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1
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Barcelos PM, Filgueiras IS, Nóbile AL, Usuda JN, Adri AS, de Alburquerque DG, Côrrea YLG, do Vale FYN, Bahia IAF, Nava RG, Boroni M, Marques AHC, Dalmolin R, Schimke LF, Cabral-Miranda G, Nakaya HI, Dias HD, Fonseca DLM, Cabral-Marques O. Gene regulatory networks analysis for the discovery of prognostic genes in gliomas. Sci Rep 2025; 15:14034. [PMID: 40269178 PMCID: PMC12018930 DOI: 10.1038/s41598-025-98542-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Accepted: 04/14/2025] [Indexed: 04/25/2025] Open
Abstract
Gliomas are the most common and aggressive primary tumors of the central nervous system. Dysregulated transcription factors (TFs) and genes have been implicated in glioma progression, yet these tumors' overall structure of gene regulatory networks (GRNs) remains undefined. We analyzed transcriptional data from 989 primary gliomas in The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) to address this. GRNs were reconstructed using the RTN package which identifies regulons-sets of genes regulated by a common TF based on co-expression and mutual information. Regulon activity was evaluated through Gene Set Enrichment Analysis. Elastic net regularization and Cox regression identified 31 and 32 prognostic genes in the TCGA and CGGA datasets, respectively, with 11 genes overlapping, many of which are associated with neural development and synaptic processes. GAS2L3, HOXD13, and OTP demonstrated the strongest correlations with survival outcomes among these. Single-cell RNA-seq analysis of 201,986 cells revealed distinct expression patterns for these genes in glioma subpopulations, particularly oligoprogenitor cells. This study uncovers key GRNs and prognostic genes in gliomas, offering new insights into tumor biology and potential therapeutic targets.
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Affiliation(s)
- Pedro Marçal Barcelos
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brazil.
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Adriel Leal Nóbile
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brazil
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Júlia Nakanishi Usuda
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brazil
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Anny Silva Adri
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brazil
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Débora Gomes de Alburquerque
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
- Interunit Postgraduate Program on Bioinformatics, Institute of Chemistry (IQ), University of São Paulo (USP), Matão Street, 1010, São Paulo, SP, 05508-090, Brazil
| | - Yohan Lucas Gonçalves Côrrea
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brazil
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Fernando Yuri Nery do Vale
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brazil
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Ian Antunes Ferreira Bahia
- Interunit Postgraduate Program on Bioinformatics, Institute of Chemistry (IQ), University of São Paulo (USP), Matão Street, 1010, São Paulo, SP, 05508-090, Brazil
| | - Roseane Galdioli Nava
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
- Interunit Postgraduate Program on Bioinformatics, Institute of Chemistry (IQ), University of São Paulo (USP), Matão Street, 1010, São Paulo, SP, 05508-090, Brazil
| | - Mariana Boroni
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Alexandre H C Marques
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Rodrigo Dalmolin
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Gustavo Cabral-Miranda
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | | | - Haroldo Dutra Dias
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, School of Medicine, University of São Paulo (USP) School of Medicine, Avenida Dr. Arnaldo, 455, São Paulo, SP, 01246-903, Brazil
| | - Dennyson Leandro M Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Chemistry (IQ), University of São Paulo (USP), Matão Street, 1010, São Paulo, SP, 05508-090, Brazil.
| | - Otavio Cabral-Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brazil.
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil.
- Laboratory of Psychoneuroimmunology, Selye Lab, University of São Paulo School of Medicine, São Paulo, Brazil.
- Interunit Postgraduate Program on Bioinformatics, Institute of Chemistry (IQ), University of São Paulo (USP), Matão Street, 1010, São Paulo, SP, 05508-090, Brazil.
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, School of Medicine, University of São Paulo (USP) School of Medicine, Avenida Dr. Arnaldo, 455, São Paulo, SP, 01246-903, Brazil.
- IDO'R Institute for Research, São Paulo, Brazil.
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Reno PL, Wallace S, Doelp SN, Biancaniello M, Kjosness KM. The role of the PTHrP/Ihh feedback loop in the unusual growth plate location in mammalian metatarsals and pisiforms. Dev Dyn 2025. [PMID: 40088130 DOI: 10.1002/dvdy.70013] [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: 08/28/2024] [Revised: 02/03/2025] [Accepted: 02/25/2025] [Indexed: 03/17/2025] Open
Abstract
BACKGROUND Longitudinal skeletal growth takes place in the cartilaginous growth plates. While growth plates are found at either end of conventional long bones, they occur at a variety of locations in the mammalian skeleton. For example, the metacarpals and metatarsals (MT) in the hands and feet form only a single growth plate at one end, and the pisiform in the wrist is the only carpal bone to contain a growth plate. We take advantage of this natural anatomical variation to test which components of the PTHrP/Ihh feedback loop, a fundamental regulator of chondrocyte differentiation, are specific to growth plate function. RESULTS Parathyroid hormone-like hormone (Pthlh), the gene that transcribes parathyroid hormone-related peptide (PTHrP), is expressed in the reserve zone of the growth plate-forming end of the MT. At the opposite end, the absence of a PTHrP+ reserve zone results in premature chondrocyte differentiation and Indian hedgehog (Ihh) expression. Pthlh is expressed in the reserve zone of the developing pisiform, confirming the existence of a true growth plate. CONCLUSION A pool of PTHrP+ reserve zone chondrocytes is a defining characteristic of growth plates, and its patterning may be key to evolved differences in growth plate location in the mammalian skeleton.
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Affiliation(s)
- Philip L Reno
- Department of Biomedical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
| | - Sherrie Wallace
- Department of Biomedical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
| | - Sarah N Doelp
- Department of Biomedical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
| | - Maria Biancaniello
- Department of Biomedical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
| | - Kelsey M Kjosness
- Department of Biomedical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
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Simon NM, Kim Y, Gribnau J, Bautista DM, Dutton JR, Brem RB. Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes. Heredity (Edinb) 2024; 133:308-316. [PMID: 39164520 PMCID: PMC11527988 DOI: 10.1038/s41437-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 08/22/2024] Open
Abstract
A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells from Mus musculus subspecies as a model. Using a test of directional, cis-regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa. We then mined population-genomic sequences to pursue underlying regulatory mechanisms for this expression divergence, finding robust evidence for alleles unique to M. m. castaneus at the upstream regions of the translation genes. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.
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Affiliation(s)
- Noah M Simon
- Biology of Aging Doctoral Program, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Yujin Kim
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, Rotterdam, PO Box 2040, CA, 3000, Netherlands
| | - Diana M Bautista
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - James R Dutton
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.
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Ishizaka M, Maeno A, Nakazawa H, Fujii R, Oikawa S, Tani T, Kanno H, Koita R, Kawamura A. The functional roles of zebrafish HoxA- and HoxD-related clusters in the pectoral fin development. Sci Rep 2024; 14:23602. [PMID: 39384796 PMCID: PMC11464670 DOI: 10.1038/s41598-024-74134-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 09/24/2024] [Indexed: 10/11/2024] Open
Abstract
The paralogs 9-13 Hox genes in mouse HoxA and HoxD clusters are critical for limb development. When both HoxA and HoxD clusters are deleted in mice, significant limb truncation is observed compared to the phenotypes of single and compound mutants of Hox9-13 genes in these clusters. In zebrafish, mutations in hox13 genes in HoxA- and HoxD-related clusters result in abnormal morphology of pectoral fins, homologous to forelimbs. However, the effect of the simultaneous deletions of entire HoxA- and HoxD-related clusters on pectoral fin development remains unknown. Here, we generated mutants with several combinations of hoxaa, hoxab, and hoxda cluster deletions and analyzed the pectoral fin development. In hoxaa-/-;hoxab-/-;hoxda-/- larvae, the endoskeletal disc and the fin-fold are significantly shortened in developing pectoral fins. In addition, we show that this anomaly is due to defects in the pectoral fin growth after the fin bud formation. Furthermore, in the surviving adult mutants, micro-CT scanning reveals defects in the posterior portion of the pectoral fin which is thought to represent latent regions of the limb. Our results further support that the functional role of HoxA and HoxD clusters is conserved in the paired appendage formation in bony fishes.
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Affiliation(s)
- Mizuki Ishizaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
| | - Akiteru Maeno
- Cell Architecture Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Hidemichi Nakazawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
| | - Renka Fujii
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
| | - Sae Oikawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
| | - Taisei Tani
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
| | - Haruna Kanno
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
| | - Rina Koita
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan.
