1
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Ichiyama-Kobayashi S, Hata K, Wakamori K, Takahata Y, Murakami T, Yamanaka H, Takano H, Yao R, Uzawa N, Nishimura R. Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development. JCI Insight 2024; 9:e175486. [PMID: 38855864 PMCID: PMC11382882 DOI: 10.1172/jci.insight.175486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 05/01/2024] [Indexed: 06/11/2024] Open
Abstract
The transcription factor SRY-related HMG box 9 (Sox9) is essential for chondrogenesis. Mutations in and around SOX9 cause campomelic dysplasia (CD) characterized by skeletal malformations. Although the function of Sox9 in this context is well studied, the mechanisms that regulate Sox9 expression in chondrocytes remain to be elucidated. Here, we have used genome-wide profiling to identify 2 Sox9 enhancers located in a proximal breakpoint cluster responsible for CD. Enhancer activity of E308 (located 308 kb 5' upstream) and E160 (located 160 kb 5' upstream) correlated with Sox9 expression levels, and both enhancers showed a synergistic effect in vitro. While single deletions in mice had no apparent effect, simultaneous deletion of both E308 and E160 caused a dwarf phenotype, concomitant with a reduction of Sox9 expression in chondrocytes. Moreover, bone morphogenetic protein 2-dependent chondrocyte differentiation of limb bud mesenchymal cells was severely attenuated in E308/E160 deletion mice. Finally, we found that an open chromatin region upstream of the Sox9 gene was reorganized in the E308/E160 deletion mice to partially compensate for the loss of E308 and E160. In conclusion, our findings reveal a mechanism of Sox9 gene regulation in chondrocytes that might aid in our understanding of the pathophysiology of skeletal disorders.
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Affiliation(s)
- Sachi Ichiyama-Kobayashi
- Department of Molecular and Cellular Biochemistry
- Department of Oral and Maxillofacial Oncology and Surgery, and
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry
| | - Kanta Wakamori
- Department of Molecular and Cellular Biochemistry
- Department of Oral and Maxillofacial Oncology and Surgery, and
| | - Yoshifumi Takahata
- Department of Molecular and Cellular Biochemistry
- Genome Editing Research and Development Unit, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | | | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Hiroshi Takano
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Narikazu Uzawa
- Department of Oral and Maxillofacial Oncology and Surgery, and
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2
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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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3
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Molin AN, Contentin R, Angelozzi M, Karvande A, Kc R, Haseeb A, Voskamp C, de Charleroy C, Lefebvre V. Skeletal growth is enhanced by a shared role for SOX8 and SOX9 in promoting reserve chondrocyte commitment to columnar proliferation. Proc Natl Acad Sci U S A 2024; 121:e2316969121. [PMID: 38346197 PMCID: PMC10895259 DOI: 10.1073/pnas.2316969121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 02/15/2024] Open
Abstract
SOX8 was linked in a genome-wide association study to human height heritability, but roles in chondrocytes for this close relative of the master chondrogenic transcription factor SOX9 remain unknown. We undertook here to fill this knowledge gap. High-throughput assays demonstrate expression of human SOX8 and mouse Sox8 in growth plate cartilage. In situ assays show that Sox8 is expressed at a similar level as Sox9 in reserve and early columnar chondrocytes and turned off when Sox9 expression peaks in late columnar and prehypertrophic chondrocytes. Sox8-/- mice and Sox8fl/flPrx1Cre and Sox9fl/+Prx1Cre mice (inactivation in limb skeletal cells) have a normal or near normal skeletal size. In contrast, juvenile and adult Sox8fl/flSox9fl/+Prx1Cre compound mutants exhibit a 15 to 20% shortening of long bones. Their growth plate reserve chondrocytes progress slowly toward the columnar stage, as witnessed by a delay in down-regulating Pthlh expression, in packing in columns and in elevating their proliferation rate. SOX8 or SOX9 overexpression in chondrocytes reveals not only that SOX8 can promote growth plate cell proliferation and differentiation, even upon inactivation of endogenous Sox9, but also that it is more efficient than SOX9, possibly due to greater protein stability. Altogether, these findings uncover a major role for SOX8 and SOX9 in promoting skeletal growth by stimulating commitment of growth plate reserve chondrocytes to actively proliferating columnar cells. Further, by showing that SOX8 is more chondrogenic than SOX9, they suggest that SOX8 could be preferred over SOX9 in therapies to promote cartilage formation or regeneration in developmental and degenerative cartilage diseases.
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Affiliation(s)
- Arnaud N. Molin
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Romain Contentin
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Marco Angelozzi
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Anirudha Karvande
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Ranjan Kc
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Abdul Haseeb
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Chantal Voskamp
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Charles de Charleroy
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Véronique Lefebvre
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
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4
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Huang X, Henck J, Qiu C, Sreenivasan VKA, Balachandran S, Amarie OV, Hrabě de Angelis M, Behncke RY, Chan WL, Despang A, Dickel DE, Duran M, Feuchtinger A, Fuchs H, Gailus-Durner V, Haag N, Hägerling R, Hansmeier N, Hennig F, Marshall C, Rajderkar S, Ringel A, Robson M, Saunders LM, da Silva-Buttkus P, Spielmann N, Srivatsan SR, Ulferts S, Wittler L, Zhu Y, Kalscheuer VM, Ibrahim DM, Kurth I, Kornak U, Visel A, Pennacchio LA, Beier DR, Trapnell C, Cao J, Shendure J, Spielmann M. Single-cell, whole-embryo phenotyping of mammalian developmental disorders. Nature 2023; 623:772-781. [PMID: 37968388 PMCID: PMC10665194 DOI: 10.1038/s41586-023-06548-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/16/2023] [Indexed: 11/17/2023]
Abstract
Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing3 to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions4,5. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be 'decomposable' through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution.
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Affiliation(s)
- Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Jana Henck
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Varun K A Sreenivasan
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Rose Yinghan Behncke
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Wing-Lee Chan
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Alexandra Despang
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Diane E Dickel
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Annette Feuchtinger
- Core Facility Pathology & Tissue Analytics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Natja Haag
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Rene Hägerling
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Nils Hansmeier
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | | | - Cooper Marshall
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | | | - Alessa Ringel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
| | - Michael Robson
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lauren M Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Patricia da Silva-Buttkus
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sascha Ulferts
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Yiwen Zhu
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | | | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - David R Beier
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Malte Spielmann
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany.
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5
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Pan D, Zhong J, Zhang J, Dong H, Zhao D, Zhang H, Yao B. Function and regulation of nuclear factor 1 X-type on chondrocyte proliferation and differentiation. Gene 2023; 881:147620. [PMID: 37433356 DOI: 10.1016/j.gene.2023.147620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/26/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023]
Abstract
Nuclear factor 1 X-type (Nfix) is a transcription factor related to mental and physical development. However, very few studies have reported the effects of Nfix on cartilage. This study aims to reveal the influence of Nfix on the proliferation and differentiation of chondrocytes, and to explore its potential action mechanism. We isolated primary chondrocytes from the costal cartilage of newborn C57BL/6 mice and with Nfix overexpression or silencing treatment. We used Alcian blue staining and found that Nfix overexpression significantly promoted ECM synthesis in chondrocytes while silencing inhibited ECM synthesis. Using RNA-seq technology to study the expression pattern of Nfix in primary chondrocytes. We found that Nfix overexpression significantly up-regulated genes that are related to chondrocyte proliferation and extracellular matrix (ECM) synthesis and significantly down-regulated genes related to chondrocyte differentiation and ECM degradation. Nfix silencing, however, significantly up-regulated genes associated with cartilage catabolism and significantly down-regulated genes associated with cartilage growth promotion. Furthermore, Nfix exerted a positive regulatory effect on Sox9, and we propose that Nfix may promote chondrocyte proliferation and inhibit differentiation by stimulating Sox9 and its downstream genes. Our findings suggest that Nfix may be a potential target for the regulation of chondrocyte proliferation and differentiation.
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Affiliation(s)
- Daian Pan
- Research Center of Traditional Chinese Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun 130021, China; Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China; Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Jinghong Zhong
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Jingcheng Zhang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Haisi Dong
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Daqing Zhao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - He Zhang
- Research Center of Traditional Chinese Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun 130021, China; Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Baojin Yao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
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6
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Wang X, Chen G, Du Y, Yang J, Wang W. Transcription Factor Sox9 Exacerbates Kidney Injury through Inhibition of MicroRNA-96-5p and Activation of the Trib3/IL-6 Axis. Kidney Blood Press Res 2023; 48:611-627. [PMID: 37717559 PMCID: PMC10614512 DOI: 10.1159/000533544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
INTRODUCTION Our study investigated the possible mechanisms of the role of the transcription factor Sox9 in the development and progression of kidney injury through regulation of the miR-96-5p/Trib3/IL-6 axis. METHODS Bioinformatics analysis was performed to identify differentially expressed genes in kidney injury and normal tissues. An in vivo animal model of kidney injury and an in vitro cellular model of kidney injury were constructed using LPS induction in 8-week-old female C57BL/6 mice and human normal renal tubular epithelial cells HK-2 for studying the possible roles of Sox9, miR-96-5p, Trib3, and IL-6 in kidney injury. RESULTS Sox9 was highly expressed in both mouse and cellular models of kidney injury. Sox9 was significantly enriched in the promoter region of miR-96-5p and repressed miR-96-5p expression. Trib3 was highly expressed in both mouse and cellular models of kidney injury and promoted inflammatory responses and kidney injury. In addition, Trib3 promoted IL-6 expression, which was highly expressed in kidney injury, and promoted the inflammatory response and extent of injury in kidney tissue. In vivo and in vitro experiments confirmed that the knockdown of Sox9 improved the inflammatory response and fibrosis of mouse kidney tissues and HK-2 cells, while the ameliorative effect of silencing Sox9 was inhibited by overexpression of IL-6. CONCLUSION Collectively, Sox9 up-regulates miR-96-5p-mediated Trib3 and activates the IL-6 signaling pathway to exacerbate the inflammatory response, ultimately promoting the development and progression of kidney injury.
