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Tian B, Zhang L, Zheng J, Kang X. The role of NF-κB-SOX9 signalling pathway in osteoarthritis. Heliyon 2024; 10:e37191. [PMID: 39319133 PMCID: PMC11419907 DOI: 10.1016/j.heliyon.2024.e37191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 08/28/2024] [Accepted: 08/28/2024] [Indexed: 09/26/2024] Open
Abstract
The nuclear factor-κB (NF-κB) signalling pathway exists in a variety of cells and is involved in the gene regulation of various physiological and pathological processes such as inflammation, immunity, cell proliferation and apoptosis. It has been shown that this signaling pathway is also involved in numerous events associated with osteoarthritis, including chondrocyte catabolism, chondrocyte survival, and synovial inflammation. SRY-related high mobility group-box 9(SOX9) is the "master regulator" of chondrocytes and one of the key transcription factors that maintain chondrocyte phenotype and cartilage homeostasis. NF-κB can positively regulate the expression of SOX9 by directly binding to its promoter region, and play a role in the formation and development of chondrocytes. This article reviews the regulatory effect of the NF-κB-SOX9 signaling axis on osteoarthritis.
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Affiliation(s)
- Bin Tian
- Department of Sports Medicine, Honghui Hospital, Xi'an Jiao Tong University, Shaanxi, 710054, PR China
- Department of Orthopedics, the First Afffliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Liang Zhang
- Department of Sports Medicine, Honghui Hospital, Xi'an Jiao Tong University, Shaanxi, 710054, PR China
| | - Jiang Zheng
- Department of Sports Medicine, Honghui Hospital, Xi'an Jiao Tong University, Shaanxi, 710054, PR China
| | - Xin Kang
- Department of Sports Medicine, Honghui Hospital, Xi'an Jiao Tong University, Shaanxi, 710054, PR China
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2
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Naqvi S, Kim S, Tabatabaee S, Pampari A, Kundaje A, Pritchard JK, Wysocka J. Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596078. [PMID: 38853998 PMCID: PMC11160683 DOI: 10.1101/2024.05.28.596078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Deep learning approaches have made significant advances in predicting cell type-specific chromatin patterns from the identity and arrangement of transcription factor (TF) binding motifs. However, most models have been applied in unperturbed contexts, precluding a predictive understanding of how chromatin state responds to TF perturbation. Here, we used transfer learning to train and interpret deep learning models that use DNA sequence to predict, with accuracy approaching experimental reproducibility, how the concentration of two dosage-sensitive TFs (TWIST1, SOX9) affects regulatory element (RE) chromatin accessibility in facial progenitor cells. High-affinity motifs that allow for heterotypic TF co-binding and are concentrated at the center of REs buffer against quantitative changes in TF dosage and strongly predict unperturbed accessibility. In contrast, motifs with low-affinity or homotypic binding distributed throughout REs lead to sensitive responses with minimal contributions to unperturbed accessibility. Both buffering and sensitizing features show signatures of purifying selection. We validated these predictive sequence features using reporter assays and showed that a biophysical model of TF-nucleosome competition can explain the sensitizing effect of low-affinity motifs. Our approach of combining transfer learning and quantitative measurements of the chromatin response to TF dosage therefore represents a powerful method to reveal additional layers of the cis-regulatory code.
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Affiliation(s)
- Sahin Naqvi
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Lead contact
| | - Seungsoo Kim
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - Saman Tabatabaee
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joanna Wysocka
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
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3
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Hojo H, Ohba S. Runt-related Transcription Factors and Gene Regulatory Mechanisms in Skeletal Development and Diseases. Curr Osteoporos Rep 2023; 21:485-492. [PMID: 37436583 PMCID: PMC10543954 DOI: 10.1007/s11914-023-00808-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/13/2023]
Abstract
PURPOSE OF REVIEW Runt-related transcription factors (RUNX) play critical roles in skeletal development, metabolism, and diseases. In mammals, three RUNX members, namely RUNX1, RUNX2, and RUNX3, play distinct and redundant roles, although RUNX2 is a dominant factor in skeletal development and several skeletal diseases. This review is to provide an overview of the current understanding of RUNX-mediated transcriptional regulation in different skeletal cell types. RECENT FINDINGS Advances in chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) have revealed genome-wide RUNX-mediated gene regulatory mechanisms, including their association with cis-regulatory elements and putative target genes. Further studies with genome-wide analysis and biochemical assays have shed light on RUNX-mediated pioneering action and involvements of RUNX2 in lipid-lipid phase separation. Emerging multi-layered mechanisms of RUNX-mediated gene regulations help us better understanding of skeletal development and diseases, which also provides clues to think how genome-wide studies can help develop therapeutic strategies for skeletal diseases.
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Affiliation(s)
- Hironori Hojo
- Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655 Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8655 Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Graduate School of Dentistry, Osaka University, 1-8 Yamadaoka, Suita, Osaka 565-0871 Japan
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Di J, Chen Z, Wang Z, He T, Wu D, Weng C, Deng J, Mai L, Wang K, He L, Rong L. Cartilage tissue from sites of weight bearing in patients with osteoarthritis exhibits a differential phenotype with distinct chondrocytes subests. RMD Open 2023; 9:e003255. [PMID: 37848267 PMCID: PMC10582868 DOI: 10.1136/rmdopen-2023-003255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/12/2023] [Indexed: 10/19/2023] Open
Abstract
OBJECTIVE Osteoarthritis (OA) is a degenerative joint disease associated with excessive mechanical loading. The aim here was to elucidate whether different subpopulations of chondrocytes exhibit distinct phenotypes in response to variations in loading conditions. Furthermore, we seek to investigate the transcriptional switches and cell crosstalk among these chondrocytes subsets. METHODS Proteomic analysis was performed on cartilage tissues isolated from weight-bearing and non-weight-bearing regions. Additionally, single-cell RNA sequencing was employed to identify different subsets of chondrocytes. For disease-specific cells, in vitro differentiation induction was performed, and their presence was confirmed in human cartilage tissue sections using immunofluorescence. The molecular mechanisms underlying transcriptional changes in these cells were analysed through whole-transcriptome sequencing. RESULTS In the weight-bearing regions of OA cartilage tissue, a subpopulation of chondrocytes called OA hypertrophic chondrocytes (OAHCs) expressing the marker genes SLC39A14 and COL10A1 are present. These cells exhibit unique characteristics of active cellular interactions mediated by the TGFβ signalling pathway and express OA phenotypes, distinct from hypertrophic chondrocytes in healthy cartilage. OAHCs are mainly distributed in the superficial region of damaged cartilage in human OA tissue, and on TGFβ stimulation, exhibit activation of transcriptional expression of iron metabolism-related genes, along with enrichment of associated pathways. CONCLUSION This study identified and validated the existence of a subset of OAHCs in the weight-bearing area of OA cartilage tissue. Our findings provide a theoretical basis for targeting OAHCs to slow down the progression of OA and facilitate the repair of cartilage injuries.
