malerba
- Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona 37134, Italy
| | - Satu Männistö
- Department of Health, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Angela Matchan
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Carolina Medina-Gomez
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Sarah J Metrustry
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Nigel W Rayner
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan 20132, Italy
| | - William R Scott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Cardiology, Ealing Hospital NHS Trust, Middlesex UB1 3EU, UK
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Lorraine Southam
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Beate St Pourcain
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK; Max Planck Institute for Psycholinguistics, Nijmegen 6500, the Netherlands
| | - Michela Traglia
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Katerina Trajanoska
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Gialuigi Zaza
- Renal Unit, Department of Medicine, Verona University Hospital, Verona 37126, Italy
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Cardiology, Ealing Hospital NHS Trust, Middlesex UB1 3EU, UK
| | - María S Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Narinder Bansal
- Cardiovascular Epidemiology Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Marianne Benn
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Zhongsheng Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Petr Danecek
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Wei-Yu Lin
- Cardiovascular Epidemiology Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Adam Locke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Alisa K Manning
- Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Medicine, Harvard University Medical School, Boston, MA 02115, USA
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB-CNR), Cagliari 09100, Italy; Università degli Studi di Sassari, Sassari 07100, Italy
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica (IRGB-CNR), Cagliari 09100, Italy
| | - Anne Tybjaerg-Hansen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Anette Varbo
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | | | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London WC1E 6BT, UK
| | | | - Audrey E Hendricks
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - John P Kemp
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK; University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD 4072, Australia
| | - Alireza Moayyeri
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK; Institute of Health Informatics, University College London, London NW1 2DA, UK
| | | | - Michal Szpak
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Scott G Wilson
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK; School of Medicine and Pharmacology, The University of Western Australia, Crawley, WA 6009, Australia; Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB-CNR), Cagliari 09100, Italy; Università degli Studi di Sassari, Sassari 07100, Italy
| | - Emanuele Di Angelantonio
- Cardiovascular Epidemiology Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Cambridge CB1 8RN, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Cecilia Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Li Ka Shing Centre for Health Information and Discovery, The Big Data Institute, University of Oxford, Oxford OX3 7BN, UK
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Department of Biostatistics, University of Liverpool, Liverpool L69 3GL, UK; Estonian Genome Center, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Børge G Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | | | | | - Paul Burton
- D2K Research Group, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Cardiology, Ealing Hospital NHS Trust, Middlesex UB1 3EU, UK; Imperial College Healthcare NHS Trust, London W2 1NY, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens 17671, Greece
| | - Janine F Felix
- The Generation R Study Group, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Giovanni Gambaro
- Division of Nephrology and Dialysis, Columbus-Gemelli University Hospital, Catholic University, Rome 00168, Italy
| | - Paolo Gasparini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34100, Italy; Medical Genetics, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste 34100, Italy
| | - Christopher J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Marcus Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital NHS Trust, Middlesex UB1 3EU, UK; Imperial College Healthcare NHS Trust, London W2 1NY, UK; National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Markus Perola
- Department of Health, National Institute for Health and Welfare, Helsinki 00271, Finland; Estonian Genome Center, University of Tartu, Tartu, Tartumaa 51010, Estonia; Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan 20132, Italy
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | | | | | | | - Inês Barroso
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; University of Cambridge Metabolic Research Laboratories, and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 1A2, Canada; Department of Oncology, McGill University, Montréal, QC H2W 1S6, Canada
| | - John R B Perry
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK; MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Brian R Walker
- BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Adam S Butterworth
- Cardiovascular Epidemiology Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Cambridge CB1 8RN, UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Richard Durbin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Nicole Soranzo
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Cambridge CB1 8RN, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AH, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Eleftheria Zeggini
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
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17
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Liu CF, Samsa WE, Zhou G, Lefebvre V. Transcriptional control of chondrocyte specification and differentiation. Semin Cell Dev Biol 2016; 62:34-49. [PMID: 27771362 DOI: 10.1016/j.semcdb.2016.10.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 12/20/2022]
Abstract
A milestone in the evolutionary emergence of vertebrates was the invention of cartilage, a tissue that has key roles in modeling, protecting and complementing the bony skeleton. Cartilage is elaborated and maintained by chondrocytes. These cells derive from multipotent skeletal progenitors and they perform highly specialized functions as they proceed through sequential lineage commitment and differentiation steps. They form cartilage primordia, the primary skeleton of the embryo. They then transform these primordia either into cartilage growth plates, temporary drivers of skeletal elongation and endochondral ossification, or into permanent tissues, namely articular cartilage. Chondrocyte fate decisions and differentiated activities are controlled by numerous extrinsic and intrinsic cues, and they are implemented at the gene expression level by transcription factors. The latter are the focus of this review. Meritorious efforts from many research groups have led over the last two decades to the identification of dozens of key chondrogenic transcription factors. These regulators belong to all types of transcription factor families. Some have master roles at one or several differentiation steps. They include SOX9 and RUNX2/3. Others decisively assist or antagonize the activities of these masters. They include TWIST1, SOX5/6, and MEF2C/D. Many more have tissue-patterning roles and regulate cell survival, proliferation and the pace of cell differentiation. They include, but are not limited to, homeodomain-containing proteins and growth factor signaling mediators. We here review current knowledge of all these factors, one superclass, class, and family at a time. We then compile all knowledge into transcriptional networks. We also identify remaining gaps in knowledge and directions for future research to fill these gaps and thereby provide novel insights into cartilage disease mechanisms and treatment options.
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Affiliation(s)
- Chia-Feng Liu
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA.
| | - William E Samsa
- Department of Orthopaedics, Case Western Reserve University, Cleveland, OH, USA
| | - Guang Zhou
- Department of Orthopaedics, Case Western Reserve University, Cleveland, OH, USA; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Véronique Lefebvre
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA.
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18
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A GWA study reveals genetic loci for body conformation traits in Chinese Laiwu pigs and its implications for human BMI. Mamm Genome 2016; 27:610-621. [PMID: 27473603 DOI: 10.1007/s00335-016-9657-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/06/2016] [Indexed: 12/20/2022]
Abstract
Pigs share numerous physiological and phenotypic similarities with human and thus have been considered as a good model in nonrodent mammals for the study of genetic basis of human obesity. Researches on candidate genes for obesity traits have successfully identified some common genes between humans and pigs. However, few studies have assessed how many similarities exist between the genetic architecture of obesity in pigs and humans by large-scale comparative genomics. Here, we performed a genome-wide association study (GWAS) using the porcine 60 K SNP Beadchip for BMI and other four conformation traits at three different ages in a Chinese Laiwu pig population, which shows a large variability in fat deposition. In total, 35 SNPs were found to be significant at Bonferroni-corrected 5 % chromosome-wise level (P = 2.13 × 10-5) and 88 SNPs had suggestive (P < 10-4) association with the conformation traits. Some SNPs showed age-dependent association. Intriguingly, out of 32 regions associated with BMI in pigs, 18 were homologous with the loci for BMI in humans. Furthermore, five closest genes to GWAS peaks including HIF1AN, SMYD3, COX10, SLMAP, and GBE1 have been already associated with BMI in humans, which makes them very promising candidates for these QTLs. The result of GO analysis provided strong support to the fact that mitochondria and synapse play important roles in obesity susceptibility, which is consistent with previous findings on human obesity, and it also implicated new gene sets related to chromatin modification and Ig-like C2-type 5 domain. Therefore, these results not only provide new insights into the genetic architecture of BMI in pigs but also highlight that humans and pigs share the significant overlap of obesity-related genes.
