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Peraldi R, Kmita M. 40 years of the homeobox: mechanisms of Hox spatial-temporal collinearity in vertebrates. Development 2024; 151:dev202508. [PMID: 39167089 DOI: 10.1242/dev.202508] [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] [Indexed: 08/23/2024]
Abstract
Animal body plans are established during embryonic development by the Hox genes. This patterning process relies on the differential expression of Hox genes along the head-to-tail axis. Hox spatial collinearity refers to the relationship between the organization of Hox genes in clusters and the differential Hox expression, whereby the relative order of the Hox genes within a cluster mirrors the spatial sequence of expression in the developing embryo. In vertebrates, the cluster organization is also associated with the timing of Hox activation, which harmonizes Hox expression with the progressive emergence of axial tissues. Thereby, in vertebrates, Hox temporal collinearity is intimately linked to Hox spatial collinearity. Understanding the mechanisms contributing to Hox temporal and spatial collinearity is thus key to the comprehension of vertebrate patterning. Here, we provide an overview of the main discoveries pertaining to the mechanisms of Hox spatial-temporal collinearity.
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Affiliation(s)
- Rodrigue Peraldi
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
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2
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Soussi G, Girdziusaite A, Jhanwar S, Palacio V, Notaro M, Sheth R, Zeller R, Zuniga A. TBX3 is essential for establishment of the posterior boundary of anterior genes and upregulation of posterior genes together with HAND2 during the onset of limb bud development. Development 2024; 151:dev202722. [PMID: 38828908 PMCID: PMC11190573 DOI: 10.1242/dev.202722] [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: 01/21/2024] [Accepted: 04/26/2024] [Indexed: 06/05/2024]
Abstract
During limb bud formation, axis polarities are established as evidenced by the spatially restricted expression of key regulator genes. In particular, the mutually antagonistic interaction between the GLI3 repressor and HAND2 results in distinct and non-overlapping anterior-distal Gli3 and posterior Hand2 expression domains. This is a hallmark of the establishment of antero-posterior limb axis polarity, together with spatially restricted expression of homeodomain and other transcriptional regulators. Here, we show that TBX3 is required for establishment of the posterior expression boundary of anterior genes in mouse limb buds. ChIP-seq and differential gene expression analysis of wild-type and mutant limb buds identifies TBX3-specific and shared TBX3-HAND2 target genes. High sensitivity fluorescent whole-mount in situ hybridisation shows that the posterior expression boundaries of anterior genes are positioned by TBX3-mediated repression, which excludes anterior genes such as Gli3, Alx4, Hand1 and Irx3/5 from the posterior limb bud mesenchyme. This exclusion delineates the posterior mesenchymal territory competent to establish the Shh-expressing limb bud organiser. In turn, HAND2 is required for Shh activation and cooperates with TBX3 to upregulate shared posterior identity target genes in early limb buds.
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Affiliation(s)
- Geoffrey Soussi
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Ausra Girdziusaite
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Shalu Jhanwar
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Victorio Palacio
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | | | - Rushikesh Sheth
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
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3
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Wellik DM. Hox genes and patterning the vertebrate body. Curr Top Dev Biol 2024; 159:1-27. [PMID: 38729674 DOI: 10.1016/bs.ctdb.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
The diversity of vertebrate body plans is dizzying, yet stunning for the many things they have in common. Vertebrates have inhabited virtually every part of the earth from its coldest to warmest climates. They locomote by swimming, flying, walking, slithering, or climbing, or combinations of these behaviors. And they exist in many different sizes, from the smallest of frogs, fish and lizards to giraffes, elephants, and blue whales. Despite these differences, vertebrates follow a remarkably similar blueprint for the establishment of their body plan. Within the relatively small amount of time required to complete gastrulation, the process through which the three germ layers, ectoderm, mesoderm, and endoderm are created, the embryo also generates its body axis and is simultaneously patterned. For the length of this axis, the genes that distinguish the neck from the rib cage or the trunk from the sacrum are the Hox genes. In vertebrates, there was evolutionary pressure to maintain this set of genes in the organism. Over the past decades, much has been learned regarding the regulatory mechanisms that ensure the appropriate expression of these genes along the main body axes. Genetic functions continue to be explored though much has been learned. Much less has been discerned on the identity of co-factors used by Hox proteins for the specificity of transcriptional regulation or what downstream targets and pathways are critical for patterning events, though there are notable exceptions. Current work in the field is demonstrating that Hox genes continue to function in many organs long after directing early patterning events. It is hopeful continued research will shed light on remaining questions regarding mechanisms used by this important and conserved set of transcriptional regulators.
