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Wu Q, Liu H, Yang Q, Qi J, Xi Y, Tang Q, Wang R, Hu J, Li L. Transcriptome-based comparison reveals key genes regulating allometry growth of forelimb and hindlimb bone in duck embryos. Poult Sci 2024; 103:103317. [PMID: 38160613 PMCID: PMC10792745 DOI: 10.1016/j.psj.2023.103317] [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: 08/24/2023] [Revised: 10/29/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Allometric growth of the forelimb and hindlimb is a widespread phenomenon observed in vertebrates. As a typical precocial bird, ducks exhibit more advanced development of their hindlimbs compared to their forelimbs, enabling them to walk shortly after hatching. This phenomenon is closely associated with the development of long bones in the embryonic stage. However, the molecular mechanism governing the allometric growth of duck forelimb and hindlimb bones is remains elusive. In this study, we employed phenotypic, histological, and gene expression analyses to investigate developmental differences between the humerus (forelimb bone) and tibia/femur (hindlimb bones) in duck embryos. Our results revealed a gradual increase in weight and length disparity between the tibia and humerus from E12 to E28 (embryo age). At E12, endochondral ossification was observed solely in the tibia but not in the humerus. The number of differentially expressed genes (DEGs) gradually increased at H12 vs. T12, H20 vs. T20, and H28 vs. T28 stages consistent with phenotypic variations. A total of 38 DEGs were found across all 3 stages. Protein-protein interaction network analysis demonstrated strong interactions among members of HOXD gene family (HOXD3/8/9/10/11/12), HOXB gene family (HOXB8/9), TBX gene family (TBX4/5/20), HOXA11, SHOX2, and MEIS2. Gene expression profiling indicated higher expression levels for all HOXD genes in the humerus compared to tibia while opposite trends were observed for HOXA/HOXB genes with low or no expression detected in the humerus. These findings suggest distinct roles played by different clusters within HOX gene family during skeletal development regulation of duck embryo's forelimbs versus hind limbs. Notably, TBX4 exhibited high expression levels specifically in tibia whereas TBX5 showed similar patterns exclusively within humerus as seen previously across other species' studies. In summary, this study identified key regulatory genes involved in allometric growth of duck forelimb and hindlimb bones during embryonic development. Skeletal development is a complex physiological process, and further research is needed to elucidate the regulatory role of candidate genes in endochondral ossification.
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Affiliation(s)
- Qifan Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China; Ministry of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinglan Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingjing Qi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qian Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Rui Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Lemdjo G, Kengne AP, Nouthe B, Lucas M, Carpentier A, Ngueta G. Humero-femoral index and diabetes risk in the US population- a case study. J Diabetes Metab Disord 2023; 22:1327-1335. [PMID: 37975100 PMCID: PMC10638166 DOI: 10.1007/s40200-023-01251-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/13/2023] [Indexed: 11/18/2023]
Abstract
Background The between-subject variability in diabetes risk persists in epidemiological studies, even after accounting for obesity. We investigated whether the humero-femoral index (HFI) was associated with prevalence of type 2 diabetes mellitus (T2DM) and assessed the incremental value of HFI as a marker of T2DM. Methods This population-based cross-sectional study used data from the National Health and Nutrition Examination Survey from 1999 to 2018. We assessed 42,088 adults aged ≥ 30 years. HFI was defined as the upper arm length/upper leg length ratio. The outcome included undiagnosed diabetes (based on 2-hour plasma glucose levels, fasting glucose and hemoglobin A1C) and history of diabetes (diagnosed diabetes or taking antidiabetic drugs). Results As compared with the bottom quartile, the prevalence ratio of T2DM was 1.28 (95% CI 1.19-1.38) in the second, 1.61 (95% CI 1.50-1.72) in the third, and 1.75 (95% CI 1.64-1.88) in the fourth quartile of HFI (P for trend < 0.0001). The positive association remained consistent within different patterns of BMI and WC in men but was rendered null in women. After adding HFI to the reference model (including WC only), the discrimination slopes increased by 60.0% in men and 51.1% in women. Conclusion Our findings suggest that HFI may be a key component in body structure contributing to the risk of T2DM. In men, the highest HFI was associated with elevated prevalence of T2DM, independent of BMI and WC. Supplementary Information The online version contains supplementary material available at 10.1007/s40200-023-01251-z.