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19
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Jeong DU, Choi JY, Kim DW. Cartilage-Specific and Cre-Dependent Nkx3.2 Overexpression In Vivo Causes Skeletal Dwarfism by Delaying Cartilage Hypertrophy. J Cell Physiol 2016; 232:78-90. [DOI: 10.1002/jcp.25446] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/01/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Da-Un Jeong
- Department of Biochemistry; College of Life Science and Biotechnology; Yonsei University; Seoul Republic of Korea
| | - Je-Yong Choi
- Department of Biochemistry and Cell Biology; School of Medicine, Kyungpook National University; Daegu Republic of Korea
| | - Dae-Won Kim
- Department of Biochemistry; College of Life Science and Biotechnology; Yonsei University; Seoul Republic of Korea
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20
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Caron MMJ, Emans PJ, Surtel DAM, van der Kraan PM, van Rhijn LW, Welting TJM. BAPX-1/NKX-3.2 Acts as a Chondrocyte Hypertrophy Molecular Switch in Osteoarthritis. Arthritis Rheumatol 2015; 67:2944-56. [DOI: 10.1002/art.39293] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 07/14/2015] [Indexed: 12/28/2022]
Affiliation(s)
| | - Pieter J. Emans
- Maastricht University Medical Centre; Maastricht The Netherlands
| | - Don A. M. Surtel
- Maastricht University Medical Centre; Maastricht The Netherlands
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21
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Suppression of Nkx3.2 by phosphatidylinositol-3-kinase signaling regulates cartilage development by modulating chondrocyte hypertrophy. Cell Signal 2015; 27:2389-400. [PMID: 26363466 DOI: 10.1016/j.cellsig.2015.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/07/2015] [Indexed: 01/04/2023]
Abstract
Phosphatidylinositol-3-kinase (PI3K) is a key regulator of diverse biological processes including cell proliferation, migration, survival, and differentiation. While a role of PI3K in chondrocyte differentiation has been suggested, its precise mechanisms of action are poorly understood. Here we show that PI3K signaling can down-regulate Nkx3.2 at both mRNA and protein levels in various chondrocyte cultures in vitro. In addition, we have intriguingly found that p85β, not p85α, is specifically employed as a regulatory subunit for PI3K-mediated Nkx3.2 suppression. Furthermore, we found that regulation of Nkx3.2 by PI3K requires Rac1-PAK1, but not Akt, signaling downstream of PI3K. Finally, using embryonic limb bud cultures, ex vivo long bone cultures, and p85β knockout mice, we demonstrated that PI3K-mediated suppression of Nkx3.2 in chondrocytes plays a role in the control of cartilage hypertrophy during skeletal development in vertebrates.
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22
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Tsang KY, Tsang SW, Chan D, Cheah KSE. The chondrocytic journey in endochondral bone growth and skeletal dysplasia. ACTA ACUST UNITED AC 2015; 102:52-73. [PMID: 24677723 DOI: 10.1002/bdrc.21060] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 02/23/2014] [Indexed: 12/29/2022]
Abstract
The endochondral bones of the skeleton develop from a cartilage template and grow via a process involving a cascade of chondrocyte differentiation steps culminating in formation of a growth plate and the replacement of cartilage by bone. This process of endochondral ossification, driven by the generation of chondrocytes and their subsequent proliferation, differentiation, and production of extracellular matrix constitute a journey, deviation from which inevitably disrupts bone growth and development, and is the basis of human skeletal dysplasias with a wide range of phenotypic severity, from perinatal lethality to progressively deforming. This highly coordinated journey of chondrocyte specification and fate determination is controlled by a myriad of intrinsic and extrinsic factors. SOX9 is the master transcription factor that, in concert with varying partners along the way, directs the different phases of the journey from mesenchymal condensation, chondrogenesis, differentiation, proliferation, and maturation. Extracellular signals, including bone morphogenetic proteins, wingless-related MMTV integration site (WNT), fibroblast growth factor, Indian hedgehog, and parathyroid hormone-related peptide, are all indispensable for growth plate chondrocytes to align and organize into the appropriate columnar architecture and controls their maturation and transition to hypertrophy. Chondrocyte hypertrophy, marked by dramatic volume increase in phases, is controlled by transcription factors SOX9, Runt-related transcription factor, and FOXA2. Hypertrophic chondrocytes mediate the cartilage to bone transition and concomitantly face a live-or-die situation, a subject of much debate. We review recent insights into the coordination of the phases of the chondrocyte journey, and highlight the need for a systems level understanding of the regulatory networks that will facilitate the development of therapeutic approaches for skeletal dysplasia.