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Contriciani RE, Grade CVC, Buzzatto-Leite I, da Veiga FC, Ledur MC, Reverter A, Alexandre PA, Cesar ASM, Coutinho LL, Alvares LE. Phenotypic divergence between broiler and layer chicken lines is regulated at the molecular level during development. BMC Genomics 2024; 25:168. [PMID: 38347479 PMCID: PMC10863267 DOI: 10.1186/s12864-024-10083-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/02/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Understanding the molecular underpinnings of phenotypic variations is critical for enhancing poultry breeding programs. The Brazilian broiler (TT) and laying hen (CC) lines exhibit striking differences in body weight, growth potential, and muscle mass. Our work aimed to compare the global transcriptome of wing and pectoral tissues during the early development (days 2.5 to 3.5) of these chicken lines, unveiling disparities in gene expression and regulation. RESULTS Different and bona-fide transcriptomic profiles were identified for the compared lines. A similar number of up- and downregulated differentially expressed genes (DEGs) were identified, considering the broiler line as a reference. Upregulated DEGs displayed an enrichment of protease-encoding genes, whereas downregulated DEGs exhibited a prevalence of receptors and ligands. Gene Ontology analysis revealed that upregulated DEGs were mainly associated with hormone response, mitotic cell cycle, and different metabolic and biosynthetic processes. In contrast, downregulated DEGs were primarily linked to communication, signal transduction, cell differentiation, and nervous system development. Regulatory networks were constructed for the mitotic cell cycle and cell differentiation biological processes, as their contrasting roles may impact the development of distinct postnatal traits. Within the mitotic cell cycle network, key upregulated DEGs included CCND1 and HSP90, with central regulators being NF-κB subunits (RELA and REL) and NFATC2. The cell differentiation network comprises numerous DEGs encoding transcription factors (e.g., HOX genes), receptors, ligands, and histones, while the main regulatory hubs are CREB, AR and epigenetic modifiers. Clustering analyses highlighted PIK3CD as a central player within the differentiation network. CONCLUSIONS Our study revealed distinct developmental transcriptomes between Brazilian broiler and layer lines. The gene expression profile of broiler embryos seems to favour increased cell proliferation and delayed differentiation, which may contribute to the subsequent enlargement of pectoral tissues during foetal and postnatal development. Our findings pave the way for future functional studies and improvement of targeted traits of economic interest in poultry.
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Affiliation(s)
- Renata Erbert Contriciani
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla Vermeulen Carvalho Grade
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Universidade Federal da Integração Latino-Americana (UNILA), Foz do Iguaçu, Brazil
| | - Igor Buzzatto-Leite
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Cristina da Veiga
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (USP), Piracicaba, Brazil
| | | | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Brisbane, QLD, Australia
| | - Pamela Almeida Alexandre
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Brisbane, QLD, Australia
| | - Aline Silva Mello Cesar
- Department of Agri-Food Industry, Food and Nutrition, Luiz de Queiroz College of Agriculture, University of São Paulo (USP), Piracicaba, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (USP), Piracicaba, Brazil.
| | - Lúcia Elvira Alvares
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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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: 2] [Impact Index Per Article: 2.0] [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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7
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Wanninger A. Hox, homology, and parsimony: An organismal perspective. Semin Cell Dev Biol 2024; 152-153:16-23. [PMID: 36670036 DOI: 10.1016/j.semcdb.2023.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/21/2022] [Accepted: 01/08/2023] [Indexed: 01/20/2023]
Abstract
Hox genes are important regulators in animal development. They often show a mosaic of conserved (e.g., longitudinal axis patterning) and lineage-specific novel functions (e.g., development of skeletal, sensory, or locomotory systems). Despite extensive research over the past decades, it remains controversial at which node in the animal tree of life the Hox cluster evolved. Its presence already in the last common metazoan ancestor has been proposed, although the genomes of both putative earliest extant metazoan offshoots, the ctenophores and the poriferans, are devoid of Hox sequences. The lack of Hox genes in the supposedly "simple"-built poriferans and their low number in cnidarians and the basally branching bilaterians, the xenacoelomorphs, seems to support the classical notion that the number of Hox genes is correlated with the degree of animal complexity. However, the 4-fold increase of the Hox cluster in xiphosurans, a basally branching chelicerate clade, as well as the situation in some teleost fishes that show a multitude of Hox genes compared to, e.g., human, demonstrates, that there is no per se direct correlation between organismal complexity and Hox number. Traditional approaches have tried to base homology on the morphological level on shared expression profiles of individual genes, but recent data have shown that, in particular with respect to Hox and other regulatory genes, complex gene-gene interactions rather than expression signatures of individual genes alone are responsible for shaping morphological traits during ontogeny. Accordingly, for sound homology assessments and reconstructions of character evolution on organ system level, additional independent datasets (e.g., morphological, developmental) need to be included in any such analyses. If supported by solid data, proposed structural homology should be regarded as valid and not be rejected solely on the grounds of non-parsimonious distribution of the character over a given phylogenetic topology.
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Affiliation(s)
- Andreas Wanninger
- University of Vienna, Department of Evolutionary Biology, Unit for Integrative Zoology, Djerassiplatz 1, 1030 Vienna, Austria.
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8
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Ludington AJ, Hammond JM, Breen J, Deveson IW, Sanders KL. New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 2023; 21:284. [PMID: 38066641 PMCID: PMC10709897 DOI: 10.1186/s12915-023-01772-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Sea snakes underwent a complete transition from land to sea within the last ~ 15 million years, yet they remain a conspicuous gap in molecular studies of marine adaptation in vertebrates. RESULTS Here, we generate four new annotated sea snake genomes, three of these at chromosome-scale (Hydrophis major, H. ornatus and H. curtus), and perform detailed comparative genomic analyses of sea snakes and their closest terrestrial relatives. Phylogenomic analyses highlight the possibility of near-simultaneous speciation at the root of Hydrophis, and synteny maps show intra-chromosomal variations that will be important targets for future adaptation and speciation genomic studies of this system. We then used a strict screen for positive selection in sea snakes (against a background of seven terrestrial snake genomes) to identify genes over-represented in hypoxia adaptation, sensory perception, immune response and morphological development. CONCLUSIONS We provide the best reference genomes currently available for the prolific and medically important elapid snake radiation. Our analyses highlight the phylogenetic complexity and conserved genome structure within Hydrophis. Positively selected marine-associated genes provide promising candidates for future, functional studies linking genetic signatures to the marine phenotypes of sea snakes and other vertebrates.
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Affiliation(s)
- Alastair J Ludington
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Jillian M Hammond
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute, Adelaide, Australia
- John Curtin School of Medical Research, College of Health & Medicine, Australian National University, Canberra, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kate L Sanders
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
- The South Australian Museum, Adelaide, Australia.
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9
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Sedas Perez S, McQueen C, Stainton H, Pickering J, Chinnaiya K, Saiz-Lopez P, Placzek M, Ros MA, Towers M. Fgf signalling triggers an intrinsic mesodermal timer that determines the duration of limb patterning. Nat Commun 2023; 14:5841. [PMID: 37730682 PMCID: PMC10511490 DOI: 10.1038/s41467-023-41457-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023] Open
Abstract
Complex signalling between the apical ectodermal ridge (AER - a thickening of the distal epithelium) and the mesoderm controls limb patterning along the proximo-distal axis (humerus to digits). However, the essential in vivo requirement for AER-Fgf signalling makes it difficult to understand the exact roles that it fulfils. To overcome this barrier, we developed an amenable ex vivo chick wing tissue explant system that faithfully replicates in vivo parameters. Using inhibition experiments and RNA-sequencing, we identify a transient role for Fgfs in triggering the distal patterning phase. Fgfs are then dispensable for the maintenance of an intrinsic mesodermal transcriptome, which controls proliferation/differentiation timing and the duration of patterning. We also uncover additional roles for Fgf signalling in maintaining AER-related gene expression and in suppressing myogenesis. We describe a simple logic for limb patterning duration, which is potentially applicable to other systems, including the main body axis.
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Affiliation(s)
- Sofia Sedas Perez
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Caitlin McQueen
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Chester Medical School, Chester, CH2 1BR, UK
| | - Holly Stainton
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Joseph Pickering
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Kavitha Chinnaiya
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Patricia Saiz-Lopez
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria), 39011, Santander, Spain
- Departamento de Anatomía y Biología Celular Facultad de Medicina, Universidad de Cantabria, 39011, Santander, Spain
| | - Marysia Placzek
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Maria A Ros
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria), 39011, Santander, Spain
- Departamento de Anatomía y Biología Celular Facultad de Medicina, Universidad de Cantabria, 39011, Santander, Spain
| | - Matthew Towers
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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10
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Yadav US, Biswas T, Singh PN, Gupta P, Chakraborty S, Delgado I, Zafar H, Capellini TD, Torres M, Bandyopadhyay A. Molecular mechanism of synovial joint site specification and induction in developing vertebrate limbs. Development 2023; 150:dev201335. [PMID: 37272420 PMCID: PMC10323242 DOI: 10.1242/dev.201335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
The vertebrate appendage comprises three primary segments, the stylopod, zeugopod and autopod, each separated by joints. The molecular mechanisms governing the specification of joint sites, which define segment lengths and thereby limb architecture, remain largely unknown. Existing literature suggests that reciprocal gradients of retinoic acid (RA) and fibroblast growth factor (FGF) signaling define the expression domains of the putative segment markers Meis1, Hoxa11 and Hoxa13. Barx1 is expressed in the presumptive joint sites. Our data demonstrate that RA-FGF signaling gradients define the expression domain of Barx1 in the first presumptive joint site. When misexpressed, Barx1 induces ectopic interzone-like structures, and its loss of function partially blocks interzone development. Simultaneous perturbations of RA-FGF signaling gradients result in predictable shifts of Barx1 expression domains along the proximo-distal axis and, consequently, in the formation of repositioned joints. Our data suggest that during early limb bud development in chick, Meis1 and Hoxa11 expression domains are overlapping, whereas the Barx1 expression domain resides within the Hoxa11 expression domain. However, once the interzone is formed, the expression domains are refined and the Barx1 expression domain becomes congruent with the border of these two putative segment markers.
