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Warin J, Vedrenne N, Tam V, Zhu M, Yin D, Lin X, Guidoux-D’halluin B, Humeau A, Roseiro L, Paillat L, Chédeville C, Chariau C, Riemers F, Templin M, Guicheux J, Tryfonidou MA, Ho JW, David L, Chan D, Camus A. In vitro and in vivo models define a molecular signature reference for human embryonic notochordal cells. iScience 2024; 27:109018. [PMID: 38357665 PMCID: PMC10865399 DOI: 10.1016/j.isci.2024.109018] [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: 08/11/2023] [Revised: 11/13/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Understanding the emergence of human notochordal cells (NC) is essential for the development of regenerative approaches. We present a comprehensive investigation into the specification and generation of bona fide NC using a straightforward pluripotent stem cell (PSC)-based system benchmarked with human fetal notochord. By integrating in vitro and in vivo transcriptomic data at single-cell resolution, we establish an extended molecular signature and overcome the limitations associated with studying human notochordal lineage at early developmental stages. We show that TGF-β inhibition enhances the yield and homogeneity of notochordal lineage commitment in vitro. Furthermore, this study characterizes regulators of cell-fate decision and matrisome enriched in the notochordal niche. Importantly, we identify specific cell-surface markers opening avenues for differentiation refinement, NC purification, and functional studies. Altogether, this study provides a human notochord transcriptomic reference that will serve as a resource for notochord identification in human systems, diseased-tissues modeling, and facilitating future biomedical research.
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Affiliation(s)
- Julie Warin
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Nicolas Vedrenne
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
- Inserm, Univ. Limoges, Pharmacology & Transplantation, U1248, CHU Limoges, Service de Pharmacologie, toxicologie et pharmacovigilance, FHU SUPORT, 87000 Limoges, France
| | - Vivian Tam
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Mengxia Zhu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Danqing Yin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Xinyi Lin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Bluwen Guidoux-D’halluin
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Antoine Humeau
- Inserm, Univ. Limoges, Pharmacology & Transplantation, U1248, CHU Limoges, Service de Pharmacologie, toxicologie et pharmacovigilance, FHU SUPORT, 87000 Limoges, France
| | - Luce Roseiro
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Lily Paillat
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Claire Chédeville
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Caroline Chariau
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, 44000 Nantes, France
| | - Frank Riemers
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Markus Templin
- NMI Natural and Medical Sciences Institute, Markwiesenstraße 55, 72770 Reutlingen, Germany
| | - Jérôme Guicheux
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Marianna A. Tryfonidou
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Joshua W.K. Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Laurent David
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, 44000 Nantes, France
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Danny Chan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Anne Camus
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
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Veithen M, Huyghe A, Van Den Ackerveken P, Fukada SI, Kokubo H, Breuskin I, Nguyen L, Delacroix L, Malgrange B. Sox9 Inhibits Cochlear Hair Cell Fate by Upregulating Hey1 and HeyL Antagonists of Atoh1. Cells 2023; 12:2148. [PMID: 37681879 PMCID: PMC10486728 DOI: 10.3390/cells12172148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
It is widely accepted that cell fate determination in the cochlea is tightly controlled by different transcription factors (TFs) that remain to be fully defined. Here, we show that Sox9, initially expressed in the entire sensory epithelium of the cochlea, progressively disappears from differentiating hair cells (HCs) and is finally restricted to supporting cells (SCs). By performing ex vivo electroporation of E13.5-E14.5 cochleae, we demonstrate that maintenance of Sox9 expression in the progenitors committed to HC fate blocks their differentiation, even if co-expressed with Atoh1, a transcription factor necessary and sufficient to form HC. Sox9 inhibits Atoh1 transcriptional activity by upregulating Hey1 and HeyL antagonists, and genetic ablation of these genes induces extra HCs along the cochlea. Although Sox9 suppression from sensory progenitors ex vivo leads to a modest increase in the number of HCs, it is not sufficient in vivo to induce supernumerary HC production in an inducible Sox9 knockout model. Taken together, these data show that Sox9 is downregulated from nascent HCs to allow the unfolding of their differentiation program. This may be critical for future strategies to promote fully mature HC formation in regeneration approaches.
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Affiliation(s)
- Mona Veithen
- Laboratory of Developmental Neurobiology, GIGA-Neurosciences, University of Liege, 4000 Liege, Belgium; (M.V.); (A.H.); (P.V.D.A.); (I.B.); (L.D.)
| | - Aurélia Huyghe
- Laboratory of Developmental Neurobiology, GIGA-Neurosciences, University of Liege, 4000 Liege, Belgium; (M.V.); (A.H.); (P.V.D.A.); (I.B.); (L.D.)
| | - Priscilla Van Den Ackerveken
- Laboratory of Developmental Neurobiology, GIGA-Neurosciences, University of Liege, 4000 Liege, Belgium; (M.V.); (A.H.); (P.V.D.A.); (I.B.); (L.D.)
| | - So-ichiro Fukada
- Laboratory of Stem Cell Regeneration and Adaptation, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan;
| | - Hiroki Kokubo
- Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan;
| | - Ingrid Breuskin
- Laboratory of Developmental Neurobiology, GIGA-Neurosciences, University of Liege, 4000 Liege, Belgium; (M.V.); (A.H.); (P.V.D.A.); (I.B.); (L.D.)
| | - Laurent Nguyen
- Laboratory of Molecular Regulation of Neurogenesis, GIGA-Neurosciences, University of Liege, 4000 Liege, Belgium;
| | - Laurence Delacroix
- Laboratory of Developmental Neurobiology, GIGA-Neurosciences, University of Liege, 4000 Liege, Belgium; (M.V.); (A.H.); (P.V.D.A.); (I.B.); (L.D.)
| | - Brigitte Malgrange
- Laboratory of Developmental Neurobiology, GIGA-Neurosciences, University of Liege, 4000 Liege, Belgium; (M.V.); (A.H.); (P.V.D.A.); (I.B.); (L.D.)
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Liu H, Tsai H, Yang M, Li G, Bian Q, Ding G, Wu D, Dai J. Three-dimensional genome structure and function. MedComm (Beijing) 2023; 4:e326. [PMID: 37426677 PMCID: PMC10329473 DOI: 10.1002/mco2.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.
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Affiliation(s)
- Hao Liu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Hsiangyu Tsai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Maoquan Yang
- School of Clinical MedicineWeifang Medical UniversityWeifangChina
| | - Guozhi Li
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Qian Bian
- Shanghai Institute of Precision MedicineShanghaiChina
| | - Gang Ding
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Dandan Wu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Jiewen Dai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
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Bmp5 Mutation Alters mRNA Expression During External Ear Development. J Craniofac Surg 2023; 34:790-796. [PMID: 36166492 DOI: 10.1097/scs.0000000000009025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
To understand changes in gene regulation and mRNA expression in external ear development, we used a bone morphogenetic protein 5 (BMP5) short-ear mouse model. External ear tissues at E15.5 and E17.5 were collected, and mRNA expression profiles were analyzed. Upregulated and downregulated mRNA expression was identified using find_circ and CIRI2 software. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed using the differentially expressed mRNAs. Alterations in related signal pathways were identified from the upregulated and downregulated mRNA transcripts. The results showed a correlation between the mRNA expression during external ear development in BMP5 short-ear mice, including key regulatory mRNA changes after point mutations of the Bmp5 gene. This study provides evidence for the mechanism underlying mRNA regulation during external ear development. Changes in mRNA expression profiles also provide clues for future studies regarding the regulatory mechanisms underlying external ear development.
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Chen Q, Dai J, Bian Q. Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects. SCIENCE ADVANCES 2022; 8:eabo3648. [PMID: 36417512 PMCID: PMC9683718 DOI: 10.1126/sciadv.abo3648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Aberrations in tissue-specific enhancers underlie many developmental defects. Disrupting a noncoding region distal from the human SOX9 gene causes the Pierre Robin sequence (PRS) characterized by the undersized lower jaw. Such a craniofacial-specific defect has been previously linked to enhancers transiently active in cranial neural crest cells (CNCCs). We demonstrate that the PRS region also strongly regulates Sox9 in CNCC-derived Meckel's cartilage (MC), but not in limb cartilages, even after decommissioning of CNCC enhancers. Such an MC-specific regulatory effect correlates with the MC-specific chromatin contacts between the PRS region and Sox9, highlighting the importance of lineage-dependent chromatin topology in instructing enhancer usage. By integrating the enhancer signatures and chromatin topology, we uncovered >10,000 enhancers that function differentially between MC and limb cartilages and demonstrated their association with human diseases. Our findings provide critical insights for understanding the choreography of gene regulation during development and interpreting the genetic basis of craniofacial pathologies.
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Affiliation(s)
- Qiming Chen
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
| | - Jiewen Dai
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
- Corresponding author. (J.D.); (Q.B.)
| | - Qian Bian
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Corresponding author. (J.D.); (Q.B.)
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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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Transcriptome Analyses Provide Insights into the Auditory Function in Trachemys scripta elegans. Animals (Basel) 2022; 12:ani12182410. [PMID: 36139269 PMCID: PMC9495000 DOI: 10.3390/ani12182410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
An auditory ability is essential for communication in vertebrates, and considerable attention has been paid to auditory sensitivity in mammals, birds, and frogs. Turtles were thought to be deaf for a long time; however, recent studies have confirmed the presence of an auditory ability in Trachemys scripta elegans as well as sex-related differences in hearing sensitivity. Earlier studies mainly focused on the morphological and physiological functions of the hearing organ in turtles; thus, the gene expression patterns remain unclear. In this study, 36 transcriptomes from six tissues (inner ear, tympanic membrane, brain, eye, lung, and muscle) were sequenced to explore the gene expression patterns of the hearing system in T. scripta elegans. A weighted gene co-expression network analysis revealed that hub genes related to the inner ear and tympanic membrane are involved in development and signal transduction. Moreover, we identified six differently expressed genes (GABRA1, GABRG2, GABBR2, GNAO1, SLC38A1, and SLC12A5) related to the GABAergic synapse pathway as candidate genes to explain the differences in sexually dimorphic hearing sensitivity. Collectively, this study provides a critical foundation for genetic research on auditory functions in turtles.