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Affiliation(s)
- Deneen M Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States.
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4
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Wang H, Chen X, Meng X, Cao Y, Han S, Liu K, Zhao X, Zhao X, Zhang X. The pathogenic mechanism of syndactyly type V identified in a Hoxd13Q50R knock-in mice. Bone Res 2024; 12:21. [PMID: 38561387 PMCID: PMC10984994 DOI: 10.1038/s41413-024-00322-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
Syndactyly type V (SDTY5) is an autosomal dominant extremity malformation characterized by fusion of the fourth and fifth metacarpals. In the previous publication, we first identified a heterozygous missense mutation Q50R in homeobox domain (HD) of HOXD13 in a large Chinese family with SDTY5. In order to substantiate the pathogenicity of the variant and elucidate the underlying pathogenic mechanism causing limb malformation, transcription-activator-like effector nucleases (TALEN) was employed to generate a Hoxd13Q50R mutant mouse. The mutant mice exhibited obvious limb malformations including slight brachydactyly and partial syndactyly between digits 2-4 in the heterozygotes, and severe syndactyly, brachydactyly and polydactyly in homozygotes. Focusing on BMP2 and SHH/GREM1/AER-FGF epithelial mesenchymal (e-m) feedback, a crucial signal pathway for limb development, we found the ectopically expressed Shh, Grem1 and Fgf8 and down-regulated Bmp2 in the embryonic limb bud at E10.5 to E12.5. A transcriptome sequencing analysis was conducted on limb buds (LBs) at E11.5, revealing 31 genes that exhibited notable disparities in mRNA level between the Hoxd13Q50R homozygotes and the wild-type. These genes are known to be involved in various processes such as limb development, cell proliferation, migration, and apoptosis. Our findings indicate that the ectopic expression of Shh and Fgf8, in conjunction with the down-regulation of Bmp2, results in a failure of patterning along both the anterior-posterior and proximal-distal axes, as well as a decrease in interdigital programmed cell death (PCD). This cascade ultimately leads to the development of syndactyly and brachydactyly in heterozygous mice, and severe limb malformations in homozygous mice. These findings suggest that abnormal expression of SHH, FGF8, and BMP2 induced by HOXD13Q50R may be responsible for the manifestation of human SDTY5.
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Affiliation(s)
- Han Wang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
- Department of Orthopedics, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Xiumin Chen
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xiaolu Meng
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yixuan Cao
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Shirui Han
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Keqiang Liu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Ximeng Zhao
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xiuli Zhao
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
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Wang L, Wang X, Sun H, Wang W, Cao L. A pan-cancer analysis of the role of HOXD1, HOXD3, and HOXD4 and validation in renal cell carcinoma. Aging (Albany NY) 2023; 15:10746-10766. [PMID: 37827698 PMCID: PMC10599751 DOI: 10.18632/aging.205116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
HOXD1, HOXD3, and HOXD4 are members of the HOXD genes family and are related to tumorigenesis of the tumor. However, whether HOXDs (1, 3, 4) have a crucial role across pan-cancer is still unknown. HOXD1, HOXD3, and HOXD4 expressions were analyzed using public databases in 33 types of tumors. The UCSC Xena website was carried out to investigate the relationship between the expression of genes and the progress of cancers. The biological functions of HOXD3 were tested by colony forming, transwell, wound healing, and xenograft assay in vitro and in vivo. GSEA was used to identify the associated cancer hallmarks with HOXDs expression. Immune cell infiltration analysis was applied to verify the immune cell infiltrations related to genes. The results showed HOXD1, HOXD3, and HOXD4 co-low expressed in BRCA, COAD, KICH, KIRC, KIRP, READ, and TGCT. In the KIRC, all of HOXDs expression was connected with tumor stage and histological grade. Upregulation of HOXDs was associated with improved OS, DSS, and PFI. Down-expression of HOXD3 induced cell proliferation, migration, and invasion in vivo and in vitro. In addition, HOXDs were connected with immune-activated hallmarks and cancer immune cell infiltrations. These findings demonstrated that HOXDs may be indicative biomarkers for the prognosis and immunotherapy in pan-cancer.