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Affiliation(s)
- Upendra S. Yadav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Tathagata Biswas
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Pratik N. Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Pankaj Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Soura Chakraborty
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Irene Delgado
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, 28029 Madrid, Spain
| | - Hamim Zafar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- Department of Computer Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Terence D. Capellini
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Miguel Torres
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, 28029 Madrid, Spain
| | - Amitabha Bandyopadhyay
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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11
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Zhu M, Tabin CJ. The role of timing in the development and evolution of the limb. Front Cell Dev Biol 2023; 11:1135519. [PMID: 37200627 PMCID: PMC10185760 DOI: 10.3389/fcell.2023.1135519] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/13/2023] [Indexed: 05/20/2023] Open
Abstract
The term heterochrony was coined to describe changes in the timing of developmental processes relative to an ancestral state. Limb development is a well-suited system to address the contribution of heterochrony to morphological evolution. We illustrate how timing mechanisms have been used to establish the correct pattern of the limb and provide cases where natural variations in timing have led to changes in limb morphology.
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12
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The molecular genetics of human appendicular skeleton. Mol Genet Genomics 2022; 297:1195-1214. [PMID: 35907958 DOI: 10.1007/s00438-022-01930-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/09/2022] [Indexed: 10/16/2022]
Abstract
Disorders that result from de-arrangement of growth, development and/or differentiation of the appendages (limbs and digit) are collectively called as inherited abnormalities of human appendicular skeleton. The bones of appendicular skeleton have central role in locomotion and movement. The different types of appendicular skeletal abnormalities are well described in the report of "Nosology and Classification of Genetic skeletal disorders: 2019 Revision". In the current article, we intend to present the embryology, developmental pathways, disorders and the molecular genetics of the appendicular skeletal malformations. We mainly focused on the polydactyly, syndactyly, brachydactyly, split-hand-foot malformation and clubfoot disorders. To our knowledge, only nine genes of polydactyly, five genes of split-hand-foot malformation, nine genes for syndactyly, eight genes for brachydactyly and only single gene for clubfoot have been identified to be involved in disease pathophysiology. The current molecular genetic data will help life sciences researchers working on the rare skeletal disorders. Moreover, the aim of present systematic review is to gather the published knowledge on molecular genetics of appendicular skeleton, which would help in genetic counseling and molecular diagnosis.
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13
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Roscito JG, Sameith K, Kirilenko BM, Hecker N, Winkler S, Dahl A, Rodrigues MT, Hiller M. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Rep 2022; 38:110280. [DOI: 10.1016/j.celrep.2021.110280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 01/02/2023] Open
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14
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Swank S, Sanger TJ, Stuart YE. (Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss. Ecol Evol 2021; 11:15484-15497. [PMID: 34824770 PMCID: PMC8601893 DOI: 10.1002/ece3.8226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/31/2021] [Accepted: 09/21/2021] [Indexed: 01/16/2023] Open
Abstract
Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. The multiple routes to appendage reduction and loss suggest that adaptive loss of function phenotypes might arise routinely through changes in expression of key developmental genes.
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Affiliation(s)
- Samantha Swank
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Thomas J. Sanger
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Yoel E. Stuart
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
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15
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Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nat Commun 2021; 12:6094. [PMID: 34667153 PMCID: PMC8526749 DOI: 10.1038/s41467-021-26234-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 09/14/2021] [Indexed: 11/09/2022] Open
Abstract
Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant. Activation of the zygotic genome is a critical transition during development, though the link to tissue-specific gene regulation remains unclear. Here the authors demonstrate distinct functions for Satb2 before and after zygotic genome activation, highlighting the temporal coordination of these roles.
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16
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Bolt CC, Lopez-Delisle L, Mascrez B, Duboule D. Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations. Nat Commun 2021; 12:5013. [PMID: 34408147 PMCID: PMC8373931 DOI: 10.1038/s41467-021-25330-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Human families with chromosomal rearrangements at 2q31, where the human HOXD locus maps, display mesomelic dysplasia, a severe shortening and bending of the limb. In mice, the dominant Ulnaless inversion of the HoxD cluster produces a similar phenotype suggesting the same origin for these malformations in humans and mice. Here we engineer 1 Mb inversion including the HoxD gene cluster, which positioned Hoxd13 close to proximal limb enhancers. Using this model, we show that these enhancers contact and activate Hoxd13 in proximal cells, inducing the formation of mesomelic dysplasia. We show that a secondary Hoxd13 null mutation in-cis with the inversion completely rescues the alterations, demonstrating that ectopic HOXD13 is directly responsible for this bone anomaly. Single-cell expression analysis and evaluation of HOXD13 binding sites suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.
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MESH Headings
- Abnormalities, Multiple/embryology
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Animals
- Bone Diseases, Developmental/embryology
- Bone Diseases, Developmental/genetics
- Bone Diseases, Developmental/metabolism
- Disease Models, Animal
- Female
- Gene Deletion
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Limb Deformities, Congenital/embryology
- Limb Deformities, Congenital/genetics
- Limb Deformities, Congenital/metabolism
- Loss of Function Mutation
- Male
- Mice, Inbred C57BL
- Multigene Family
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Mice
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Affiliation(s)
- Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
- Collège de France, Paris, France.
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17
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Contreras O, Rossi FMV, Theret M. Origins, potency, and heterogeneity of skeletal muscle fibro-adipogenic progenitors-time for new definitions. Skelet Muscle 2021; 11:16. [PMID: 34210364 PMCID: PMC8247239 DOI: 10.1186/s13395-021-00265-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Striated muscle is a highly plastic and regenerative organ that regulates body movement, temperature, and metabolism-all the functions needed for an individual's health and well-being. The muscle connective tissue's main components are the extracellular matrix and its resident stromal cells, which continuously reshape it in embryonic development, homeostasis, and regeneration. Fibro-adipogenic progenitors are enigmatic and transformative muscle-resident interstitial cells with mesenchymal stem/stromal cell properties. They act as cellular sentinels and physiological hubs for adult muscle homeostasis and regeneration by shaping the microenvironment by secreting a complex cocktail of extracellular matrix components, diffusible cytokines, ligands, and immune-modulatory factors. Fibro-adipogenic progenitors are the lineage precursors of specialized cells, including activated fibroblasts, adipocytes, and osteogenic cells after injury. Here, we discuss current research gaps, potential druggable developments, and outstanding questions about fibro-adipogenic progenitor origins, potency, and heterogeneity. Finally, we took advantage of recent advances in single-cell technologies combined with lineage tracing to unify the diversity of stromal fibro-adipogenic progenitors. Thus, this compelling review provides new cellular and molecular insights in comprehending the origins, definitions, markers, fate, and plasticity of murine and human fibro-adipogenic progenitors in muscle development, homeostasis, regeneration, and repair.
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Affiliation(s)
- Osvaldo Contreras
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Kensington, 2052, Australia.
- Departamento de Biología Celular y Molecular and Center for Aging and Regeneration (CARE-ChileUC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile.
| | - Fabio M V Rossi
- Biomedical Research Centre, Department of Medical Genetics and School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Marine Theret
- Biomedical Research Centre, Department of Medical Genetics and School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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18
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Fibroblast dedifferentiation as a determinant of successful regeneration. Dev Cell 2021; 56:1541-1551.e6. [PMID: 34004152 PMCID: PMC8140481 DOI: 10.1016/j.devcel.2021.04.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/03/2021] [Accepted: 04/16/2021] [Indexed: 12/31/2022]
Abstract
Limb regeneration, while observed lifelong in salamanders, is restricted in post-metamorphic Xenopus laevis frogs. Whether this loss is due to systemic factors or an intrinsic incapability of cells to form competent stem cells has been unclear. Here, we use genetic fate mapping to establish that connective tissue (CT) cells form the post-metamorphic frog blastema, as in the case of axolotls. Using heterochronic transplantation into the limb bud and single-cell transcriptomic profiling, we show that axolotl CT cells dedifferentiate and integrate to form lineages, including cartilage. In contrast, frog blastema CT cells do not fully re-express the limb bud progenitor program, even when transplanted into the limb bud. Correspondingly, transplanted cells contribute to extraskeletal CT, but not to the developing cartilage. Furthermore, using single-cell RNA-seq analysis we find that embryonic and adult frog cartilage differentiation programs are molecularly distinct. This work defines intrinsic restrictions in CT dedifferentiation as a limitation in adult regeneration.
Fibroblast-derived Prrx1+ cells are the main constituent of a frog limb blastema Frog fibroblasts only undergo partial dedifferentiation due to intrinsic limitations Adult chondrogenesis is distinct from the embryonic program
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19
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Hawkins MB, Henke K, Harris MP. Latent developmental potential to form limb-like skeletal structures in zebrafish. Cell 2021; 184:899-911.e13. [PMID: 33545089 DOI: 10.1016/j.cell.2021.01.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 10/28/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Changes in appendage structure underlie key transitions in vertebrate evolution. Addition of skeletal elements along the proximal-distal axis facilitated critical transformations, including the fin-to-limb transition that permitted generation of diverse modes of locomotion. Here, we identify zebrafish mutants that form supernumerary long bones in their pectoral fins. These new bones integrate into musculature, form joints, and articulate with neighboring elements. This phenotype is caused by activating mutations in previously unrecognized regulators of appendage patterning, vav2 and waslb, that function in a common pathway. This pathway is required for appendage development across vertebrates, and loss of Wasl in mice causes defects similar to those seen in murine Hox mutants. Concordantly, formation of supernumerary bones requires Hox11 function, and mutations in the vav2/wasl pathway drive enhanced expression of hoxa11b, indicating developmental homology with the forearm. Our findings reveal a latent, limb-like pattern ability in fins that is activated by simple genetic perturbation.