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Hörnblad A, Remeseiro S. Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency. Cells 2022; 11:cells11091404. [PMID: 35563711 PMCID: PMC9105757 DOI: 10.3390/cells11091404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022] Open
Abstract
Genome architecture, epigenetics and enhancer function control the fate and identity of cells. Reprogramming to induced pluripotent stem cells (iPSCs) changes the transcriptional profile and chromatin landscape of the starting somatic cell to that of the pluripotent cell in a stepwise manner. Changes in the regulatory networks are tightly regulated during normal embryonic development to determine cell fate, and similarly need to function in cell fate control during reprogramming. Switching off the somatic program and turning on the pluripotent program involves a dynamic reorganization of the epigenetic landscape, enhancer function, chromatin accessibility and 3D chromatin topology. Within this context, we will review here the current knowledge on the processes that control the establishment and maintenance of pluripotency during somatic cell reprogramming.
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Affiliation(s)
- Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
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Migale R, Neumann M, Lovell-Badge R. Long-Range Regulation of Key Sex Determination Genes. Sex Dev 2021; 15:360-380. [PMID: 34753143 DOI: 10.1159/000519891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/26/2021] [Indexed: 11/19/2022] Open
Abstract
The development of sexually dimorphic gonads is a unique process that starts with the specification of the bipotential genital ridges and culminates with the development of fully differentiated ovaries and testes in females and males, respectively. Research on sex determination has been mostly focused on the identification of sex determination genes, the majority of which encode for proteins and specifically transcription factors such as SOX9 in the testes and FOXL2 in the ovaries. Our understanding of which factors may be critical for sex determination have benefited from the study of human disorders of sex development (DSD) and animal models, such as the mouse and the goat, as these often replicate the same phenotypes observed in humans when mutations or chromosomic rearrangements arise in protein-coding genes. Despite the advances made so far in explaining the role of key factors such as SRY, SOX9, and FOXL2 and the genes they control, what may regulate these factors upstream is not entirely understood, often resulting in the inability to correctly diagnose DSD patients. The role of non-coding DNA, which represents 98% of the human genome, in sex determination has only recently begun to be fully appreciated. In this review, we summarize the current knowledge on the long-range regulation of 2 important sex determination genes, SOX9 and FOXL2, and discuss the challenges that lie ahead and the many avenues of research yet to be explored in the sex determination field.
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Takano T, Ota H, Ohishi H, Hata K, Furukawa R, Nakabayashi K. Adult acampomelic campomelic dysplasia and disorders of sex development due to a reciprocal translocation involving chromosome 17q24.3 upstream of the SOX9 gene. Eur J Med Genet 2021; 64:104332. [PMID: 34481091 DOI: 10.1016/j.ejmg.2021.104332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/06/2021] [Accepted: 08/31/2021] [Indexed: 11/19/2022]
Abstract
Balanced chromosomal rearrangements with a breakpoint located upstream of the sex determining region Y-box 9 (SOX9) gene on chromosome 17q24.3 are associated with skeletal abnormalities, campomelic dysplasia (CMPD), or acampomelic campomelic dysplasia (ACMPD). We report on a female patient with a reciprocal translocation of t (11; 17) (p15.4; q24.3), who was diagnosed with acampomelic campomelic dysplasia. The 34-year-old Japanese patient presented with distinct skeletal abnormalities, profound intellectual disability, and female phenotype despite the presence of Y chromosome and the sex determining region Y (SRY) gene. Her menarche started at 33 years and 4 months after hormone therapy of estrogen therapy followed by estrogen progesterone therapy. By conducting whole genome sequencing followed by Sanger sequencing validation, we determined the precise breakpoint positions of the reciprocal translocation, one of which was located 203 kb upstream of the SOX9 gene. Considering the phenotypic variations previously reported among the CMPD/ACMPD patients with a chromosomal translocation in the vicinity of SOX9, the identified translocation was concluded to be responsible for all major phenotypes observed in the patient.
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Affiliation(s)
- Takako Takano
- Department of Child Health, Tokyo Kasei University, Tokyo, Japan; Department of Pediatrics, Tokyo Metropolitan Tobu Medical Center for Children with Developmental Disabilities, Tokyo, Japan.
| | - Hideomi Ota
- Department of Pediatrics, Tokyo Metropolitan Tobu Medical Center for Children with Developmental Disabilities, Tokyo, Japan
| | - Hajime Ohishi
- Department of Obstetrics and Gynecology, Center Hospital of the National Center for Global Health and Medicine, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Rieko Furukawa
- Department of Pediatric Medical Imaging, Jichi Children's Medical Center, Tochigi, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
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11
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Vining B, Ming Z, Bagheri-Fam S, Harley V. Diverse Regulation but Conserved Function: SOX9 in Vertebrate Sex Determination. Genes (Basel) 2021; 12:genes12040486. [PMID: 33810596 PMCID: PMC8066042 DOI: 10.3390/genes12040486] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022] Open
Abstract
Sex determination occurs early during embryogenesis among vertebrates. It involves the differentiation of the bipotential gonad to ovaries or testes by a fascinating diversity of molecular switches. In most mammals, the switch is SRY (sex determining region Y); in other vertebrates it could be one of a variety of genes including Dmrt1 or dmy. Downstream of the switch gene, SOX9 upregulation is a central event in testes development, controlled by gonad-specific enhancers across the 2 Mb SOX9 locus. SOX9 is a ‘hub’ gene of gonadal development, regulated positively in males and negatively in females. Despite this diversity, SOX9 protein sequence and function among vertebrates remains highly conserved. This article explores the cellular, morphological, and genetic mechanisms initiated by SOX9 for male gonad differentiation.
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Affiliation(s)
- Brittany Vining
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3800, Australia
| | - Zhenhua Ming
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3800, Australia
| | - Stefan Bagheri-Fam
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
| | - Vincent Harley
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3800, Australia
- Correspondence: ; Tel.: +61-3-8572-2527
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12
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Dissection of the Fgf8 regulatory landscape by in vivo CRISPR-editing reveals extensive intra- and inter-enhancer redundancy. Nat Commun 2021; 12:439. [PMID: 33469032 PMCID: PMC7815712 DOI: 10.1038/s41467-020-20714-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
Developmental genes are often regulated by multiple elements with overlapping activity. Yet, in most cases, the relative function of those elements and their contribution to endogenous gene expression remain poorly characterized. An example of this phenomenon is that distinct sets of enhancers have been proposed to direct Fgf8 in the limb apical ectodermal ridge and the midbrain-hindbrain boundary. Using in vivo CRISPR/Cas9 genome engineering, we functionally dissect this complex regulatory ensemble and demonstrate two distinct regulatory logics. In the apical ectodermal ridge, the control of Fgf8 expression appears distributed between different enhancers. In contrast, we find that in the midbrain-hindbrain boundary, one of the three active enhancers is essential while the other two are dispensable. We further dissect the essential midbrain-hindbrain boundary enhancer to reveal that it is also composed by a mixture of essential and dispensable modules. Cross-species transgenic analysis of this enhancer suggests that its composition may have changed in the vertebrate lineage.
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13
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Long HK, Osterwalder M, Welsh IC, Hansen K, Davies JOJ, Liu YE, Koska M, Adams AT, Aho R, Arora N, Ikeda K, Williams RM, Sauka-Spengler T, Porteus MH, Mohun T, Dickel DE, Swigut T, Hughes JR, Higgs DR, Visel A, Selleri L, Wysocka J. Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder. Cell Stem Cell 2020; 27:765-783.e14. [PMID: 32991838 PMCID: PMC7655526 DOI: 10.1016/j.stem.2020.09.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 01/09/2023]
Abstract
Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence (PRS). Leveraging a human stem cell differentiation model, we identify two clusters of enhancers within the PRS-associated region that regulate SOX9 expression during a restricted window of facial progenitor development at distances up to 1.45 Mb. Enhancers within the 1.45 Mb cluster exhibit highly synergistic activity that is dependent on the Coordinator motif. Using mouse models, we demonstrate that PRS phenotypic specificity arises from the convergence of two mechanisms: confinement of Sox9 dosage perturbation to developing facial structures through context-specific enhancer activity and heightened sensitivity of the lower jaw to Sox9 expression reduction. Overall, we characterize the longest-range human enhancers involved in congenital malformations, directly demonstrate that PRS is an enhanceropathy, and illustrate how small changes in gene expression can lead to morphological variation.
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Affiliation(s)
- Hannah K Long
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian C Welsh
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Karissa Hansen
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Yiran E Liu
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mervenaz Koska
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander T Adams
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Robert Aho
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kazuya Ikeda
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Ruth M Williams
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Tim Mohun
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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14
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Nakamichi R, Kurimoto R, Tabata Y, Asahara H. Transcriptional, epigenetic and microRNA regulation of growth plate. Bone 2020; 137:115434. [PMID: 32422296 PMCID: PMC7387102 DOI: 10.1016/j.bone.2020.115434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/13/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
Endochondral ossification is a critical event in bone formation, particularly in long shaft bones. Many cellular differentiation processes work in concert to facilitate the generation of cartilage primordium to formation of trabecular structures, all of which occur within the growth plate. Previous studies have revealed that the growth plate is tightly regulated by various transcription factors, epigenetic systems, and microRNAs. Hence, understanding these mechanisms that regulate the growth plate is crucial to furthering the current understanding on skeletal diseases, and in formulating effective treatment strategies. In this review, we focus on describing the function and mechanisms of the transcription factors, epigenetic systems, and microRNAs known to regulate the growth plate.
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Affiliation(s)
- Ryo Nakamichi
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MBB-102, La Jolla, CA 92037, USA; Department of Orthopaedic Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Ryota Kurimoto
- Department of Systems Biomedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yusuke Tabata
- Department of Orthopaedic Surgery, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan
| | - Hirosi Asahara
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MBB-102, La Jolla, CA 92037, USA; Department of Systems Biomedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
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15
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Chen CH, Zheng R, Tokheim C, Dong X, Fan J, Wan C, Tang Q, Brown M, Liu JS, Meyer CA, Liu XS. Determinants of transcription factor regulatory range. Nat Commun 2020; 11:2472. [PMID: 32424124 PMCID: PMC7235260 DOI: 10.1038/s41467-020-16106-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/14/2020] [Indexed: 01/03/2023] Open
Abstract
Characterization of the genomic distances over which transcription factor (TF) binding influences gene expression is important for inferring target genes from TF chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here we systematically examine the relationship between thousands of TF and histone modification ChIP-seq data sets with thousands of gene expression profiles. We develop a model for integrating these data, which reveals two classes of TFs with distinct ranges of regulatory influence, chromatin-binding preferences, and auto-regulatory properties. We find that the regulatory range of the same TF bound within different topologically associating domains (TADs) depend on intrinsic TAD properties such as local gene density and G/C content, but also on the TAD chromatin states. Our results suggest that considering TF type, binding distance to gene locus, as well as chromatin context is important in identifying implicated TFs from GWAS SNPs.