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Affiliation(s)
- Jiawei Di
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
| | - Zihao Chen
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
| | - Zhe Wang
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Department of Joint Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tianwei He
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
| | - Depeng Wu
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
| | - Chuanggui Weng
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
| | - Jiajun Deng
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
| | - Lang Mai
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
| | - Kun Wang
- Department of Joint Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei He
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
| | - Limin Rong
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Engineering and Technology Research of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
- Guangdong Provincial Center for Quality Control of Minimally Invasive Spine Surgery, Guangzhou, Guangdong, China
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Matsuoka K, Bakiri L, Bilban M, Toegel S, Haschemi A, Yuan H, Kasper M, Windhager R, Wagner EF. Metabolic rewiring controlled by c-Fos governs cartilage integrity in osteoarthritis. Ann Rheum Dis 2023; 82:1227-1239. [PMID: 37344157 PMCID: PMC10423482 DOI: 10.1136/ard-2023-224002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/11/2023] [Indexed: 06/23/2023]
Abstract
OBJECTIVES The activator protein-1 (AP-1) transcription factor component c-Fos regulates chondrocyte proliferation and differentiation, but its involvement in osteoarthritis (OA) has not been functionally assessed. METHODS c-Fos expression was evaluated by immunohistochemistry on articular cartilage sections from patients with OA and mice subjected to the destabilisation of the medial meniscus (DMM) model of OA. Cartilage-specific c-Fos knockout (c-FosΔCh) mice were generated by crossing c-fosfl/fl to Col2a1-CreERT mice. Articular cartilage was evaluated by histology, immunohistochemistry, RNA sequencing (RNA-seq), quantitative reverse transcription PCR (qRT-PCR) and in situ metabolic enzyme assays. The effect of dichloroacetic acid (DCA), an inhibitor of pyruvate dehydrogenase kinase (Pdk), was assessed in c-FosΔCh mice subjected to DMM. RESULTS FOS-positive chondrocytes were increased in human and murine OA cartilage during disease progression. Compared with c-FosWT mice, c-FosΔCh mice exhibited exacerbated DMM-induced cartilage destruction. Chondrocytes lacking c-Fos proliferate less, have shorter collagen fibres and reduced cartilage matrix. Comparative RNA-seq revealed a prominent anaerobic glycolysis gene expression signature. Consistently decreased pyruvate dehydrogenase (Pdh) and elevated lactate dehydrogenase (Ldh) enzymatic activities were measured in situ, which are likely due to higher expression of hypoxia-inducible factor-1α, Ldha, and Pdk1 in chondrocytes. In vivo treatment of c-FosΔCh mice with DCA restored Pdh/Ldh activity, chondrocyte proliferation, collagen biosynthesis and decreased cartilage damage after DMM, thereby reverting the deleterious effects of c-Fos inactivation. CONCLUSIONS c-Fos modulates cellular bioenergetics in chondrocytes by balancing pyruvate flux between anaerobic glycolysis and the tricarboxylic acid cycle in response to OA signals. We identify a novel metabolic adaptation of chondrocytes controlled by c-Fos-containing AP-1 dimers that could be therapeutically relevant.
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Affiliation(s)
- Kazuhiko Matsuoka
- Genes and Disease group, Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Cellular and Molecular Tumor biology, Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Latifa Bakiri
- Genes and Disease group, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Martin Bilban
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Core Facilities, Medical University of Vienna, Vienna, Austria
| | - Stefan Toegel
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Vienna, Austria
| | - Arvand Haschemi
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Hao Yuan
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Maria Kasper
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Reinhard Windhager
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, Vienna, Austria
| | - Erwin F Wagner
- Genes and Disease group, Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Genes and Disease group, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
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6
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Richard D, Pregizer S, Venkatasubramanian D, Raftery RM, Muthuirulan P, Liu Z, Capellini TD, Craft AM. Lineage-specific differences and regulatory networks governing human chondrocyte development. eLife 2023; 12:e79925. [PMID: 36920035 PMCID: PMC10069868 DOI: 10.7554/elife.79925] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 03/14/2023] [Indexed: 03/16/2023] Open
Abstract
To address large gaps in our understanding of the molecular regulation of articular and growth plate cartilage development in humans, we used our directed differentiation approach to generate these distinct cartilage tissues from human embryonic stem cells. The resulting transcriptomic profiles of hESC-derived articular and growth plate chondrocytes were similar to fetal epiphyseal and growth plate chondrocytes, with respect to genes both known and previously unknown to cartilage biology. With the goal to characterize the regulatory landscapes accompanying these respective transcriptomes, we mapped chromatin accessibility in hESC-derived chondrocyte lineages, and mouse embryonic chondrocytes, using ATAC-sequencing. Integration of the expression dataset with the differentially accessible genomic regions revealed lineage-specific gene regulatory networks. We validated functional interactions of two transcription factors (TFs) (RUNX2 in growth plate chondrocytes and RELA in articular chondrocytes) with their predicted genomic targets. The maps we provide thus represent a framework for probing regulatory interactions governing chondrocyte differentiation. This work constitutes a substantial step towards comprehensive and comparative molecular characterizations of distinct chondrogenic lineages and sheds new light on human cartilage development and biology.
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Affiliation(s)
- Daniel Richard
- Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Steven Pregizer
- Department of Orthopedic Research, Boston Children’s HospitalBostonUnited States
- Department of Orthopedic Surgery, Harvard Medical SchoolBostonUnited States
| | - Divya Venkatasubramanian
- Department of Orthopedic Research, Boston Children’s HospitalBostonUnited States
- Department of Orthopedic Surgery, Harvard Medical SchoolBostonUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Rosanne M Raftery
- Department of Orthopedic Research, Boston Children’s HospitalBostonUnited States
- Department of Orthopedic Surgery, Harvard Medical SchoolBostonUnited States
| | | | - Zun Liu
- Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Terence D Capellini
- Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - April M Craft
- Department of Orthopedic Research, Boston Children’s HospitalBostonUnited States
- Department of Orthopedic Surgery, Harvard Medical SchoolBostonUnited States
- Harvard Stem Cell InstituteCambridgeUnited States
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7
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Au TYK, Yip RKH, Wynn SL, Tan TY, Fu A, Geng YH, Szeto IYY, Niu B, Yip KY, Cheung MCH, Lovell-Badge R, Cheah KSE. Hypomorphic and dominant-negative impact of truncated SOX9 dysregulates Hedgehog-Wnt signaling, causing campomelia. Proc Natl Acad Sci U S A 2023; 120:e2208623119. [PMID: 36584300 PMCID: PMC9910594 DOI: 10.1073/pnas.2208623119] [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: 06/10/2022] [Accepted: 11/02/2022] [Indexed: 01/01/2023] Open
Abstract
Haploinsufficiency for SOX9, the master chondrogenesis transcription factor, can underlie campomelic dysplasia (CD), an autosomal dominant skeletal malformation syndrome, because heterozygous Sox9 null mice recapitulate the bent limb (campomelia) and some other phenotypes associated with CD. However, in vitro cell assays suggest haploinsufficiency may not apply for certain mutations, notably those that truncate the protein, but in these cases in vivo evidence is lacking and underlying mechanisms are unknown. Here, using conditional mouse mutants, we compared the impact of a heterozygous Sox9 null mutation (Sox9+/-) with the Sox9+/Y440X CD mutation that truncates the C-terminal transactivation domain but spares the DNA-binding domain. While some Sox9+/Y440X mice survived, all Sox9+/- mice died perinatally. However, the skeletal defects were more severe and IHH signaling in developing limb cartilage was significantly enhanced in Sox9+/Y440X compared with Sox9+/-. Activating Sox9Y440X specifically in the chondrocyte-osteoblast lineage caused milder campomelia, and revealed cell- and noncell autonomous mechanisms acting on chondrocyte differentiation and osteogenesis in the perichondrium. Transcriptome analyses of developing Sox9+/Y440X limbs revealed dysregulated expression of genes for the extracellular matrix, as well as changes consistent with aberrant WNT and HH signaling. SOX9Y440X failed to interact with β-catenin and was unable to suppress transactivation of Ihh in cell-based assays. We propose enhanced HH signaling in the adjacent perichondrium induces asymmetrically localized excessive perichondrial osteogenesis resulting in campomelia. Our study implicates combined haploinsufficiency/hypomorphic and dominant-negative actions of SOX9Y440X, cell-autonomous and noncell autonomous mechanisms, and dysregulated WNT and HH signaling, as the cause of human campomelia.