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Affiliation(s)
- M Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA; Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Katrin Henke
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA.
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20
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Mammalian-specific ectodermal enhancers control the expression of Hoxc genes in developing nails and hair follicles. Proc Natl Acad Sci U S A 2020; 117:30509-30519. [PMID: 33199643 PMCID: PMC7720164 DOI: 10.1073/pnas.2011078117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Vertebrate Hox genes are critical for the establishment of structures during the development of the main body axis. Subsequently, they play important roles either in organizing secondary axial structures such as the appendages, or during homeostasis in postnatal stages and adulthood. Here, we set up to analyze their elusive function in the ectodermal compartment, using the mouse limb bud as a model. We report that the HoxC gene cluster was co-opted to be transcribed in the distal limb ectoderm, where it is activated following the rule of temporal colinearity. These ectodermal cells subsequently produce various keratinized organs such as nails or claws. Accordingly, deletion of the HoxC cluster led to mice lacking nails (anonychia), a condition stronger than the previously reported loss of function of Hoxc13, which is the causative gene of the ectodermal dysplasia 9 (ECTD9) in human patients. We further identified two mammalian-specific ectodermal enhancers located upstream of the HoxC gene cluster, which together regulate Hoxc gene expression in the hair and nail ectodermal organs. Deletion of these regulatory elements alone or in combination revealed a strong quantitative component in the regulation of Hoxc genes in the ectoderm, suggesting that these two enhancers may have evolved along with the mammalian taxon to provide the level of HOXC proteins necessary for the full development of hair and nail.
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21
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Basu S, Mackowiak SD, Niskanen H, Knezevic D, Asimi V, Grosswendt S, Geertsema H, Ali S, Jerković I, Ewers H, Mundlos S, Meissner A, Ibrahim DM, Hnisz D. Unblending of Transcriptional Condensates in Human Repeat Expansion Disease. Cell 2020; 181:1062-1079.e30. [PMID: 32386547 PMCID: PMC7261253 DOI: 10.1016/j.cell.2020.04.018] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/16/2020] [Accepted: 04/13/2020] [Indexed: 11/27/2022]
Abstract
Expansions of amino acid repeats occur in >20 inherited human disorders, and many occur in intrinsically disordered regions (IDRs) of transcription factors (TFs). Such diseases are associated with protein aggregation, but the contribution of aggregates to pathology has been controversial. Here, we report that alanine repeat expansions in the HOXD13 TF, which cause hereditary synpolydactyly in humans, alter its phase separation capacity and its capacity to co-condense with transcriptional co-activators. HOXD13 repeat expansions perturb the composition of HOXD13-containing condensates in vitro and in vivo and alter the transcriptional program in a cell-specific manner in a mouse model of synpolydactyly. Disease-associated repeat expansions in other TFs (HOXA13, RUNX2, and TBP) were similarly found to alter their phase separation. These results suggest that unblending of transcriptional condensates may underlie human pathologies. We present a molecular classification of TF IDRs, which provides a framework to dissect TF function in diseases associated with transcriptional dysregulation.
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Affiliation(s)
- Shaon Basu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Henri Niskanen
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Dora Knezevic
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vahid Asimi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefanie Grosswendt
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Hylkje Geertsema
- Institute for Chemistry and Biochemistry, Free University Berlin, 14195 Berlin, Germany
| | - Salaheddine Ali
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, 10178 Berlin, Germany
| | - Ivana Jerković
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Free University Berlin, 14195 Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, 10178 Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Daniel M Ibrahim
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, 10178 Berlin, Germany
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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22
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Lewis EMA, Sankar S, Tong C, Patterson ES, Waller LE, Gontarz P, Zhang B, Ornitz DM, Kroll KL. Geminin is required for Hox gene regulation to pattern the developing limb. Dev Biol 2020; 464:11-23. [PMID: 32450229 DOI: 10.1016/j.ydbio.2020.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/09/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023]
Abstract
Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5' Hox transcription factor expression is essential for proper limb bud patterning and elaboration of distinct limb skeletal elements. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5' Hox gene expression expanded into more proximal and anterior regions of the embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior SHH signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the HOXD13 target Shh, and the SHH target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of GLI3, a SHH pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb.
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Affiliation(s)
- Emily M A Lewis
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Savita Sankar
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Caili Tong
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ethan S Patterson
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laura E Waller
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Paul Gontarz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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23
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Wang T, Hill RC, Dzieciatkowska M, Zhu L, Infante AM, Hu G, Hansen KC, Pei M. Site-Dependent Lineage Preference of Adipose Stem Cells. Front Cell Dev Biol 2020; 8:237. [PMID: 32351957 PMCID: PMC7174673 DOI: 10.3389/fcell.2020.00237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/20/2020] [Indexed: 12/15/2022] Open
Abstract
Adult stem cells have unique properties in both proliferation and differentiation preference. In this study, we hypothesized that adipose stem cells have a depot-dependent lineage preference. Four rabbits were used to provide donor-matched adipose stem cells from either subcutaneous adipose tissue (ScAT) or infrapatellar fat pad (IPFP). Proliferation and multi-lineage differentiation were evaluated in adipose stem cells from donor-matched ScAT and IPFP. RNA sequencing (RNA-seq) and proteomics were conducted to uncover potential molecular discrepancy in adipose stem cells and their corresponding matrix microenvironments. We found that stem cells from ScAT exhibited significantly higher proliferation and adipogenic capacity compared to those from donor-matched IPFP while stem cells from IPFP displayed significantly higher chondrogenic potential compared to those from donor-matched ScAT. Our findings are strongly endorsed by supportive data from transcriptome and proteomics analyses, indicating a site-dependent lineage preference of adipose stem cells.
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Affiliation(s)
- Tingliang Wang
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopedics, West Virginia University, Morgantown, WV, United States
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital Affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, United States
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, United States
| | - Lian Zhu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital Affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aniello M. Infante
- Bioinformatics Core Facility, West Virginia University, Morgantown, WV, United States
| | - Gangqing Hu
- Bioinformatics Core Facility, West Virginia University, Morgantown, WV, United States
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, United States
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, United States
| | - Ming Pei
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopedics, West Virginia University, Morgantown, WV, United States
- WVU Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, United States
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24
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Li J, Shang S, Fang N, Zhu Y, Zhang J, Irwin DM, Zhang S, Wang Z. Accelerated Evolution of Limb-Related Gene Hoxd11 in the Common Ancestor of Cetaceans and Ruminants (Cetruminantia). G3 (BETHESDA, MD.) 2020; 10:515-524. [PMID: 31792005 PMCID: PMC7003097 DOI: 10.1534/g3.119.400512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/24/2019] [Indexed: 11/18/2022]
Abstract
Reduced numbers of carpal and tarsal bones (wrist and ankle joints) are extensively observed in the clade of Cetacea and Ruminantia (Cetruminantia). Homebox D11 (Hoxd11) is one of the important genes required for limb development in mammals. Mutations in Hoxd11 can lead to defects in particular bones of limbs, including carpus and tarsus. To test whether evolutionary changes in Hoxd11 underlie the loss of these bones in Cetruminantia, we sequenced and analyzed Hoxd11 coding sequences and compared them with other 5' HoxA and HoxD genes in a taxonomic coverage of Cetacea, Ruminantia and other mammalian relatives. Statistical tests on the Hoxd11 sequences found an accelerated evolution in the common ancestor of cetaceans and ruminants, which coincided with the reduction of carpal and tarsal bones in this clade. Five amino acid substitutions (G222S, G227A, G229S, A240T and G261V) and one amino acid deletion (G254Del) occurred in this lineage. In contrast, other 5' HoxA and HoxD genes do not show this same evolutionary pattern, but instead display a highly conserved pattern of evolution in this lineage. Accelerated evolution of Hoxd11, but not other 5' HoxA and HoxD genes, is probably related to the reduction of the carpal and tarsal bones in Cetruminantia. Moreover, we found two amino acid substitutions (G110S and D223N) in Hoxd11 that are unique to the lineage of Cetacea, which coincided with hindlimb loss in the common ancestor of cetaceans. Our results give molecular evidence of Hoxd11 adaptive evolution in cetaceans and ruminants, which could be correlated with limb morphological adaptation.