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Affiliation(s)
- Xiao Wang
- Department of Urology, Fuyang People’s Hospital, Anhui Medical University, Fuyang, China
| | - Guang Chen
- Department of Urology, Fuyang People’s Hospital, Anhui Medical University, Fuyang, China
| | - Yongqiang Du
- Department of Urology, Fuyang People’s Hospital, Anhui Medical University, Fuyang, China
| | - Jiajia Yang
- Department of Urology, Fuyang People’s Hospital, Anhui Medical University, Fuyang, China
| | - Wei Wang
- Department of Urology, First Affiliated Hospital of Anhui Medical University, Hefei, China
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7
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Pan D, Zhong J, Zhang J, Dong H, Zhao D, Zhang H, Yao B. Function and regulation of nuclear factor 1 X-type on chondrocyte proliferation and differentiation. Gene 2023; 881:147620. [DOI: org/10.1016/j.gene.2023.147620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
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8
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Chen LF, Long HK, Park M, Swigut T, Boettiger AN, Wysocka J. Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus. Mol Cell 2023; 83:1446-1461.e6. [PMID: 36996812 DOI: 10.1016/j.molcel.2023.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023]
Abstract
Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 Mb. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. We observed pronounced changes in locus topology between cell types. Subsequent analysis of single-chromatin fiber traces revealed that these ensemble-average differences arise through changes in the frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which promote stripe formation, are positioned near the domain's 3D geometric center, and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multi-loop, centrally clustered geometry. Together, we provide mechanistic insights into architectural stripe formation and gene regulation over ultra-long genomic ranges.
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Affiliation(s)
- Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hannah Katherine Long
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minhee Park
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair Nicol Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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9
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Chen Q, Dai J, Bian Q. Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects. SCIENCE ADVANCES 2022; 8:eabo3648. [PMID: 36417512 PMCID: PMC9683718 DOI: 10.1126/sciadv.abo3648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Aberrations in tissue-specific enhancers underlie many developmental defects. Disrupting a noncoding region distal from the human SOX9 gene causes the Pierre Robin sequence (PRS) characterized by the undersized lower jaw. Such a craniofacial-specific defect has been previously linked to enhancers transiently active in cranial neural crest cells (CNCCs). We demonstrate that the PRS region also strongly regulates Sox9 in CNCC-derived Meckel's cartilage (MC), but not in limb cartilages, even after decommissioning of CNCC enhancers. Such an MC-specific regulatory effect correlates with the MC-specific chromatin contacts between the PRS region and Sox9, highlighting the importance of lineage-dependent chromatin topology in instructing enhancer usage. By integrating the enhancer signatures and chromatin topology, we uncovered >10,000 enhancers that function differentially between MC and limb cartilages and demonstrated their association with human diseases. Our findings provide critical insights for understanding the choreography of gene regulation during development and interpreting the genetic basis of craniofacial pathologies.
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Affiliation(s)
- Qiming Chen
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
| | - Jiewen Dai
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
- Corresponding author. (J.D.); (Q.B.)
| | - Qian Bian
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Corresponding author. (J.D.); (Q.B.)
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10
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Ming Z, Vining B, Bagheri-Fam S, Harley V. SOX9 in organogenesis: shared and unique transcriptional functions. Cell Mol Life Sci 2022; 79:522. [PMID: 36114905 PMCID: PMC9482574 DOI: 10.1007/s00018-022-04543-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/13/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022]
Abstract
The transcription factor SOX9 is essential for the development of multiple organs including bone, testis, heart, lung, pancreas, intestine and nervous system. Mutations in the human SOX9 gene led to campomelic dysplasia, a haploinsufficiency disorder with several skeletal malformations frequently accompanied by 46, XY sex reversal. The mechanisms underlying the diverse SOX9 functions during organ development including its post-translational modifications, the availability of binding partners, and tissue-specific accessibility to target gene chromatin. Here we summarize the expression, activities, and downstream target genes of SOX9 in molecular genetic pathways essential for organ development, maintenance, and function. We also provide an insight into understanding the mechanisms that regulate the versatile roles of SOX9 in different organs.
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Affiliation(s)
- Zhenhua Ming
- Sex Development Laboratory, Hudson Institute of Medical Research, PO Box 5152, Melbourne, VIC, 3168, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, 3800, Australia
| | - Brittany Vining
- Sex Development Laboratory, Hudson Institute of Medical Research, PO Box 5152, Melbourne, VIC, 3168, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, 3800, Australia
| | - Stefan Bagheri-Fam
- Sex Development Laboratory, Hudson Institute of Medical Research, PO Box 5152, Melbourne, VIC, 3168, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, 3800, Australia
| | - Vincent Harley
- Sex Development Laboratory, Hudson Institute of Medical Research, PO Box 5152, Melbourne, VIC, 3168, Australia.
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, 3800, Australia.
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11
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Identification of candidate enhancers controlling the transcriptome during the formation of interphalangeal joints. Sci Rep 2022; 12:12835. [PMID: 35896673 PMCID: PMC9329285 DOI: 10.1038/s41598-022-16951-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
The formation of the synovial joint begins with the visible emergence of a stripe of densely packed mesenchymal cells located between distal ends of the developing skeletal anlagen called the interzone. Recently the transcriptome of the early synovial joint was reported. Knowledge about enhancers would complement these data and lead to a better understanding of the control of gene transcription at the onset of joint development. Using ChIP-sequencing we have mapped the H3-signatures H3K27ac and H3K4me1 to locate regulatory elements specific for the interzone and adjacent phalange, respectively. This one-stage atlas of candidate enhancers (CEs) was used to map the association between these respective joint tissue specific CEs and biological processes. Subsequently, integrative analysis of transcriptomic data and CEs identified new putative regulatory elements of genes expressed in interzone (e.g., GDF5, BMP2 and DACT2) and phalange (e.g., MATN1, HAPLN1 and SNAI1). We also linked such CEs to genes known as crucial in synovial joint hypermobility and osteoarthritis, as well as phalange malformations. These analyses show that the CE atlas can serve as resource for identifying, and as starting point for experimentally validating, putative disease-causing genomic regulatory regions in patients with synovial joint dysfunctions and/or phalange disorders, and enhancer-controlled synovial joint and phalange formation.
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12
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SOX9 and SATB2 Immunohistochemistry Cannot Reliably Distinguish Between Osteosarcoma and Chondrosarcoma on Biopsy Material. Hum Pathol 2022; 121:56-64. [PMID: 35016891 DOI: 10.1016/j.humpath.2021.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/23/2022]
Abstract
INTRODUCTION Limited tissue in biopsies of malignant bone lesions can preclude definitive subclassification, especially when cellular or matrix elements are sparse, absent, or confounding. It is uncertain whether IHC for SOX9 (marker of chondrogenesis) and SATB2 (marker of osteoblastic differentiation) may be discriminatory tools towards osteosarcoma and chondrosarcoma. METHODS This study interrogated the pre-resection biopsies of a cohort of osteosarcoma and chondrosarcoma with SATB2 and SOX9 in tandem, to assess their value as diagnostic adjuncts as well as their concordance with final resection diagnoses. RESULTS SATB2 was expressed more frequently in osteosarcoma (46/53, 86%) compared to chondrosarcoma (9/18, 50%); SOX9 was expressed in high frequencies in both osteosarcoma (52/53, 98%) and chondrosarcoma (17/18, 94%), and SATB2 and SOX9 were co-expressed in both osteosarcoma (46/53, 89%) and chondrosarcoma (8/18, 44%). CONCLUSIONS There exists significant overlap in expression of SATB2 and SOX9 in osteosarcoma and chondrosarcoma. These markers are not expressed in a distribution that is unique enough for application towards this particular diagnostic differential.
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13
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Agrawal P, Rao S. Super-Enhancers and CTCF in Early Embryonic Cell Fate Decisions. Front Cell Dev Biol 2021; 9:653669. [PMID: 33842482 PMCID: PMC8027350 DOI: 10.3389/fcell.2021.653669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/18/2021] [Indexed: 12/04/2022] Open
Abstract
Cell fate decisions are the backbone of many developmental and disease processes. In early mammalian development, precise gene expression changes underly the rapid division of a single cell that leads to the embryo and are critically dependent on autonomous cell changes in gene expression. To understand how these lineage specifications events are mediated, scientists have had to look past protein coding genes to the cis regulatory elements (CREs), including enhancers and insulators, that modulate gene expression. One class of enhancers, termed super-enhancers, is highly active and cell-type specific, implying their critical role in modulating cell-type specific gene expression. Deletion or mutations within these CREs adversely affect gene expression and development and can cause disease. In this mini-review we discuss recent studies describing the potential roles of two CREs, enhancers and binding sites for CTCF, in early mammalian development.