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Affiliation(s)
- Tiffany Y. K. Au
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Raymond K. H. Yip
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Sarah L. Wynn
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Tiong Y. Tan
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Alex Fu
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, New Territories, Shatin, Hong Kong SAR, China
| | - Yu Hong Geng
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Irene Y. Y. Szeto
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Ben Niu
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Kevin Y. Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, New Territories, Shatin, Hong Kong SAR, China
| | - Martin C. H. Cheung
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | | | - Kathryn S. E. Cheah
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
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8
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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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9
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Hojo H, Saito T, He X, Guo Q, Onodera S, Azuma T, Koebis M, Nakao K, Aiba A, Seki M, Suzuki Y, Okada H, Tanaka S, Chung UI, McMahon AP, Ohba S. Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages. Cell Rep 2022; 40:111315. [PMID: 36070691 PMCID: PMC9510047 DOI: 10.1016/j.celrep.2022.111315] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/31/2022] [Accepted: 08/15/2022] [Indexed: 12/12/2022] Open
Abstract
The transcriptional regulator Runx2 (runt-related transcription factor 2) has essential but distinct roles in osteoblasts and chondrocytes in skeletal development. However, Runx2-mediated regulatory mechanisms underlying the distinctive programming of osteoblasts and chondrocytes are not well understood. Here, we perform an integrative analysis to investigate Runx2-DNA binding and chromatin accessibility ex vivo using neonatal osteoblasts and chondrocytes. We find that Runx2 engages with cell-type-distinct chromatin-accessible regions, potentially interacting with different combinations of transcriptional regulators, forming cell-type-specific hotspots, and potentiating chromatin accessibility. Genetic analysis and direct cellular reprogramming studies suggest that Runx2 is essential for establishment of chromatin accessibility in osteoblasts. Functional enhancer studies identify an Sp7 distal enhancer driven by Runx2-dependent binding and osteoblast-specific chromatin accessibility, contributing to normal osteoblast differentiation. Our findings provide a framework for understanding the regulatory landscape encompassing Runx2-mediated and cell-type-distinct enhancer networks that underlie the specification of osteoblasts. Hojo et al. investigate the gene-regulatory landscape underlying specification of skeletal cell types in neonatal mice. Runx2, an osteoblast determinant, engages with cell-type-distinct chromatin-accessible regions and is essential for establishment of chromatin accessibility in osteoblasts. The study provides insights into enhancer networks in skeletal development.
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Affiliation(s)
- Hironori Hojo
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Taku Saito
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Xinjun He
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shoko Onodera
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Toshifumi Azuma
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Michinori Koebis
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kazuki Nakao
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hiroyuki Okada
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Sakae Tanaka
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ung-Il Chung
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shinsuke Ohba
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan; Department of Oral Anatomy and Developmental Biology, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan.
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10
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Gomez-Picos P, Ovens K, Eames BF. Limb Mesoderm and Head Ectomesenchyme Both Express a Core Transcriptional Program During Chondrocyte Differentiation. Front Cell Dev Biol 2022; 10:876825. [PMID: 35784462 PMCID: PMC9247276 DOI: 10.3389/fcell.2022.876825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
To explain how cartilage appeared in different parts of the vertebrate body at discrete times during evolution, we hypothesize that different embryonic populations co-opted expression of a core gene regulatory network (GRN) driving chondrocyte differentiation. To test this hypothesis, laser-capture microdissection coupled with RNA-seq was used to reveal chondrocyte transcriptomes in the developing chick humerus and ceratobranchial, which are mesoderm- and neural crest-derived, respectively. During endochondral ossification, two general types of chondrocytes differentiate. Immature chondrocytes (IMM) represent the early stages of cartilage differentiation, while mature chondrocytes (MAT) undergo additional stages of differentiation, including hypertrophy and stimulating matrix mineralization and degradation. Venn diagram analyses generally revealed a high degree of conservation between chondrocyte transcriptomes of the limb and head, including SOX9, COL2A1, and ACAN expression. Typical maturation genes, such as COL10A1, IBSP, and SPP1, were upregulated in MAT compared to IMM in both limb and head chondrocytes. Gene co-expression network (GCN) analyses of limb and head chondrocyte transcriptomes estimated the core GRN governing cartilage differentiation. Two discrete portions of the GCN contained genes that were differentially expressed in limb or head chondrocytes, but these genes were enriched for biological processes related to limb/forelimb morphogenesis or neural crest-dependent processes, respectively, perhaps simply reflecting the embryonic origin of the cells. A core GRN driving cartilage differentiation in limb and head was revealed that included typical chondrocyte differentiation and maturation markers, as well as putative novel "chondrocyte" genes. Conservation of a core transcriptional program during chondrocyte differentiation in both the limb and head suggest that the same core GRN was co-opted when cartilage appeared in different regions of the skeleton during vertebrate evolution.
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Affiliation(s)
- Patsy Gomez-Picos
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Katie Ovens
- Department of Computer Science, University of Calgary, Calgary, AB, Canada
| | - B. Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
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11
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Thielen NGM, Neefjes M, Vitters EL, van Beuningen HM, Blom AB, Koenders MI, van Lent PLEM, van de Loo FAJ, Blaney Davidson EN, van Caam APM, van der Kraan PM. Identification of Transcription Factors Responsible for a Transforming Growth Factor-β-Driven Hypertrophy-like Phenotype in Human Osteoarthritic Chondrocytes. Cells 2022; 11:cells11071232. [PMID: 35406794 PMCID: PMC8998018 DOI: 10.3390/cells11071232] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/18/2022] Open
Abstract
During osteoarthritis (OA), hypertrophy-like chondrocytes contribute to the disease process. TGF-β's signaling pathways can contribute to a hypertrophy(-like) phenotype in chondrocytes, especially at high doses of TGF-β. In this study, we examine which transcription factors (TFs) are activated and involved in TGF-β-dependent induction of a hypertrophy-like phenotype in human OA chondrocytes. We found that TGF-β, at levels found in synovial fluid in OA patients, induces hypertrophic differentiation, as characterized by increased expression of RUNX2, COL10A1, COL1A1, VEGFA and IHH. Using luciferase-based TF activity assays, we observed that the expression of these hypertrophy genes positively correlated to SMAD3:4, STAT3 and AP1 activity. Blocking these TFs using specific inhibitors for ALK-5-induced SMAD signaling (5 µM SB-505124), JAK-STAT signaling (1 µM Tofacitinib) and JNK signaling (10 µM SP-600125) led to the striking observation that only SB-505124 repressed the expression of hypertrophy factors in TGF-β-stimulated chondrocytes. Therefore, we conclude that ALK5 kinase activity is essential for TGF-β-induced expression of crucial hypertrophy factors in chondrocytes.
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12
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Shah K, Maradana MR, Joaquina Delàs M, Metidji A, Graelmann F, Llorian M, Chakravarty P, Li Y, Tolaini M, Shapiro M, Kelly G, Cheshire C, Bhurta D, Bharate SB, Stockinger B. Cell-intrinsic Aryl Hydrocarbon Receptor signalling is required for the resolution of injury-induced colonic stem cells. Nat Commun 2022; 13:1827. [PMID: 35383166 PMCID: PMC8983642 DOI: 10.1038/s41467-022-29098-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/23/2022] [Indexed: 12/17/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is an environmental sensor that integrates microbial and dietary cues to influence physiological processes within the intestinal microenvironment, protecting against colitis and colitis-associated colorectal cancer development. Rapid tissue regeneration upon injury is important for the reinstatement of barrier integrity and its dysregulation promotes malignant transformation. Here we show that AHR is important for the termination of the regenerative response and the reacquisition of mature epithelial cell identity post injury in vivo and in organoid cultures in vitro. Using an integrative multi-omics approach in colon organoids, we show that AHR is required for timely termination of the regenerative response through direct regulation of transcription factors involved in epithelial cell differentiation as well as restriction of chromatin accessibility to regeneration-associated Yap/Tead transcriptional targets. Safeguarding a regulated regenerative response places AHR at a pivotal position in the delicate balance between controlled regeneration and malignant transformation. Rapid intestinal regeneration after injury is critical to maintain barrier integrity and homeostasis, but must be tightly controlled to prevent tumorigenesis. Here they show that the aryl hydrocarbon receptor is required to terminate the regenerative response after wound healing.