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Affiliation(s)
- Gaelle Lemdjo
- Endocrinology Unit, Jordan Medical Service, Yaounde, Cameroon
| | - André Pascal Kengne
- Non-Communicable Disease Research Unit, South African Medical Research Council, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Brice Nouthe
- Fraser Health Authority/Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Michel Lucas
- Department of Social and Preventive Medicine, Faculty of medicine, Laval University, Québec, Canada
| | - André Carpentier
- Division of Endocrinology, Department of Medicine, University of Sherbrooke, Sherbrooke, Canada
- Research Center of the CHU de Sherbrooke, University of Sherbrooke, Sherbrooke, Québec Canada
| | - Gérard Ngueta
- Research Center of the CHU de Sherbrooke, University of Sherbrooke, Sherbrooke, Québec Canada
- Department of Community Health Sciences, University of Sherbrooke, Sherbrooke, Québec Canada
- Centre de recherche du CHU de Sherbrooke, CRCHUS- Hôpital Fleurimont, Axe: Diabète, Obésité, Complications cardiovasculaires), Service d’endocrinologie, 12 eme Avenue Nord, Sherbrooke, 3001 Canada
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Zhang S, Zhang X, Zhang C, Xu S, Wang D, Guo C. Developmental Genetic Basis of Hoxd9 Homeobox Domain Deletion in Pampus argenteus Pelvic Fin Deficiency. Int J Mol Sci 2023; 24:11769. [PMID: 37511526 PMCID: PMC10380636 DOI: 10.3390/ijms241411769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Pampus argenteus is important for commercial fishery catch species and is an emerging target for aquaculture production. Notably, P. argenteus has a bizarre morphology and lacks pelvic fins. However, the reason for the lack of pelvic fins remains unclear, ultimately leading to frequent upside-down floating of P. argenteus during breeding and marked consumption of physical energy. Some lineages, including whales, fugu, snakes, and seahorse, independently lost the pelvic appendages over evolutionary time. Do different taxa employ the same molecular genetic pathways when they independently evolve similar developmental morphologies? Through analysis of the gene responsible for appendage localization, Hoxd9, it was discovered that the Hox domain was absent in the Hoxd9 gene of P. argenteus, and the Hoxd9b gene lacked the Hox9 activation region, a feature not observed in the Hoxd9 gene of other fish species. Interestingly, those distinctive characteristics are not observed in the Hoxd9 gene of other fish species. To determine the association between the Hoxd9 gene characteristics and the pelvic fin deletion in P. argenteus, the full-length cDNA of the Hoxd9a gene was cloned, and morphological observations of the species' juveniles were performed using stereomicroscopy and scanning electron microscopy. Thereafter, the tissue localization of Hoxd9a in the species was analyzed at the gene and protein levels. Based on the results, deletion of the Hoxd9a structural domain possibly leads to disruptions in the protein translation and the pelvic fin localization in P. argenteus during its early ontogenetic developmental stage, resulting in the absence of pelvic fins.
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Affiliation(s)
- Shun Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Xiaodong Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Cheng Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Shanliang Xu
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo 315211, China
| | - Danli Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Green Mariculture (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, Ningbo 315211, China
| | - Chunyang Guo
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Green Mariculture (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, Ningbo 315211, China
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Gomez-Picos P, Ovens K, Eames BF. Limb Mesoderm and Head Ectomesenchyme Both Express a Core Transcriptional Program During Chondrocyte Differentiation. Front Cell Dev Biol 2022; 10:876825. [PMID: 35784462 PMCID: PMC9247276 DOI: 10.3389/fcell.2022.876825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
To explain how cartilage appeared in different parts of the vertebrate body at discrete times during evolution, we hypothesize that different embryonic populations co-opted expression of a core gene regulatory network (GRN) driving chondrocyte differentiation. To test this hypothesis, laser-capture microdissection coupled with RNA-seq was used to reveal chondrocyte transcriptomes in the developing chick humerus and ceratobranchial, which are mesoderm- and neural crest-derived, respectively. During endochondral ossification, two general types of chondrocytes differentiate. Immature chondrocytes (IMM) represent the early stages of cartilage differentiation, while mature chondrocytes (MAT) undergo additional stages of differentiation, including hypertrophy and stimulating matrix mineralization and degradation. Venn diagram analyses generally revealed a high degree of conservation between chondrocyte transcriptomes of the limb and head, including SOX9, COL2A1, and ACAN expression. Typical maturation genes, such as COL10A1, IBSP, and SPP1, were upregulated in MAT compared to IMM in both limb and head chondrocytes. Gene co-expression network (GCN) analyses of limb and head chondrocyte transcriptomes estimated the core GRN governing cartilage differentiation. Two discrete portions of the GCN contained genes that were differentially expressed in limb or head chondrocytes, but these genes were enriched for biological processes related to limb/forelimb morphogenesis or neural crest-dependent processes, respectively, perhaps simply reflecting the embryonic origin of the cells. A core GRN driving cartilage differentiation in limb and head was revealed that included typical chondrocyte differentiation and maturation markers, as well as putative novel “chondrocyte” genes. Conservation of a core transcriptional program during chondrocyte differentiation in both the limb and head suggest that the same core GRN was co-opted when cartilage appeared in different regions of the skeleton during vertebrate evolution.