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Affiliation(s)
- Puja Agrawal
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
- Versiti Blood Research Institute, Milwaukee, WI, United States
| | - Sridhar Rao
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
- Versiti Blood Research Institute, Milwaukee, WI, United States
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
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14
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Yu TT, Xu QF, Li SY, Huang HJ, Dugan S, Shao L, Roggenbuck JA, Liu XT, Liu HZ, Hirsch BA, Yue S, Liu C, Cheng SY. Deletion at an 1q24 locus reveals a critical role of long noncoding RNA DNM3OS in skeletal development. Cell Biosci 2021; 11:47. [PMID: 33653390 PMCID: PMC7923828 DOI: 10.1186/s13578-021-00559-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Skeletal development and maintenance are complex processes known to be coordinated by multiple genetic and epigenetic signaling pathways. However, the role of long non-coding RNAs (lncRNAs), a class of crucial epigenetic regulatory molecules, has been under explored in skeletal biology. RESULTS Here we report a young patient with short stature, hypothalamic dysfunction and mild macrocephaly, who carries a maternally inherited 690 kb deletion at Chr.1q24.2 encompassing a noncoding RNA gene, DNM3OS, embedded on the opposite strand in an intron of the DYNAMIN 3 (DNM3) gene. We show that lncRNA DNM3OS sustains the proliferation of chondrocytes independent of two co-cistronic microRNAs miR-199a and miR-214. We further show that nerve growth factor (NGF), a known factor of chondrocyte growth, is a key target of DNM3OS-mediated control of chondrocyte proliferation. CONCLUSIONS This work demonstrates that DNM3OS is essential for preventing premature differentiation of chondrocytes required for bone growth through endochondral ossification.
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Affiliation(s)
- Ting-Ting Yu
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China
| | - Qiu-Fan Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China
| | - Si-Yang Li
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China
| | - Hui-Jie Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China
| | - Sarah Dugan
- Department of Medical Genetics, Children's Hospital and Clinics of Minnesota, Minneapolis, MI, 55404, USA
| | - Lei Shao
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China
| | - Jennifer A Roggenbuck
- Department of Neurology, Ohio State University Medical Center, Columbus, OH, 43210, USA
| | - Xiao-Tong Liu
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China
| | - Huai-Ze Liu
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China
| | - Betsy A Hirsch
- University of Minnesota Medical Center-Fairview, Minneapolis, MI, 55404, USA
| | - Shen Yue
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China.
| | - Chen Liu
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China.
| | - Steven Y Cheng
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Jiangsu, 211166, Nanjing, P. R. China.
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15
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Nakamichi R, Kurimoto R, Tabata Y, Asahara H. Transcriptional, epigenetic and microRNA regulation of growth plate. Bone 2020; 137:115434. [PMID: 32422296 PMCID: PMC7387102 DOI: 10.1016/j.bone.2020.115434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/13/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
Endochondral ossification is a critical event in bone formation, particularly in long shaft bones. Many cellular differentiation processes work in concert to facilitate the generation of cartilage primordium to formation of trabecular structures, all of which occur within the growth plate. Previous studies have revealed that the growth plate is tightly regulated by various transcription factors, epigenetic systems, and microRNAs. Hence, understanding these mechanisms that regulate the growth plate is crucial to furthering the current understanding on skeletal diseases, and in formulating effective treatment strategies. In this review, we focus on describing the function and mechanisms of the transcription factors, epigenetic systems, and microRNAs known to regulate the growth plate.
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Affiliation(s)
- Ryo Nakamichi
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MBB-102, La Jolla, CA 92037, USA; Department of Orthopaedic Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Ryota Kurimoto
- Department of Systems Biomedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yusuke Tabata
- Department of Orthopaedic Surgery, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan
| | - Hirosi Asahara
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MBB-102, La Jolla, CA 92037, USA; Department of Systems Biomedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
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16
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Zhou Z, Yao B, Zhao D. Runx3 regulates chondrocyte phenotype by controlling multiple genes involved in chondrocyte proliferation and differentiation. Mol Biol Rep 2020; 47:5773-5792. [PMID: 32661874 DOI: 10.1007/s11033-020-05646-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/08/2020] [Indexed: 12/22/2022]
Abstract
Chondrocytes are the sole cell type present within cartilage, and play pivotal roles in controlling the formation and composition of health cartilage. Chondrocytes maintain cartilage homeostasis through proliferating, differentiating and synthesizing different types of extracellular matrices. Thus, the coordinated proliferation and differentiation of chondrocytes are essential for cartilage growth, repair and the conversion from cartilage to bone during the processes of bone formation and fracture healing. Runx3, a transcription factor that belongs to the Runx family, is significantly upregulated at the onset of cartilage mineralization and regulates both early and late markers of chondrocyte maturation. Therefore, Runx3 may serve as an accelerator of chondrocyte differentiation and maturation. However, the underlying molecular mechanism of Runx3 in regulating chondrocyte proliferation and differentiation remains largely to be elucidated. In the present study, we used state-of-the-art RNA-seq technology combined with validation methods to investigate the effect of Runx3 overexpression or silencing on primary chondrocyte proliferation and differentiation, and demonstrated that Runx3 overexpression possibly inhibited chondrocyte proliferation but accelerated differentiation, whereas Runx3 silencing possibly promoted chondrocyte proliferation but suppressed differentiation. Furthermore, Runx3 overexpression possibly decreased the expression levels of Sox9 and its downstream genes via Sox9 cartilage-specific enhancers, and vice versa for Runx3 silencing.
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Affiliation(s)
- Zhenwei Zhou
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Baojin Yao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117, China.
| | - Daqing Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117, China.
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17
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Song H, Park KH. Regulation and function of SOX9 during cartilage development and regeneration. Semin Cancer Biol 2020; 67:12-23. [PMID: 32380234 DOI: 10.1016/j.semcancer.2020.04.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 09/23/2019] [Accepted: 04/26/2020] [Indexed: 12/21/2022]
Abstract
Chondrogenesis is a highly coordinated event in embryo development, adult homeostasis, and repair of the vertebrate cartilage. Fate decisions and differentiation of chondrocytes accompany differential expression of genes critical for each step of chondrogenesis. SOX9 is a master transcription factor that participates in sequential events in chondrogenesis by regulating a series of downstream factors in a stage-specific manner. SOX9 either works alone or in combination with downstream SOX transcription factors, SOX5 and SOX6 as chondrogenic SOX Trio. SOX9 is reduced in the articular cartilage of patients with osteoarthritis while highly maintained during tumorigenesis of cartilage and bone. Gene therapy using viral and non-viral vectors accompanied by tissue engineering (scaffolds) is a promising tool to regenerate impaired cartilage. Delivery of SOX9 or chondrogenic SOX Trio into cells produces efficient therapeutic effects on chondrogenesis and this event is facilitated by scaffolds. Non-viral vector-guided delivery systems encapsulated or loaded in mechanically stable solid scaffolds are useful for the regeneration of articular cartilage. Here we review major milestones and most recent studies focusing on regulation and function of chondrogenic SOX Trio, during chondrogenesis and cartilage regeneration, and on the development of advanced technologies in gene delivery with tissue engineering to improve efficiency of cartilage repair process.
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Affiliation(s)
- Haengseok Song
- Department of Biomedical Science, CHA University, Seongnam, Republic of Korea
| | - Keun-Hong Park
- Department of Biomedical Science, CHA University, Seongnam, Republic of Korea.
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18
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Rice SJ, Beier F, Young DA, Loughlin J. Interplay between genetics and epigenetics in osteoarthritis. Nat Rev Rheumatol 2020; 16:268-281. [PMID: 32273577 DOI: 10.1038/s41584-020-0407-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Research into the molecular genetics of osteoarthritis (OA) has been substantially bolstered in the past few years by the implementation of powerful genome-wide scans that have revealed a large number of novel risk loci associated with the disease. This refreshing wave of discovery has occurred concurrently with epigenetic studies of joint tissues that have examined DNA methylation, histone modifications and regulatory RNAs. These epigenetic analyses have involved investigations of joint development, homeostasis and disease and have used both human samples and animal models. What has become apparent from a comparison of these two complementary approaches is that many OA genetic risk signals interact with, map to or correlate with epigenetic mediators. This discovery implies that epigenetic mechanisms, and their effect on gene expression, are a major conduit through which OA genetic risk polymorphisms exert their functional effects. This observation is particularly exciting as it provides mechanistic insight into OA susceptibility. Furthermore, this knowledge reveals avenues for attenuating the negative effect of risk-conferring alleles by exposing the epigenome as an exploitable target for therapeutic intervention in OA.
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Affiliation(s)
- Sarah J Rice
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Frank Beier
- Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada.,Western Bone and Joint Institute, The University of Western Ontario, London, ON, Canada
| | - David A Young
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John Loughlin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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19
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Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, Housman G, García-Pérez R, Lizano E, Cheronet O, Mallick S, Nieves-Colón MA, Li H, Alpaslan-Roodenberg S, Novak M, Gu H, Osinski JM, Ferrando-Bernal M, Gelabert P, Lipende I, Mjungu D, Kondova I, Bontrop R, Kullmer O, Weber G, Shahar T, Dvir-Ginzberg M, Faerman M, Quillen EE, Meissner A, Lahav Y, Kandel L, Liebergall M, Prada ME, Vidal JM, Gronostajski RM, Stone AC, Yakir B, Lalueza-Fox C, Pinhasi R, Reich D, Marques-Bonet T, Meshorer E, Carmel L. Differential DNA methylation of vocal and facial anatomy genes in modern humans. Nat Commun 2020; 11:1189. [PMID: 32132541 PMCID: PMC7055320 DOI: 10.1038/s41467-020-15020-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.