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Affiliation(s)
| | | | | | - Amina Metidji
- Department of Oncology, St Jude Children's Hospital, Memphis, TN, USA
| | - Frederike Graelmann
- Immunology and Environment, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | | | - Ying Li
- The Francis Crick Institute, London, UK
| | | | | | | | | | - Deendyal Bhurta
- Natural Products & Medicinal Chemistry Division, CSIR - Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR - Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
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13
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The Evolution of Biomineralization through the Co-Option of Organic Scaffold Forming Networks. Cells 2022; 11:cells11040595. [PMID: 35203246 PMCID: PMC8870065 DOI: 10.3390/cells11040595] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/05/2022] Open
Abstract
Biomineralization is the process in which organisms use minerals to generate hard structures like teeth, skeletons and shells. Biomineralization is proposed to have evolved independently in different phyla through the co-option of pre-existing developmental programs. Comparing the gene regulatory networks (GRNs) that drive biomineralization in different species could illuminate the molecular evolution of biomineralization. Skeletogenesis in the sea urchin embryo was extensively studied and the underlying GRN shows high conservation within echinoderms, larval and adult skeletogenesis. The organic scaffold in which the calcite skeletal elements form in echinoderms is a tubular compartment generated by the syncytial skeletogenic cells. This is strictly different than the organic cartilaginous scaffold that vertebrates mineralize with hydroxyapatite to make their bones. Here I compare the GRNs that drive biomineralization and tubulogenesis in echinoderms and in vertebrates. The GRN that drives skeletogenesis in the sea urchin embryo shows little similarity to the GRN that drives bone formation and high resemblance to the GRN that drives vertebrates’ vascular tubulogenesis. On the other hand, vertebrates’ bone-GRNs show high similarity to the GRNs that operate in the cells that generate the cartilage-like tissues of basal chordate and invertebrates that do not produce mineralized tissue. These comparisons suggest that biomineralization in deuterostomes evolved through the phylum specific co-option of GRNs that control distinct organic scaffolds to mineralization.
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14
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Ohba S. Genome-scale actions of master regulators directing skeletal development. JAPANESE DENTAL SCIENCE REVIEW 2021; 57:217-223. [PMID: 34745394 PMCID: PMC8556520 DOI: 10.1016/j.jdsr.2021.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/14/2021] [Accepted: 10/10/2021] [Indexed: 11/03/2022] Open
Abstract
The mammalian skeleton develops through two distinct modes of ossification: intramembranous ossification and endochondral ossification. During the process of skeletal development, SRY-box containing gene 9 (Sox9), runt-related transcription factor 2 (Runx2), and Sp7 work as master transcription factors (TFs) or transcriptional regulators, underlying cell fate specification of the two distinct populations: bone-forming osteoblasts and cartilage-forming chondrocytes. In the past two decades, core transcriptional circuits underlying skeletal development have been identified mainly through mouse genetics and biochemical approaches. Recently emerging next-generation sequencer (NGS)-based studies have provided genome-scale views on the gene regulatory landscape programmed by the master TFs/transcriptional regulators. With particular focus on Sox9, Runx2, and Sp7, this review aims to discuss the gene regulatory landscape in skeletal development, which has been identified by genome-scale data, and provide future perspectives in this field.
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Affiliation(s)
- Shinsuke Ohba
- Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
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15
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Ono K, Hata K, Nakamura E, Ishihara S, Kobayashi S, Nakanishi M, Yoshida M, Takahata Y, Murakami T, Takenoshita S, Komori T, Nishimura R, Yoneda T. Dmrt2 promotes transition of endochondral bone formation by linking Sox9 and Runx2. Commun Biol 2021; 4:326. [PMID: 33707608 PMCID: PMC7952723 DOI: 10.1038/s42003-021-01848-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
Endochondral bone formation is fundamental for skeletal development. During this process, chondrocytes undergo multiple steps of differentiation and coordinated transition from a proliferating to a hypertrophic stage, which is critical to advance skeletal development. Here, we identified the transcription factor Dmrt2 (double-sex and mab-3 related transcription factor 2) as a Sox9-inducible gene that promotes chondrocyte hypertrophy in pre-hypertrophic chondrocytes. Epigenetic analysis further demonstrated that Sox9 regulates Dmrt2 expression through an active enhancer located 18 kb upstream of the Dmrt2 gene and that this enhancer's chromatin status is progressively activated through chondrocyte differentiation. Dmrt2-knockout mice exhibited a dwarf phenotype with delayed initiation of chondrocyte hypertrophy. Dmrt2 augmented hypertrophic chondrocyte gene expression including Ihh through physical and functional interaction with Runx2. Furthermore, Dmrt2 deficiency reduced Runx2-dependent Ihh expression. Our findings suggest that Dmrt2 is critical for sequential chondrocyte differentiation during endochondral bone formation and coordinates the transcriptional network between Sox9 and Runx2.
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Affiliation(s)
- Koichiro Ono
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
- Department of Orthopedics, Nippon Medical School, Tokyo, Japan
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan.
| | - Eriko Nakamura
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Shota Ishihara
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Sachi Kobayashi
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Masako Nakanishi
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
- Department of Pathology, Wakayama Medical University, Wakayama, Japan
| | - Michiko Yoshida
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Yoshifumi Takahata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Tomohiko Murakami
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Seiichi Takenoshita
- Advanced Clinical Research Center, Fukushima Medical University, Fukushima, Japan
| | - Toshihisa Komori
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Riko Nishimura
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan.
| | - Toshiyuki Yoneda
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
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16
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Edelman HE, McClymont SA, Tucker TR, Pineda S, Beer RL, McCallion AS, Parsons MJ. SOX9 modulates cancer biomarker and cilia genes in pancreatic cancer. Hum Mol Genet 2021; 30:485-499. [PMID: 33693707 DOI: 10.1093/hmg/ddab064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/02/2021] [Accepted: 02/24/2021] [Indexed: 12/21/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive form of cancer with high mortality. The cellular origins of PDAC are largely unknown; however, ductal cells, especially centroacinar cells (CACs), have several characteristics in common with PDAC, such as expression of SOX9 and components of the Notch-signaling pathway. Mutations in KRAS and alterations to Notch signaling are common in PDAC, and both these pathways regulate the transcription factor SOX9. To identify genes regulated by SOX9, we performed siRNA knockdown of SOX9 followed by RNA-seq in PANC-1s, a human PDAC cell line. We report 93 differentially expressed (DE) genes, with convergence on alterations to Notch-signaling pathways and ciliogenesis. These results point to SOX9 and Notch activity being in a positive feedback loop and SOX9 regulating cilia production in PDAC. We additionally performed ChIP-seq in PANC-1s to identify direct targets of SOX9 binding and integrated these results with our DE gene list. Nine of the top 10 downregulated genes have evidence of direct SOX9 binding at their promoter regions. One of these targets was the cancer stem cell marker EpCAM. Using whole-mount in situ hybridization to detect epcam transcript in zebrafish larvae, we demonstrated that epcam is a CAC marker and that Sox9 regulation of epcam expression is conserved in zebrafish. Additionally, we generated an epcam null mutant and observed pronounced defects in ciliogenesis during development. Our results provide a link between SOX9, EpCAM and ciliary repression that can be exploited in improving our understanding of the cellular origins and mechanisms of PDAC.