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Affiliation(s)
- Patsy Gomez-Picos
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Katie Ovens
- Department of Computer Science, University of Calgary, Calgary, AB, Canada
| | - B. Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: B. Frank Eames,
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Saxena A, Sharma V, Muthuirulan P, Neufeld SJ, Tran MP, Gutierrez HL, Chen KD, Erberich JM, Birmingham A, Capellini TD, Cobb J, Hiller M, Cooper KL. Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas. Curr Biol 2022; 32:289-303.e6. [PMID: 34793695 PMCID: PMC8792248 DOI: 10.1016/j.cub.2021.10.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/16/2021] [Accepted: 10/28/2021] [Indexed: 01/26/2023]
Abstract
Despite the great diversity of vertebrate limb proportion and our deep understanding of the genetic mechanisms that drive skeletal elongation, little is known about how individual bones reach different lengths in any species. Here, we directly compare the transcriptomes of homologous growth cartilages of the mouse (Mus musculus) and bipedal jerboa (Jaculus jaculus), the latter of which has "mouse-like" arms but extremely long metatarsals of the feet. Intersecting gene-expression differences in metatarsals and forearms of the two species revealed that about 10% of orthologous genes are associated with the disproportionately rapid elongation of neonatal jerboa feet. These include genes and enriched pathways not previously associated with endochondral elongation as well as those that might diversify skeletal proportion in addition to their known requirements for bone growth throughout the skeleton. We also identified transcription regulators that might act as "nodes" for sweeping differences in genome expression between species. Among these, Shox2, which is necessary for proximal limb elongation, has gained expression in jerboa metatarsals where it has not been detected in other vertebrates. We show that Shox2 is sufficient to increase mouse distal limb length, and a nearby putative cis-regulatory region is preferentially accessible in jerboa metatarsals. In addition to mechanisms that might directly promote growth, we found evidence that jerboa foot elongation may occur in part by de-repressing latent growth potential. The genes and pathways that we identified here provide a framework to understand the modular genetic control of skeletal growth and the remarkable malleability of vertebrate limb proportion.
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Affiliation(s)
- Aditya Saxena
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Pushpanathan Muthuirulan
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - Stanley J Neufeld
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Mai P Tran
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Haydee L Gutierrez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kevin D Chen
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joel M Erberich
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - John Cobb
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Zfhx4 regulates endochondral ossification as the transcriptional platform of Osterix in mice. Commun Biol 2021; 4:1258. [PMID: 34732852 PMCID: PMC8566502 DOI: 10.1038/s42003-021-02793-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/18/2021] [Indexed: 11/08/2022] Open
Abstract
Endochondral ossification is regulated by transcription factors that include SRY-box transcription factor 9, runt-related protein 2 (Runx2), and Osterix. However, the sequential and harmonious regulation of the multiple steps of endochondral ossification is unclear. This study identified zinc finger homeodomain 4 (Zfhx4) as a crucial transcriptional partner of Osterix. We found that Zfhx4 was highly expressed in cartilage and that Zfhx4 deficient mice had reduced expression of matrix metallopeptidase 13 and inhibited calcification of cartilage matrices. These phenotypes were very similar to impaired chondrogenesis in Osterix deficient mice. Coimmunoprecipitation and immunofluorescence indicated a physical interaction between Zfhx4 and Osterix. Notably, Zfhx4 and Osterix double mutant mice showed more severe phenotype than Zfhx4 deficient mice. Additionally, Zfhx4 interacted with Runx2 that functions upstream of Osterix. Our findings suggest that Zfhx4 coordinates the transcriptional network of Osterix and, consequently, endochondral ossification.
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Hong Q, Li XD, Xie P, Du SX. All-trans-retinoic acid suppresses rat embryo hindlimb bud mesenchymal chondrogenesis by modulating HoxD9 expression. Bioengineered 2021; 12:3900-3911. [PMID: 34288810 PMCID: PMC8806522 DOI: 10.1080/21655979.2021.1940613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In vertebrates, 5ʹ-Hoxd genes (Hoxd9), which are expressed in the hindlimb bud mesenchyme, participate in limb growth and patterning in early embryonic development. In the present study, We investigated the mechanisms by which ATRA regulates cultured E12.5 rat embryo hindlimb bud mesenchymal cells (rEHBMCs). Following exposure to ATRA over 24 h, mRNA and protein expression levels of HoxD9 were evaluated by reverse transcription-polymerase chain reaction (RT-PCR), quantitative real-time PCR (qPCR), and western blotting. Flow cytometry was used to detect apoptosis. ATRA inhibited the condensation and proliferation, and promoted the apoptosis rate of the rEHBMCs in a dose-dependent manner. Sox9 and Col2a1 in rEHBMCs were downregulated by ATRA in a dose-dependent manner at both mRNA and protein levels. Similarly, HoxD9 was downregulated by ATRA in a dose-dependent manner, in parallel with the cartilage-specific molecules Sox9 and Col2a1. Both qPCR and western blotting showed that both Shh and Gli3 were downregulated. Overexpression of HoxD9 reversed the effects of ATRA. These results demonstrate that ATRA suppresses chondrogenesis in rEHBMCs by inhibiting the expression of HoxD9 and its downstream protein targets, including Sox9 and Col2a1. This effect may also be correlated with inhibition of the Shh-Gli3 signaling pathway.