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Affiliation(s)
- David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Malka Nissim-Rafinia
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Lily Agranat-Tamir
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Swapan Mallick
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Heng Li
- Broad Institute, Cambridge, MA, 02138, USA
| | | | - Mario Novak
- Institute for Anthropological Research, 10000, Zagreb, Croatia
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | | | - Jason M Osinski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | | | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Iddi Lipende
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Deus Mjungu
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Ivanela Kondova
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ottmar Kullmer
- Department of Palaeoanthropology and Messel Research, Senckenberg Center of Human Evolution and Paleoecology, Frankfurt am Main, Germany
| | - Gerhard Weber
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Tal Shahar
- Department of Neurosurgery, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Mona Dvir-Ginzberg
- Laboratory of Cartilage Biology, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Marina Faerman
- Laboratory of Bioanthropology and Ancient DNA, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 85287, USA
| | - Alexander Meissner
- Broad Institute, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yonatan Lahav
- Otolaryngology - Head & Neck Surgery Department, Laryngeal Surgery Unit, Kaplan Medical Center, Rehovot, Israel
- The Hebrew University Medical School, Jerusalem, Israel
| | - Leonid Kandel
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Meir Liebergall
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - María E Prada
- I.E.S.O. 'Los Salados'. Junta de Castilla y León, León, Spain
| | - Julio M Vidal
- Junta de Castilla y León, Servicio de Cultura de León, León, Spain
| | - Richard M Gronostajski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
- Genetics, Genomics and Bioinformatics Program, New York State Center of Excellence in Bioinformatics and Life Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | - Benjamin Yakir
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - David Reich
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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20
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Tariq A, Hao Q, Sun Q, Singh DK, Jadaliha M, Zhang Y, Chetlangia N, Ma J, Holton SE, Bhargava R, Lal A, Prasanth SG, Prasanth KV. LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells. RNA (NEW YORK, N.Y.) 2020; 26:175-185. [PMID: 31690584 PMCID: PMC6961546 DOI: 10.1261/rna.073254.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/30/2019] [Indexed: 05/08/2023]
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) subtypes with a poor prognosis and high recurrence rate. Recent studies have identified vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type-specific expression of lncRNAs and their potential role in regulating the expression of oncogenic and tumor suppressor genes have made them promising cancer drug targets. By performing a transcriptome screen in an isogenic TNBC/basal subtype BC progression cell line model, we recently reported ∼1800 lncRNAs that display aberrant expression during breast cancer progression. Mechanistic studies on one such nuclear-retained lncRNA, linc02095, reveal that it promotes breast cancer proliferation by facilitating the expression of oncogenic transcription factor, SOX9. Both linc02095 and SOX9 display coregulated expression in BC patients as well in basal subtype BC cell lines. Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase II occupancy at the SOX9 gene body as well as defective SOX9 mRNA export, implying that linc02095 positively regulates SOX9 transcription and mRNA export. Finally, we identify a positive feedback loop in BC cells that controls the expression of both linc02095 and SOX9 Thus, our results unearth tumor-promoting activities of a nuclear lncRNA linc02095 by facilitating the expression of key oncogenic transcription factor in BC.
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Affiliation(s)
- Aamira Tariq
- Department of Biosciences, Comsats Institute of Information Technology, Islamabad 45550, Pakistan
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Sun
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mahdieh Jadaliha
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Sarah E Holton
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Rohit Bhargava
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions. Sci Rep 2020; 10:1169. [PMID: 31980739 PMCID: PMC6981252 DOI: 10.1038/s41598-020-58093-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/21/2019] [Indexed: 12/12/2022] Open
Abstract
Regulation of transcription occurs in a cell type specific manner orchestrated by epigenetic mechanisms including DNA methylation. Methylation changes may also play a key role in lineage specification during stem cell differentiation. To further our understanding of epigenetic regulation in chondrocytes we characterised the DNA methylation changes during chondrogenesis of mesenchymal stem cells (MSCs) by Infinium 450 K methylation array. Significant DNA hypomethylation was identified during chondrogenic differentiation including changes at many key cartilage gene loci. Integration with chondrogenesis gene expression data revealed an enrichment of significant CpGs in upregulated genes, while characterisation of significant CpG loci indicated their predominant localisation to enhancer regions. Comparison with methylation profiles of other tissues, including healthy and diseased adult cartilage, identified chondrocyte-specific regions of hypomethylation and the overlap with differentially methylated CpGs in osteoarthritis. Taken together we have associated DNA methylation levels with the chondrocyte phenotype. The consequences of which has potential to improve cartilage generation for tissue engineering purposes and also to provide context for observed methylation changes in cartilage diseases such as osteoarthritis.
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Gulyaeva O, Nguyen H, Sambeat A, Heydari K, Sul HS. Sox9-Meis1 Inactivation Is Required for Adipogenesis, Advancing Pref-1 + to PDGFRα + Cells. Cell Rep 2019; 25:1002-1017.e4. [PMID: 30355480 PMCID: PMC6903418 DOI: 10.1016/j.celrep.2018.09.086] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/27/2018] [Accepted: 09/26/2018] [Indexed: 12/28/2022] Open
Abstract
Adipocytes arise from the commitment and differentiation of adipose precursors in white adipose tissue (WAT). In studying adipogenesis, precursor markers, including Pref-1 and PDGFRα, are used to isolate precursors from stromal vascular fractions of WAT, but the relation among the markers is not known. Here, we used the Pref-1 promoter-rtTA system in mice for labeling Pref-1+ cells and for inducible inactivation of the Pref-1 target Sox9. We show the requirement of Sox9 for the maintenance of Pref-1+ proliferative, early precursors. Upon Sox9 inactivation, these Pref-1+ cells become PDGFRα+ cells that express early adipogenic markers. Thus, we show that Pref-1+ cells precede PDGFRα+ cells in the adipogenic pathway and that Sox9 inactivation is required for WAT growth and expansion. Furthermore, we show that in maintaining early adipose precursors, Sox9 activates Meis1, which prevents adipogenic differentiation. Our study also demonstrates the Pref-1 promoter-rtTA system for inducible gene inactivation in early adipose precursor populations. The relationship among Sox9+, Pref-1+, and PDGFRα+ WAT precursors has not been studied. Gulyaeva et al. show that Pref-1+ cells are early adipose precursors and, upon Sox9 inactivation, they become PDGFRα+ cells at a later stage of the adipogenic pathway. In maintaining Pref-1+ adipose precursors, Sox9 activates Meis1, which prevents adipogenic differentiation.
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Affiliation(s)
- Olga Gulyaeva
- Endocrinology Program, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hai Nguyen
- Endocrinology Program, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Audrey Sambeat
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kartoosh Heydari
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hei Sook Sul
- Endocrinology Program, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Kawata M, Mori D, Kanke K, Hojo H, Ohba S, Chung UI, Yano F, Masaki H, Otsu M, Nakauchi H, Tanaka S, Saito T. Simple and Robust Differentiation of Human Pluripotent Stem Cells toward Chondrocytes by Two Small-Molecule Compounds. Stem Cell Reports 2019; 13:530-544. [PMID: 31402337 PMCID: PMC6739881 DOI: 10.1016/j.stemcr.2019.07.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 01/08/2023] Open
Abstract
A simple induction protocol to differentiate chondrocytes from pluripotent stem cells (PSCs) using small-molecule compounds is beneficial for cartilage regenerative medicine and mechanistic studies of chondrogenesis. Here, we demonstrate that chondrocytes are robustly induced from human PSCs by simple combination of two compounds, CHIR99021, a glycogen synthase kinase 3 inhibitor, and TTNPB, a retinoic acid receptor (RAR) agonist, under serum- and feeder-free conditions within 5-9 days. An excellent differentiation efficiency and potential to form hyaline cartilaginous tissues in vivo were demonstrated. Comprehensive gene expression and open chromatin analyses at each protocol stage revealed step-by-step differentiation toward chondrocytes. Genome-wide analysis of RAR and β-catenin association with DNA showed that retinoic acid and Wnt/β-catenin signaling collaboratively regulated the key marker genes at each differentiation stage. This method provides a promising cell source for regenerative medicine and, as an in vitro model, may facilitate elucidation of the molecular mechanisms underlying chondrocyte differentiation.
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Affiliation(s)
- Manabu Kawata
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Mori
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kosuke Kanke
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinsuke Ohba
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ung-Il Chung
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fumiko Yano
- Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Masaki
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Makoto Otsu
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sakae Tanaka
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taku Saito
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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24
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SOX9 in cartilage development and disease. Curr Opin Cell Biol 2019; 61:39-47. [PMID: 31382142 DOI: 10.1016/j.ceb.2019.07.008] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 07/06/2019] [Indexed: 12/18/2022]
Abstract
SOX9 is a pivotal transcription factor in chondrocytes, a lineage essential in skeletogenesis. Its mandatory role in transactivating many cartilage-specific genes is well established, whereas its pioneer role in lineage specification, which along with transactivation defines master transcription factors, remains to be better defined. Abundant, but yet incomplete evidence exists that intricate molecular networks control SOX9 activity during the multi-step chondrogenesis pathway. They include a highly modular genetic regulation, post-transcriptional and post-translational modifications, and varying sets of functional partners. Fully uncovering SOX9 actions and regulation is fundamental to explain mechanisms underlying many diseases that directly or indirectly affect SOX9 activities and to design effective disease treatments. We here review current knowledge, highlight recent discoveries, and propose new research directions to answer remaining questions.