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Affiliation(s)
- Hannah E Edelman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, 470 Miller Research Building, Baltimore, MD 21205, USA
| | - Sarah A McClymont
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, 470 Miller Research Building, Baltimore, MD 21205, USA
| | - Tori R Tucker
- Department of Developmental and Cell Biology, University of California, Irvine, Natural Sciences II, CA 92697, USA
| | - Santiago Pineda
- Department of Developmental and Cell Biology, University of California, Irvine, Natural Sciences II, CA 92697, USA
| | - Rebecca L Beer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, 470 Miller Research Building, Baltimore, MD 21205, USA
| | - Andrew S McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, 470 Miller Research Building, Baltimore, MD 21205, USA
| | - Michael J Parsons
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, 470 Miller Research Building, Baltimore, MD 21205, USA.,Department of Developmental and Cell Biology, University of California, Irvine, Natural Sciences II, CA 92697, USA
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17
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Shneider BL, Cortes-Santiago N, Schady DA, Krishnamoorthy S, Thevananther S, Rajapakshe K, Perera D, Huang S, Coarfa C. Constitutive activation of mitogen-activated protein kinase kinase (MEK1) in ileal enterocytes leads to dysplasia and a predisposition to cancer. Am J Physiol Gastrointest Liver Physiol 2021; 320:G366-G379. [PMID: 33470189 PMCID: PMC8202241 DOI: 10.1152/ajpgi.00065.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Activation of mitogen-activated protein kinases (MAPKs) is a key factor in the pathogenesis of cancer, although the specific role of mitogen-activated protein kinase kinase (MEK1) is not well understood. Villin promoter-driven Cre expression was used to excise a floxed stop cassette from a phosphomimetically constitutively activated MEK1 (caMEK1) expression construct in the intestine of C57BL/6 mice. Zygosity status of caMEK1 afforded assessment of the dose dependence of the effect. The expected mendelian distribution of genotypes and sex was observed in 443 progenies. Between 21 and 63 days of life, caMEK1 had no effect on body weight in male mice, but reduced body weight in female mice homozygous for caMEK1. At 10 wk of age, the ileum of caMEK1-expressing mice was characterized by the finding of dysplasia and profound changes in overall architecture. Paneth cells were nearly absent in caMEK1 homozygotes. Targeted proteomic profiling via reverse phase protein array analyses with confirmatory Western blotting revealed significant changes in protein and phosphoprotein expression, including upregulation of proteins downstream of MEK1, associated with enhanced markers of proliferation, diminished apoptosis, alterations in cell-fate determination, cell-cell interactions, and tight junctions. Long-term viability of caMEK1 homozygous mice was reduced with no survival beyond 1 yr. Invasive adenocarcinoma developed in three of ten older mice [15 wk (homozygous), 26 wk (homozygous), and 35 wk (heterozygous) of age]. Expression of caMEK1 in enterocytes leads to marked derangements in the intestinal epithelium, which is associated with a predisposition to the development of invasive cancer.NEW & NOTEWORTHY The ileum of mice with constitutive expression of activated MEK1 (via phosphomimetic changes) in enterocytes is markedly abnormal with architectural distortion and cytologic atypia, which evolves into an adenoma invasive carcinoma sequence. Phosphoproteomic analysis reveals upregulation of proteins downstream of MEK1, associated with enhanced markers of proliferation, diminished apoptosis, alterations in cell-fate determination, cell-cell interactions, and tight junctions. This novel model provides new insights into intestinal homeostasis and carcinogenesis.
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Affiliation(s)
- Benjamin L. Shneider
- 1Section of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | | | - Deborah A. Schady
- 2Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Swapna Krishnamoorthy
- 1Section of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Sundararajah Thevananther
- 1Section of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Kimal Rajapakshe
- 3Department of Molecular and Cellular Biology, Dan L. Duncan Comprehensive Cancer Center, Houston, Texas
| | - Dimuthu Perera
- 3Department of Molecular and Cellular Biology, Dan L. Duncan Comprehensive Cancer Center, Houston, Texas
| | - Shixia Huang
- 3Department of Molecular and Cellular Biology, Dan L. Duncan Comprehensive Cancer Center, Houston, Texas
| | - Cristian Coarfa
- 3Department of Molecular and Cellular Biology, Dan L. Duncan Comprehensive Cancer Center, Houston, Texas,4Center for Prevention and Environmental Health, Baylor College of Medicine, Houston, Texas
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18
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Ultra-processed food targets bone quality via endochondral ossification. Bone Res 2021; 9:14. [PMID: 33637698 PMCID: PMC7910299 DOI: 10.1038/s41413-020-00127-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/11/2020] [Accepted: 11/01/2020] [Indexed: 01/31/2023] Open
Abstract
Ultra-processed foods have known negative implications for health; however, their effect on skeletal development has never been explored. Here, we show that young rats fed ultra-processed food rich in fat and sugar suffer from growth retardation due to lesions in their tibial growth plates. The bone mineral density decreases significantly, and the structural parameters of the bone deteriorate, presenting a sieve-like appearance in the cortices and poor trabecular parameters in long bones and vertebrae. This results in inferior mechanical performance of the entire bone with a high fracture risk. RNA sequence analysis of the growth plates demonstrated an imbalance in extracellular matrix formation and degradation and impairment of proliferation, differentiation and mineralization processes. Our findings highlight, for the first time, the severe impact of consuming ultra-processed foods on the growing skeleton. This pathology extends far beyond that explained by the known metabolic effects, highlighting bone as a new target for studies of modern diets.
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19
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Xie J, Deng Z, Alahdal M, Liu J, Zhao Z, Chen X, Wang G, Hu X, Duan L, Wang D, Li W. Screening and verification of hub genes involved in osteoarthritis using bioinformatics. Exp Ther Med 2021; 21:330. [PMID: 33732303 PMCID: PMC7903481 DOI: 10.3892/etm.2021.9761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022] Open
Abstract
Osteoarthritis (OA) is one of the most common causes of disability and its development is associated with numerous factors. A major challenge in the treatment of OA is the lack of early diagnosis. In the present study, a bioinformatics method was employed to filter key genes that may be responsible for the pathogenesis of OA. From the Gene Expression Omnibus database, the datasets GSE55457, GSE12021 and GSE55325 were downloaded, which comprised 59 samples. Of these, 30 samples were from patients diagnosed with osteoarthritis and 29 were normal. Differentially expressed genes (DEGs) were obtained by downloading and analyzing the original data using bioinformatics. The Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathways were analyzed using the Database for Annotation, Visualization and Integrated Discovery online database. Protein-protein interaction network analysis was performed using the Search Tool for the Retrieval of Interacting Genes/proteins online database. BSCL2 lipid droplet biogenesis associated, seipin, FOS-like 2, activator protein-1 transcription factor subunit (FOSL2), cyclin-dependent kinase inhibitor 1A (CDKN1A) and kinectin 1 (KTN1) genes were identified as key genes by using Cytoscape software. Functional enrichment revealed that the DEGs were mainly accumulated in the ErbB, MAPK and PI3K-Akt pathways. Reverse transcription-quantitative PCR analysis confirmed a significant reduction in the expression levels of FOSL2, CDKN1A and KTN1 in OA samples. These genes have the potential to become novel diagnostic and therapeutic targets for OA.