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Affiliation(s)
- Jun Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Songyang Shang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Na Fang
- State Key Laboratory of Estuarine and Coastal Research, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China, and
| | - Yubo Zhu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China,
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25
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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: 3.2] [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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26
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Pigeon foot feathering reveals conserved limb identity networks. Dev Biol 2019; 454:128-144. [PMID: 31247188 DOI: 10.1016/j.ydbio.2019.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022]
Abstract
The tetrapod limb is a stunning example of evolutionary diversity, with dramatic variation not only among distantly related species, but also between the serially homologous forelimbs (FLs) and hindlimbs (HLs) within species. Despite this variation, highly conserved genetic and developmental programs underlie limb development and identity in all tetrapods, raising the question of how limb diversification is generated from a conserved toolkit. In some breeds of domestic pigeon, shifts in the expression of two conserved limb identity transcription factors, PITX1 and TBX5, are associated with the formation of feathered HLs with partial FL identity. To determine how modulation of PITX1 and TBX5 expression affects downstream gene expression, we compared the transcriptomes of embryonic limb buds from pigeons with scaled and feathered HLs. We identified a set of differentially expressed genes enriched for genes encoding transcription factors, extracellular matrix proteins, and components of developmental signaling pathways with important roles in limb development. A subset of the genes that distinguish scaled and feathered HLs are also differentially expressed between FL and scaled HL buds in pigeons, pinpointing a set of gene expression changes downstream of PITX1 and TBX5 in the partial transformation from HL to FL identity. We extended our analyses by comparing pigeon limb bud transcriptomes to chicken, anole lizard, and mammalian datasets to identify deeply conserved PITX1- and TBX5-responsive components of the limb identity program. Our analyses reveal a suite of predominantly low-level gene expression changes that are conserved across amniotes to regulate the identity of morphologically distinct limbs.
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27
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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28
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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: 1.8] [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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29
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Giffin JL, Gaitor D, Franz-Odendaal TA. The Forgotten Skeletogenic Condensations: A Comparison of Early Skeletal Development Amongst Vertebrates. J Dev Biol 2019; 7:jdb7010004. [PMID: 30717314 PMCID: PMC6473759 DOI: 10.3390/jdb7010004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 01/13/2023] Open
Abstract
The development of a skeletogenic condensation is perhaps the most critical yet considerably overlooked stage of skeletogenesis. Described in this comprehensive review are the mechanisms that facilitate skeletogenic condensation formation, growth, and maintenance to allow for overt differentiation into a skeletal element. This review discusses the current knowledge of gene regulation and characterization of skeletogenic condensations in the chicken, mouse, zebrafish, and other developmental models. We limited our scope to condensations that give rise to the bones and cartilages of the vertebrate skeleton, with a particular focus on craniofacial and limb bud regions. While many of the skeletogenic processes are similar among vertebrate lineages, differences are apparent in the site and timing of the initial epithelial⁻mesenchymal interactions as well as in whether the condensation has an osteogenic or chondrogenic fate, both within and among species. Further comparative studies are needed to clarify and broaden the existing knowledge of this intricate phenomenon.
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Affiliation(s)
- Jennifer L Giffin
- Department of Biology, Mount Saint Vincent University, 166 Bedford Highway, Halifax, NS B3M 2J6, Canada.
| | - Danielle Gaitor
- Department of Biology, Mount Saint Vincent University, 166 Bedford Highway, Halifax, NS B3M 2J6, Canada.
- Department of Medical Neuroscience, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Tamara A Franz-Odendaal
- Department of Biology, Mount Saint Vincent University, 166 Bedford Highway, Halifax, NS B3M 2J6, Canada.
- Department of Medical Neuroscience, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
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30
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Mucientes A, Herranz E, Moro E, Lajas C, Candelas G, Fernández-Gutiérrez B, Lamas JR. Differential Expression of HOX Genes in Mesenchymal Stem Cells from Osteoarthritic Patients Is Independent of Their Promoter Methylation. Cells 2018; 7:cells7120244. [PMID: 30563049 PMCID: PMC6316585 DOI: 10.3390/cells7120244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Skeletogenesis, remodeling, and maintenance in adult tissues are regulated by sequential activation of genes coding for specific transcription factors. The conserved Homeobox genes (HOX, in humans) are involved in several skeletal pathologies. Osteoarthritis (OA) is characterized by homeostatic alterations of cartilage and bone synthesis, resulting in cartilage destruction and increased bone formation. We postulate that alterations in HOX expression in Mesenchymal Stem cells (MSCs) are likely one of the causes explaining the homeostatic alterations in OA and that this altered expression could be the result of epigenetic regulation. The expression of HOX genes in osteoarthritic-derived MSCs was screened using PCR arrays. Epigenetic regulation of HOX was analyzed measuring the degree of DNA methylation in their promoters. We demonstrate the downregulated expression of HOXA9 and HOXC8 in OA-MSCs. However, their expression does not correlate with promoter methylation status, suggesting that other epigenetic mechanisms could be implicated in the regulation of HOX expression. Studies on the role of these genes under active differentiation conditions need to be addressed for a better knowledge of the mechanisms regulating the expression of HOX, to allow a better understanding of OA pathology and to define possible biomarkers for therapeutic treatment.
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Affiliation(s)
- Arkaitz Mucientes
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC). UGC de Reumatología, Hospital Clínico San Carlos, 28040 Madrid, Spain.
| | - Eva Herranz
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC). UGC de Reumatología, Hospital Clínico San Carlos, 28040 Madrid, Spain.
| | - Enrique Moro
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC). UGC de Traumatología, Hospital Clínico San Carlos, 28040 Madrid, Spain.
| | - Cristina Lajas
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC). UGC de Reumatología, Hospital Clínico San Carlos, 28040 Madrid, Spain.
| | - Gloria Candelas
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC). UGC de Reumatología, Hospital Clínico San Carlos, 28040 Madrid, Spain.
| | - Benjamín Fernández-Gutiérrez
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC). UGC de Reumatología, Hospital Clínico San Carlos, 28040 Madrid, Spain.
| | - José Ramón Lamas
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC). UGC de Reumatología, Hospital Clínico San Carlos, 28040 Madrid, Spain.
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31
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Expression of meis and hoxa11 in dipnoan and teleost fins provides new insights into the evolution of vertebrate appendages. EvoDevo 2018; 9:11. [PMID: 29719716 PMCID: PMC5924435 DOI: 10.1186/s13227-018-0099-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/20/2018] [Indexed: 11/22/2022] Open
Abstract
Background The concerted activity of Meis and Hoxa11 transcription factors is essential for the subdivision of tetrapod limbs into proximo-distal (PD) domains; however, little is know about the evolution of this patterning mechanism. Here, we aim to study the expression of meis and hoxa11 orthologues in the median and paired rayed fins of zebrafish and in the lobed fins of the Australian lungfish. Results First, a late phase of expression of meis1.1 and hoxa11b in zebrafish dorsal and anal fins relates with segmentation of endochondral elements in proximal and distal radials. Second, our zebrafish in situ hybridization results reveal spatial and temporal changes between pectoral and pelvic fins. Third, in situ analysis of meis1, meis3 and hoxa11 genes in Neoceratodus pectoral fins identifies decoupled domains of expression along the PD axis. Conclusions Our data raise the possibility that the origin of stylopod and zeugopod lies much deeper in gnathostome evolution and that variation in meis and hoxa11 expression has played a substantial role in the transformation of appendage anatomy. Moreover, these observations provide evidence that the Meis/Hoxa11 profile considered a hallmark of stylopod/zeugopod patterning is present in Neoceratodus. Electronic supplementary material The online version of this article (10.1186/s13227-018-0099-9) contains supplementary material, which is available to authorized users.
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Kamkar F, Xaymardan M, Asli NS. Hox-Mediated Spatial and Temporal Coding of Stem Cells in Homeostasis and Neoplasia. Stem Cells Dev 2017; 25:1282-9. [PMID: 27462829 DOI: 10.1089/scd.2015.0352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Hox genes are fundamental components of embryonic patterning and morphogenesis with expression persisting into adulthood. They are also implicated in the development of diseases, particularly neoplastic transformations. The tight spatio-temporal regulation of Hox genes in concordance with embryonic patterning is an outstanding feature of these genes. In this review we have systematically analyzed Hox functions within the stem/progenitor cell compartments and asked whether their temporo-spatial topography is retained within the stem cell domain throughout development and adulthood. In brief, evidence support involvement of Hox genes at several levels along the stem cell hierarchy, including positional identity, stem cell self-renewal, and differentiation. There is also strong evidence to suggest a role for Hox genes during neoplasia. Although fundamental questions are yet to be addressed through more targeted and high- throughput approaches, existing evidence suggests a central role for Hox genes within a continuum along the developmental axes persisting into adult homeostasis and disease.