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Affiliation(s)
- Chen-Hao Chen
- Department of Data Sciences, Dana-Farber Cancer Institute. Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Biological and Biomedical Science Program, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rongbin Zheng
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Collin Tokheim
- Department of Data Sciences, Dana-Farber Cancer Institute. Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xin Dong
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jingyu Fan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Changxin Wan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qin Tang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Clifford A Meyer
- Department of Data Sciences, Dana-Farber Cancer Institute. Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - X Shirley Liu
- Department of Data Sciences, Dana-Farber Cancer Institute. Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Statistics, Harvard University, Cambridge, MA, USA.
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16
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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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17
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Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, Housman G, García-Pérez R, Lizano E, Cheronet O, Mallick S, Nieves-Colón MA, Li H, Alpaslan-Roodenberg S, Novak M, Gu H, Osinski JM, Ferrando-Bernal M, Gelabert P, Lipende I, Mjungu D, Kondova I, Bontrop R, Kullmer O, Weber G, Shahar T, Dvir-Ginzberg M, Faerman M, Quillen EE, Meissner A, Lahav Y, Kandel L, Liebergall M, Prada ME, Vidal JM, Gronostajski RM, Stone AC, Yakir B, Lalueza-Fox C, Pinhasi R, Reich D, Marques-Bonet T, Meshorer E, Carmel L. Differential DNA methylation of vocal and facial anatomy genes in modern humans. Nat Commun 2020; 11:1189. [PMID: 32132541 PMCID: PMC7055320 DOI: 10.1038/s41467-020-15020-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.
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Affiliation(s)
- David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Malka Nissim-Rafinia
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Lily Agranat-Tamir
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Swapan Mallick
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Heng Li
- Broad Institute, Cambridge, MA, 02138, USA
| | | | - Mario Novak
- Institute for Anthropological Research, 10000, Zagreb, Croatia
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | | | - Jason M Osinski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | | | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Iddi Lipende
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Deus Mjungu
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Ivanela Kondova
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ottmar Kullmer
- Department of Palaeoanthropology and Messel Research, Senckenberg Center of Human Evolution and Paleoecology, Frankfurt am Main, Germany
| | - Gerhard Weber
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Tal Shahar
- Department of Neurosurgery, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Mona Dvir-Ginzberg
- Laboratory of Cartilage Biology, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Marina Faerman
- Laboratory of Bioanthropology and Ancient DNA, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 85287, USA
| | - Alexander Meissner
- Broad Institute, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yonatan Lahav
- Otolaryngology - Head & Neck Surgery Department, Laryngeal Surgery Unit, Kaplan Medical Center, Rehovot, Israel
- The Hebrew University Medical School, Jerusalem, Israel
| | - Leonid Kandel
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Meir Liebergall
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - María E Prada
- I.E.S.O. 'Los Salados'. Junta de Castilla y León, León, Spain
| | - Julio M Vidal
- Junta de Castilla y León, Servicio de Cultura de León, León, Spain
| | - Richard M Gronostajski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
- Genetics, Genomics and Bioinformatics Program, New York State Center of Excellence in Bioinformatics and Life Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | - Benjamin Yakir
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - David Reich
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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18
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NOTO Transcription Factor Directs Human Induced Pluripotent Stem Cell-Derived Mesendoderm Progenitors to a Notochordal Fate. Cells 2020; 9:cells9020509. [PMID: 32102328 PMCID: PMC7072849 DOI: 10.3390/cells9020509] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022] Open
Abstract
The founder cells of the Nucleus pulposus, the centre of the intervertebral disc, originate in the embryonic notochord. After birth, mature notochordal cells (NC) are identified as key regulators of disc homeostasis. Better understanding of their biology has great potential in delaying the onset of disc degeneration or as a regenerative-cell source for disc repair. Using human pluripotent stem cells, we developed a two-step method to generate a stable NC-like population with a distinct molecular signature. Time-course analysis of lineage-specific markers shows that WNT pathway activation and transfection of the notochord-related transcription factor NOTO are sufficient to induce high levels of mesendoderm progenitors and favour their commitment toward the notochordal lineage instead of paraxial and lateral mesodermal or endodermal lineages. This study results in the identification of NOTO-regulated genes including some that are found expressed in human healthy disc tissue and highlights NOTO function in coordinating the gene network to human notochord differentiation.
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19
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Di Gregorio A. The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to vertebrates. Curr Top Dev Biol 2020; 139:325-374. [PMID: 32450965 DOI: 10.1016/bs.ctdb.2020.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The notochord is a structure required for support and patterning of all chordate embryos, from sea squirts to humans. An increasing amount of information on notochord development and on the molecular strategies that ensure its proper morphogenesis has been gleaned through studies in the sea squirt Ciona. This invertebrate chordate offers a fortunate combination of experimental advantages, ranging from translucent, fast-developing embryos to a compact genome and impressive biomolecular resources. These assets have enabled the rapid identification of numerous notochord genes and cis-regulatory regions, and provide a rather unique opportunity to reconstruct the gene regulatory network that controls the formation of this developmental and evolutionary chordate landmark. This chapter summarizes the morphogenetic milestones that punctuate notochord formation in Ciona, their molecular effectors, and the current knowledge of the gene regulatory network that ensures the accurate spatial and temporal orchestration of these processes.
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Affiliation(s)
- Anna Di Gregorio
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY, United States.
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20
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Barešić A, Nash AJ, Dahoun T, Howes O, Lenhard B. Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks. Mol Psychiatry 2020; 25:6-18. [PMID: 31616042 PMCID: PMC6906185 DOI: 10.1038/s41380-019-0518-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 06/18/2019] [Accepted: 07/09/2019] [Indexed: 01/30/2023]
Abstract
Recent genome-wide association studies have identified numerous loci associated with neuropsychiatric disorders. The majority of these are in non-coding regions, and are commonly assigned to the nearest gene along the genome. However, this approach neglects the three-dimensional organisation of the genome, and the fact that the genome contains arrays of extremely conserved non-coding elements termed genomic regulatory blocks (GRBs), which can be utilized to detect genes under long-range developmental regulation. Here we review a GRB-based approach to assign loci in non-coding regions to potential target genes, and apply it to reanalyse the results of one of the largest schizophrenia GWAS (SWG PGC, 2014). We further apply this approach to GWAS data from two related neuropsychiatric disorders-autism spectrum disorder and bipolar disorder-to show that it is applicable to developmental disorders in general. We find that disease-associated SNPs are overrepresented in GRBs and that the GRB model is a powerful tool for linking these SNPs to their correct target genes under long-range regulation. Our analysis identifies novel genes not previously implicated in schizophrenia and corroborates a number of predicted targets from the original study. The results are available as an online resource in which the genomic context and the strength of enhancer-promoter associations can be browsed for each schizophrenia-associated SNP.
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Affiliation(s)
- Anja Barešić
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Alexander Jolyon Nash
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Tarik Dahoun
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX37 JX, UK
| | - Oliver Howes
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008, Bergen, Norway.
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21
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Wakamatsu Y, Suzuki K. Sequence alteration in the enhancer contributes to the heterochronic Sox9 expression in marsupial cranial neural crest. Dev Biol 2019; 456:31-39. [PMID: 31430446 DOI: 10.1016/j.ydbio.2019.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 11/29/2022]
Abstract
Neonates of marsupial mammals are altricial at birth, because their gestation period is relatively short compared to placental mammals. Yet, as they need to travel to the teat from the birth canal, and suckle on the mother's milk, forelimbs and jaws develop significantly early. Previous studies in opossum (Monodelphis domestica), an experimental marsupial model, have revealed that cranial neural crest cells are generated significantly early compared to those in placental mammals, such as mouse, leading to an early development of jaw primordia. We have previously found that Sox9, an important neural crest-specifier gene, is expressed in the future cranial neural crest of the opossum embryonic ectoderm significantly earlier than that in mouse or quail embryos. As Sox9 is essential for neural crest formation in various vertebrates, it seems likely that the heterochronic expression of Sox9 is critical for the early cranial neural crest formation in the marsupial embryos. In this study, we show a marsupial-specific sequence in the Sox9 neural crest enhancer E3. We also reveal that the mouse E3 enhancer is activated in the cranial neural crest cells of quail embryos, that the E3 enhancer with marsupial-specific sequence is activated earlier in the Pax7-expressing neural border prior to the onset of endogenous Sox9 expression, and that a misexpression of cMyb, which is also a transcriptional activator of Pax7, in the neural border can ectopically activate the "marsupialized" enhancer. Thus, we suggest that the modification of the E3 enhancer sequence in the marsupial ancestor would have promoted the early expression of Sox9 in the neural border, facilitating the early formation of the cranial neural crest cells and the subsequent heterochronic development of the jaw primordia.
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Affiliation(s)
- Yoshio Wakamatsu
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan.
| | - Kunihiro Suzuki
- Department of Biology, Nihon University School of Dentistry at Matsudo, Chiba, 271-8587, Japan
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22
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Pasupathy M, Radhakrishnan V, Adenwalla HS, Narayanan PV. A case report of acampomelic campomelic dysplasia and operative difficulties in cleft palate reconstruction. Indian J Plast Surg 2019; 49:253-257. [PMID: 27833291 PMCID: PMC5053001 DOI: 10.4103/0970-0358.191310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Acampomelic campomelic dysplasia (CD) is a type of CD (CD; OMIM #114290), a rare form of congenital short-limbed dwarfism and is due to mutations in SOX9 gene family. Characteristic phenotypes of CD include bowing of the lower limbs, a narrow thoracic cage, 11 pairs of ribs, hypoplastic scapulae, macrocephaly, flattened supraorbital ridges and nasal bridge, cleft palate and micrognathia. The bending of the long bones is not an obligatory feature and is absent in about 10% of cases, referred to as acampomelic CD. A child previously diagnosed with acampomelic CD was brought to our outpatient clinic for cleft palate reconstruction. Our neurosurgeon cautioned us against performing surgery with extension of the neck in view of the possibility of producing quadriparesis, due to narrowing of the spinal canal as part of the osseous anomaly noted in the magnetic resonance imaging study of the spine, thus making the anaesthesia, surgical and post-operative procedures difficult. The cleft palate reconstruction was performed with all precautions and was uneventful.