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Affiliation(s)
- Junxiong Xie
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China.,University of South China, School of Clinical Medicine, Hengyang, Hunan 421001, P.R. China
| | - Zhiqin Deng
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China
| | - Murad Alahdal
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China
| | - Jianquan Liu
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China
| | - Zhe Zhao
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China
| | - Xiaoqiang Chen
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China
| | - Guanghui Wang
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China
| | - Xiaotian Hu
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China
| | - Li Duan
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China
| | - Daping Wang
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China.,University of South China, School of Clinical Medicine, Hengyang, Hunan 421001, P.R. China
| | - Wencui Li
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong 518000, P.R. China
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20
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Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful tool to identify binding profiles of transcriptional regulators and chromatin regulators as well as histone modification patterns in a genome-wide manner. ChIP-seq consists of five major steps: (1) preparation of cells and chromatin, (2) ChIP, (3) ChIP-seq library construction, (4) sequencing of ChIP DNA with a next-generation sequencer (NGS), and (5) computational analysis of sequence data. Recent ChIP-seq studies in skeletal tissues enable us to understand the modes of action of key skeletal regulators, functional interaction among the enhancers bound by the regulators, the complex nature of regulatory inputs, and thereby the gene regulatory landscape in skeletal development. Here we describe a ChIP-seq protocol that we have employed in our studies, with particular focus on chromatin preparation and subsequent ChIP in skeletal cells, including chondrocytes.
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Affiliation(s)
- Akira Yamakawa
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Shinsuke Ohba
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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21
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Neefjes M, van Caam APM, van der Kraan PM. Transcription Factors in Cartilage Homeostasis and Osteoarthritis. BIOLOGY 2020; 9:biology9090290. [PMID: 32937960 PMCID: PMC7563835 DOI: 10.3390/biology9090290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Osteoarthritis (OA) is the most common degenerative joint disease, and it is characterized by articular cartilage loss. In part, OA is caused by aberrant anabolic and catabolic activities of the chondrocyte, the only cell type present in cartilage. These chondrocyte activities depend on the intra- and extracellular signals that the cell receives and integrates into gene expression. The key proteins for this integration are transcription factors. A large number of transcription factors exist, and a better understanding of the transcription factors activated by the various signaling pathways active during OA can help us to better understand the complex etiology of OA. In addition, establishing such a profile can help to stratify patients in different subtypes, which can be a very useful approach towards personalized therapy. In this review, we discuss crucial transcription factors for extracellular matrix metabolism, chondrocyte hypertrophy, chondrocyte senescence, and autophagy in chondrocytes. In addition, we discuss how insight into these factors can be used for treatment purposes.
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22
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Ma SKY, Chan ASF, Rubab A, Chan WCW, Chan D. Extracellular Matrix and Cellular Plasticity in Musculoskeletal Development. Front Cell Dev Biol 2020; 8:781. [PMID: 32984311 PMCID: PMC7477050 DOI: 10.3389/fcell.2020.00781] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Cellular plasticity refers to the ability of cell fates to be reprogrammed given the proper signals, allowing for dedifferentiation or transdifferentiation into different cell fates. In vitro, this can be induced through direct activation of gene expression, however this process does not naturally occur in vivo. Instead, the microenvironment consisting of the extracellular matrix (ECM) and signaling factors, directs the signals presented to cells. Often the ECM is involved in regulating both biochemical and mechanical signals. In stem cell populations, this niche is necessary for maintenance and proper function of the stem cell pool. However, recent studies have demonstrated that differentiated or lineage restricted cells can exit their current state and transform into another state under different situations during development and regeneration. This may be achieved through (1) cells responding to a changing niche; (2) cells migrating and encountering a new niche; and (3) formation of a transitional niche followed by restoration of the homeostatic niche to sequentially guide cells along the regenerative process. This review focuses on examples in musculoskeletal biology, with the concept of ECM regulating cells and stem cells in development and regeneration, extending beyond the conventional concept of small population of progenitor cells, but under the right circumstances even “lineage-restricted” or differentiated cells can be reprogrammed to enter into a different fate.
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Affiliation(s)
- Sophia Ka Yan Ma
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | | | - Aqsa Rubab
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Wilson Cheuk Wing Chan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.,Department of Orthopedics Surgery and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.,The University of Hong Kong Shenzhen Institute of Research and Innovation (HKU-SIRI), Shenzhen, China
| | - Danny Chan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.,The University of Hong Kong Shenzhen Institute of Research and Innovation (HKU-SIRI), Shenzhen, China
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23
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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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24
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Cheung K, Barter MJ, Falk J, Proctor CJ, Reynard LN, Young DA. Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity. FASEB J 2020; 34:5317-5331. [PMID: 32058623 PMCID: PMC7187454 DOI: 10.1096/fj.201902061rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterized the epigenome during the in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next‐generation sequencing (ChIP‐seq) was used to assess a range of N‐terminal posttranscriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3, and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterized using histone ChIP‐seq and cis‐regulatory elements were identified in chondrocytes. Chondrocyte enhancers were associated with chondrogenesis‐related gene ontology (GO) terms. In silico analysis and integration of DNA methylation data with chondrogenesis chromatin states revealed that enhancers marked by histone marks H3K4me1 and H3K27ac were de‐methylated during in vitro chondrogenesis. Similarity analysis between hMSC and chondrocyte chromatin states defined in this study with epigenomes of cell‐types defined by the Roadmap Epigenomics project revealed that enhancers are more distinct between cell‐types compared to other chromatin states. Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers. Luciferase reporter assays confirmed that chondrocyte enhancers characterized in this study exhibited enhancer activity which may be modulated by DNA methylation and SOX9 overexpression. Altogether, these integrated data illustrate the cross‐talk between different epigenetic mechanisms during chondrocyte differentiation.
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Affiliation(s)
- Kathleen Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Julia Falk
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Carole J Proctor
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Louise N Reynard
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
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25
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Sox100B Regulates Progenitor-Specific Gene Expression and Cell Differentiation in the Adult Drosophila Intestine. Stem Cell Reports 2020; 14:226-240. [PMID: 32032550 PMCID: PMC7013235 DOI: 10.1016/j.stemcr.2020.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 01/03/2020] [Accepted: 01/08/2020] [Indexed: 01/30/2023] Open
Abstract
Robust production of terminally differentiated cells from self-renewing resident stem cells is essential to maintain proper tissue architecture and physiological functions, especially in high-turnover tissues. However, the transcriptional networks that precisely regulate cell transition and differentiation are poorly understood in most tissues. Here, we identified Sox100B, a Drosophila Sox E family transcription factor, as a critical regulator of adult intestinal stem cell differentiation. Sox100B is expressed in stem and progenitor cells and required for differentiation of enteroblast progenitors into absorptive enterocytes. Mechanistically, Sox100B regulates the expression of another critical stem cell differentiation factor, Sox21a. Supporting a direct control of Sox21a by Sox100B, we identified a Sox21a intronic enhancer that is active in all intestinal progenitors and directly regulated by Sox100B. Taken together, our results demonstrate that the activity and regulation of two Sox transcription factors are essential to coordinate stem cell differentiation and proliferation and maintain intestinal tissue homeostasis. Sox100B is expressed in progenitor cells in the adult intestine Sox100B is required for stem cell differentiation Sox100B is required for Sox21a expression Sox100B directly controls the activity of a Sox21a intronic enhancer
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26
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Liao J, Zhang Z, Jia X, Zou Z, Liang K, Wang Y. Transcriptional Regulation of Vih by Oct4 and Sox9 in Scylla paramamosain. Front Endocrinol (Lausanne) 2020; 11:650. [PMID: 33178132 PMCID: PMC7593643 DOI: 10.3389/fendo.2020.00650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/10/2020] [Indexed: 01/28/2023] Open
Abstract
Mud crab (Scylla paramamosain) is one of the most economically-important marine crabs in China. However, research on mechanisms of reproductive regulation is not sufficient. Vitellogenesis-inhibiting hormone (VIH) is a member of the crustacean hyperglycemia hormones (CHH) family, which plays an essential role in the regulation of gonadal development and maturation in crustaceans, and current studies on the regulation of Vih transcription in crabs are relatively rare. Our previous studies on the transcriptional regulation of mud crab Vih (SpVih) have proved that the binding site of Oct4/Sox9 transcription factor may be the key region for positively regulating the expression of SpVih. In this study, the electrophoretic mobility shift assay (EMSA) experiment confirmed that the nuclear protein extracted from the eyestalk could bind to the key region of SpVih promoter, and these specific bindings were dependent on the presence of Oct4/Sox9 binding sites. Two specific binding complex bands were detected in the supershift group of EMSA supershift experiments by Oct4 and Sox9 antibodies, further confirming the specific recognition of these two transcription factors on the key regulatory region of SpVih. In vitro, Oct4 and Sox9 gene overexpression vectors and SpVih core promoter fragment vector were constructed and co-transfected into HEK293T cells. As a result, SpVih activity increased with the concentration of transcription factors. In vivo, when Oct4 and Sox9 dsRNA were injected into the eyestalks of mud crab, respectively, the expression level of SpVih decreased significantly after interference with Oct4 or Sox9, and the expression level of SpVtg in the ovary and hepatopancreatic increased. Both in vitro and in vivo experiments showed that Oct4 and Sox9 had a positive regulatory effect on SpVih. The GST pull-down experiment was carried out by purified Oct4 and Sox9 proteins, and the results showed that there was an interaction between them. It was speculated that they regulated the expression of SpVih through the interaction.