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Angelozzi M, Lefebvre V. SOXopathies: Growing Family of Developmental Disorders Due to SOX Mutations. Trends Genet 2019; 35:658-671. [PMID: 31288943 DOI: 10.1016/j.tig.2019.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022]
Abstract
The SRY-related (SOX) transcription factor family pivotally contributes to determining cell fate and identity in many lineages. Since the original discovery that SRY deletions cause sex reversal, mutations in half of the 20 human SOX genes have been associated with rare congenital disorders, henceforward called SOXopathies. Mutations are generally de novo, heterozygous, and inactivating, revealing gene haploinsufficiency, but other types, including duplications, have been reported too. Missense variants primarily target the HMG domain, the SOX hallmark that mediates DNA binding and bending, nuclear trafficking, and protein-protein interactions. We here review key clinical and molecular features of SOXopathies and discuss the prospect that the disease family likely involves more SOX genes and larger clinical and genetic spectrums than currently appreciated.
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Affiliation(s)
- Marco Angelozzi
- Department of Surgery/Division of Orthopaedic Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Véronique Lefebvre
- Department of Surgery/Division of Orthopaedic Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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26
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Wu N, Liu B, Du H, Zhao S, Li Y, Cheng X, Wang S, Lin J, Zhou J, Qiu G, Wu Z, Zhang J. The Progress of CRISPR/Cas9-Mediated Gene Editing in Generating Mouse/Zebrafish Models of Human Skeletal Diseases. Comput Struct Biotechnol J 2019; 17:954-962. [PMID: 31360334 PMCID: PMC6639410 DOI: 10.1016/j.csbj.2019.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/28/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
Genetic factors play a substantial role in the etiology of skeletal diseases, which involve 1) defects in skeletal development, including intramembranous ossification and endochondral ossification; 2) defects in skeletal metabolism, including late bone growth and bone remodeling; 3) defects in early developmental processes related to skeletal diseases, such as neural crest cell (NCC) and cilia functions; 4) disturbance of the cellular signaling pathways which potentially affect bone growth. Efficient and high-throughput genetic methods have enabled the exploration and verification of disease-causing genes and variants. Animal models including mouse and zebrafish have been extensively used in functional mechanism studies of causal genes and variants. The conventional approaches of generating mutant animal models include spontaneous mutagenesis, random integration, and targeted integration via mouse embryonic stem cells. These approaches are costly and time-consuming. Recent development and application of gene-editing tools, especially the CRISPR/Cas9 system, has significantly accelerated the process of gene-editing in diverse organisms. Here we review both mice and zebrafish models of human skeletal diseases generated by CRISPR/Cas9 system, and their contributions to deciphering the underpins of disease mechanisms.
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Affiliation(s)
- Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Bowen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yaqi Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Xi Cheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Junde Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | | | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
- Central Laboratory & Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Central Laboratory & Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
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27
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Hong SH, You JS. SOX9 is controlled by the BRD4 inhibitor JQ1 via multiple regulation mechanisms. Biochem Biophys Res Commun 2019; 511:746-752. [PMID: 30833074 DOI: 10.1016/j.bbrc.2019.02.135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 01/10/2023]
Abstract
SOX9 is a key transcription factor during cell differentiation, sex determination, and tumorigenesis. However, the detailed mechanisms of its targeting strategy remain elusive. To investigate possibilities of targeting SOX9 with epigenetic drugs and the precise underlying mechanisms, two human cancer cell lines were chosen as model systems, which showed high SOX9 expression and anti-tumorigenic effects upon loss of SOX9. Histone acetylation-related screening of a small panel of epigenetic drugs revealed that the bromodomain reader inhibitor JQ1 dramatically downregulated SOX9 through multiple regulation steps, namely, transcription, BRD4-SOX9 protein-protein interaction, and further protein stability. These findings suggest that BRD4 inhibition is a novel therapeutic strategy for diseases characterized by SOX9 overexpression.
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Affiliation(s)
- Seong Hwi Hong
- Department of Biochemistry, School of Medicine, Konkuk University, Seoul, 05029, South Korea
| | - Jueng Soo You
- Department of Biochemistry, School of Medicine, Konkuk University, Seoul, 05029, South Korea; Research Institute of Medical Science, Konkuk University School of Medicine, South Korea.
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28
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Abstract
SOX transcription factors participate in the specification, differentiation and activities of many cell types in development and beyond. The 20 mammalian family members are distributed into eight groups based on sequence identity, and while co-expressed same-group proteins often have redundant functions, different-group proteins typically have distinct functions. More than a handful of SOX proteins have pivotal roles in skeletogenesis. Heterozygous mutations in their genes cause human diseases, in which skeletal dysmorphism is a major feature, such as campomelic dysplasia (SOX9), or a minor feature, such as LAMSHF syndrome (SOX5) and Coffin-Siris-like syndromes (SOX4 and SOX11). Loss- and gain-of-function experiments in animal models have revealed that SOX4 and SOX11 (SOXC group) promote skeletal progenitor survival and control skeleton patterning and growth; SOX8 (SOXE group) delays the differentiation of osteoblast progenitors; SOX9 (SOXE group) is essential for chondrocyte fate maintenance and differentiation, and works in cooperation with SOX5 and SOX6 (SOXD group) and other types of transcription factors. These and other SOX proteins have also been proposed, mainly through in vitro experiments, to have key roles in other aspects of skeletogenesis, such as SOX2 in osteoblast stem cell self-renewal. We here review current knowledge of well-established and proposed skeletogenic roles of SOX proteins, their transcriptional and non-transcriptional actions, and their modes of regulation at the gene, RNA and protein levels. We also discuss gaps in knowledge and directions for future research to further decipher mechanisms underlying skeletogenesis in health and diseases and identify treatment options for skeletal malformation and degeneration diseases.
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Affiliation(s)
- Véronique Lefebvre
- The Children's Hospital of Philadelphia, Philadelphia, PA, United States.
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29
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microRNA-690 regulates induced pluripotent stem cells (iPSCs) differentiation into insulin-producing cells by targeting Sox9. Stem Cell Res Ther 2019; 10:59. [PMID: 30767782 PMCID: PMC6376733 DOI: 10.1186/s13287-019-1154-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/14/2019] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
Background The regulatory mechanism of insulin-producing cells (IPCs) differentiation from induced pluripotent stem cells (iPSCs) in vitro is very important in the phylogenetics of pancreatic islets, the molecular pathogenesis of diabetes, and the acquisition of high-quality pancreatic β-cells derived from stem cells for cell therapy. Methods miPSCs were induced for IPCs differentiation. miRNA microarray assays were performed by using total RNA from our iPCs-derived IPCs containing undifferentiated iPSCs and iPSCs-derived IPCSs at day 4, day 14, and day 21 during step 3 to screen the differentially expressed miRNAs (DEmiRNAs) related to IPCs differentiation, and putative target genes of DEmiRNAs were predicted by bioinformatics analysis. miR-690 was selected for further research, and MPCs were transfected by miR-690-agomir to confirm whether it was involved in the regulation of IPCs differentiation in iPSCs. Quantitative Real-Time PCR (qRT-PCR), Western blotting, and immunostaining assays were performed to examine the pancreatic function of IPCs at mRNA and protein level respectively. Flow cytometry and ELISA were performed to detect differentiation efficiency and insulin content and secretion from iPSCs-derived IPCs in response to stimulation at different concentration of glucose. The targeting of the 3′-untranslated region of Sox9 by miR-690 was examined by luciferase assay. Results We found that miR-690 was expressed dynamically during IPCs differentiation according to the miRNA array results and that overexpression of miR-690 significantly impaired the maturation and insulinogenesis of IPCs derived from iPSCs both in vitro and in vivo. Bioinformatic prediction and mechanistic analysis revealed that miR-690 plays a pivotal role during the differentiation of IPCs by directly targeting the transcription factor sex-determining region Y (SRY)-box9. Furthermore, downstream experiments indicated that miR-690 is likely to act as an inactivated regulator of the Wnt signaling pathway in this process. Conclusions We discovered a previously unknown interaction between miR-690 and sox9 but also revealed a new regulatory signaling pathway of the miR-690/Sox9 axis during iPSCs-induced IPCs differentiation. Electronic supplementary material The online version of this article (10.1186/s13287-019-1154-8) contains supplementary material, which is available to authorized users.
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Abstract
The bipotential nature of cell types in the early developing gonad and the process of sex determination leading to either testis or ovary differentiation makes this an interesting system in which to study transcriptional regulation of gene expression and cell fate decisions. SOX9 is a transcription factor with multiple roles during development, including being a key player in mediating testis differentiation and therefore subsequent male development. Loss of Sox9 expression in both humans and mice results in XY female development, whereas its inappropriate activation in XX embryonic gonads can give male development. Multiple cases of Disorders of Sex Development in human patients or sex reversal in mice and other vertebrates can be explained by mutations affecting upstream regulators of Sox9 expression, such as the product of the Y chromosome gene Sry that triggers testis differentiation. Other cases are due to mutations in the Sox9 gene itself, including its own regulatory region. Indeed, rearrangements in and around the Sox9 genomic locus indicate the presence of multiple critical enhancers and the complex nature of its regulation. Here we summarize what is known about the role of Sox9 and its regulation during gonad development, including recently discovered critical enhancers. We also discuss higher order chromatin organization and how this might be involved. We end with some interesting future directions that have the potential to further enrich our understanding on the complex, multi-layered regulation controlling Sox9 expression in the gonads.