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Affiliation(s)
- M Pasupathy
- The Charles Pinto Centre for Cleft Lip, Palate and Craniofacial Anomalies, Jubilee Mission Medical College and Research Institute, Trissur, Kerala, India
| | - Vasant Radhakrishnan
- The Charles Pinto Centre for Cleft Lip, Palate and Craniofacial Anomalies, Jubilee Mission Medical College and Research Institute, Trissur, Kerala, India
| | - Hirji Sorab Adenwalla
- Department of Plastic Surgery, Burns and The Charles Pinto Centre for Cleft Lip, Palate and Craniofacial Anomalies, Jubilee Mission Medical College and Research Institute, Trissur, Kerala, India
| | - Puthucode V Narayanan
- The Charles Pinto Centre for Cleft Lip, Palate and Craniofacial Anomalies, Jubilee Mission Medical College and Research Institute, Trissur, Kerala, India
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23
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Kawata M, Mori D, Kanke K, Hojo H, Ohba S, Chung UI, Yano F, Masaki H, Otsu M, Nakauchi H, Tanaka S, Saito T. Simple and Robust Differentiation of Human Pluripotent Stem Cells toward Chondrocytes by Two Small-Molecule Compounds. Stem Cell Reports 2019; 13:530-544. [PMID: 31402337 PMCID: PMC6739881 DOI: 10.1016/j.stemcr.2019.07.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 01/08/2023] Open
Abstract
A simple induction protocol to differentiate chondrocytes from pluripotent stem cells (PSCs) using small-molecule compounds is beneficial for cartilage regenerative medicine and mechanistic studies of chondrogenesis. Here, we demonstrate that chondrocytes are robustly induced from human PSCs by simple combination of two compounds, CHIR99021, a glycogen synthase kinase 3 inhibitor, and TTNPB, a retinoic acid receptor (RAR) agonist, under serum- and feeder-free conditions within 5-9 days. An excellent differentiation efficiency and potential to form hyaline cartilaginous tissues in vivo were demonstrated. Comprehensive gene expression and open chromatin analyses at each protocol stage revealed step-by-step differentiation toward chondrocytes. Genome-wide analysis of RAR and β-catenin association with DNA showed that retinoic acid and Wnt/β-catenin signaling collaboratively regulated the key marker genes at each differentiation stage. This method provides a promising cell source for regenerative medicine and, as an in vitro model, may facilitate elucidation of the molecular mechanisms underlying chondrocyte differentiation.
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Affiliation(s)
- Manabu Kawata
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Mori
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kosuke Kanke
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinsuke Ohba
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ung-Il Chung
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fumiko Yano
- Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Masaki
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Makoto Otsu
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sakae Tanaka
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taku Saito
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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24
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SOX9 in cartilage development and disease. Curr Opin Cell Biol 2019; 61:39-47. [PMID: 31382142 DOI: 10.1016/j.ceb.2019.07.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [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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25
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Wu N, Liu B, Du H, Zhao S, Li Y, Cheng X, Wang S, Lin J, Zhou J, Qiu G, Wu Z, Zhang J. The Progress of CRISPR/Cas9-Mediated Gene Editing in Generating Mouse/Zebrafish Models of Human Skeletal Diseases. Comput Struct Biotechnol J 2019; 17:954-962. [PMID: 31360334 PMCID: PMC6639410 DOI: 10.1016/j.csbj.2019.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/28/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
Genetic factors play a substantial role in the etiology of skeletal diseases, which involve 1) defects in skeletal development, including intramembranous ossification and endochondral ossification; 2) defects in skeletal metabolism, including late bone growth and bone remodeling; 3) defects in early developmental processes related to skeletal diseases, such as neural crest cell (NCC) and cilia functions; 4) disturbance of the cellular signaling pathways which potentially affect bone growth. Efficient and high-throughput genetic methods have enabled the exploration and verification of disease-causing genes and variants. Animal models including mouse and zebrafish have been extensively used in functional mechanism studies of causal genes and variants. The conventional approaches of generating mutant animal models include spontaneous mutagenesis, random integration, and targeted integration via mouse embryonic stem cells. These approaches are costly and time-consuming. Recent development and application of gene-editing tools, especially the CRISPR/Cas9 system, has significantly accelerated the process of gene-editing in diverse organisms. Here we review both mice and zebrafish models of human skeletal diseases generated by CRISPR/Cas9 system, and their contributions to deciphering the underpins of disease mechanisms.
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Affiliation(s)
- Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Bowen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yaqi Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Xi Cheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Junde Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | | | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
- Central Laboratory & Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Central Laboratory & Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
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26
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Wang L, Yang H, Zamperone A, Diolaiti D, Palmbos PL, Abel EV, Purohit V, Dolgalev I, Rhim AD, Ljungman M, Hadju CH, Halbrook CJ, Bar-Sagi D, di Magliano MP, Crawford HC, Simeone DM. ATDC is required for the initiation of KRAS-induced pancreatic tumorigenesis. Genes Dev 2019; 33:641-655. [PMID: 31048544 PMCID: PMC6546061 DOI: 10.1101/gad.323303.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/08/2019] [Indexed: 12/15/2022]
Abstract
Pancreatic adenocarcinoma (PDA) is an aggressive disease driven by oncogenic KRAS and characterized by late diagnosis and therapeutic resistance. Here we show that deletion of the ataxia-telangiectasia group D-complementing (Atdc) gene, whose human homolog is up-regulated in the majority of pancreatic adenocarcinoma, completely prevents PDA development in the context of oncogenic KRAS. ATDC is required for KRAS-driven acinar-ductal metaplasia (ADM) and its progression to pancreatic intraepithelial neoplasia (PanIN). As a result, mice lacking ATDC are protected from developing PDA. Mechanistically, we show ATDC promotes ADM progression to PanIN through activation of β-catenin signaling and subsequent SOX9 up-regulation. These results provide new insight into PDA initiation and reveal ATDC as a potential target for preventing early tumor-initiating events.
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Affiliation(s)
- Lidong Wang
- Department of Surgery, New York University School of Medicine, New York, New York 10016, USA.,Perlmutter Cancer Center, NYU Langone Medical Center, New York University, New York, New York 10016, USA
| | - Huibin Yang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andrea Zamperone
- Department of Surgery, New York University School of Medicine, New York, New York 10016, USA.,Perlmutter Cancer Center, NYU Langone Medical Center, New York University, New York, New York 10016, USA
| | - Daniel Diolaiti
- Department of Surgery, New York University School of Medicine, New York, New York 10016, USA.,Perlmutter Cancer Center, NYU Langone Medical Center, New York University, New York, New York 10016, USA
| | - Phillip L Palmbos
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ethan V Abel
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vinee Purohit
- Department of Surgery, New York University School of Medicine, New York, New York 10016, USA.,Perlmutter Cancer Center, NYU Langone Medical Center, New York University, New York, New York 10016, USA
| | - Igor Dolgalev
- Perlmutter Cancer Center, NYU Langone Medical Center, New York University, New York, New York 10016, USA
| | - Andrew D Rhim
- Department of Gastroenterology, Hepatology, and Nutrition, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Christina H Hadju
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
| | - Christopher J Halbrook
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Dafna Bar-Sagi
- Perlmutter Cancer Center, NYU Langone Medical Center, New York University, New York, New York 10016, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.,Department of Medicine, New York University School of Medicine, New York, New York 10016, USA
| | - Marina Pasca di Magliano
- Department of Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Howard C Crawford
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Diane M Simeone
- Department of Surgery, New York University School of Medicine, New York, New York 10016, USA.,Perlmutter Cancer Center, NYU Langone Medical Center, New York University, New York, New York 10016, USA.,Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
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27
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Hong SH, You JS. SOX9 is controlled by the BRD4 inhibitor JQ1 via multiple regulation mechanisms. Biochem Biophys Res Commun 2019; 511:746-752. [PMID: 30833074 DOI: 10.1016/j.bbrc.2019.02.135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 01/10/2023]
Abstract
SOX9 is a key transcription factor during cell differentiation, sex determination, and tumorigenesis. However, the detailed mechanisms of its targeting strategy remain elusive. To investigate possibilities of targeting SOX9 with epigenetic drugs and the precise underlying mechanisms, two human cancer cell lines were chosen as model systems, which showed high SOX9 expression and anti-tumorigenic effects upon loss of SOX9. Histone acetylation-related screening of a small panel of epigenetic drugs revealed that the bromodomain reader inhibitor JQ1 dramatically downregulated SOX9 through multiple regulation steps, namely, transcription, BRD4-SOX9 protein-protein interaction, and further protein stability. These findings suggest that BRD4 inhibition is a novel therapeutic strategy for diseases characterized by SOX9 overexpression.
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Affiliation(s)
- Seong Hwi Hong
- Department of Biochemistry, School of Medicine, Konkuk University, Seoul, 05029, South Korea
| | - Jueng Soo You
- Department of Biochemistry, School of Medicine, Konkuk University, Seoul, 05029, South Korea; Research Institute of Medical Science, Konkuk University School of Medicine, South Korea.