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Affiliation(s)
- Jiaqian Liao
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen, China
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiwei Jia
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen, China
| | - Zhihua Zou
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen, China
| | - Keying Liang
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen, China
| | - Yilei Wang
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen, China
- *Correspondence: Yilei Wang
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27
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Hojo H, Ohba S. Insights into Gene Regulatory Networks in Chondrocytes. Int J Mol Sci 2019; 20:ijms20246324. [PMID: 31847446 PMCID: PMC6940734 DOI: 10.3390/ijms20246324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
Abstract
Chondrogenesis is a key developmental process that molds the framework of our body and generates the skeletal tissues by coupling with osteogenesis. The developmental processes are well-coordinated by spatiotemporal gene expressions, which are hardwired with gene regulatory elements. Those elements exist as thousands of modules of DNA sequences on the genome. Transcription factors function as key regulatory proteins by binding to regulatory elements and recruiting cofactors. Over the past 30 years, extensive attempts have been made to identify gene regulatory mechanisms in chondrogenesis, mainly through biochemical approaches and genetics. More recently, newly developed next-generation sequencers (NGS) have identified thousands of gene regulatory elements on a genome scale, and provided novel insights into the multiple layers of gene regulatory mechanisms, including the modes of actions of transcription factors, post-translational histone modifications, chromatin accessibility, the concept of pioneer factors, and three-dimensional chromatin architecture. In this review, we summarize the studies that have improved our understanding of the gene regulatory mechanisms in chondrogenesis, from the historical studies to the more recent works using NGS. Finally, we consider the future perspectives, including efforts to improve our understanding of the gene regulatory landscape in chondrogenesis and potential applications to the treatment of chondrocyte-related diseases.
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Affiliation(s)
- Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan;
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan
| | - Shinsuke Ohba
- Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan
- Correspondence: ; Tel.: +81-95-819-7630
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28
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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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29
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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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30
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Bai Y, Gong X, Dou C, Cao Z, Dong S. Redox control of chondrocyte differentiation and chondrogenesis. Free Radic Biol Med 2019; 132:83-89. [PMID: 30394290 DOI: 10.1016/j.freeradbiomed.2018.10.443] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 10/14/2018] [Accepted: 10/26/2018] [Indexed: 11/24/2022]
Abstract
Chondrogenesis involves the recruitment and migration of mesenchymal cells, mesenchymal condensation, and chondrocyte differentiation and hypertrophy. Multiple factors precisely regulate chondrogenesis. Recent studies have demonstrated that the redox status of chondrocytes plays an essential role in the regulation of chondrocyte differentiation and chondrogenesis. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are important factors that change the intracellular redox status. Physiological levels of ROS/RNS act as intracellular signals in chondrocytes, and oxidative stress impairs the metabolism of chondrocytes. Under physiological conditions, the balance between ROS/RNS production and elimination ensures that redox-sensitive signalling proteins function correctly. The redox homeostasis of chondrocytes ensures that they respond appropriately to endogenous and exogenous stimuli. This review focuses on the redox regulation of key signalling pathways and transcription factors that control chondrogenesis and chondrocyte differentiation. Additionally, the mechanism by which ROS/RNS regulate signalling proteins and transcription factors in chondrocytes is also reviewed.
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Affiliation(s)
- Yun Bai
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University, Gaotanyan Street No.30, Chongqing 400038, China
| | - Xiaoshan Gong
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University, Gaotanyan Street No.30, Chongqing 400038, China
| | - Ce Dou
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University, Gaotanyan Street No.30, Chongqing 400038, China
| | - Zhen Cao
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University, Gaotanyan Street No.30, Chongqing 400038, China
| | - Shiwu Dong
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University, Gaotanyan Street No.30, Chongqing 400038, China; State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China.
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31
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Abstract
Accumulating evidence supports the idea that stem and progenitor cells play important roles in skeletal development. Over the last decade, the definition of skeletal stem and progenitor cells has evolved from cells simply defined by their in vitro behaviors to cells fully defined by a combination of sophisticated approaches, including serial transplantation assays and in vivo lineage-tracing experiments. These approaches have led to better identification of the characteristics of skeletal stem cells residing in multiple sites, including the perichondrium of the fetal bone, the resting zone of the postnatal growth plate, the bone marrow space and the periosteum in adulthood. These diverse groups of skeletal stem cells appear to closely collaborate and achieve a number of important biological functions of bones, including not only bone development and growth, but also bone maintenance and repair. Although these are important findings, we are only beginning to understand the diversity and the nature of skeletal stem and progenitor cells, and how they actually behave in vivo.
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Affiliation(s)
- Noriaki Ono
- University of Michigan School of Dentistry, Ann Arbor, MI, United States.
| | - Deepak H Balani
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Henry M Kronenberg
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
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32
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Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis. Sci Rep 2018; 8:15499. [PMID: 30341348 PMCID: PMC6195601 DOI: 10.1038/s41598-018-33779-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022] Open
Abstract
Osteoarthritis (OA) is a common joint disorder with increasing impact in an aging society. While genetic and transcriptomic analyses have revealed some genes and non-coding loci associated to OA, the pathogenesis remains incompletely understood. Chromatin profiling, which provides insight into gene regulation, has not been reported in OA mainly due to technical difficulties. Here, we employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients. We identified 109,215 accessible chromatin regions for cartilages, of which 71% were annotated as enhancers. By overlaying them with genetic and DNA methylation data, we have determined potential OA-relevant enhancers and their putative target genes. Furthermore, through integration with RNA-seq data, we characterized genes that are altered both at epigenomic and transcriptomic levels in OA. These genes are enriched in pathways regulating ossification and mesenchymal stem cell (MSC) differentiation. Consistently, the differentially accessible regions in OA are enriched for MSC-specific enhancers and motifs of transcription factor families involved in osteoblast differentiation. In conclusion, we demonstrate how direct chromatin profiling of clinical tissues can provide comprehensive epigenetic information for a disease and suggest candidate genes and enhancers of translational potential.