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Affiliation(s)
- Nitzan Gonen
- The Francis Crick Institute, London, United Kingdom.
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31
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Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9. Nat Commun 2018; 9:5319. [PMID: 30552336 PMCID: PMC6293998 DOI: 10.1038/s41467-018-07784-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 11/22/2018] [Indexed: 12/03/2022] Open
Abstract
Disorders of sex development (DSDs) are conditions affecting development of the gonads or genitalia. Variants in two key genes, SRY and its target SOX9, are an established cause of 46,XY DSD, but the genetic basis of many DSDs remains unknown. SRY-mediated SOX9 upregulation in the early gonad is crucial for testis development, yet the regulatory elements underlying this have not been identified in humans. Here, we identified four DSD patients with overlapping duplications or deletions upstream of SOX9. Bioinformatic analysis identified three putative enhancers for SOX9 that responded to different combinations of testis-specific regulators. All three enhancers showed synergistic activity and together drive SOX9 in the testis. This is the first study to identify SOX9 enhancers that, when duplicated or deleted, result in 46,XX or 46,XY sex reversal, respectively. These enhancers provide a hitherto missing link by which SRY activates SOX9 in humans, and establish SOX9 enhancer mutations as a significant cause of DSD. SRY and its target SOX9 are known key determinants in testis development. Here the authors by studying duplications and deletions upstream of SOX9 from patient samples with disorders of sex development (DSD) reveal enhancers for SOX9 critical for human sex development and DSD.
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Mochizuki Y, Chiba T, Kataoka K, Yamashita S, Sato T, Kato T, Takahashi K, Miyamoto T, Kitazawa M, Hatta T, Natsume T, Takai S, Asahara H. Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression. Dev Cell 2018; 46:794-806.e6. [PMID: 30146478 PMCID: PMC6324936 DOI: 10.1016/j.devcel.2018.07.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 04/23/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022]
Abstract
SRY-box 9 (SOX9) is a master transcription factor that regulates cartilage development. SOX9 haploinsufficiency resulting from breakpoints in a ∼1-Mb region upstream of SOX9 was reported in acampomelic campomelic dysplasia (ACD) patients, suggesting that essential enhancer regions of SOX9 for cartilage development are located in this long non-coding sequence. However, the cis-acting enhancer region regulating cartilage-specific SOX9 expression remains to be identified. To identify distant cartilage Sox9 enhancers, we utilized the combination of multiple CRISPR/Cas9 technologies including enrichment of the promoter-enhancer complex followed by next-generation sequencing and mass spectrometry (MS), SIN3A-dCas9-mediated epigenetic silencing, and generation of enhancer deletion mice. As a result, we could identify a critical far-upstream cis-element and Stat3 as a trans-acting factor, regulating cartilage-specific Sox9 expression and subsequent skeletal development. Our strategy could facilitate definitive ACD diagnosis and should be useful to reveal the detailed chromatin conformation and regulation.
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Affiliation(s)
- Yusuke Mochizuki
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Department of Orthopaedic Surgery, Nippon Medical School, Tokyo 113-0022, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kensuke Kataoka
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Satoshi Yamashita
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tempei Sato
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tomomi Kato
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kenji Takahashi
- Department of Orthopaedic Surgery, Nippon Medical School, Tokyo 113-0022, Japan
| | - Takeshi Miyamoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Masashi Kitazawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Shinro Takai
- Department of Orthopaedic Surgery, Nippon Medical School, Tokyo 113-0022, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Department of Molecular and Experimental Medicine, The Scripps Research Institute, San Diego, CA 92037, USA.
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Liu CF, Angelozzi M, Haseeb A, Lefebvre V. SOX9 is dispensable for the initiation of epigenetic remodeling and the activation of marker genes at the onset of chondrogenesis. Development 2018; 145:dev164459. [PMID: 30021842 PMCID: PMC6078338 DOI: 10.1242/dev.164459] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
Abstract
SOX9 controls cell lineage fate and differentiation in major biological processes. It is known as a potent transcriptional activator of differentiation-specific genes, but its earliest targets and its contribution to priming chromatin for gene activation remain unknown. Here, we address this knowledge gap using chondrogenesis as a model system. By profiling the whole transcriptome and the whole epigenome of wild-type and Sox9-deficient mouse embryo limb buds, we uncover multiple structural and regulatory genes, including Fam101a, Myh14, Sema3c and Sema3d, as specific markers of precartilaginous condensation, and we provide evidence of their direct transactivation by SOX9. Intriguingly, we find that SOX9 helps remove epigenetic signatures of transcriptional repression and establish active-promoter and active-enhancer marks at precartilage- and cartilage-specific loci, but is not absolutely required to initiate these changes and activate transcription. Altogether, these findings widen our current knowledge of SOX9 targets in early chondrogenesis and call for new studies to identify the pioneer and transactivating factors that act upstream of or along with SOX9 to prompt chromatin remodeling and specific gene activation at the onset of chondrogenesis and other processes.
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Affiliation(s)
- Chia-Feng Liu
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Marco Angelozzi
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Abdul Haseeb
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Véronique Lefebvre
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
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Tan Z, Niu B, Tsang KY, Melhado IG, Ohba S, He X, Huang Y, Wang C, McMahon AP, Jauch R, Chan D, Zhang MQ, Cheah KSE. Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions. PLoS Genet 2018; 14:e1007346. [PMID: 29659575 PMCID: PMC5919691 DOI: 10.1371/journal.pgen.1007346] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/26/2018] [Accepted: 03/29/2018] [Indexed: 11/18/2022] Open
Abstract
The growth plate mediates bone growth where SOX9 and GLI factors control chondrocyte proliferation, differentiation and entry into hypertrophy. FOXA factors regulate hypertrophic chondrocyte maturation. How these factors integrate into a Gene Regulatory Network (GRN) controlling these differentiation transitions is incompletely understood. We adopted a genome-wide whole tissue approach to establish a Growth Plate Differential Gene Expression Library (GP-DGEL) for fractionated proliferating, pre-hypertrophic, early and late hypertrophic chondrocytes, as an overarching resource for discovery of pathways and disease candidates. De novo motif discovery revealed the enrichment of SOX9 and GLI binding sites in the genes preferentially expressed in proliferating and prehypertrophic chondrocytes, suggesting the potential cooperation between SOX9 and GLI proteins. We integrated the analyses of the transcriptome, SOX9, GLI1 and GLI3 ChIP-seq datasets, with functional validation by transactivation assays and mouse mutants. We identified new SOX9 targets and showed SOX9-GLI directly and cooperatively regulate many genes such as Trps1, Sox9, Sox5, Sox6, Col2a1, Ptch1, Gli1 and Gli2. Further, FOXA2 competes with SOX9 for the transactivation of target genes. The data support a model of SOX9-GLI-FOXA phasic GRN in chondrocyte development. Together, SOX9-GLI auto-regulate and cooperate to activate and repress genes in proliferating chondrocytes. Upon hypertrophy, FOXA competes with SOX9, and control toward terminal differentiation passes to FOXA, RUNX, AP1 and MEF2 factors. In the development of the mammalian growth plate, while several transcription factors are individually well known for their key roles in regulating phases of chondrocyte differentiation, there is little information on how they interact and cooperate with each other. We took an unbiased genome wide approach to identify the transcription factors and signaling pathways that play dominant roles in the chondrocyte differentiation cascade. We developed a searchable library of differentially expressed genes, GP-DGEL, which has fine spatial resolution and global transcriptomic coverage for discovery of processes, pathways and disease candidates. Our work identifies a novel regulatory mechanism that integrates the action of three transcription factors, SOX9, GLI and FOXA. SOX9-GLI auto-regulate and cooperate to activate and repress genes in proliferating chondrocytes. Upon entry into prehypertrophy, FOXA competes with SOX9, and control of hypertrophy passes to FOXA, RUNX, AP1 and MEF2 factors.
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Affiliation(s)
- Zhijia Tan
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Ben Niu
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Kwok Yeung Tsang
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Ian G. Melhado
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Shinsuke Ohba
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, W.M. Keck School of Medicine of the University of Southern California, Los Angeles, California, United States of America
| | - Xinjun He
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, W.M. Keck School of Medicine of the University of Southern California, Los Angeles, California, United States of America
| | - Yongheng Huang
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Cheng Wang
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, W.M. Keck School of Medicine of the University of Southern California, Los Angeles, California, United States of America
| | - Ralf Jauch
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Danny Chan
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Michael Q. Zhang
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Dallas, Texas, United States of America
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing, China
| | - Kathryn S. E. Cheah
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
- * E-mail:
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Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network. BMC Genomics 2017; 18:983. [PMID: 29262782 PMCID: PMC5738906 DOI: 10.1186/s12864-017-4378-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 12/11/2017] [Indexed: 01/05/2023] Open
Abstract
Background Chondrogenesis is the earliest stage of skeletal development and is a highly dynamic process, integrating the activities and functions of transcription factors, cell signaling molecules and extracellular matrix proteins. The molecular mechanisms underlying chondrogenesis have been extensively studied and multiple key regulators of this process have been identified. However, a genome-wide overview of the gene regulatory network in chondrogenesis has not been achieved. Results In this study, employing RNA sequencing, we identified 332 protein coding genes and 34 long non-coding RNA (lncRNA) genes that are highly selectively expressed in human fetal growth plate chondrocytes. Among the protein coding genes, 32 genes were associated with 62 distinct human skeletal disorders and 153 genes were associated with skeletal defects in knockout mice, confirming their essential roles in skeletal formation. These gene products formed a comprehensive physical interaction network and participated in multiple cellular processes regulating skeletal development. The data also revealed 34 transcription factors and 11,334 distal enhancers that were uniquely active in chondrocytes, functioning as transcriptional regulators for the cartilage-selective genes. Conclusions Our findings revealed a complex gene regulatory network controlling skeletal development whereby transcription factors, enhancers and lncRNAs participate in chondrogenesis by transcriptional regulation of key genes. Additionally, the cartilage-selective genes represent candidate genes for unsolved human skeletal disorders. Electronic supplementary material The online version of this article (10.1186/s12864-017-4378-y) contains supplementary material, which is available to authorized users.