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Affiliation(s)
- Lumin Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710004, P.R. China
| | - Xiaofei Wang
- Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi 710061, P.R. China
| | - Haifeng Sun
- The Third Department of Medical Oncology, Shaanxi Provincial Cancer Hospital Affiliated to Medical College of Xi’an Jiaotong University, Xi’an, Shaanxi 710065, P.R. China
| | - Wenjing Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710061, P.R. China
| | - Li Cao
- Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi 710061, P.R. China
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6
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Losa M, Barozzi I, Osterwalder M, Hermosilla-Aguayo V, Morabito A, Chacón BH, Zarrineh P, Girdziusaite A, Benazet JD, Zhu J, Mackem S, Capellini TD, Dickel D, Bobola N, Zuniga A, Visel A, Zeller R, Selleri L. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2. Nat Commun 2023; 14:3993. [PMID: 37414772 PMCID: PMC10325989 DOI: 10.1038/s41467-023-39443-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023] Open
Abstract
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Viviana Hermosilla-Aguayo
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Angela Morabito
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Brandon H Chacón
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Ausra Girdziusaite
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Jean Denis Benazet
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Aimée Zuniga
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
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7
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Jia X, Lin W, Wang W. Regulation of chromatin organization during animal regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:19. [PMID: 37259007 DOI: 10.1186/s13619-023-00162-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/21/2023] [Indexed: 06/02/2023]
Abstract
Activation of regeneration upon tissue damages requires the activation of many developmental genes responsible for cell proliferation, migration, differentiation, and tissue patterning. Ample evidence revealed that the regulation of chromatin organization functions as a crucial mechanism for establishing and maintaining cellular identity through precise control of gene transcription. The alteration of chromatin organization can lead to changes in chromatin accessibility and/or enhancer-promoter interactions. Like embryogenesis, each stage of tissue regeneration is accompanied by dynamic changes of chromatin organization in regeneration-responsive cells. In the past decade, many studies have been conducted to investigate the contribution of chromatin organization during regeneration in various tissues, organs, and organisms. A collection of chromatin regulators were demonstrated to play critical roles in regeneration. In this review, we will summarize the progress in the understanding of chromatin organization during regeneration in different research organisms and discuss potential common mechanisms responsible for the activation of regeneration response program.
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Affiliation(s)
- Xiaohui Jia
- National Institute of Biological Sciences, Beijing, 102206, China
- China Agricultural University, Beijing, 100083, China
| | - Weifeng Lin
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Wei Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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Leclerc K, Remark LH, Ramsukh M, Josephson AM, Palma L, Parente PEL, Sambon M, Lee S, Lopez EM, Morgani SM, Leucht P. Hox genes are crucial regulators of periosteal stem cell identity. Development 2023; 150:dev201391. [PMID: 36912250 PMCID: PMC10112919 DOI: 10.1242/dev.201391] [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: 10/19/2022] [Accepted: 02/20/2023] [Indexed: 03/14/2023]
Abstract
Periosteal stem and progenitor cells (PSPCs) are major contributors to bone maintenance and repair. Deciphering the molecular mechanisms that regulate their function is crucial for the successful generation and application of future therapeutics. Here, we pinpoint Hox transcription factors as necessary and sufficient for periosteal stem cell function. Hox genes are transcriptionally enriched in periosteal stem cells and their overexpression in more committed progenitors drives reprogramming to a naïve, self-renewing stem cell-like state. Crucially, individual Hox family members are expressed in a location-specific manner and their stem cell-promoting activity is only observed when the Hox gene is matched to the anatomical origin of the PSPC, demonstrating a role for the embryonic Hox code in adult stem cells. Finally, we demonstrate that Hoxa10 overexpression partially restores the age-related decline in fracture repair. Together, our data highlight the importance of Hox genes as key regulators of PSPC identity in skeletal homeostasis and repair.