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Affiliation(s)
- Quan Hong
- Department of Orthopedics, Jieyang People's Hospital (Jieyang Affiliated Hospital, Sun Yat-sen University), Jieyang, Guangdong, China
| | - Xue-Dong Li
- Department of Orthopedics, Shenzhen Luohu Hospital Group Luohu People's Hospital (The Third Affiliated Hospital of Shenzhen University), Shenzhen, Guangdong, China
| | - Peng Xie
- Department of Orthopedics, Shenzhen Luohu Hospital Group Luohu People's Hospital (The Third Affiliated Hospital of Shenzhen University), Shenzhen, Guangdong, China
| | - Shi-Xin Du
- Department of Orthopedics, Shenzhen Luohu Hospital Group Luohu People's Hospital (The Third Affiliated Hospital of Shenzhen University), Shenzhen, Guangdong, China
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Fernandez-Guerrero M, Zdral S, Castilla-Ibeas A, Lopez-Delisle L, Duboule D, Ros MA. Time-sequenced transcriptomes of developing distal mouse limb buds: A comparative tissue layer analysis. Dev Dyn 2021; 251:1550-1575. [PMID: 34254395 DOI: 10.1002/dvdy.394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The development of the amniote limb has been an important model system to study patterning mechanisms and morphogenesis. For proper growth and patterning, it requires the interaction between the distal sub-apical mesenchyme and the apical ectodermal ridge (AER) that involve the separate implementation of coordinated and tissue-specific genetic programs. RESULTS Here, we produce and analyze the transcriptomes of both distal limb mesenchymal progenitors and the overlying ectodermal cells, following time-coursed dissections that cover from limb bud initiation to fully patterned limbs. The comparison of transcriptomes within each layer as well as between layers over time, allowed the identification of specific transcriptional signatures for each of the developmental stages. Special attention was given to the identification of genes whose transcription dynamics suggest a previously unnoticed role in the context of limb development and also to signaling pathways enriched between layers. CONCLUSION We interpret the transcriptomic data in light of the known development pattern and we conclude that a major transcriptional transition occurs in distal limb buds between E9.5 and E10.5, coincident with the switch from an early phase continuation of the signature of trunk progenitors, related to the initial proximo distal specification, to a late intrinsic phase of development.
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Affiliation(s)
- Marc Fernandez-Guerrero
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-University of Cantabria-SODERCAN), Santander, Spain
| | - Sofia Zdral
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-University of Cantabria-SODERCAN), Santander, Spain
| | - Alejandro Castilla-Ibeas
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-University of Cantabria-SODERCAN), Santander, Spain
| | | | - Denis Duboule
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland.,Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Collège de France, Paris, France
| | - Marian A Ros
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-University of Cantabria-SODERCAN), Santander, Spain.,Facultad de Medicina, Departamento de Anatomía y Biología Celular, Universidad de Cantabria, Santander, Spain
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9
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Xi H, Langerman J, Sabri S, Chien P, Young CS, Younesi S, Hicks M, Gonzalez K, Fujiwara W, Marzi J, Liebscher S, Spencer M, Van Handel B, Evseenko D, Schenke-Layland K, Plath K, Pyle AD. A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells. Cell Stem Cell 2020; 27:158-176.e10. [PMID: 32396864 PMCID: PMC7367475 DOI: 10.1016/j.stem.2020.04.017] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/12/2020] [Accepted: 04/23/2020] [Indexed: 12/17/2022]
Abstract
The developmental trajectory of human skeletal myogenesis and the transition between progenitor and stem cell states are unclear. We used single-cell RNA sequencing to profile human skeletal muscle tissues from embryonic, fetal, and postnatal stages. In silico, we identified myogenic as well as other cell types and constructed a "roadmap" of human skeletal muscle ontogeny across development. In a similar fashion, we also profiled the heterogeneous cell cultures generated from multiple human pluripotent stem cell (hPSC) myogenic differentiation protocols and mapped hPSC-derived myogenic progenitors to an embryonic-to-fetal transition period. We found differentially enriched biological processes and discovered co-regulated gene networks and transcription factors present at distinct myogenic stages. This work serves as a resource for advancing our knowledge of human myogenesis. It also provides a tool for a better understanding of hPSC-derived myogenic progenitors for translational applications in skeletal muscle-based regenerative medicine.