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Barter MJ, Gomez R, Hyatt S, Cheung K, Skelton AJ, Xu Y, Clark IM, Young DA. The long non-coding RNA ROCR contributes to SOX9 expression and chondrogenic differentiation of human mesenchymal stem cells. Development 2017; 144:4510-4521. [PMID: 29084806 PMCID: PMC5769619 DOI: 10.1242/dev.152504] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/25/2017] [Indexed: 12/31/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed in a highly tissue-specific manner and function in various aspects of cell biology, often as key regulators of gene expression. In this study, we established a role for lncRNAs in chondrocyte differentiation. Using RNA sequencing we identified a human articular chondrocyte repertoire of lncRNAs from normal hip cartilage donated by neck of femur fracture patients. Of particular interest are lncRNAs upstream of the master chondrocyte transcription factor SOX9 locus. SOX9 is an HMG-box transcription factor that plays an essential role in chondrocyte development by directing the expression of chondrocyte-specific genes. Two of these lncRNAs are upregulated during chondrogenic differentiation of mesenchymal stem cells (MSCs). Depletion of one of these lncRNAs, LOC102723505, which we termed ROCR (regulator of chondrogenesis RNA), by RNA interference disrupted MSC chondrogenesis, concomitant with reduced cartilage-specific gene expression and incomplete matrix component production, indicating an important role in chondrocyte biology. Specifically, SOX9 induction was significantly ablated in the absence of ROCR, and overexpression of SOX9 rescued the differentiation of MSCs into chondrocytes. Our work sheds further light on chondrocyte-specific SOX9 expression and highlights a novel method of chondrocyte gene regulation involving a lncRNA. Summary: This study identified a chondrocyte repertoire of lncRNAs and discovered that ROCR (regulator of chondrogenesis RNA) is important for MSC chondrogenesis and cartilage gene expression by promoting the expression of SOX9.
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Affiliation(s)
- Matt J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Rodolfo Gomez
- Musculoskeletal Pathology Group, Institute IDIS, Travesia choupana s/n, Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706, Spain
| | - Sam Hyatt
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Kat Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Andrew J Skelton
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Yaobo Xu
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Ian M Clark
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
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Li W, Yue H. Thymidine phosphorylase: A potential new target for treating cardiovascular disease. Trends Cardiovasc Med 2017; 28:157-171. [PMID: 29108898 DOI: 10.1016/j.tcm.2017.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/03/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022]
Abstract
We recently found that thymidine phosphorylase (TYMP), also known as platelet-derived endothelial cell growth factor, plays an important role in platelet activation in vitro and thrombosis in vivo by participating in multiple signaling pathways. Platelets are a major source of TYMP. Since platelet-mediated clot formation is a key event in several fatal diseases, such as myocardial infarction, stroke and pulmonary embolism, understanding TYMP in depth may lead to uncovering novel mechanisms in the development of cardiovascular diseases. Targeting TYMP may become a novel therapeutic for cardiovascular disorders. In this review article, we summarize the discovery of TYMP and the potential molecular mechanisms of TYMP involved in the development of various diseases, especially cardiovascular diseases. We also offer insights regarding future studies exploring the role of TYMP in the development of cardiovascular disease as well as in therapy.
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Affiliation(s)
- Wei Li
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall, University, Huntington, WV; Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, WV.
| | - Hong Yue
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall, University, Huntington, WV
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Symon A, Harley V. SOX9: A genomic view of tissue specific expression and action. Int J Biochem Cell Biol 2017; 87:18-22. [DOI: 10.1016/j.biocel.2017.03.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 03/09/2017] [Accepted: 03/11/2017] [Indexed: 11/29/2022]
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Hojo H, Chung UI, Ohba S. Identification of the gene-regulatory landscape in skeletal development and potential links to skeletal regeneration. Regen Ther 2017; 6:100-107. [PMID: 30271844 PMCID: PMC6134913 DOI: 10.1016/j.reth.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 12/21/2022] Open
Abstract
A class of gene-regulatory elements called enhancers are the main mediators controlling quantitative, temporal and spatial gene expressions. In the course of evolution, the enhancer landscape of higher organisms such as mammals has become quite complex, exerting biological functions precisely and coordinately. In mammalian skeletal development, the master transcription factors Sox9, Runx2 and Sp7/Osterix function primarily through enhancers on the genome to achieve specification and differentiation of skeletal cells. Recently developed genome-scale analyses have shed light on multiple layers of gene regulations, uncovering not only the primary mode of actions of these transcription factors on skeletal enhancers, but also the relation of the epigenetic landscape to three-dimensional chromatin architecture. Here, we review findings on the emerging framework of gene-regulatory networks involved in skeletal development. We further discuss the power of genome-scale analyses to provide new insights into genetic diseases and regenerative medicine in skeletal tissues. Skeletal development is coordinated by master transcription factors. ChIP-seq analyses for the skeletal regulators identified their modes of actions. Analyses of epigenetic landscape features distinct cell types in skeletal tissues. Integrated analyses of the gene regulatory networks link to skeletal regeneration.
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Affiliation(s)
- Hironori Hojo
- Department of Bioengineering, The University of Tokyo Graduate School of Engineering, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ung-Il Chung
- Department of Bioengineering, The University of Tokyo Graduate School of Engineering, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinsuke Ohba
- Department of Bioengineering, The University of Tokyo Graduate School of Engineering, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Hall MD, Murray CA, Valdez MJ, Perantoni AO. Mesoderm-specific Stat3 deletion affects expression of Sox9 yielding Sox9-dependent phenotypes. PLoS Genet 2017; 13:e1006610. [PMID: 28166224 PMCID: PMC5319801 DOI: 10.1371/journal.pgen.1006610] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 02/21/2017] [Accepted: 01/30/2017] [Indexed: 01/14/2023] Open
Abstract
To date, mutations within the coding region and translocations around the SOX9 gene both constitute the majority of genetic lesions underpinning human campomelic dysplasia (CD). While pathological coding-region mutations typically result in a non-functional SOX9 protein, little is known about what mechanism(s) controls normal SOX9 expression, and subsequently, which signaling pathways may be interrupted by alterations occurring around the SOX9 gene. Here, we report the identification of Stat3 as a key modulator of Sox9 expression in nascent cartilage and developing chondrocytes. Stat3 expression is predominant in tissues of mesodermal origin, and its conditional ablation using mesoderm-specific TCre, in vivo, causes dwarfism and skeletal defects characteristic of CD. Specifically, Stat3 loss results in the expansion of growth plate hypertrophic chondrocytes and deregulation of normal endochondral ossification in all bones examined. Conditional deletion of Stat3 with a Sox9Cre driver produces palate and tracheal irregularities similar to those described in Sox9+/- mice. Furthermore, mesodermal deletion of Stat3 causes global embryonic down regulation of Sox9 expression and function in vivo. Mechanistic experiments ex vivo suggest Stat3 can directly activate the expression of Sox9 by binding to its proximal promoter following activation. These findings illuminate a novel role for Stat3 in chondrocytes during skeletal development through modulation of a critical factor, Sox9. Importantly, they further provide the first evidence for the modulation of a gene product other than Sox9 itself which is capable of modeling pathological aspects of CD and underscore a potentially valuable therapeutic target for patients with the disorder.
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Affiliation(s)
- Michael D. Hall
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Caroline A. Murray
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Michael J. Valdez
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Alan O. Perantoni
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
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Smyk M, Akdemir KC, Stankiewicz P. SOX9 chromatin folding domains correlate with its real and putative distant cis-regulatory elements. Nucleus 2017; 8:182-187. [PMID: 28085555 DOI: 10.1080/19491034.2017.1279776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Evolutionary conserved transcription factor SOX9, encoded by the dosage sensitive SOX9 gene on chromosome 17q24.3, plays an important role in development of multiple organs, including bones and testes. Heterozygous point mutations and genomic copy-number variant (CNV) deletions involving SOX9 have been reported in patients with campomelic dysplasia (CD), a skeletal malformation syndrome often associated with male-to-female sex reversal. Balanced and unbalanced structural genomic variants with breakpoints mapping up to 1.3 Mb up- and downstream to SOX9 have been described in patients with milder phenotypes, including acampomelic campomelic dysplasia, sex reversal, and Pierre Robin sequence. Based on the localization of breakpoints of genomic rearrangements causing different phenotypes, 5 genomic intervals mapping upstream to SOX9 have been defined. We have analyzed the publically available database of high-throughput chromosome conformation capture (Hi-C) in multiple cell lines in the genomic regions flanking SOX9. Consistent with the literature data, chromatin domain boundaries in the SOX9 locus exhibit conservation across species and remain largely constant across multiple cell types. Interestingly, we have found that chromatin folding domains in the SOX9 locus associate with the genomic intervals harboring real and putative regulatory elements of SOX9, implicating that variation in intra-domain interactions may be critical for dynamic regulation of SOX9 expression in a cell type-specific fashion. We propose that tissue-specific enhancers for other transcription factor genes may similarly utilize chromatin folding sub-domains in gene regulation.