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Affiliation(s)
- Kevin Leclerc
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Lindsey H. Remark
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Malissa Ramsukh
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Anne Marie Josephson
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Laura Palma
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Paulo E. L. Parente
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Margaux Sambon
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Sooyeon Lee
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Institute of Comparative Molecular Endocrinology, Ulm University, Ulm 89081, Germany
| | - Emma Muiños Lopez
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Cell Therapy Area, Clínica Universidad de Navarra, Pamplona 31008, Spain
| | - Sophie M. Morgani
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Philipp Leucht
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
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9
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Shaping Hox gene activity to generate morphological diversity across vertebrate phylogeny. Essays Biochem 2022; 66:717-726. [PMID: 35924372 DOI: 10.1042/ebc20220050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 02/07/2023]
Abstract
The importance of Hox genes for the development and evolution of the vertebrate axial skeleton and paired appendages has been recognized for already several decades. The steady growth of genomic sequence data from an increasing number of vertebrate species, together with the improvement of methods to analyze genomic structure and interactions, as well as to control gene activity in various species has refined our understanding of Hox gene activity in development and evolution. Here, I will review recent data addressing the influence of Hox regulatory processes in the evolution of the fins and the emergence of the tetrapod limb. In addition, I will discuss the involvement of posterior Hox genes in the control of vertebrate axial extension, focusing on an apparently divergent activity that Hox13 paralog group genes have on the regulation of tail bud development in mouse and zebrafish embryos.
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10
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Shim J, Park J, Abudureyimu G, Kim MH, Shim JS, Jang KT, Kwon EJ, Jang HS, Yeo E, Lee JH, Lee D. Comparative Spatial Transcriptomic and Single-Cell Analyses of Human Nail Units and Hair Follicles Show Transcriptional Similarities between the Onychodermis and Follicular Dermal Papilla. J Invest Dermatol 2022; 142:3146-3157.e12. [PMID: 35853486 DOI: 10.1016/j.jid.2022.06.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 01/05/2023]
Abstract
The nail unit and hair follicle are both hard keratin-producing organs that share various biological features. In this study, we used digital spatial profiling and single-cell RNA sequencing to define a spatially resolved expression profile of the human nail unit and hair follicle. Our approach showed the presence of a nail-specific mesenchymal population called onychofibroblasts within the onychodermis. Onychodermis and follicular dermal papilla both expressed Wnt and bone morphogenetic protein signaling molecules. In addition, nail matrix epithelium and hair matrix showed very similar expressions profile, including the expression of hard keratins and HOXC13, a transcriptional regulator of the hair shaft. Integration of single-cell RNA sequencing and digital spatial profiling data through computational deconvolution methods estimated epithelial and mesenchymal cell abundance in the nail- and hair-specific regions of interest and revealed close transcriptional similarity between these major skin appendages. To analyze the function of bone morphogenetic proteins in nail differentiation, we treated cultured human nail matrix keratinocytes with BMP5, which are highly expressed by onychofibroblasts. We observed increased expressions of hard keratin and its regulator genes such as HOXC13. Collectively, our data suggest that onychodermis is the counterpart of dermal papilla and that BMP5 in onychofibroblasts plays a key role in the differentiation of nail matrix keratinocytes.