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28
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Abstract
SOX transcription factors participate in the specification, differentiation and activities of many cell types in development and beyond. The 20 mammalian family members are distributed into eight groups based on sequence identity, and while co-expressed same-group proteins often have redundant functions, different-group proteins typically have distinct functions. More than a handful of SOX proteins have pivotal roles in skeletogenesis. Heterozygous mutations in their genes cause human diseases, in which skeletal dysmorphism is a major feature, such as campomelic dysplasia (SOX9), or a minor feature, such as LAMSHF syndrome (SOX5) and Coffin-Siris-like syndromes (SOX4 and SOX11). Loss- and gain-of-function experiments in animal models have revealed that SOX4 and SOX11 (SOXC group) promote skeletal progenitor survival and control skeleton patterning and growth; SOX8 (SOXE group) delays the differentiation of osteoblast progenitors; SOX9 (SOXE group) is essential for chondrocyte fate maintenance and differentiation, and works in cooperation with SOX5 and SOX6 (SOXD group) and other types of transcription factors. These and other SOX proteins have also been proposed, mainly through in vitro experiments, to have key roles in other aspects of skeletogenesis, such as SOX2 in osteoblast stem cell self-renewal. We here review current knowledge of well-established and proposed skeletogenic roles of SOX proteins, their transcriptional and non-transcriptional actions, and their modes of regulation at the gene, RNA and protein levels. We also discuss gaps in knowledge and directions for future research to further decipher mechanisms underlying skeletogenesis in health and diseases and identify treatment options for skeletal malformation and degeneration diseases.
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Affiliation(s)
- Véronique Lefebvre
- The Children's Hospital of Philadelphia, Philadelphia, PA, United States.
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29
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Abstract
The bipotential nature of cell types in the early developing gonad and the process of sex determination leading to either testis or ovary differentiation makes this an interesting system in which to study transcriptional regulation of gene expression and cell fate decisions. SOX9 is a transcription factor with multiple roles during development, including being a key player in mediating testis differentiation and therefore subsequent male development. Loss of Sox9 expression in both humans and mice results in XY female development, whereas its inappropriate activation in XX embryonic gonads can give male development. Multiple cases of Disorders of Sex Development in human patients or sex reversal in mice and other vertebrates can be explained by mutations affecting upstream regulators of Sox9 expression, such as the product of the Y chromosome gene Sry that triggers testis differentiation. Other cases are due to mutations in the Sox9 gene itself, including its own regulatory region. Indeed, rearrangements in and around the Sox9 genomic locus indicate the presence of multiple critical enhancers and the complex nature of its regulation. Here we summarize what is known about the role of Sox9 and its regulation during gonad development, including recently discovered critical enhancers. We also discuss higher order chromatin organization and how this might be involved. We end with some interesting future directions that have the potential to further enrich our understanding on the complex, multi-layered regulation controlling Sox9 expression in the gonads.
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Affiliation(s)
- Nitzan Gonen
- The Francis Crick Institute, London, United Kingdom.
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30
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Tarchini B, Longo-Guess C, Tian C, Tadenev ALD, Devanney N, Johnson KR. A spontaneous mouse deletion in Mctp1 uncovers a long-range cis-regulatory region crucial for NR2F1 function during inner ear development. Dev Biol 2018; 443:153-164. [PMID: 30217595 PMCID: PMC6214362 DOI: 10.1016/j.ydbio.2018.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/12/2022]
Abstract
Hundreds of thousands of cis-regulatory DNA sequences are predicted in vertebrate genomes, but unlike genes themselves, few have been characterized at the functional level or even unambiguously paired with a target gene. Here we serendipitously identified and started investigating the first reported long-range regulatory region for the Nr2f1 (Coup-TFI) transcription factor gene. NR2F1 is temporally and spatially regulated during development and required for patterning and regionalization in the nervous system, including sensory hair cell organization in the auditory epithelium of the cochlea. Analyzing the deaf wanderer (dwnd) spontaneous mouse mutation, we traced back the cause of its associated circling behavior to a 53 kb deletion removing five exons and adjacent intronic regions of the poorly characterized Mctp1 gene. Interestingly, loss of Mctp1 function cannot account for the hearing loss, inner ear dysmorphology and sensory hair cell disorganization observed in dwnd mutants. Instead, we found that the Mctp1dwnd deletion affects the Nr2f1 gene located 1.4 Mb away, downregulating transcription and protein expression in the embryonic cochlea. Remarkably, the Mctp1dwnd allele failed to complement a targeted inactivation allele of Nr2f1, and transheterozygotes or Mctp1dwnd homozygotes exhibit the same morphological defects observed in inner ears of Nr2f1 mutants without sharing their early life lethality. Defects include improper separation of the utricle and saccule in the vestibule not described previously, which can explain the circling behavior that first brought the spontaneous mutation to attention. By contrast, mice homozygous for a targeted inactivation of Mctp1 have normal hearing and inner ear structures. We conclude that the 53 kb Mctp1dwnd deletion encompasses a long-range cis-regulatory region essential for proper Nr2f1 expression in the embryonic inner ear, providing a first opportunity to investigate Nr2f1 function in postnatal inner ears. This work adds to the short list of long-range regulatory regions characterized as essential to drive expression of key developmental control genes.
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Affiliation(s)
- Basile Tarchini
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Department of Medicine, Tufts University, Boston 02111, MA, USA; Graduate School of Biomedical Science and Engineering (GSBSE), University of Maine, Orono 04469, ME, USA.
| | | | - Cong Tian
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Science and Engineering (GSBSE), University of Maine, Orono 04469, ME, USA
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31
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Bertolini F, Schiavo G, Tinarelli S, Santoro L, Utzeri VJ, Dall'Olio S, Nanni Costa L, Gallo M, Fontanesi L. Exploiting phenotype diversity in a local animal genetic resource: Identification of a single nucleotide polymorphism associated with the tail shape phenotype in the autochthonous Casertana pig breed. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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32
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Mochizuki Y, Chiba T, Kataoka K, Yamashita S, Sato T, Kato T, Takahashi K, Miyamoto T, Kitazawa M, Hatta T, Natsume T, Takai S, Asahara H. Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression. Dev Cell 2018; 46:794-806.e6. [PMID: 30146478 PMCID: PMC6324936 DOI: 10.1016/j.devcel.2018.07.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 04/23/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022]
Abstract
SRY-box 9 (SOX9) is a master transcription factor that regulates cartilage development. SOX9 haploinsufficiency resulting from breakpoints in a ∼1-Mb region upstream of SOX9 was reported in acampomelic campomelic dysplasia (ACD) patients, suggesting that essential enhancer regions of SOX9 for cartilage development are located in this long non-coding sequence. However, the cis-acting enhancer region regulating cartilage-specific SOX9 expression remains to be identified. To identify distant cartilage Sox9 enhancers, we utilized the combination of multiple CRISPR/Cas9 technologies including enrichment of the promoter-enhancer complex followed by next-generation sequencing and mass spectrometry (MS), SIN3A-dCas9-mediated epigenetic silencing, and generation of enhancer deletion mice. As a result, we could identify a critical far-upstream cis-element and Stat3 as a trans-acting factor, regulating cartilage-specific Sox9 expression and subsequent skeletal development. Our strategy could facilitate definitive ACD diagnosis and should be useful to reveal the detailed chromatin conformation and regulation.
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Affiliation(s)
- Yusuke Mochizuki
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Department of Orthopaedic Surgery, Nippon Medical School, Tokyo 113-0022, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kensuke Kataoka
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Satoshi Yamashita
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tempei Sato
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tomomi Kato
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kenji Takahashi
- Department of Orthopaedic Surgery, Nippon Medical School, Tokyo 113-0022, Japan
| | - Takeshi Miyamoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Masashi Kitazawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Shinro Takai
- Department of Orthopaedic Surgery, Nippon Medical School, Tokyo 113-0022, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Department of Molecular and Experimental Medicine, The Scripps Research Institute, San Diego, CA 92037, USA.
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Li IMH, Liu K, Neal A, Clegg PD, De Val S, Bou-Gharios G. Differential tissue specific, temporal and spatial expression patterns of the Aggrecan gene is modulated by independent enhancer elements. Sci Rep 2018; 8:950. [PMID: 29343853 PMCID: PMC5772622 DOI: 10.1038/s41598-018-19186-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/22/2017] [Indexed: 02/06/2023] Open
Abstract
The transcriptional mechanism through which chondrocytes control the spatial and temporal composition of the cartilage tissue has remained largely elusive. The central aim of this study was to identify whether transcriptional enhancers played a role in the organisation of the chondrocytes in cartilaginous tissue. We focused on the Aggrecan gene (Acan) as it is essential for the normal structure and function of cartilage and it is expressed developmentally in different stages of chondrocyte maturation. Using transgenic reporter studies in mice we identified four elements, two of which showed individual chondrocyte developmental stage specificity. In particular, one enhancer (-80) distinguishes itself from the others by being predominantly active in adult cartilage. Furthermore, the -62 element uniquely drove reporter activity in early chondrocytes. The remaining chondrocyte specific enhancers, +28 and -30, showed no preference to chondrocyte type. The transcription factor SOX9 interacted with all the enhancers in vitro and mutation of SOX9 binding sites in one of the enhancers (-30) resulted in a loss of its chondrocyte specificity and ectopic enhancer reporter activity. Thus, the Acan enhancers orchestrate the precise spatiotemporal expression of this gene in cartilage types at different stages of development and adulthood.
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Affiliation(s)
- Ian M H Li
- Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, Liverpool, L7 8TX, UK
| | - Ke Liu
- Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, Liverpool, L7 8TX, UK
| | - Alice Neal
- Ludwig Cancer Research Ltd, University of Oxford, Oxford, UK
| | - Peter D Clegg
- Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, Liverpool, L7 8TX, UK
| | - Sarah De Val
- Ludwig Cancer Research Ltd, University of Oxford, Oxford, UK
| | - George Bou-Gharios
- Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, Liverpool, L7 8TX, UK.
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Maguire JE, Pandey A, Wu Y, Di Gregorio A. Investigating Evolutionarily Conserved Molecular Mechanisms Controlling Gene Expression in the Notochord. TRANSGENIC ASCIDIANS 2018. [DOI: 10.1007/978-981-10-7545-2_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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35
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Baetens D, Mendonça BB, Verdin H, Cools M, De Baere E. Non-coding variation in disorders of sex development. Clin Genet 2017; 91:163-172. [PMID: 27801941 DOI: 10.1111/cge.12911] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/26/2023]
Abstract
Genetic studies in Disorders of Sex Development (DSD), representing a wide spectrum of developmental or functional conditions of the gonad, have mainly been oriented towards the coding genome. Application of genomic technologies, such as whole-exome sequencing, result in a molecular genetic diagnosis in ∼50% of cases with DSD. Many of the genes mutated in DSD encode transcription factors such as SRY, SOX9, NR5A1, and FOXL2, characterized by a strictly regulated spatiotemporal expression. Hence, it can be hypothesized that at least part of the missing genetic variation in DSD can be explained by non-coding mutations in regulatory elements that alter gene expression, either by reduced, mis- or overexpression of their target genes. In addition, structural variations such as translocations, deletions, duplications or inversions can affect the normal chromatin conformation by different mechanisms. Here, we review non-coding defects in human DSD phenotypes and in animal models. The wide variety of non-coding defects found in DSD emphasizes that the regulatory landscape of known and to be discovered DSD genes has to be taken into consideration when investigating the molecular pathogenesis of DSD.