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Affiliation(s)
- Fatemeh Kamkar
- 1 Department of Cell and Molecular Medicine, Faculty of Medicine, University of Ottawa , Ontario, Canada
| | - Munira Xaymardan
- 2 Discipline of Life Sciences, Faculty of Dentistry, University of Sydney , Westmead Hospital, Westmead, Australia
| | - Naisana S Asli
- 2 Discipline of Life Sciences, Faculty of Dentistry, University of Sydney , Westmead Hospital, Westmead, Australia
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Rux DR, Song JY, Pineault KM, Mandair GS, Swinehart IT, Schlientz AJ, Garthus KN, Goldstein SA, Kozloff KM, Wellik DM. Hox11 Function Is Required for Region-Specific Fracture Repair. J Bone Miner Res 2017; 32:1750-1760. [PMID: 28470721 PMCID: PMC5550340 DOI: 10.1002/jbmr.3166] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/26/2017] [Accepted: 05/01/2017] [Indexed: 12/23/2022]
Abstract
The processes that govern fracture repair rely on many mechanisms that recapitulate embryonic skeletal development. Hox genes are transcription factors that perform critical patterning functions in regional domains along the axial and limb skeleton during development. Much less is known about roles for these genes in the adult skeleton. We recently reported that Hox11 genes, which function in zeugopod development (radius/ulna and tibia/fibula), are also expressed in the adult zeugopod skeleton exclusively in PDGFRα+/CD51+/LepR+ mesenchymal stem/stromal cells (MSCs). In this study, we use a Hoxa11eGFP reporter allele and loss-of-function Hox11 alleles, and we show that Hox11 expression expands after zeugopod fracture injury, and that loss of Hox11 function results in defects in endochondral ossification and in the bone remodeling phase of repair. In Hox11 compound mutant fractures, early chondrocytes are specified but show defects in differentiation, leading to an overall deficit in the cartilage production. In the later stages of the repair process, the hard callus remains incompletely remodeled in mutants due, at least in part, to abnormal bone matrix organization. Overall, our data supports multiple roles for Hox11 genes following fracture injury in the adult skeleton. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Danielle R. Rux
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Jane Y. Song
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Kyriel M. Pineault
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Gurjit S. Mandair
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA
| | - Ilea T. Swinehart
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Aleesa J. Schlientz
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Kayla N. Garthus
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Steve A. Goldstein
- Department of Orthopedic Surgery, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Ken M. Kozloff
- Department of Orthopedic Surgery, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Deneen M Wellik
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2200, USA
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109-2200, USA
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Firulli BA, Milliar H, Toolan KP, Harkin J, Fuchs RK, Robling AG, Firulli AB. Defective Hand1 phosphoregulation uncovers essential roles for Hand1 in limb morphogenesis. Development 2017; 144:2480-2489. [PMID: 28576769 PMCID: PMC5536869 DOI: 10.1242/dev.149963] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/18/2017] [Indexed: 11/20/2022]
Abstract
The morphogenesis of the vertebrate limbs is a complex process in which cell signaling and transcriptional regulation coordinate diverse structural adaptations in diverse species. In this study, we examine the consequences of altering Hand1 dimer choice regulation within developing vertebrate limbs. Although Hand1 deletion via the limb-specific Prrx1-Cre reveals a non-essential role for Hand1 in mouse limb morphogenesis, altering Hand1 phosphoregulation, and consequently Hand1 dimerization affinities, results in a severe truncation of proximal-anterior limb elements. Molecular analysis reveals a non-cell-autonomous mechanism that causes widespread cell death within the embryonic limb bud. In addition, we observe changes in proximal-anterior gene regulation, including a reduction in the expression of Irx3, Irx5, Gli3 and Alx4, all of which are upregulated in Hand2 limb conditional knockouts. A reduction of Hand2 and Shh gene dosage improves the integrity of anterior limb structures, validating the importance of the Twist-family bHLH dimer pool in limb morphogenesis. Summary: Altering Hand1 phosphoregulation, and consequently Hand1 dimerization affinities, results in a severe truncation of anterior-proximal limb elements in mice.
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Affiliation(s)
- Beth A Firulli
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Departments of Anatomy and Cell Biology, Biochemistry, Medical and Molecular Genetics, Indiana University School of Medicine
| | - Hannah Milliar
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Departments of Anatomy and Cell Biology, Biochemistry, Medical and Molecular Genetics, Indiana University School of Medicine
| | - Kevin P Toolan
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Departments of Anatomy and Cell Biology, Biochemistry, Medical and Molecular Genetics, Indiana University School of Medicine
| | - Jade Harkin
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Departments of Anatomy and Cell Biology, Biochemistry, Medical and Molecular Genetics, Indiana University School of Medicine
| | - Robyn K Fuchs
- Department of Physical Therapy and the Center for Translational Musculoskeletal Research, School of Health and Rehabilitation Science, Indiana University, Indianapolis, IN 46202, USA
| | - Alex G Robling
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202-5225, USA
| | - Anthony B Firulli
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Departments of Anatomy and Cell Biology, Biochemistry, Medical and Molecular Genetics, Indiana University School of Medicine
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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: 71] [Impact Index Per Article: 8.9] [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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Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF. PLoS Genet 2017; 13:e1006567. [PMID: 28103242 PMCID: PMC5289628 DOI: 10.1371/journal.pgen.1006567] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/02/2017] [Accepted: 01/04/2017] [Indexed: 11/29/2022] Open
Abstract
Homeotic genes code for key transcription factors (HOX-TFs) that pattern the animal body plan. During embryonic development, Hox genes are expressed in overlapping patterns and function in a partially redundant manner. In vitro biochemical screens probing the HOX-TF sequence specificity revealed largely overlapping sequence preferences, indicating that co-factors might modulate the biological function of HOX-TFs. However, due to their overlapping expression pattern, high protein homology, and insufficiently specific antibodies, little is known about their genome-wide binding preferences. In order to overcome this problem, we virally expressed tagged versions of limb-expressed posterior HOX genes (HOXA9-13, and HOXD9-13) in primary chicken mesenchymal limb progenitor cells (micromass). We determined the effect of each HOX-TF on cellular differentiation (chondrogenesis) and gene expression and found that groups of HOX-TFs induce distinct regulatory programs. We used ChIP-seq to determine their individual genome-wide binding profiles and identified between 12,721 and 28,572 binding sites for each of the nine HOX-TFs. Principal Component Analysis (PCA) of binding profiles revealed that the HOX-TFs are clustered in two subgroups (Group 1: HOXA/D9, HOXA/D10, HOXD12, and HOXA13 and Group 2: HOXA/D11 and HOXD13), which are characterized by differences in their sequence specificity and by the presence of cofactor motifs. Specifically, we identified CTCF binding sites in Group 1, indicating that this subgroup of HOX-proteins cooperates with CTCF. We confirmed this interaction by an independent biological assay (Proximity Ligation Assay) and demonstrated that CTCF is a novel HOX cofactor that specifically associates with Group 1 HOX-TFs, pointing towards a possible interplay between HOX-TFs and chromatin architecture. Hox genes encode transcription factors that determine the vertebrate body plan and pattern structures and organs in the developing embryo. Despite decades of effort and research on Hox genes, little is known about the HOX-DNA binding properties in vivo. This lack of knowledge is mainly due to the absence of appropriate antibodies to distinguish between different HOX transcription factors. Here, we adapt a cell culture system that allows us to investigate HOX-DNA binding on a genome-wide scale. With this approach, we define and directly compare the genome-wide binding sites of nine posterior HOXA and HOXD transcription factors. We report that the in vivo HOX binding specificity differs from the in vitro specificity and find that HOX-TFs largely rely on co-factor binding and not only on direct HOX-DNA binding. Finally, we identify a novel HOX co-factor, a genome architecture protein, CTCF suggesting a possible interplay between HOX-TF function and chromatin architecture.
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Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper. Nat Commun 2016; 7:13107. [PMID: 27708285 PMCID: PMC5059746 DOI: 10.1038/ncomms13107] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 09/02/2016] [Indexed: 12/29/2022] Open
Abstract
Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution. Snakes have many characteristics that distinguish them from their relatives. Here, Yin et al. sequence the genome of the five-pacer viper, Deinagkistrodon acutus, and use comparative genomic analyses to elucidate the evolution of transposable elements, developmental genes and sex chromosomes in snakes.
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Reno PL, Kjosness KM, Hines JE. The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:303-21. [DOI: 10.1002/jez.b.22688] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 06/13/2016] [Accepted: 06/28/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Philip L. Reno
- Department of Anthropology; The Pennsylvania State University; University Park Pennsylvania
| | - Kelsey M. Kjosness
- Department of Anthropology; The Pennsylvania State University; University Park Pennsylvania
| | - Jasmine E. Hines
- Department of Anthropology; The Pennsylvania State University; University Park Pennsylvania
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HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution. Sci Rep 2016; 6:22720. [PMID: 26940624 PMCID: PMC4778128 DOI: 10.1038/srep22720] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 02/18/2016] [Indexed: 11/24/2022] Open
Abstract
The role of Homeobox transcription factors during fin and limb development have been the focus of recent work investigating the evolutionary origin of limb-specific morphologies. Here we characterize the expression of HoxD genes, as well as the cluster-associated genes Evx2 and LNP, in the paddlefish Polyodon spathula, a basal ray-finned fish. Our results demonstrate a collinear pattern of nesting in early fin buds that includes HoxD14, a gene previously thought to be isolated from global Hox regulation. We also show that in both Polyodon and the catshark Scyliorhinus canicula (a representative chondrichthyan) late phase HoxD transcripts are present in cells of the fin-fold and co-localize with And1, a component of the dermal skeleton. These new data support an ancestral role for HoxD genes in patterning the fin-folds of jawed vertebrates, and fuel new hypotheses about the evolution of cluster regulation and the potential downstream differentiation outcomes of distinct HoxD-regulated compartments.