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Affiliation(s)
- Haibin Xi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Justin Langerman
- Deparment of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shan Sabri
- Deparment of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peggie Chien
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Courtney S Young
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shahab Younesi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael Hicks
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karen Gonzalez
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wakana Fujiwara
- Department of Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julia Marzi
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls University Tübingen, Tübingen, Germany; The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
| | - Simone Liebscher
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Melissa Spencer
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ben Van Handel
- Department of Orthopaedic Surgery, Keck School of Medicine, Stem Cell Research and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Denis Evseenko
- Department of Orthopaedic Surgery, Keck School of Medicine, Stem Cell Research and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Katja Schenke-Layland
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls University Tübingen, Tübingen, Germany; The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany; Department of Medicine/Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kathrin Plath
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Deparment of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
| | - April D Pyle
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
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10
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Eyal S, Kult S, Rubin S, Krief S, Felsenthal N, Pineault KM, Leshkowitz D, Salame TM, Addadi Y, Wellik DM, Zelzer E. Bone morphology is regulated modularly by global and regional genetic programs. Development 2019; 146:dev.167882. [PMID: 31221640 DOI: 10.1242/dev.167882] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/13/2019] [Indexed: 01/09/2023]
Abstract
Bone protrusions provide stable anchoring sites for ligaments and tendons and define the unique morphology of each long bone. Despite their importance, the mechanism by which superstructures are patterned is unknown. Here, we identify components of the genetic program that control the patterning of Sox9 +/Scx + superstructure progenitors in mouse and show that this program includes both global and regional regulatory modules. Using light-sheet fluorescence microscopy combined with genetic lineage labeling, we mapped the broad contribution of the Sox9 +/Scx + progenitors to the formation of bone superstructures. Then, by combining literature-based evidence, comparative transcriptomic analysis and genetic mouse models, we identified Gli3 as a global regulator of superstructure patterning, whereas Pbx1, Pbx2, Hoxa11 and Hoxd11 act as proximal and distal regulators, respectively. Moreover, by demonstrating a dose-dependent pattern regulation in Gli3 and Pbx1 compound mutations, we show that the global and regional regulatory modules work in a coordinated manner. Collectively, our results provide strong evidence for genetic regulation of superstructure patterning, which further supports the notion that long bone development is a modular process.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Shai Eyal
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot 76100, Israel
| | - Shiri Kult
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot 76100, Israel
| | - Sarah Rubin
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot 76100, Israel
| | - Sharon Krief
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot 76100, Israel
| | - Neta Felsenthal
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot 76100, Israel
| | - Kyriel M Pineault
- University of Wisconsin-Madison, Department of Cell & Regenerative Biology, Madison, WI 53705, USA
| | - Dena Leshkowitz
- Weizmann Institute of Science, Department of Life Sciences Core Facilities, Rehovot 76100, Israel
| | - Tomer-Meir Salame
- Weizmann Institute of Science, Department of Life Sciences Core Facilities, Rehovot 76100, Israel
| | - Yoseph Addadi
- Weizmann Institute of Science, Department of Life Sciences Core Facilities, Rehovot 76100, Israel
| | - Deneen M Wellik
- University of Wisconsin-Madison, Department of Cell & Regenerative Biology, Madison, WI 53705, USA
| | - Elazar Zelzer
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot 76100, Israel
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11
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Reinhardt R, Gullotta F, Nusspaumer G, Ünal E, Ivanek R, Zuniga A, Zeller R. Molecular signatures identify immature mesenchymal progenitors in early mouse limb buds that respond differentially to morphogen signaling. Development 2019; 146:dev.173328. [PMID: 31076486 PMCID: PMC6550019 DOI: 10.1242/dev.173328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/01/2019] [Indexed: 12/31/2022]
Abstract
The key molecular interactions governing vertebrate limb bud development are a paradigm for studying the mechanisms controlling progenitor cell proliferation and specification during vertebrate organogenesis. However, little is known about the cellular heterogeneity of the mesenchymal progenitors in early limb buds that ultimately contribute to the chondrogenic condensations prefiguring the skeleton. We combined flow cytometric and transcriptome analyses to identify the molecular signatures of several distinct mesenchymal progenitor cell populations present in early mouse forelimb buds. In particular, jagged 1 (JAG1)-positive cells located in the posterior-distal mesenchyme were identified as the most immature limb bud mesenchymal progenitors (LMPs), which crucially depend on SHH and FGF signaling in culture. The analysis of gremlin 1 (Grem1)-deficient forelimb buds showed that JAG1-expressing LMPs are protected from apoptosis by GREM1-mediated BMP antagonism. At the same stage, the osteo-chondrogenic progenitors (OCPs) located in the core mesenchyme are already actively responding to BMP signaling. This analysis sheds light on the cellular heterogeneity of the early mouse limb bud mesenchyme and on the distinct response of LMPs and OCPs to morphogen signaling.