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Affiliation(s)
- D Baetens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - B B Mendonça
- Laboratório de Hormônios e Genética Molecular, LIM/42, Unidade de Adrenal, Disc. de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - H Verdin
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - M Cools
- Department of Pediatrics, Division of Pediatric Endocrinology, Ghent University Hospital and Ghent University, Ghent, Belgium
| | - E De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
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Symon A, Harley V. SOX9: A genomic view of tissue specific expression and action. Int J Biochem Cell Biol 2017; 87:18-22. [DOI: 10.1016/j.biocel.2017.03.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 03/09/2017] [Accepted: 03/11/2017] [Indexed: 11/29/2022]
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Sreenivasan R, Gordon CT, Benko S, de Iongh R, Bagheri-Fam S, Lyonnet S, Harley V. Altered SOX9 genital tubercle enhancer region in hypospadias. J Steroid Biochem Mol Biol 2017; 170:28-38. [PMID: 27989796 DOI: 10.1016/j.jsbmb.2016.10.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/17/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022]
Abstract
Human mutations in the SOX9 gene or its regulatory region can disrupt testicular development, leading to disorders of sex development (DSDs). Our previous work involving the genomic analysis of isolated DSD patients revealed a 78kb minimal sex determining region (RevSex) far upstream of SOX9 that was duplicated in 46,XX and deleted in 46,XY DSDs. It was postulated that RevSex contains a gonadal enhancer. However, the most highly conserved sub-region within RevSex, called SR4, was neither responsive to sex determining factors in vitro nor active in the gonads of transgenic mice, suggesting that SR4 may not be functioning as a testicular enhancer. Interestingly, SR4 transgenic mice showed reporter activity in the genital tubercle, the primordium of the penis and clitoris, a previously unreported domain of Sox9 expression. SOX9 protein was detected in the genital tubercle, notably in the urethral plate epithelium, preputial glands, ventral surface ectoderm and corpus cavernosa. SR4 may therefore function as a Sox9 genital tubercle enhancer, mutations of which could possibly lead to hypospadias, a birth defect seen in the DSD patients in the RevSex study. SR4 activity and the observed SOX9 expression pattern suggest that SR4 may function as a Sox9 genital tubercle enhancer. However, conditional ablation of Sox9 in the genital tubercle using Shh-Cre/+;Sox9flox/flox mice revealed no genital tubercle abnormalities, possibly due to compensation by similar Sox factors. To conclude, we have identified a novel regulatory enhancer driving Sox9 expression during external genitalia development.
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Affiliation(s)
- Rajini Sreenivasan
- Molecular Genetics and Development, Hudson Institute of Medical Research, Melbourne, Victoria, Australia; Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, Australia; Monash University, Melbourne, Victoria, Australia
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Sabina Benko
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Robb de Iongh
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, Australia
| | - Stefan Bagheri-Fam
- Molecular Genetics and Development, Hudson Institute of Medical Research, Melbourne, Victoria, Australia; Monash University, Melbourne, Victoria, Australia
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Vincent Harley
- Molecular Genetics and Development, Hudson Institute of Medical Research, Melbourne, Victoria, Australia; Monash University, Melbourne, Victoria, Australia.
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Hall MD, Murray CA, Valdez MJ, Perantoni AO. Mesoderm-specific Stat3 deletion affects expression of Sox9 yielding Sox9-dependent phenotypes. PLoS Genet 2017; 13:e1006610. [PMID: 28166224 PMCID: PMC5319801 DOI: 10.1371/journal.pgen.1006610] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 02/21/2017] [Accepted: 01/30/2017] [Indexed: 01/14/2023] Open
Abstract
To date, mutations within the coding region and translocations around the SOX9 gene both constitute the majority of genetic lesions underpinning human campomelic dysplasia (CD). While pathological coding-region mutations typically result in a non-functional SOX9 protein, little is known about what mechanism(s) controls normal SOX9 expression, and subsequently, which signaling pathways may be interrupted by alterations occurring around the SOX9 gene. Here, we report the identification of Stat3 as a key modulator of Sox9 expression in nascent cartilage and developing chondrocytes. Stat3 expression is predominant in tissues of mesodermal origin, and its conditional ablation using mesoderm-specific TCre, in vivo, causes dwarfism and skeletal defects characteristic of CD. Specifically, Stat3 loss results in the expansion of growth plate hypertrophic chondrocytes and deregulation of normal endochondral ossification in all bones examined. Conditional deletion of Stat3 with a Sox9Cre driver produces palate and tracheal irregularities similar to those described in Sox9+/- mice. Furthermore, mesodermal deletion of Stat3 causes global embryonic down regulation of Sox9 expression and function in vivo. Mechanistic experiments ex vivo suggest Stat3 can directly activate the expression of Sox9 by binding to its proximal promoter following activation. These findings illuminate a novel role for Stat3 in chondrocytes during skeletal development through modulation of a critical factor, Sox9. Importantly, they further provide the first evidence for the modulation of a gene product other than Sox9 itself which is capable of modeling pathological aspects of CD and underscore a potentially valuable therapeutic target for patients with the disorder.
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Affiliation(s)
- Michael D. Hall
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Caroline A. Murray
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Michael J. Valdez
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Alan O. Perantoni
- The Cancer and Developmental Biology Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
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Smyk M, Akdemir KC, Stankiewicz P. SOX9 chromatin folding domains correlate with its real and putative distant cis-regulatory elements. Nucleus 2017; 8:182-187. [PMID: 28085555 DOI: 10.1080/19491034.2017.1279776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Evolutionary conserved transcription factor SOX9, encoded by the dosage sensitive SOX9 gene on chromosome 17q24.3, plays an important role in development of multiple organs, including bones and testes. Heterozygous point mutations and genomic copy-number variant (CNV) deletions involving SOX9 have been reported in patients with campomelic dysplasia (CD), a skeletal malformation syndrome often associated with male-to-female sex reversal. Balanced and unbalanced structural genomic variants with breakpoints mapping up to 1.3 Mb up- and downstream to SOX9 have been described in patients with milder phenotypes, including acampomelic campomelic dysplasia, sex reversal, and Pierre Robin sequence. Based on the localization of breakpoints of genomic rearrangements causing different phenotypes, 5 genomic intervals mapping upstream to SOX9 have been defined. We have analyzed the publically available database of high-throughput chromosome conformation capture (Hi-C) in multiple cell lines in the genomic regions flanking SOX9. Consistent with the literature data, chromatin domain boundaries in the SOX9 locus exhibit conservation across species and remain largely constant across multiple cell types. Interestingly, we have found that chromatin folding domains in the SOX9 locus associate with the genomic intervals harboring real and putative regulatory elements of SOX9, implicating that variation in intra-domain interactions may be critical for dynamic regulation of SOX9 expression in a cell type-specific fashion. We propose that tissue-specific enhancers for other transcription factor genes may similarly utilize chromatin folding sub-domains in gene regulation.
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Affiliation(s)
- Marta Smyk
- a Department of Medical Genetics , Institute of Mother and Child , Warsaw , Poland
| | - Kadir Caner Akdemir
- b Genomic Medicine Department , MD Anderson Cancer Center , Houston , TX , USA
| | - Paweł Stankiewicz
- c Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
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Abstract
SOX9 is a pivotal transcription factor in developing and adult cartilage. Its gene is expressed from the multipotent skeletal progenitor stage and is active throughout chondrocyte differentiation. While it is repressed in hypertrophic chondrocytes in cartilage growth plates, it remains expressed throughout life in permanent chondrocytes of healthy articular cartilage. SOX9 is required for chondrogenesis: it secures chondrocyte lineage commitment, promotes cell survival, and transcriptionally activates the genes for many cartilage-specific structural components and regulatory factors. Since heterozygous mutations within and around SOX9 were shown to cause the severe skeletal malformation syndrome called campomelic dysplasia, researchers around the world have worked assiduously to decipher the many facets of SOX9 actions and regulation in chondrogenesis. The more we learn, the more we realize the complexity of the molecular networks in which SOX9 fulfills its functions and is regulated at the levels of its gene, RNA, and protein, and the more we measure the many gaps remaining in knowledge. At the same time, new technologies keep giving us more means to push further the frontiers of knowledge. Research efforts must be pursued to fill these gaps and to better understand and treat many types of cartilage diseases in which SOX9 has or could have a critical role. These diseases include chondrodysplasias and cartilage degeneration diseases, namely osteoarthritis, a prevalent and still incurable joint disease. We here review the current state of knowledge of SOX9 actions and regulation in the chondrocyte lineage, and propose new directions for future fundamental and translational research projects.
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Affiliation(s)
- Véronique Lefebvre
- Department of Cellular & Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Mona Dvir-Ginzberg
- Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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41
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Fujita K, Ogawa R, Ito K. CHD7, Oct3/4, Sox2, and Nanog control FoxD3 expression during mouse neural crest-derived stem cell formation. FEBS J 2016; 283:3791-3806. [PMID: 27579714 DOI: 10.1111/febs.13843] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 08/02/2016] [Accepted: 08/30/2016] [Indexed: 11/29/2022]
Abstract
Neural crest-derived stem cells (NCSCs) are tissue-specific stem cells derived from multipotent neural crest cells. NCSCs are present in some adult tissues such as dorsal root ganglia, sciatic nerve, and bone marrow. However, little is known about the formation mechanisms of these cells. We have shown that BMP2/Wnt3a signaling and a chromatin remodeler, CHD7, in mice help to maintain the multipotency of neural crest cells and lead to the formation of NCSCs. In the present study, we analyzed a regulatory gene cascade in the formation of mouse NCSCs. The inhibition of FoxD3 expression significantly suppressed the expression of Sox10, which is an indispensable transcription factor for mouse NCSC formation, in the presence of BMP2/Wnt3a. CHD7, Oct3/4, Sox2, and Nanog occupied multiple conserved regions of mouse FoxD3, mE1, mE2, and mE3, in a BMP2/Wnt3a-dependent manner. Furthermore, siRNA of CHD7, Oct3/4, Sox2, and Nanog significantly suppressed FoxD3 expression. The inhibition of histone H3K4 mono- or trimethylation also repressed FoxD3 expression. The present data suggest that CHD7, Oct3/4, Sox2, and Nanog directly induce FoxD3 expression when stimulated by BMP2/Wnt3a signaling, that FoxD3 promotes Sox10 expression, and that histone H3K4 methylation plays important roles in this process of mouse NCSC formation.