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Chen X, Bai G, Scholl TO. Spontaneous Preterm Delivery, Particularly with Reduced Fetal Growth, is Associated with DNA Hypomethylation of Tumor Related Genes. ACTA ACUST UNITED AC 2016; 3. [PMID: 27500275 PMCID: PMC4975560 DOI: 10.4172/2376-127x.1000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background Preterm delivery and sub-optimal fetal growth are associated with each other and affect both mother and infant. Our aim was to determine (i) whether there are detectable differences in DNA methylation between early and late gestation and (ii) whether changes in DNA methylation from entry are associated with spontaneous preterm delivery with and without reduced fetal growth. Methods We conducted a case-control study nested within a large prospective cohort. Gene specific methylation was measured by Methyl-Profiler PCR Array in a Human Breast Cancer Signature Panel of 24 genes from maternal peripheral leukocytes genomic DNA at entry and 3rd trimester (sampled at 16 and 30 weeks of gestation, respectively). Clonal bisulfite DNA sequencing was performed to confirm the changes in selected genes (CYP1B1, GADD45A and CXCL12). Multivariable analysis was used for data analysis. Results There was significantly decrease in DNA methylation in 15 of 24 genes during the 3rd trimester in cases of spontaneous preterm delivery (n=23) as compared to the controls (n=19) (p<0.05–p<0.01 for each gene). Similar results were observed by bisulfite sequencing for 3 genes. The change in DNA methylation between late and early gestation was significantly different in cases (overall decrease in methylation was −4.0 ± 1.5%) compared to the controls (overall increase in methylation was 12.6 ± 2.19%, p<0.0001). A graded pattern of DNA methylation was observed in 15 genes. Cases who delivered preterm with reduced fetal growth had the lowest level of methylation, cases delivering preterm without reduced fetal growth were next and term controls were highest in methylation (p for trend <0.05 to p<0.01 for each gene). Cases of preterm delivery also had significantly lower dietary choline intake. Conclusions These data suggest that epigenetic modification is associated with an increased risk of spontaneous preterm delivery, spontaneous preterm delivery with reduced fetal growth in particular.
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Affiliation(s)
- Xinhua Chen
- Department of Obstetrics and Gynecology, Rowan University - School of Osteopathic Medicine, Stratford, NJ, USA
| | - Guang Bai
- Department of Neural and Pain Sciences, University of Maryland, School of Dentistry, Baltimore, MD, USA
| | - Theresa O Scholl
- Department of Obstetrics and Gynecology, Rowan University - School of Osteopathic Medicine, Stratford, NJ, USA
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Linkage between the mechanisms of thrombocytopenia and thrombopoiesis. Blood 2016; 127:1234-41. [PMID: 26787737 DOI: 10.1182/blood-2015-07-607903] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/19/2015] [Indexed: 12/30/2022] Open
Abstract
Thrombocytopenia is defined as a status in which platelet numbers are reduced. Imbalance between the homeostatic regulation of platelet generation and destruction is 1 potential cause of thrombocytopenia. In adults, platelet generation is a 2-stage process entailing the differentiation of hematopoietic stem cells into mature megakaryocytes (MKs; known as megakaryopoiesis) and release of platelets from MKs (known as thrombopoiesis or platelet biogenesis). Until recently, information about the genetic defects responsible for congenital thrombocytopenia was only available for a few forms of the disease. However, investigations over the past 15 years have identified mutations in genes encoding >20 different proteins that are responsible for these disorders, which has advanced our understanding of megakaryopoiesis and thrombopoiesis. The underlying pathogenic mechanisms can be categorized as (1) defects in MK lineage commitment and differentiation, (2) defects in MK maturation, and (3) defect in platelet release. Using these developmental stage categories, we here update recently described mechanisms underlying megakaryopoiesis and thrombopoiesis and discuss the association between platelet generation systems and thrombocytopenia.
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Pineault KM, Swinehart IT, Garthus KN, Ho E, Yao Q, Schipani E, Kozloff KM, Wellik DM. Hox11 genes regulate postnatal longitudinal bone growth and growth plate proliferation. Biol Open 2015; 4:1538-48. [PMID: 26500224 PMCID: PMC4728342 DOI: 10.1242/bio.012500] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hox genes are critical regulators of skeletal development and Hox9-13 paralogs, specifically, are necessary for appendicular development along the proximal to distal axis. Loss of function of both Hoxa11 and Hoxd11 results in severe malformation of the forelimb zeugopod. In the radius and ulna of these mutants, chondrocyte development is perturbed, growth plates are not established, and skeletal growth and maturation fails. In compound mutants in which one of the four Hox11 alleles remains wild-type, establishment of a growth plate is preserved and embryos develop normally through newborn stages, however, skeletal phenotypes become evident postnatally. During postnatal development, the radial and ulnar growth rate slows compared to wild-type controls and terminal bone length is reduced. Growth plate height is decreased in mutants and premature growth plate senescence occurs along with abnormally high levels of chondrocyte proliferation in the reserve and proliferative zones. Compound mutants additionally develop an abnormal curvature of the radius, which causes significant distortion of the carpal elements. The progressive bowing of the radius appears to result from physical constraint caused by the disproportionately slower growth of the ulna than the radius. Collectively, these data are consistent with premature depletion of forelimb zeugopod progenitor cells in the growth plate of Hox11 compound mutants, and demonstrate a continued function for Hox genes in postnatal bone growth and patterning.
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Affiliation(s)
- Kyriel M Pineault
- Program in Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Ilea T Swinehart
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Kayla N Garthus
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Edward Ho
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Qing Yao
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ernestina Schipani
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kenneth M Kozloff
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deneen M Wellik
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109-2200, USA
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Raines AM, Magella B, Adam M, Potter SS. Key pathways regulated by HoxA9,10,11/HoxD9,10,11 during limb development. BMC DEVELOPMENTAL BIOLOGY 2015; 15:28. [PMID: 26186931 PMCID: PMC4506574 DOI: 10.1186/s12861-015-0078-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/07/2015] [Indexed: 11/17/2022]
Abstract
Background The 39 mammalian Hox genes show problematic patterns of functional overlap. In order to more fully define the developmental roles of Hox genes it is necessary to remove multiple combinations of paralogous and flanking genes. In addition, the downstream molecular pathways regulated by Hox genes during limb development remain incompletely delineated. Results In this report we examine limb development in mice with frameshift mutations in six Hox genes, Hoxa9,10,11 and Hoxd9,10,11. The mice were made with a novel recombineering method that allows the simultaneous targeting of frameshift mutations into multiple flanking genes. The Hoxa9,10,11−/−/Hoxd9,10,11−/− mutant mice show a reduced ulna and radius that is more severe than seen in Hoxa11−/−/Hoxd11−/− mice, indicating a minor role for the flanking Hox9,10 genes in zeugopod development, as well as their primary function in stylopod development. The mutant mice also show severe reduction of Shh expression in the zone of polarizing activity, and decreased Fgf8 expression in the apical ectodermal ridge, thereby better defining the roles of these specific Hox genes in the regulation of critical signaling centers during limb development. Importantly, we also used laser capture microdissection coupled with RNA-Seq to characterize the gene expression programs in wild type and mutant limbs. Resting, proliferative and hypertrophic compartments of E15.5 forelimb zeugopods were examined. The results provide an RNA-Seq characterization of the progression of gene expression patterns during normal endochondral bone formation. In addition of the Hox mutants showed strongly altered expression of Pknox2, Zfp467, Gdf5, Bmpr1b, Dkk3, Igf1, Hand2, Shox2, Runx3, Bmp7 and Lef1, all of which have been previously shown to play important roles in bone formation. Conclusions The recombineering based frameshift mutation of the six flanking and paralogous Hoxa9,10,11 and Hoxd9,10,11 genes provides a resource for the analysis of their overlapping functions. Analysis of the Hoxa9,10,11−/−/Hoxd9,10,11−/− mutant limbs confirms and extends the results of previous studies using mice with Hox mutations in single paralogous groups or with entire Hox cluster deletions. The RNA-Seq analysis of specific compartments of the normal and mutant limbs defines the multiple key perturbed pathways downstream of these Hox genes. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0078-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna M Raines
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
| | - Bliss Magella
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
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Seifert A, Werheid DF, Knapp SM, Tobiasch E. Role of Hox genes in stem cell differentiation. World J Stem Cells 2015; 7:583-595. [PMID: 25914765 PMCID: PMC4404393 DOI: 10.4252/wjsc.v7.i3.583] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 11/20/2014] [Accepted: 12/17/2014] [Indexed: 02/06/2023] Open
Abstract
Hox genes are an evolutionary highly conserved gene family. They determine the anterior-posterior body axis in bilateral organisms and influence the developmental fate of cells. Embryonic stem cells are usually devoid of any Hox gene expression, but these transcription factors are activated in varying spatial and temporal patterns defining the development of various body regions. In the adult body, Hox genes are among others responsible for driving the differentiation of tissue stem cells towards their respective lineages in order to repair and maintain the correct function of tissues and organs. Due to their involvement in the embryonic and adult body, they have been suggested to be useable for improving stem cell differentiations in vitro and in vivo. In many studies Hox genes have been found as driving factors in stem cell differentiation towards adipogenesis, in lineages involved in bone and joint formation, mainly chondrogenesis and osteogenesis, in cardiovascular lineages including endothelial and smooth muscle cell differentiations, and in neurogenesis. As life expectancy is rising, the demand for tissue reconstruction continues to increase. Stem cells have become an increasingly popular choice for creating therapies in regenerative medicine due to their self-renewal and differentiation potential. Especially mesenchymal stem cells are used more and more frequently due to their easy handling and accessibility, combined with a low tumorgenicity and little ethical concerns. This review therefore intends to summarize to date known correlations between natural Hox gene expression patterns in body tissues and during the differentiation of various stem cells towards their respective lineages with a major focus on mesenchymal stem cell differentiations. This overview shall help to understand the complex interactions of Hox genes and differentiation processes all over the body as well as in vitro for further improvement of stem cell treatments in future regenerative medicine approaches.