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Affiliation(s)
- Kwok Yeung Tsang
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
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23
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Abstract
Transcription factor, Nkx3.2, is a member of the NK family of developmental genes and is expressed during embryogenesis in a variety of mammalian model organisms, including chicken and mouse. It was first identified in Drosophila as the Bagpipe (bap) gene, where it has been demonstrated to be essential during formation of the midgut musculature. However, mammalian homolog Nkx3.2 has been shown to play a significant role in axial and limb skeletogenesis; in particular, the human skeletal disease, spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD), is associated with mutations of the Nkx3.2 gene. In this review, we highlight the role of Nkx3.2 during musculoskeletal development, with an emphasis on the factor's role in determining chondrogenic cell fate and its subsequent role in endochondral ossification and chondrocyte survival.
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Li X, Hu J, Zhang J, Jin Q, Wang DM, Yu J, Zhang Q, Zhang YB. Genome-wide linkage study suggests a susceptibility locus for isolated bilateral microtia on 4p15.32-4p16.2. PLoS One 2014; 9:e101152. [PMID: 24983964 PMCID: PMC4077761 DOI: 10.1371/journal.pone.0101152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022] Open
Abstract
Microtia is a congenital deformity where the external ear is underdeveloped. Genetic investigations have identified many susceptibility genes of microtia-related syndromes. However, no causal genes were reported for isolated microtia, the main form of microtia. We conducted a genome-wide linkage analysis on a 5-generation Chinese pedigree with isolated bilateral microtia. We identified a suggestive linkage locus on 4p15.32-4p16.2 with parametric LOD score of 2.70 and nonparametric linkage score (Zmean) of 12.28 (simulated occurrence per genome scan equal to 0.46 and 0.47, respectively). Haplotype reconstruction analysis of the 4p15.32-4p16.2 region further confined the linkage signal to a 10-Mb segment located between rs12505562 and rs12649803 (9.65-30.24 cM; 5.54-15.58 Mb). Various human organ developmental genes reside in this 10-Mb susceptibility region, such as EVC, EVC2, SLC2A9, NKX3-2, and HMX1. The coding regions of three genes, EVC known for cartilage development and NKX3-2, HMX1 involved in microtia, were selected for sequencing with 5 individuals from the pedigree. Of the 38 identified sequence variants, none segregates along with the disease phenotype. Other genes or DNA sequences of the 10-Mb region warrant for further investigation. In conclusion, we report a susceptibility locus of isolated microtia, and this finding will encourage future studies on the genetic basis of ear deformity.
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Affiliation(s)
- Xin Li
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
- Department of Cardiology, Beijing Anzhen Hospital of the Capital University of Medical Sciences, Beijing, P. R. China
| | - Jintian Hu
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Jiao Zhang
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Qian Jin
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Duen-Mei Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
| | - Qingguo Zhang
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Yong-Biao Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
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25
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Simon M, Campos-Xavier AB, Mittaz-Crettol L, Valadares ER, Carvalho D, Speck-Martins CE, Nampoothiri S, Alanay Y, Mihci E, van Bever Y, Garcia-Segarra N, Cavalcanti D, Mortier G, Bonafé L, Superti-Furga A. Severe neurologic manifestations from cervical spine instability in spondylo-megaepiphyseal-metaphyseal dysplasia. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2012; 160C:230-7. [DOI: 10.1002/ajmg.c.31339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Cairns DM, Liu R, Sen M, Canner JP, Schindeler A, Little DG, Zeng L. Interplay of Nkx3.2, Sox9 and Pax3 regulates chondrogenic differentiation of muscle progenitor cells. PLoS One 2012; 7:e39642. [PMID: 22768305 PMCID: PMC3388093 DOI: 10.1371/journal.pone.0039642] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 05/26/2012] [Indexed: 01/04/2023] Open
Abstract