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Affiliation(s)
- Joonho Shim
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jihye Park
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Gulimila Abudureyimu
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Min-Hee Kim
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong Sup Shim
- Department of Orthopedic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kee-Taek Jang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eun Ji Kwon
- Department of Dermatology, Columbia University Irving Medical Center, New York, New York, USA
| | - Hyung-Suk Jang
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eunhye Yeo
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Jong Hee Lee
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Dongyoun Lee
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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11
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Johnson GL, Glasser MB, Charles JF, Duryea J, Lehoczky JA. En1 and Lmx1b do not recapitulate embryonic dorsal-ventral limb patterning functions during mouse digit tip regeneration. Cell Rep 2022; 41:111701. [PMID: 36417876 PMCID: PMC9727699 DOI: 10.1016/j.celrep.2022.111701] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/09/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
The mouse digit tip regenerates following amputation. How the regenerate is patterned is unknown, but a long-standing hypothesis proposes developmental patterning mechanisms are re-used during regeneration. The digit tip bone exhibits dorsal-ventral (DV) polarity, so we focus on En1 and Lmx1b, two factors necessary for DV patterning during limb development. We investigate whether they are re-expressed during regeneration in a developmental-like pattern and whether they direct DV morphology of the regenerate. We find that both En1 and Lmx1b are expressed in the regenerating digit tip epithelium and mesenchyme, respectively, but without DV polarity. Conditional genetics and quantitative analysis of digit tip bone morphology determine that genetic deletion of En1 or Lmx1b in adult digit tip regeneration modestly reduces bone regeneration but does not affect DV patterning. Collectively, our data suggest that, while En1 and Lmx1b are re-expressed during mouse digit tip regeneration, they do not define the DV axis during regeneration.
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Affiliation(s)
- Gemma L. Johnson
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Morgan B. Glasser
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Julia F. Charles
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jeffrey Duryea
- Department of Radiology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jessica A. Lehoczky
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA,Lead contact,Correspondence:
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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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Koyano-Nakagawa N, Gong W, Das S, Theisen JWM, Swanholm TB, Van Ly D, Dsouza N, Singh BN, Kawakami H, Young S, Chen KQ, Kawakami Y, Garry DJ. Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud. Nat Commun 2022; 13:4221. [PMID: 35864091 PMCID: PMC9304341 DOI: 10.1038/s41467-022-31848-6] [Citation(s) in RCA: 5] [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: 09/21/2019] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
Sonic hedgehog (Shh) is essential for limb development, and the mechanisms that govern the propagation and maintenance of its expression has been well studied; however, the mechanisms that govern the initiation of Shh expression are incomplete. Here we report that ETV2 initiates Shh expression by changing the chromatin status of the developmental limb enhancer, ZRS. Etv2 expression precedes Shh in limb buds, and Etv2 inactivation prevents the opening of limb chromatin, including the ZRS, resulting in an absence of Shh expression. Etv2 overexpression in limb buds causes nucleosomal displacement at the ZRS, ectopic Shh expression, and polydactyly. Areas of nucleosome displacement coincide with ETS binding site clusters. ETV2 also functions as a transcriptional activator of ZRS and is antagonized by ETV4/5 repressors. Known human polydactyl mutations introduce novel ETV2 binding sites in the ZRS, suggesting that ETV2 dosage regulates ZRS activation. These studies identify ETV2 as a pioneer transcription factor (TF) regulating the onset of Shh expression, having both a chromatin regulatory role and a transcriptional activation role.
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Affiliation(s)
- Naoko Koyano-Nakagawa
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA
- Hamre, Schumann, Mueller & Larson, P.C., Minneapolis, MN, 55402, USA
- Mitchell Hamline School of Law, St. Paul, MN, 55105, USA
| | - Wuming Gong
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Satyabrata Das
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joshua W M Theisen
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Tran B Swanholm
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel Van Ly
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Nikita Dsouza
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Bhairab N Singh
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Hiroko Kawakami
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Samantha Young
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Yasuhiko Kawakami
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
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14
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Purushothaman S, Lopez Aviña BB, Seifert AW. Sonic hedgehog is Essential for Proximal-Distal Outgrowth of the Limb Bud in Salamanders. Front Cell Dev Biol 2022; 10:797352. [PMID: 35433673 PMCID: PMC9010949 DOI: 10.3389/fcell.2022.797352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
The developing forelimb has been a foundational model to understand how specified progenitor cells integrate genetic information to produce the tetrapod limb bauplan. Although the reigning hypothesis is that all tetrapods develop limbs in a similar manner, recent work suggests that urodeles have evolved a derived mode of limb dvelopment. Here, we demonstrate through pharmacological and genetic inactivation of Sonic hedgehog (Shh) signaling in axolotls that Shh directs expansion and survival of limb progenitor cells in addition to patterning the limb across the proximodistal and antero-posterior axis. In contrast to inactivation of Shh in mouse or chick embryos where a humerus, radius, and single digit develop, Shh crispant axolotls completely lack forelimbs. In rescuing limb development by implanting SHH-N protein beads into the nascent limb field of Shh crispants, we show that the limb field is specified in the absence of Shh and that hedgehog pathway activation is required to initiate proximodistal outgrowth. When our results are examined alongside other derived aspects of salamander limb development and placed in a phylogenetic context, a new hypothesis emerges whereby the ability for cells at an amputation plane to activate morphogenesis and regenerate a limb may have evolved uniquely in urodeles.