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Affiliation(s)
- Kyohei Fujita
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Ryuhei Ogawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Kazuo Ito
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
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42
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Suryo Rahmanto A, Savov V, Brunner A, Bolin S, Weishaupt H, Malyukova A, Rosén G, Čančer M, Hutter S, Sundström A, Kawauchi D, Jones DT, Spruck C, Taylor MD, Cho YJ, Pfister SM, Kool M, Korshunov A, Swartling FJ, Sangfelt O. FBW7 suppression leads to SOX9 stabilization and increased malignancy in medulloblastoma. EMBO J 2016; 35:2192-2212. [PMID: 27625374 PMCID: PMC5069553 DOI: 10.15252/embj.201693889] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 08/18/2016] [Indexed: 12/02/2022] Open
Abstract
SOX9 is a master transcription factor that regulates development and stem cell programs. However, its potential oncogenic activity and regulatory mechanisms that control SOX9 protein stability are poorly understood. Here, we show that SOX9 is a substrate of FBW7, a tumor suppressor, and a SCF (SKP1/CUL1/F‐box)‐type ubiquitin ligase. FBW7 recognizes a conserved degron surrounding threonine 236 (T236) in SOX9 that is phosphorylated by GSK3 kinase and consequently degraded by SCFFBW7α. Failure to degrade SOX9 promotes migration, metastasis, and treatment resistance in medulloblastoma, one of the most common childhood brain tumors. FBW7 is either mutated or downregulated in medulloblastoma, and in cases where FBW7 mRNA levels are low, SOX9 protein is significantly elevated and this phenotype is associated with metastasis at diagnosis and poor patient outcome. Transcriptional profiling of medulloblastoma cells expressing a degradation‐resistant SOX9 mutant reveals activation of pro‐metastatic genes and genes linked to cisplatin resistance. Finally, we show that pharmacological inhibition of PI3K/AKT/mTOR pathway activity destabilizes SOX9 in a GSK3/FBW7‐dependent manner, rendering medulloblastoma cells sensitive to cytostatic treatment.
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Affiliation(s)
| | - Vasil Savov
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Andrä Brunner
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sara Bolin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Holger Weishaupt
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Alena Malyukova
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gabriela Rosén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Matko Čančer
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Sonja Hutter
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anders Sundström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Daisuke Kawauchi
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Tw Jones
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Charles Spruck
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Yoon-Jae Cho
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Stefan M Pfister
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Marcel Kool
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, University Hospital, Heidelberg, Germany
| | - Fredrik J Swartling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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McDermott B, Ellis S, Bou-Gharios G, Clegg P, Tew S. RNA binding proteins regulate anabolic and catabolic gene expression in chondrocytes. Osteoarthritis Cartilage 2016; 24:1263-73. [PMID: 26853752 PMCID: PMC4917896 DOI: 10.1016/j.joca.2016.01.988] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 01/21/2016] [Accepted: 01/29/2016] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Regulation of anabolic and catabolic factors is considered essential in maintaining the homoeostasis of healthy articular cartilage. In this study we investigated the influence of RNA binding proteins (RNABPs) in this process. DESIGN Using small interfering RNA (siRNA), RNABP expression was knocked down in SW1353 chondrosarcoma cells and human articular chondrocytes. Gene expression and messenger RNA (mRNA) decay of anabolic (SOX9, Aggrecan) and catabolic (matrix metalloproteinase (MMP)13) factors were analysed using reverse transcription quantitative polymerase chain reaction (RT-qPCR). RNA-electromobility shift assays (EMSAs) were used to investigate RNABP interactions with the SOX9 mRNA 3' untranslated region (UTR). Immunohistochemical localisation of MMP13 and the RNABP human antigen R (HuR) was performed in E13.5 and E16.5 mouse embryo sections. RESULTS SOX9 mRNA, mRNA half-life and protein expression were increased with siRNA targeting the RNABP tristetraprolin (TTP) in both HACs and SW1353s. TTP knockdown also stimulated aggrecan mRNA expression but did not affect its stability. RNA-EMSAs demonstrated that adenine uracil (AU)-rich elements in the SOX9 mRNA 3'UTR interacted with chondrocyte proteins with three specific elements interacting with TTP. HuR knockdown significantly increased MMP13 expression and also regulated the expression of a number of known transcriptional repressors of MMP13. HuR was ubiquitously expressed within mouse embryos yet displayed regional down-regulation within developing skeletal structures. CONCLUSION This study demonstrates for the first time how RNABPs are able to affect the balance of anabolic and catabolic gene expression in human chondrocytes. The post-transcriptional mechanisms controlled by RNABPs present novel avenues of regulation and potential points of intervention for controlling the expression of SOX9 and MMP13 in chondrocytes.
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Affiliation(s)
| | | | | | | | - S.R. Tew
- Address correspondence and reprint requests to: S.R. Tew, Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst Campus, Neston, Cheshire CH64 7TE, UK. Tel: 44-(0)-151-7956235; Fax: 44-(0)-151-7946034.
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44
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Burns FR, Lanham KA, Xiong KM, Gooding AJ, Peterson RE, Heideman W. Analysis of the zebrafish sox9b promoter: Identification of elements that recapitulate organ-specific expression of sox9b. Gene 2015; 578:281-9. [PMID: 26721460 DOI: 10.1016/j.gene.2015.12.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 11/28/2015] [Accepted: 12/17/2015] [Indexed: 01/09/2023]
Abstract
The SRY-related high-mobility box 9 (SOX9) gene is expressed in many different tissues. To better understand the DNA elements that control tissue-specific expression, we cloned and sequenced a 2.5 kb fragment lying 5' to the zebrafish sox9b gene transcriptional start site. Three regions of this clone contained stable secondary structures that hindered cloning, sequencing, and amplification. This segment and smaller fragmentswere inserted 5' of an EGFP reporter and transgenic fish were raised with the different reporters. Reporter expression was also observed in embryos directly injected with the constructs to transiently express the reporter. Heart expression required only a very short 5' sequence, as a 0.6 kb sox9b fragment produced reporter expression in heart in transgenic zebrafish, and transient experiments showed heart expression from a minimal sox9b promoter region containing a conserved TATA box and an EGR2 element (-74/+29 bp). Reporter expression in transgenic skeletal muscle was consistently lower than in other tissues. Jaw, brain, and notochord expression was strong with the full-length clone, but was dramatically reduced as the size of the fragment driving the reporter decreased from approximately 1.8 to 0.9 kb. The 2.5 kb region 5' of the sox9b contained 7 conserved non-coding elements (CNEs) that included putative hypoxia inducible factor 1α (HIF1α), CAAT box (CCAAT), early growth response protein 2 (EGR2), and core promoter elements. While a synthetic fragment containing all 7 CNEs produced some degree of reporter expression in muscle, jaw, heart and brain, the degree of reporter expression was considerably lower than that produced by the full length clone. These results can account for the tissue-specific expression of sox9b in the developing zebrafish.
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Affiliation(s)
- Felipe R Burns
- Molecular and Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA.
| | - Kevin A Lanham
- Molecular and Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA; Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705, USA
| | - Kong M Xiong
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705, USA; Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, 420 Henry Mall, Madison, WI 53705, USA; Immunoassay Research and Development, Beckman Coulter Inc., 1000 Lake Hazeltine Dr., Chaska, MN 55318, USA
| | - Alex J Gooding
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705, USA
| | - Richard E Peterson
- Molecular and Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA; Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705, USA
| | - Warren Heideman
- Molecular and Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA; Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705, USA
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Castori M, Bottillo I, Morlino S, Barone C, Cascone P, Grammatico P, Laino L. Variability in a three-generation family with Pierre Robin sequence, acampomelic campomelic dysplasia, and intellectual disability due to a novel ∼1 Mb deletion upstream of SOX9, and including KCNJ2 and KCNJ16. ACTA ACUST UNITED AC 2015; 106:61-8. [PMID: 26663529 DOI: 10.1002/bdra.23463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Campomelic dysplasia and acampomelic campomelic dysplasia (ACD) are allelic disorders due to heterozygous mutations in or around SOX9. Translocations and deletions involving the SOX9 5' regulatory region are rare causes of these disorders, as well as Pierre Robin sequence (PRS) and 46,XY gonadal dysgenesis. Genotype-phenotype correlations are not straightforward due to the complex epigenetic regulation of SOX9 expression during development. METHODS We report a three-generation pedigree with a novel ∼1 Mb deletion upstream of SOX9 and including KCNJ2 and KCNJ16, and ascertained for dominant transmission of PRS. RESULTS Further characterization of the family identified subtle appendicular anomalies and a variable constellation of axial skeletal features evocative of ACD in several members. Affected males showed learning disability. CONCLUSION The identified deletion was smaller than all other chromosome rearrangements associated with ACD. Comparison with other reported translocations and deletions involving this region allowed further refining of genotype-phenotype correlations and an update of the smallest regions of overlap associated with the different phenotypes. Intrafamilial variability in this pedigree suggests a phenotypic continuity between ACD and PRS in patients carrying mutations in the SOX9 5' regulatory region.