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Abstract
In the musculoskeletal system, muscle, tendon, and bone tissues develop in a spatially and temporally coordinated manner, and integrate into a cohesive functional unit by forming specific connections unique to each region of the musculoskeletal system. The mechanisms of these patterning and integration events are an area of great interest in musculoskeletal biology. Hox genes are a family of important developmental regulators and play critical roles in skeletal patterning throughout the axial and appendicular skeleton. Unexpectedly, Hox genes are not expressed in the differentiated cartilage or other skeletal cells, but rather are highly expressed in the tightly associated stromal connective tissues as well as regionally expressed in tendons and muscle connective tissue. Recent work has revealed a previously unappreciated role for Hox in patterning all the musculoskeletal tissues of the limb. These observations suggest that integration of the musculoskeletal system is regulated, at least in part, by Hox function in the stromal connective tissue. This review will outline our current understanding of Hox function in patterning and integrating the musculoskeletal tissues.
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Affiliation(s)
- Kyriel M Pineault
- Program in Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Deneen M Wellik
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109-2200, USA
- Corresponding author: , Phone: 734-936-8902, Fax: 734-763-2162
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Kjosness KM, Hines JE, Lovejoy CO, Reno PL. The pisiform growth plate is lost in humans and supports a role for Hox in growth plate formation. J Anat 2014; 225:527-38. [PMID: 25279687 PMCID: PMC4292754 DOI: 10.1111/joa.12235] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2014] [Indexed: 12/29/2022] Open
Abstract
The human pisiform is a small, nodular, although functionally significant, bone of the wrist. In most other mammals, including apes and Australopithecus afarensis, pisiforms are elongate. An underappreciated fact is that the typical mammalian pisiform forms from two ossification centers. We hypothesize that: (i) the presence of a secondary ossification center in mammalian pisiforms indicates the existence of a growth plate; and (ii) human pisiform reduction results from growth plate loss. To address these hypotheses, we surveyed African ape pisiform ossification and confirmed the presence of a late-forming secondary ossification center in chimpanzees and gorillas. Identification of the initial ossification center occurs substantially earlier in apes relative to humans, raising questions concerning the homology of the human pisiform and the two mammalian ossification centers. Second, we conducted histological and immunohistochemical analyses of pisiform ossification in mice. We confirm the presence of two ossification centers separated by organized columnar and hypertrophic chondrocyte zones. Flattened chondrocytes were highly mitotic, indicating the presence of a growth plate. Hox genes have been proposed to play a fundamental role in growth plate patterning. The existence of a pisiform growth plate presents an interesting test case for the association between Hox expression and growth plate formation, and could explain the severe effects on the pisiform observed in Hoxa11 and Hoxd11 knockout mice. Consistent with this hypothesis, we show that Hoxd11 is expressed adjacent to the pisiform in late-stage embryonic mouse limbs supporting a role for Hox genes in growth plate specification. This raises questions concerning the mechanisms regulating Hox expression in the developing carpus.
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Affiliation(s)
- Kelsey M Kjosness
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
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Introduction to Evolutionary Teratology, with an Application to the Forelimbs of Tyrannosauridae and Carnotaurinae (Dinosauria: Theropoda). Evol Biol 2014. [DOI: 10.1007/s11692-014-9296-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb. Genetics 2014; 198:1117-26. [PMID: 25217052 DOI: 10.1534/genetics.114.167460] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The growth and development of the vertebrate limb relies on homeobox genes of the Hox and Shox families, with their independent mutation often giving dose-dependent effects. Here we investigate whether Shox2 and Hox genes function together during mouse limb development by modulating their relative dosage and examining the limb for nonadditive effects on growth. Using double mRNA fluorescence in situ hybridization (FISH) in single embryos, we first show that Shox2 and Hox genes have associated spatial expression dynamics, with Shox2 expression restricted to the proximal limb along with Hoxd9 and Hoxa11 expression, juxtaposing the distal expression of Hoxa13 and Hoxd13. By generating mice with all possible dosage combinations of mutant Shox2 alleles and HoxA/D cluster deletions, we then show that their coordinated proximal limb expression is critical to generate normally proportioned limb segments. These epistatic interactions tune limb length, where Shox2 underexpression enhances, and Shox2 overexpression suppresses, Hox-mutant phenotypes. Disruption of either Shox2 or Hox genes leads to a similar reduction in Runx2 expression in the developing humerus, suggesting their concerted action drives cartilage maturation during normal development. While we furthermore provide evidence that Hox gene function influences Shox2 expression, this regulation is limited in extent and is unlikely on its own to be a major explanation for their genetic interaction. Given the similar effect of human SHOX mutations on regional limb growth, Shox and Hox genes may generally function as genetic interaction partners during the growth and development of the proximal vertebrate limb.
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González-Martín MC, Mallo M, Ros MA. Long bone development requires a threshold of Hox function. Dev Biol 2014; 392:454-65. [PMID: 24930703 DOI: 10.1016/j.ydbio.2014.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 05/30/2014] [Accepted: 06/04/2014] [Indexed: 11/30/2022]
Abstract
The Hoxd(Del(11-13)) mutant is one of the animal models for human synpolydactyly, characterized by short and syndactylous digits. Here we have characterized in detail the cartilage and bone defects in these mutants. We report two distinct phenotypes: (i) a delay and change in pattern of chondrocyte maturation of metacarpals/metatarsals and (ii) formation of a poor and not centrally positioned primary ossification center in the proximal-intermediate phalanx. In the metacarpals of Hoxd(Del(11-13)) mutants, ossification occurs postnataly, in the absence of significant Ihh expression and without the establishment of growth plates, following patterns similar to those of short bones. The strong downregulation in Ihh expression is associated with a corresponding increase of the repressor form of Gli3. To evaluate the contribution of this alteration to the phenotype, we generated double Hoxd(Del(11-13));Gli3 homozygous mutants. Intriguingly, these double mutants showed a complete rescue of the phenotype in metatarsals but only partial phenotypic rescue in metacarpals. Our results support Hox genes being required in a dose-dependent manner for long bone cartilage maturation and suggest that and excess of Gli3R mediates a significant part of the Hoxd(Del(11-13)) chondrogenic phenotype.
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Affiliation(s)
- Ma Carmen González-Martín
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria-SODERCAN., 39011 Santander, Spain
| | - Moises Mallo
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Marian A Ros
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria-SODERCAN., 39011 Santander, Spain; Dpto. de Anatomía y Biología Celular, Universidad de Cantabria, 39011 Santander, Spain.
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Li Z, Wu G, Sher RB, Khavandgar Z, Hermansson M, Cox GA, Doschak MR, Murshed M, Beier F, Vance DE. Choline kinase beta is required for normal endochondral bone formation. Biochim Biophys Acta Gen Subj 2014; 1840:2112-22. [PMID: 24637075 DOI: 10.1016/j.bbagen.2014.03.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/05/2014] [Accepted: 03/07/2014] [Indexed: 11/28/2022]
Abstract
BACKGROUND Choline kinase has three isoforms encoded by the genes Chka and Chkb. Inactivation of Chka in mice results in embryonic lethality, whereas Chkb(-/-) mice display neonatal forelimb bone deformations. METHODS To understand the mechanisms underlying the bone deformations, we compared the biology and biochemistry of bone formation from embryonic to young adult wild-type (WT) and Chkb(-/-) mice. RESULTS The deformations are specific to the radius and ulna during the late embryonic stage. The radius and ulna of Chkb(-/-) mice display expanded hypertrophic zones, unorganized proliferative columns in their growth plates, and delayed formation of primary ossification centers. The differentiation of chondrocytes of Chkb(-/-) mice was impaired, as was chondrocyte proliferation and expression of matrix metalloproteinases 9 and 13. In chondrocytes from Chkb(-/-) mice, phosphatidylcholine was slightly lower than in WT mice whereas the amount of phosphocholine was decreased by approximately 75%. In addition, the radius and ulna from Chkb(-/-) mice contained fewer osteoclasts along the cartilage/bone interface. CONCLUSIONS Chkb has a critical role in the normal embryogenic formation of the radius and ulna in mice. GENERAL SIGNIFICANCE Our data indicate that choline kinase beta plays an important role in endochondral bone formation by modulating growth plate physiology.
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Affiliation(s)
- Zhuo Li
- Group on the Molecular and Cell Biology of Lipids and Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2 Canada
| | - Gengshu Wu
- Group on the Molecular and Cell Biology of Lipids and Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2 Canada
| | | | | | - Martin Hermansson
- Group on the Molecular and Cell Biology of Lipids and Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2 Canada
| | | | - Michael R Doschak
- Faculty of Pharmacy & Pharmaceutical Sciences, University of Alberta, Canada
| | - Monzur Murshed
- Faculty of Dentistry, McGill University, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Frank Beier
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Dennis E Vance
- Group on the Molecular and Cell Biology of Lipids and Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S2 Canada.
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