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Affiliation(s)
- Robert Reinhardt
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Fabiana Gullotta
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Gretel Nusspaumer
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland.,Development and Evolution, Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Erkan Ünal
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,Bioinformatics Core Facility, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
| | - Robert Ivanek
- Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,Bioinformatics Core Facility, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
| | - Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
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12
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Yamamoto S, Uchida Y, Ohtani T, Nozaki E, Yin C, Gotoh Y, Yakushiji-Kaminatsui N, Higashiyama T, Suzuki T, Takemoto T, Shiraishi YI, Kuroiwa A. Hoxa13 regulates expression of common Hox target genes involved in cartilage development to coordinate the expansion of the autopodal anlage. Dev Growth Differ 2019; 61:228-251. [PMID: 30895612 PMCID: PMC6850407 DOI: 10.1111/dgd.12601] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 02/04/2023]
Abstract
To elucidate the role of Hox genes in limb cartilage development, we identified the target genes of HOXA11 and HOXA13 by ChIP‐Seq. The ChIP DNA fragment contained evolutionarily conserved sequences and multiple highly conserved HOX binding sites. A substantial portion of the HOXA11 ChIP fragment overlapped with the HOXA13 ChIP fragment indicating that both factors share common targets. Deletion of the target regions neighboring Bmp2 or Tshz2 reduced their expression in the autopod suggesting that they function as the limb bud‐specific enhancers. We identified the Hox downstream genes as exhibiting expression changes in the Hoxa13 knock out (KO) and Hoxd11‐13 deletion double mutant (Hox13 dKO) autopod by Genechip analysis. The Hox downstream genes neighboring the ChIP fragment were defined as the direct targets of Hox. We analyzed the spatial expression pattern of the Hox target genes that encode two different categories of transcription factors during autopod development and Hox13dKO limb bud. (a) Bcl11a, encoding a repressor of cartilage differentiation, was expressed in the E11.5 autopod and was substantially reduced in the Hox13dKO. (b) The transcription factors Aff3, Bnc2, Nfib and Runx1t1 were expressed in the zeugopodal cartilage but not in the autopod due to the repressive or relatively weak transcriptional activity of Hox13 at E11.5. Interestingly, the expression of these genes was later observed in the autopodal cartilage at E12.5. These results indicate that Hox13 transiently suspends the cartilage differentiation in the autopodal anlage via multiple pathways until establishing the paddle‐shaped structure required to generate five digits.
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Affiliation(s)
- Shiori Yamamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Yuji Uchida
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Tomomi Ohtani
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Erina Nozaki
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Chunyang Yin
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Yoshihiro Gotoh
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | | | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai-shi, Aichi-ken, Japan
| | - Tatsuya Takemoto
- Laboratory for Embryology, Institute for Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Yo-Ichi Shiraishi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
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13
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Tung YC, Lee NC, Hwu WL, Liu SY, Lee CT, Chien YH, Tsai WY. SHOX deficiency in short Taiwanese children: A single-center experience. J Formos Med Assoc 2017; 117:909-914. [PMID: 29254682 DOI: 10.1016/j.jfma.2017.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 10/25/2017] [Accepted: 11/28/2017] [Indexed: 10/18/2022] Open
Abstract
BACKGROUND SHOX deficiency is a common cause of idiopathic short stature. The aim of this study was to describe the clinical characteristics and molecular findings of patients with SHOX deficiency in Taiwan. METHODS A phenotype scoring system was used to evaluate several anthropometric measures in patients with idiopathic short stature. Twenty-three patients with a phenotype score >7 were enrolled for SHOX gene analysis by MLPA and sequencing. Another patient with a deletion/insertion of the short arm of the X chromosome containing the SHOX gene was enrolled for the assessment. RESULTS SHOX deficiency was detected in 26% of short children with a phenotype score >7. The arm-span-to-height ratio was significantly lower in SHOX-D patients than in non-SHOX-D patients. In patients with SHOX deficiency, an arm-span-to-height ratio <96.5% and short forearm were the most common characteristics. Three patients also exhibited typical radiological findings. A molecular analysis of the SHOX gene revealed five patients with intragenic deletions, one with a deletion in the regulatory region, and one with a missense mutation at exon 5. CONCLUSION The phenotype scoring system is useful to select children with SHOX deficiency in Taiwan. Family history and radiological image of the radius are also of value for the diagnosis. This study may aid physicians in the early diagnosis of children with SHOX deficiency.
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Affiliation(s)
- Yi-Ching Tung
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan
| | - Ni-Chung Lee
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan; Department of Medical Genetics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan; Department of Medical Genetics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan
| | - Shih-Yao Liu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan
| | - Cheng-Ting Lee
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan; Department of Medical Genetics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan
| | - Wen-Yu Tsai
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taiwan.
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14
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Feiner N. Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards. Proc Biol Sci 2017; 283:rspb.2016.1555. [PMID: 27733546 DOI: 10.1098/rspb.2016.1555] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/14/2016] [Indexed: 12/20/2022] Open
Abstract
Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region (Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis, TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards.
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Affiliation(s)
- Nathalie Feiner
- Department of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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15
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Yi J, Jin L, Chen J, Feng B, He Z, Chen L, Song H. MiR-375 suppresses invasion and metastasis by direct targeting of SHOX2 in esophageal squamous cell carcinoma. Acta Biochim Biophys Sin (Shanghai) 2017; 49:159-169. [PMID: 28069583 DOI: 10.1093/abbs/gmw131] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Indexed: 12/15/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the most common histological type in China. MicroRNAs are endogenously expressed in mammals and play a significant role in tumor invasion and metastasis by targeting potential downstream genes. In the present study, microarray analysis showed that miR-375 expression was distinctly downregulated in ESCC compared with that in normal esophageal epithelium tissues. Then, luciferase reporter assay showed that SHOX2 was the direct downstream target of miR-375 and this interaction was confirmed by the rescue experiments. Quantitative polymerase chain reaction results also showed that SHOX2 expression was upregulated in ESCC cells and tissues. Further analysis showed that SHOX2 induced proliferation, invasion, and metastasis of ESCC both in vivo and in vitro. Moreover, the interaction between miR-375 and SHOX2 affected the epithelial-to-mesenchymal transition. We conclude that miR-375 may suppress invasion and metastasis of ESCC by directly targeting SHOX2. The miR-375/SHOX2 axis may be a novel therapeutic target for ESCC.