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Affiliation(s)
- Marta Smyk
- a Department of Medical Genetics , Institute of Mother and Child , Warsaw , Poland
| | - Kadir Caner Akdemir
- b Genomic Medicine Department , MD Anderson Cancer Center , Houston , TX , USA
| | - Paweł Stankiewicz
- c Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
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Abstract
SOX9 is a pivotal transcription factor in developing and adult cartilage. Its gene is expressed from the multipotent skeletal progenitor stage and is active throughout chondrocyte differentiation. While it is repressed in hypertrophic chondrocytes in cartilage growth plates, it remains expressed throughout life in permanent chondrocytes of healthy articular cartilage. SOX9 is required for chondrogenesis: it secures chondrocyte lineage commitment, promotes cell survival, and transcriptionally activates the genes for many cartilage-specific structural components and regulatory factors. Since heterozygous mutations within and around SOX9 were shown to cause the severe skeletal malformation syndrome called campomelic dysplasia, researchers around the world have worked assiduously to decipher the many facets of SOX9 actions and regulation in chondrogenesis. The more we learn, the more we realize the complexity of the molecular networks in which SOX9 fulfills its functions and is regulated at the levels of its gene, RNA, and protein, and the more we measure the many gaps remaining in knowledge. At the same time, new technologies keep giving us more means to push further the frontiers of knowledge. Research efforts must be pursued to fill these gaps and to better understand and treat many types of cartilage diseases in which SOX9 has or could have a critical role. These diseases include chondrodysplasias and cartilage degeneration diseases, namely osteoarthritis, a prevalent and still incurable joint disease. We here review the current state of knowledge of SOX9 actions and regulation in the chondrocyte lineage, and propose new directions for future fundamental and translational research projects.
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Affiliation(s)
- Véronique Lefebvre
- Department of Cellular & Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Mona Dvir-Ginzberg
- Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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Gonen N, Quinn A, O’Neill HC, Koopman P, Lovell-Badge R. Normal Levels of Sox9 Expression in the Developing Mouse Testis Depend on the TES/TESCO Enhancer, but This Does Not Act Alone. PLoS Genet 2017; 13:e1006520. [PMID: 28045957 PMCID: PMC5207396 DOI: 10.1371/journal.pgen.1006520] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/02/2016] [Indexed: 01/18/2023] Open
Abstract
During mouse sex determination, transient expression of the Y-linked gene Sry up-regulates its direct target gene Sox9, via a 3.2 kb testis specific enhancer of Sox9 (TES), which includes a core 1.4 kb element, TESCO. SOX9 activity leads to differentiation of Sertoli cells, rather than granulosa cells from the bipotential supporting cell precursor lineage. Here, we present functional analysis of TES/TESCO, using CRISPR/Cas9 genome editing in mice. Deletion of TESCO or TES reduced Sox9 expression levels in XY fetal gonads to 60 or 45% respectively relative to wild type gonads, and reduced expression of the SOX9 target Amh. Although human patients heterozygous for null mutations in SOX9, which are assumed to have 50% of normal expression, often show XY female sex reversal, mice deleted for one copy of Sox9 do not. Consistent with this, we did not observe sex reversal in either TESCO-/- or TES-/- XY embryos or adult mice. However, embryos carrying both a conditional Sox9 null allele and the TES deletion developed ovotestes. Quantitative analysis of these revealed levels of 23% expression of Sox9 compared to wild type, and a significant increase in the expression of the granulosa cell marker Foxl2. This indicates that the threshold in mice where sex reversal begins to be seen is about half that of the ~50% levels predicted in humans. Our results demonstrate that TES/TESCO is a crucial enhancer regulating Sox9 expression in the gonad, but point to the existence of additional enhancers that act redundantly.
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Affiliation(s)
- Nitzan Gonen
- The Francis Crick Institute, Midland Road, London, United Kingdom
| | - Alexander Quinn
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Helen C. O’Neill
- The Francis Crick Institute, Midland Road, London, United Kingdom
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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An Emerging Regulatory Landscape for Skeletal Development. Trends Genet 2016; 32:774-787. [PMID: 27814929 DOI: 10.1016/j.tig.2016.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/21/2016] [Accepted: 10/04/2016] [Indexed: 02/02/2023]
Abstract
Skeletal development creates the physical framework that shapes our body and its actions. In the past two decades, genetic studies have provided important insights into the molecular processes at play, including the roles of signaling pathways and transcriptional effectors that coordinate an orderly, progressive emergence and expansion of distinct cartilage and bone cell fates in an invariant temporal and spatial pattern for any given skeletal element within that specific vertebrate species. Genome-scale studies have provided additional layers of understanding, moving from individual genes to the gene regulatory landscape, integrating regulatory information through cis-regulatory modules into cell type-specific gene regulatory programs. This review discusses our current understanding of the transcriptional control of mammalian skeletal development, focusing on recent genome-scale studies.
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Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature 2016; 538:265-269. [DOI: 10.1038/nature19800] [Citation(s) in RCA: 455] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 08/23/2016] [Indexed: 01/10/2023]
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Reynard LN, Ratnayake M, Santibanez-Koref M, Loughlin J. Functional Characterization of the Osteoarthritis Susceptibility Mapping to CHST11-A Bioinformatics and Molecular Study. PLoS One 2016; 11:e0159024. [PMID: 27391021 PMCID: PMC4938163 DOI: 10.1371/journal.pone.0159024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/24/2016] [Indexed: 02/07/2023] Open
Abstract
The single nucleotide polymorphism (SNP) rs835487 is associated with hip osteoarthritis (OA) at the genome-wide significance level and is located within CHST11, which codes for carbohydrate sulfotransferase 11. This enzyme post-translationally modifies proteoglycan prior to its deposition in the cartilage extracellular matrix. Using bioinformatics and experimental analyses, our aims were to characterise the rs835487 association signal and to identify the causal functional variant/s. Database searches revealed that rs835487 resides within a linkage disequilibrium (LD) block of only 2.7 kb and is in LD (r2 ≥ 0.8) with six other SNPs. These are all located within intron 2 of CHST11, in a region that has predicted enhancer activity and which shows a high degree of conservation in primates. Luciferase reporter assays revealed that of the seven SNPs, rs835487 and rs835488, which have a pairwise r2 of 0.962, are the top functional candidates; the haplotype composed of the OA-risk conferring G allele of rs835487 and the corresponding T allele of rs835488 (the G-T haplotype) demonstrated significantly different enhancer activity relative to the haplotype composed of the non-risk A allele of rs835487 and the corresponding C allele of rs835488 (the A-C haplotype) (p < 0.001). Electrophoretic mobility shift assays and supershifts identified several transcription factors that bind more strongly to the risk-conferring G and T alleles of the two SNPs, including SP1, SP3, YY1 and SUB1. CHST11 was found to be upregulated in OA versus non-OA cartilage (p < 0.001) and was expressed dynamically during chondrogenesis. Its expression in adult cartilage did not however correlate with rs835487 genotype. Our data demonstrate that the OA susceptibility is mediated by differential protein binding to the alleles of rs835487 and rs835488, which are located within an enhancer whose target may be CHST11 during chondrogenesis or an alternative gene.
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Affiliation(s)
- Louise N. Reynard
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
| | - Madhushika Ratnayake
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mauro Santibanez-Koref
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John Loughlin
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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Affiliation(s)
| | - Jeffrey Baron
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD.
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Liu CF, Lefebvre V. The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis. Nucleic Acids Res 2015; 43:8183-203. [PMID: 26150426 PMCID: PMC4787819 DOI: 10.1093/nar/gkv688] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/24/2015] [Indexed: 12/21/2022] Open
Abstract
SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We use here genome-wide approaches to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio. Using the RCS cell line as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes, we uncover that SOX6 and SOX9 bind thousands of genomic sites, frequently and most efficiently near each other. SOX9 recognizes pairs of inverted SOX motifs, whereas SOX6 favors pairs of tandem SOX motifs. The SOX proteins primarily target enhancers. While binding to a small fraction of typical enhancers, they bind multiple sites on almost all super-enhancers (SEs) present in RCS cells. These SEs are predominantly linked to cartilage-specific genes. The SOX proteins effectively work together to activate these SEs and are required for in vivo expression of their associated genes. These genes encode key regulatory factors, including the SOX trio proteins, and all essential cartilage extracellular matrix components. Chst11, Fgfr3, Runx2 and Runx3 are among many other newly identified SOX trio targets. SOX9 and SOX5/SOX6 thus cooperate genome-wide, primarily through SEs, to implement the growth plate chondrocyte differentiation program.
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Affiliation(s)
- Chia-Feng Liu
- Department of Cellular & Molecular Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Véronique Lefebvre
- Department of Cellular & Molecular Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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