Muscle satellite cells make up a stem cell population that is capable of differentiating into myocytes and contributing to muscle regeneration upon injury. In this work we investigate the mechanism by which these muscle progenitor cells adopt an alternative cell fate, the cartilage fate. We show that chick muscle satellite cells that normally would undergo myogenesis can be converted to express cartilage matrix proteins in vitro when cultured in chondrogenic medium containing TGFß3 or BMP2. In the meantime, the myogenic program is repressed, suggesting that muscle satellite cells have undergone chondrogenic differentiation. Furthermore, ectopic expression of the myogenic factor Pax3 prevents chondrogenesis in these cells, while chondrogenic factors Nkx3.2 and Sox9 act downstream of TGFß or BMP2 to promote this cell fate transition. We found that Nkx3.2 and Sox9 repress the activity of the Pax3 promoter and that Nkx3.2 acts as a transcriptional repressor in this process. Importantly, a reverse function mutant of Nkx3.2 blocks the ability of Sox9 to both inhibit myogenesis and induce chondrogenesis, suggesting that Nkx3.2 is required for Sox9 to promote chondrogenic differentiation in satellite cells. Finally, we found that in an in vivo mouse model of fracture healing where muscle progenitor cells were lineage-traced, Nkx3.2 and Sox9 are significantly upregulated while Pax3 is significantly downregulated in the muscle progenitor cells that give rise to chondrocytes during fracture repair. Thus our in vitro and in vivo analyses suggest that the balance of Pax3, Nkx3.2 and Sox9 may act as a molecular switch during the chondrogenic differentiation of muscle progenitor cells, which may be important for fracture healing.
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Affiliation(s)
- Dana M. Cairns
- Program in Cellular, Molecular and Developmental Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Renjing Liu
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Westmead, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Manpreet Sen
- Building Diversity in Biomedical Research Program (BDBS), Tufts University School of Medicine, Massachusetts, United States of America
- Department of Anatomy and Cellular Biology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - James P. Canner
- Program in Cellular, Molecular and Developmental Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Aaron Schindeler
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Westmead, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - David G. Little
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Westmead, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Li Zeng
- Program in Cellular, Molecular and Developmental Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Building Diversity in Biomedical Research Program (BDBS), Tufts University School of Medicine, Massachusetts, United States of America
- Department of Anatomy and Cellular Biology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Department of Orthopaedic Surgery, Tufts Medical Center, Boston, Massachusetts, United States of America
- * E-mail:
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27
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Nkx3.2 promotes primary chondrogenic differentiation by upregulating Col2a1 transcription. PLoS One 2012; 7:e34703. [PMID: 22511961 PMCID: PMC3325257 DOI: 10.1371/journal.pone.0034703] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 03/05/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The Nkx3.2 transcription factor promotes chondrogenesis by forming a positive regulatory loop with a crucial chondrogenic transcription factor, Sox9. Previous studies have indicated that factors other than Sox9 may promote chondrogenesis directly, but these factors have not been identified. Here, we test the hypothesis that Nkx3.2 promotes chondrogenesis directly by Sox9-independent mechanisms and indirectly by previously characterized Sox9-dependent mechanisms. METHODOLOGY/PRINCIPAL FINDINGS C3H10T1/2 pluripotent mesenchymal cells were cultured with bone morphogenetic protein 2 (BMP2) to induce endochondral ossification. Overexpression of wild-type Nkx3.2 (WT-Nkx3.2) upregulated glycosaminoglycan (GAG) production and expression of type II collagen α1 (Col2a1) mRNA, and these effects were evident before WT-Nkx3.2-mediated upregulation of Sox9. RNAi-mediated inhibition of Nkx3.2 abolished GAG production and expression of Col2a1 mRNA. Dual luciferase reporter assays revealed that WT-Nkx3.2 upregulated Col2a1 enhancer activity in a dose-dependent manner in C3H10T1/2 cells and also in N1511 chondrocytes. In addition, WT-Nkx3.2 partially restored downregulation of GAG production, Col2 protein expression, and Col2a1 mRNA expression induced by Sox9 RNAi. ChIP assays revealed that Nkx3.2 bound to the Col2a1 enhancer element. CONCLUSIONS/SIGNIFICANCE Nkx3.2 promoted primary chondrogenesis by two mechanisms: Direct and Sox9-independent upregulation of Col2a1 transcription and upregulation of Sox9 mRNA expression under positive feedback system.
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