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Affiliation(s)
- Jun Yi
- Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing 210002, China
| | - Li Jin
- Department of Medical Oncology, Jinling Hospital, Nanjing 210002, China
| | - Jing Chen
- Department of Medical Oncology, Jinling Hospital, Nanjing 210002, China
| | - Bing Feng
- Department of Medical Oncology, Jinling Hospital, Nanjing 210002, China
| | - Zhenyue He
- Department of Medical Oncology, Jinling Hospital, Nanjing 210002, China
| | - Longbang Chen
- Department of Medical Oncology, Jinling Hospital, Nanjing 210002, China
| | - Haizhu Song
- Department of Medical Oncology, Jinling Hospital, Nanjing 210002, China
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16
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Rux DR, Wellik DM. Hox genes in the adult skeleton: Novel functions beyond embryonic development. Dev Dyn 2017; 246:310-317. [PMID: 28026082 DOI: 10.1002/dvdy.24482] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 12/20/2022] Open
Abstract
Hox genes encode evolutionarily conserved transcription factors that control skeletal patterning in the developing embryo. They are expressed in regionally restricted domains and function to regulate the morphology of specific vertebral and long bone elements. Recent work has provided evidence that Hox genes continue to be regionally expressed in adult tissues. Fibroblasts cultured from adult tissues show broadly maintained Hox gene expression patterns. In the adult skeleton, Hox genes are expressed in progenitor-enriched populations of mesenchymal stem/stromal cells (MSCs), and genetic loss-of-function analyses have provided evidence that Hox genes function during the fracture healing process. This review will highlight our current understanding of Hox expression in the adult animal and its function in skeletal regeneration. Developmental Dynamics 246:310-317, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Danielle R Rux
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Deneen M Wellik
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan.,Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, Michigan
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17
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Marchini A, Ogata T, Rappold GA. A Track Record on SHOX: From Basic Research to Complex Models and Therapy. Endocr Rev 2016; 37:417-48. [PMID: 27355317 PMCID: PMC4971310 DOI: 10.1210/er.2016-1036] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SHOX deficiency is the most frequent genetic growth disorder associated with isolated and syndromic forms of short stature. Caused by mutations in the homeobox gene SHOX, its varied clinical manifestations include isolated short stature, Léri-Weill dyschondrosteosis, and Langer mesomelic dysplasia. In addition, SHOX deficiency contributes to the skeletal features in Turner syndrome. Causative SHOX mutations have allowed downstream pathology to be linked to defined molecular lesions. Expression levels of SHOX are tightly regulated, and almost half of the pathogenic mutations have affected enhancers. Clinical severity of SHOX deficiency varies between genders and ranges from normal stature to profound mesomelic skeletal dysplasia. Treatment options for children with SHOX deficiency are available. Two decades of research support the concept of SHOX as a transcription factor that integrates diverse aspects of bone development, growth plate biology, and apoptosis. Due to its absence in mouse, the animal models of choice have become chicken and zebrafish. These models, therefore, together with micromass cultures and primary cell lines, have been used to address SHOX function. Pathway and network analyses have identified interactors, target genes, and regulators. Here, we summarize recent data and give insight into the critical molecular and cellular functions of SHOX in the etiopathogenesis of short stature and limb development.
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Affiliation(s)
- Antonio Marchini
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Tsutomu Ogata
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Gudrun A Rappold
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
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18
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Ye W, Song Y, Huang Z, Osterwalder M, Ljubojevic A, Xu J, Bobick B, Abassah-Oppong S, Ruan N, Shamby R, Yu D, Zhang L, Cai CL, Visel A, Zhang Y, Cobb J, Chen Y. A unique stylopod patterning mechanism by Shox2-controlled osteogenesis. Development 2016; 143:2548-60. [PMID: 27287812 PMCID: PMC4958343 DOI: 10.1242/dev.138750] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/31/2016] [Indexed: 02/05/2023]
Abstract
Vertebrate appendage patterning is programmed by Hox-TALE factor-bound regulatory elements. However, it remains unclear which cell lineages are commissioned by Hox-TALE factors to generate regional specific patterns and whether other Hox-TALE co-factors exist. In this study, we investigated the transcriptional mechanisms controlled by the Shox2 transcriptional regulator in limb patterning. Harnessing an osteogenic lineage-specific Shox2 inactivation approach we show that despite widespread Shox2 expression in multiple cell lineages, lack of the stylopod observed upon Shox2 deficiency is a specific result of Shox2 loss of function in the osteogenic lineage. ChIP-Seq revealed robust interaction of Shox2 with cis-regulatory enhancers clustering around skeletogenic genes that are also bound by Hox-TALE factors, supporting a lineage autonomous function of Shox2 in osteogenic lineage fate determination and skeleton patterning. Pbx ChIP-Seq further allowed the genome-wide identification of cis-regulatory modules exhibiting co-occupancy of Pbx, Meis and Shox2 transcriptional regulators. Integrative analysis of ChIP-Seq and RNA-Seq data and transgenic enhancer assays indicate that Shox2 patterns the stylopod as a repressor via interaction with enhancers active in the proximal limb mesenchyme and antagonizes the repressive function of TALE factors in osteogenesis.