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33
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Li T, Huang H, Shi G, Zhao L, Li T, Zhang Z, Liu R, Hu Y, Liu H, Yu J, Li G. TGF-β1-SOX9 axis-inducible COL10A1 promotes invasion and metastasis in gastric cancer via epithelial-to-mesenchymal transition. Cell Death Dis 2018; 9:849. [PMID: 30154451 PMCID: PMC6113209 DOI: 10.1038/s41419-018-0877-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/22/2018] [Accepted: 06/13/2018] [Indexed: 12/14/2022]
Abstract
Molecular biomarkers that predict disease progression might promote drug development and therapeutic strategies in aggressive cancers, such as gastric cancer (GC). High-throughput mRNA sequencing (RNA-seq) revealed that collagen type X alpha 1 (COL10A1) is a disease progression-associated gene. Analysis of 103 GC patients showed that high COL10A1 mRNA expression was associated with GC metastasis and reduced survival. We analyzed the COL10A1 promoter using the UCSC genome website and JASPAR database, and we found potential SOX9 binding site. Here, we demonstrated that SOX9 and COL10A1 were both up-regulated in GC. We observed a positive correlation between the expression patterns of SOX9 and COL10A1 in GC cells and tissues. The results of electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP) assay and promoter reporter indicated that SOX9 could directly bind to the COL10A1 gene promoter and activate its transcription. Biological function experiments showed that COL10A1 regulated the migration and invasion of GC cells. Knockdown COL10A1 inhibited lung and abdominal cavity metastasis in a nude mouse model. Moreover, transforming growth factor-β1 (TGF-β1) treatment up-regulated the phosphorylation of Smad2 and increased SOX9 and COL10A1 expression. COL10A1 was confirmed to be a potential inducer of epithelial-to-mesenchymal transition (EMT). SOX9 was essential for COL10A1-mediated EMT, and cell migration, invasion and metastasis. Co-expression of SOX9 and COL10A1 was associated with tumor progression and was strongly predictive of overall survival in GC patients. In summary, this study elucidated the mechanistic link between COL10A1 and the TGF-β1-SOX9 axis. These findings indicated that COL10A1 might play a crucial role in GC progression and serve as a potential biomarker and therapeutic target in GC patients.
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Affiliation(s)
- Tingting Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haipeng Huang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Gastrointestinal Surgery, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Guangyao Shi
- Division of Cardiology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liying Zhao
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tuanjie Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ze Zhang
- Departments of Maxillofacial and Otorhinolaryngology Oncology; Department of Head and Neck Surgery, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ruoyan Liu
- Department of Gynecologic Oncology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yanfeng Hu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Liu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Jiang Yu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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34
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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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Nishimura R, Hata K, Nakamura E, Murakami T, Takahata Y. Transcriptional network systems in cartilage development and disease. Histochem Cell Biol 2018; 149:353-363. [PMID: 29308531 DOI: 10.1007/s00418-017-1628-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2017] [Indexed: 12/13/2022]
Abstract
Transcription factors play important roles in the regulation of cartilage development by controlling the expression of chondrogenic genes. Genetic studies have revealed that Sox9/Sox5/Sox6, Runx2/Runx3 and Osterix in particular are essential for the sequential steps of cartilage development. Importantly, these transcription factors form network systems that are also required for appropriate cartilage development. Molecular cloning approaches have largely contributed to the identification of several transcriptional partners for Sox9 and Runx2 during cartilage development. Although the importance of a negative-feedback loop between Indian hedgehog (Ihh) and parathyroid hormone-related protein (PTHrP) in chondrocyte hypertrophy has been well established, recent studies indicate that several transcription factors interact with the Ihh-PTHrP loop and demonstrated that Ihh has multiple functions in the regulation of cartilage development. The most common cartilage disorder, osteoarthritis, has been reported to result from the pathological action of several transcription factors, including Runx2, C/EBPβ and HIF-2α. On the other hand, NFAT family members appear to play roles in the protection of cartilage from osteoarthritis. It is also becoming important to understand the homeostasis and regulation of articular chondrocytes, because they have different cellular and molecular features from chondrocytes of the growth plate. This review summarizes the regulation and roles of transcriptional network systems in cartilage development and their pathological roles in osteoarthritis.
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Affiliation(s)
- Riko Nishimura
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eriko Nakamura
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomohiko Murakami
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshifumi Takahata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Abstract
Endochondral ossification is the fundamental process of skeletal development in vertebrates. Chondrocytes undergo sequential steps of differentiation, including mesenchymal condensation, proliferation, hypertrophy, and mineralization. These steps, which are required for the morphological and functional changes in differentiating chondrocytes, are strictly regulated by a complex transcriptional network. Biochemical and mice genetic studies identified chondrogenic transcription factors critical for endochondral ossification. The transcription factor sex-determining region Y (SRY)-box 9 (Sox9) is essential for early chondrogenesis, and impaired Sox9 function causes severe chondrodysplasia in humans and mice. In addition, recent genome-wide chromatin immunoprecipitation-sequencing studies revealed the precise regulatory mechanism of Sox9 during early chondrogenesis. Runt-related transcription factor 2 promotes chondrocyte hypertrophy and terminal differentiation. Interestingly, endoplasmic reticulum (ER) stress-related transcription factors have recently emerged as novel regulators of chondrocyte differentiation. Here we review the transcriptional mechanisms that regulate endochondral ossification, with a focus on Sox9.
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Affiliation(s)
- Kenji Hata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Yoshifumi Takahata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Tomohiko Murakami
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Riko Nishimura
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
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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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38
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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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Liu CF, Samsa WE, Zhou G, Lefebvre V. Transcriptional control of chondrocyte specification and differentiation. Semin Cell Dev Biol 2016; 62:34-49. [PMID: 27771362 DOI: 10.1016/j.semcdb.2016.10.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 12/20/2022]
Abstract
A milestone in the evolutionary emergence of vertebrates was the invention of cartilage, a tissue that has key roles in modeling, protecting and complementing the bony skeleton. Cartilage is elaborated and maintained by chondrocytes. These cells derive from multipotent skeletal progenitors and they perform highly specialized functions as they proceed through sequential lineage commitment and differentiation steps. They form cartilage primordia, the primary skeleton of the embryo. They then transform these primordia either into cartilage growth plates, temporary drivers of skeletal elongation and endochondral ossification, or into permanent tissues, namely articular cartilage. Chondrocyte fate decisions and differentiated activities are controlled by numerous extrinsic and intrinsic cues, and they are implemented at the gene expression level by transcription factors. The latter are the focus of this review. Meritorious efforts from many research groups have led over the last two decades to the identification of dozens of key chondrogenic transcription factors. These regulators belong to all types of transcription factor families. Some have master roles at one or several differentiation steps. They include SOX9 and RUNX2/3. Others decisively assist or antagonize the activities of these masters. They include TWIST1, SOX5/6, and MEF2C/D. Many more have tissue-patterning roles and regulate cell survival, proliferation and the pace of cell differentiation. They include, but are not limited to, homeodomain-containing proteins and growth factor signaling mediators. We here review current knowledge of all these factors, one superclass, class, and family at a time. We then compile all knowledge into transcriptional networks. We also identify remaining gaps in knowledge and directions for future research to fill these gaps and thereby provide novel insights into cartilage disease mechanisms and treatment options.
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Affiliation(s)
- Chia-Feng Liu
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA.
| | - William E Samsa
- Department of Orthopaedics, Case Western Reserve University, Cleveland, OH, USA
| | - Guang Zhou
- Department of Orthopaedics, Case Western Reserve University, Cleveland, OH, USA; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Véronique Lefebvre
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA.
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