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15
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Takeuchi T, Matsubara H, Minamitani F, Satoh Y, Tozawa S, Moriyama T, Maruyama K, Suzuki KIT, Shigenobu S, Inoue T, Tamura K, Agata K, Hayashi T. Newt Hoxa13 has an essential and predominant role in digit formation during development and regeneration. Development 2022; 149:274659. [DOI: 10.1242/dev.200282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/21/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The 5′Hox genes play crucial roles in limb development and specify regions in the proximal-distal axis of limbs. However, there is no direct genetic evidence that Hox genes are essential for limb development in non-mammalian tetrapods or for limb regeneration. Here, we produced single to quadruple Hox13 paralog mutants using the CRISPR/Cas9 system in newts (Pleurodeles waltl), which have strong regenerative capacities, and also produced germline mutants. We show that Hox13 genes are essential for digit formation in development, as in mice. In addition, Hoxa13 has a predominant role in digit formation, unlike in mice. The predominance is probably due to the restricted expression pattern of Hoxd13 in limb buds and the strong dependence of Hoxd13 expression on Hoxa13. Finally, we demonstrate that Hox13 genes are also necessary for digit formation in limb regeneration. Our findings reveal that the general function of Hox13 genes is conserved between limb development and regeneration, and across taxa. The predominance of Hoxa13 function both in newt limbs and fish fins, but not in mouse limbs, suggests a potential contribution of Hoxa13 function in fin-to-limb transition.
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Affiliation(s)
- Takashi Takeuchi
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Haruka Matsubara
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Fumina Minamitani
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Yukio Satoh
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Sayo Tozawa
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Tomoki Moriyama
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Kohei Maruyama
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Ken-ichi T. Suzuki
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Gakushuin University, Toyoshima-Ku, Tokyo 171-8588, Japan
| | - Koji Tamura
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kiyokazu Agata
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department of Life Science, Faculty of Science, Gakushuin University, Toyoshima-Ku, Tokyo 171-8588, Japan
| | - Toshinori Hayashi
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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16
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Essay the (unusual) heuristic value of Hox gene clusters; a matter of time? Dev Biol 2022; 484:75-87. [PMID: 35182536 DOI: 10.1016/j.ydbio.2022.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/22/2022]
Abstract
Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.