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Affiliation(s)
- Wenduo Ye
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Yingnan Song
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | - Zhen Huang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | | | - Anja Ljubojevic
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Jue Xu
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Brent Bobick
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Samuel Abassah-Oppong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Ningsheng Ruan
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | - Ross Shamby
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Diankun Yu
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Lu Zhang
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chen-Leng Cai
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA School of Natural Sciences, University of California at Merced, Merced, CA 95343, USA
| | - Yanding Zhang
- Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | - John Cobb
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - YiPing Chen
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
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19
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Beccari L, Yakushiji-Kaminatsui N, Woltering JM, Necsulea A, Lonfat N, Rodríguez-Carballo E, Mascrez B, Yamamoto S, Kuroiwa A, Duboule D. A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus. Genes Dev 2016; 30:1172-86. [PMID: 27198226 PMCID: PMC4888838 DOI: 10.1101/gad.281055.116] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/22/2016] [Indexed: 11/24/2022]
Abstract
During vertebrate limb development, Hoxd genes are regulated following a bimodal strategy involving two topologically associating domains (TADs) located on either side of the gene cluster. These regulatory landscapes alternatively control different subsets of Hoxd targets, first into the arm and subsequently into the digits. We studied the transition between these two global regulations, a switch that correlates with the positioning of the wrist, which articulates these two main limb segments. We show that the HOX13 proteins themselves help switch off the telomeric TAD, likely through a global repressive mechanism. At the same time, they directly interact with distal enhancers to sustain the activity of the centromeric TAD, thus explaining both the sequential and exclusive operating processes of these two regulatory domains. We propose a model in which the activation of Hox13 gene expression in distal limb cells both interrupts the proximal Hox gene regulation and re-enforces the distal regulation. In the absence of HOX13 proteins, a proximal limb structure grows without any sign of wrist articulation, likely related to an ancestral fish-like condition.
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Affiliation(s)
- Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
| | | | - Joost M Woltering
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
| | - Anamaria Necsulea
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Lonfat
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
| | | | - Benedicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
| | - Shiori Yamamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland; School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
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Vernon LL, Vance DD, Wang L, Rampersaud E, Vance JM, Pericak-Vance M, Huang CYC, Kaplan LD. Regional Differential Genetic Response of Human Articular Cartilage to Impact Injury. Cartilage 2016; 7:163-73. [PMID: 27047639 PMCID: PMC4797239 DOI: 10.1177/1947603515618483] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVE Normal physiological movement creates different weightbearing zones within a human knee: the medial condyle bearing the highest and the trochlea bearing the lowest weight. Adaptation to different physiological loading conditions results in different tissue and cellular properties within a knee. The objective of this study was to use microarray analysis to examine gene expression differences among three anatomical regions of human knee articular cartilage at baseline and following induction of an acute impact injury. DESIGN Cartilage explants were harvested from 7 cadaveric knees (12 plugs per knee). A drop tower was utilized to introduce injury. Plugs were examined 24 hours after impact for gene expression using microarray. The primary analysis is the comparison of baseline versus impacted samples within each region separately. In addition, pairwise comparisons among the three regions were performed at baseline and after impact. False discovery rate (FDR) was used to evaluate significance of differential gene expression. RESULTS In the comparison of before and after injury, the trochlear had 130 differentially expressed genes (FDR ≤ 0.05) while the condyles had none. In the comparison among regions, smaller sets of differentially expressed genes (n ≤ 21) were found, with trochlea being more different than the condyles. Most of more frequently expressed genes in trochlea are developmental genes. CONCLUSIONS Within the experimental setup of this study, only the trochlea was displaying an acute genetic response on injury. Our data demonstrated the regional-specific response to injury in human articular cartilage.
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Affiliation(s)
- Lauren L. Vernon
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL, USA,Division of Sports Medicine, UHealth Sports Performance and Wellness Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Danica D. Vance
- Division of Sports Medicine, UHealth Sports Performance and Wellness Institute, University of Miami Miller School of Medicine, Miami, FL, USA,John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Evadnie Rampersaud
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - C.-Y. Charles Huang
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL, USA
| | - Lee D. Kaplan
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL, USA,Division of Sports Medicine, UHealth Sports Performance and Wellness Institute, University of Miami Miller School of Medicine, Miami, FL, USA,Lee D. Kaplan, Division of Sports Medicine, UHealth Sports Performance and Wellness Institute, University of Miami, 1400 NW 12th Avenue, First Floor Sports Medicine Clinic, Miami, FL 33136, USA.
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