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Affiliation(s)
- Marco Castori
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Irene Bottillo
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Silvia Morlino
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Chiara Barone
- Center for Genetic Counseling and Reproductive Teratology, Maternal and Child Health Department, Garibaldi Nesima Hospital, Catania, Italy
| | - Piero Cascone
- Division of Maxillo-Facial Surgery, Sapienza University, Policlinico Umberto I Hospital, Rome, Italy
| | | | - Paola Grammatico
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Luigi Laino
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
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Remeseiro S, Hörnblad A, Spitz F. Gene regulation during development in the light of topologically associating domains. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:169-85. [PMID: 26558551 DOI: 10.1002/wdev.218] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 08/31/2015] [Accepted: 09/15/2015] [Indexed: 01/20/2023]
Abstract
During embryonic development, complex transcriptional programs govern the precision of gene expression. Many key developmental genes are regulated via cis-regulatory elements that are located far away in the linear genome. How sequences located hundreds of kilobases away from a promoter can influence its activity has been the subject of numerous speculations, which all underline the importance of the 3D-organization of the genome. The recent advent of chromosome conformation capture techniques has put into focus the subdivision of the genome into topologically associating domains (TADs). TADs may influence regulatory activities on multiple levels. The relative invariance of TAD limits across cell types suggests that they may form fixed structural domains that could facilitate and/or confine long-range regulatory interactions. However, most recent studies suggest that interactions within TADs are more variable and dynamic than initially described. Hence, different models are emerging regarding how TADs shape the complex 3D conformations, and thereafter influence the networks of cis-interactions that govern gene expression during development. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Hörnblad
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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Katoh-Fukui Y, Igarashi M, Nagasaki K, Horikawa R, Nagai T, Tsuchiya T, Suzuki E, Miyado M, Hata K, Nakabayashi K, Hayashi K, Matsubara Y, Baba T, Morohashi KI, Igarashi A, Ogata T, Takada S, Fukami M. Testicular dysgenesis/regression without campomelic dysplasia in patients carrying missense mutations and upstream deletion of SOX9. Mol Genet Genomic Med 2015; 3:550-7. [PMID: 26740947 PMCID: PMC4694128 DOI: 10.1002/mgg3.165] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 11/28/2022] Open
Abstract
SOX9 haploinsufficiency underlies campomelic dysplasia (CD) with or without testicular dysgenesis. Current understanding of the phenotypic variability and mutation spectrum of SOX9 abnormalities remains fragmentary. Here, we report three patients with hitherto unreported SOX9 abnormalities. These patients were identified through molecular analysis of 33 patients with 46,XY disorders of sex development (DSD). Patients 1–3 manifested testicular dysgenesis or regression without CD. Patients 1 and 2 carried probable damaging mutations p.Arg394Gly and p.Arg437Cys, respectively, in the SOX9 C‐terminal domain but not in other known 46,XY DSD causative genes. These substitutions were absent from ~120,000 alleles in the exome database. These mutations retained normal transactivating activity for the Col2a1 enhancer, but showed impaired activity for the Amh promoter. Patient 3 harbored a maternally inherited ~491 kb SOX9 upstream deletion that encompassed the known 32.5 kb XY sex reversal region. Breakpoints of the deletion resided within nonrepeat sequences and were accompanied by a short‐nucleotide insertion. The results imply that testicular dysgenesis and regression without skeletal dysplasia may be rare manifestations of SOX9 abnormalities. Furthermore, our data broaden pathogenic SOX9 abnormalities to include C‐terminal missense substitutions which lead to target‐gene‐specific protein dysfunction, and enhancer‐containing upstream microdeletions mediated by nonhomologous end‐joining.
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Affiliation(s)
- Yuko Katoh-Fukui
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Maki Igarashi
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Keisuke Nagasaki
- Division of Pediatrics Department of Homeostatic Regulation and Development Niigata University Graduate School of Medical and Dental Sciences Niigata Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism National Center for Child Health and Development Tokyo Japan
| | - Toshiro Nagai
- Department of Pediatrics Dokkyo Medical University Koshigaya Hospital Koshigaya Japan
| | - Takayoshi Tsuchiya
- Department of Pediatrics Dokkyo Medical University Koshigaya Hospital Koshigaya Japan
| | - Erina Suzuki
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Mami Miyado
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology National Research Institute for Child Health and Development Tokyo Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology National Research Institute for Child Health and Development Tokyo Japan
| | - Keiko Hayashi
- Department of Maternal-Fetal Biology National Research Institute for Child Health and Development Tokyo Japan
| | - Yoichi Matsubara
- National Research Institute for Child Health and Development Tokyo Japan
| | - Takashi Baba
- Department of Molecular Biology Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Ken-Ichirou Morohashi
- Department of Molecular Biology Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Arisa Igarashi
- Department of Systems BioMedicine National Research Institute for Child Health and Development Tokyo Japan
| | - Tsutomu Ogata
- Department of Molecular EndocrinologyNational Research Institute for Child Health and DevelopmentTokyoJapan; Department of PediatricsHamamatsu University School of MedicineHamamatsuJapan
| | - Shuji Takada
- Department of Systems BioMedicine National Research Institute for Child Health and Development Tokyo Japan
| | - Maki Fukami
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
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Shida H, Mende M, Takano-Yamamoto T, Osumi N, Streit A, Wakamatsu Y. Otic placode cell specification and proliferation are regulated by Notch signaling in avian development. Dev Dyn 2015; 244:839-51. [PMID: 25970828 DOI: 10.1002/dvdy.24291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 04/26/2015] [Accepted: 05/01/2015] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The entire inner ear including the cochlear-vestibular ganglion arises from a simple epithelium, the otic placode. Precursors for the placode originate from a pool of progenitors located in ectoderm next to the future hindbrain, the pre-otic field, where they are intermingled with future epibranchial and epidermal cells. While the importance of secreted proteins, such as FGFs and Wnts, in imparting otic identity has been well studied, how precursors for these different fates segregate locally is less well understood. RESULTS (1) The Notch ligand Delta1 and the Notch target Hes5-2 are expressed in a part of pre-otic field before otic commitment, indicative of active Notch signaling, and this is confirmed using a Notch reporter. (2) Loss and gain-of-function approaches reveal that Notch signaling regulates both proliferation and specification of pre-otic progenitors. CONCLUSIONS Our results identify a novel function of Notch signaling in cell fate determination in the pre-otic field of avian embryos.
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Affiliation(s)
- Hiroko Shida
- Department of Developmental Neuroscience, Center for Translational and Advanced Animal Research, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Division of Orthodontics and Dentofacial Orthopedics, Tohoku University Graduate School of Dentistry, Miyagi, Japan
| | - Michael Mende
- Department of Craniofacial Development and Stem Cell Biology, King's College London
| | - Teruko Takano-Yamamoto
- Division of Orthodontics and Dentofacial Orthopedics, Tohoku University Graduate School of Dentistry, Miyagi, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, Center for Translational and Advanced Animal Research, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Andrea Streit
- Department of Craniofacial Development and Stem Cell Biology, King's College London
| | - Yoshio Wakamatsu
- Department of Developmental Neuroscience, Center for Translational and Advanced Animal Research, Tohoku University Graduate School of Medicine, Miyagi, Japan
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Smyk M, Roeder E, Cheung SW, Szafranski P, Stankiewicz P. A de novo 1.58 Mb deletion, including MAP2K6 and mapping 1.28 Mb upstream to SOX9, identified in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Am J Med Genet A 2015; 167A:1842-50. [PMID: 26059046 DOI: 10.1002/ajmg.a.37057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/23/2015] [Indexed: 12/18/2022]
Abstract
Defects of long-range regulatory elements of dosage-sensitive genes represent an under-recognized mechanism underlying genetic diseases. Haploinsufficiency of SOX9, the gene essential for development of testes and differentiation of chondrocytes, results in campomelic dysplasia, a skeletal malformation syndrome often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.6 Mb up- and downstream to SOX9, and disrupting its distant cis-regulatory elements, have been described in patients with milder forms of campomelic dysplasia, Pierre Robin sequence, and sex reversal. We present an ∼1.58 Mb deletion mapping ∼1.28 Mb upstream to SOX9 that encompasses its putative long-range cis-regulatory element(s) and MAP2K6 in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Low bone mass panel testing using massively parallel sequencing of 23 nuclear genes, including COL1A1 and COL1A2 was negative. Based on the previous mouse model of Map2k6, suggesting that Sox9 is likely a downstream target of the p38 MAPK pathway, and our previous chromosome conformation capture-on-chip (4C) data showing potential interactions between SOX9 promoter and MAP2K6, we hypothesize that deletion of MAP2K6 might have affected SOX9 expression and contributed to our patient's phenotype.
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Affiliation(s)
- Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Elizabeth Roeder
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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50
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Yao B, Wang Q, Liu CF, Bhattaram P, Li W, Mead TJ, Crish JF, Lefebvre V. The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers. Nucleic Acids Res 2015; 43:5394-408. [PMID: 25940622 PMCID: PMC4477657 DOI: 10.1093/nar/gkv426] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 04/17/2015] [Indexed: 01/18/2023] Open
Abstract
Two decades after the discovery that heterozygous mutations within and around SOX9 cause campomelic dysplasia, a generalized skeleton malformation syndrome, it is well established that SOX9 is a master transcription factor in chondrocytes. In contrast, the mechanisms whereby translocations in the –350/–50-kb region 5′ of SOX9 cause severe disease and whereby SOX9 expression is specified in chondrocytes remain scarcely known. We here screen this upstream region and uncover multiple enhancers that activate Sox9-promoter transgenes in the SOX9 expression domain. Three of them are primarily active in chondrocytes. E250 (located at –250 kb) confines its activity to condensed prechondrocytes, E195 mainly targets proliferating chondrocytes, and E84 is potent in all differentiated chondrocytes. E84 and E195 synergize with E70, previously shown to be active in most Sox9-expressing somatic tissues, including cartilage. While SOX9 protein powerfully activates E70, it does not control E250. It requires its SOX5/SOX6 chondrogenic partners to robustly activate E195 and additional factors to activate E84. Altogether, these results indicate that SOX9 expression in chondrocytes relies on widely spread transcriptional modules whose synergistic and overlapping activities are driven by SOX9, SOX5/SOX6 and other factors. They help elucidate mechanisms underlying campomelic dysplasia and will likely help uncover other disease mechanisms.
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Affiliation(s)
- Baojin Yao
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Qiuqing Wang
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Chia-Feng Liu
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Pallavi Bhattaram
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Wei Li
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Timothy J Mead
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - James F Crish
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Véronique Lefebvre
- Department of Cellular & Molecular Medicine, and Orthopaedic and Rheumatologic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
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