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17
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Janowska-Sejda EI, Adeleye Y, Currie RA. Exploration of the DARTable Genome- a Resource Enabling Data-Driven NAMs for Developmental and Reproductive Toxicity Prediction. FRONTIERS IN TOXICOLOGY 2022; 3:806311. [PMID: 35295108 PMCID: PMC8915813 DOI: 10.3389/ftox.2021.806311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/22/2021] [Indexed: 12/12/2022] Open
Abstract
The identification of developmental and reproductive toxicity (DART) is a critical component of toxicological evaluations of chemical safety. Adverse Outcome Pathways (AOPs) provide a framework to describe biological processes leading to a toxic effect and can provide insights in understanding the mechanisms underlying toxicological endpoints and aid the development of new approach methods (NAMs). Integrated approaches to testing and assessment (IATA) can be developed based on AOP knowledge and can serve as pragmatic approaches to chemical hazard characterization using NAMs. However, DART effects remain difficult to predict given the diversity of biological mechanisms operating during ontogenesis and consequently, the considerable number of potential molecular initiating events (MIEs) that might trigger a DART Adverse Outcome (DART AO). Consequently, two challenges that need to be overcome to create an AOP-based DART IATA are having sufficient knowledge of relevant biology and using this knowledge to determine the appropriate selection of cell systems that provide sufficient coverage of that biology. The wealth of modern biological and bioinformatics data can be used to provide this knowledge. Here we demonstrate the utility of bioinformatics analyses to address these questions. We integrated known DART MIEs with gene-developmental phenotype information to curate the hypothetical human DARTable genome (HDG, ∼5 k genes) which represents the comprehensive set of biomarkers for DART. Using network analysis of the human interactome, we show that HDG genes have distinct connectivity compared to other genes. HDG genes have higher node degree with lower neighborhood connectivity, betweenness centralities and average shortest path length. Therefore, HDG is highly connected to itself and to the wider network and not only to their local community. Also, by comparison with the Druggable Genome we show how the HDG can be prioritized to identify potential MIEs based on potential to interact with small molecules. We demonstrate how the HDG in combination with gene expression data can be used to select a panel of relevant cell lines (RD-1, OVCAR-3) for inclusion in an IATA and conclude that bioinformatic analyses can provide the necessary insights and serve as a resource for the development of a screening panel for a DART IATA.
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18
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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: 1.0] [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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19
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Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Front Cell Dev Biol 2021; 9:718308. [PMID: 34458272 PMCID: PMC8386295 DOI: 10.3389/fcell.2021.718308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis of a developing bilaterian embryo. Early work suggested a possible role of clustering and ordering of Hox to regulate their expression in a spatially restricted manner along the AP axis. However, the recent availability of many genome assemblies for different organisms uncovered several examples that defy this constraint. With recent advancements in genomics, the current review discusses the arrangement of Hox in various organisms. Further, we revisit their discovery and regulation in Drosophila melanogaster. We also review their regulation in different arthropods and vertebrates, with a significant focus on Hox expression in the crustacean Parahyale hawaiensis. It is noteworthy that subtle changes in the levels of Hox gene expression can contribute to the development of novel features in an organism. We, therefore, delve into the distinct regulation of these genes during primary axis formation, segment identity, and extra-embryonic roles such as in the formation of hair follicles or misregulation leading to cancer. Toward the end of each section, we emphasize the possibilities of several experiments involving various organisms, owing to the advancements in the field of genomics and CRISPR-based genome engineering. Overall, we present a holistic view of the functioning of Hox in the animal world.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Rakesh K. Mishra
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- AcSIR – Academy of Scientific and Innovative Research, Ghaziabad, India
- Tata Institute for Genetics and Society (TIGS), Bangalore, India
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20
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Degani N, Lubelsky Y, Perry RBT, Ainbinder E, Ulitsky I. Highly conserved and cis-acting lncRNAs produced from paralogous regions in the center of HOXA and HOXB clusters in the endoderm lineage. PLoS Genet 2021; 17:e1009681. [PMID: 34280202 PMCID: PMC8330917 DOI: 10.1371/journal.pgen.1009681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/03/2021] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play important roles in gene regulatory networks acting in early development. There has been rapid turnover of lncRNA loci during vertebrate evolution, with few human lncRNAs conserved beyond mammals. The sequences of these rare deeply conserved lncRNAs are typically not similar to each other. Here, we characterize HOXA-AS3 and HOXB-AS3, lncRNAs produced from the central regions of the HOXA and HOXB clusters. Sequence-similar orthologs of both lncRNAs are found in multiple vertebrate species and there is evident sequence similarity between their promoters, suggesting that the production of these lncRNAs predates the duplication of the HOX clusters at the root of the vertebrate lineage. This conservation extends to similar expression patterns of the two lncRNAs, in particular in cells transiently arising during early development or in the adult colon. Functionally, the RNA products of HOXA-AS3 and HOXB-AS3 regulate the expression of their overlapping HOX5-7 genes both in HT-29 cells and during differentiation of human embryonic stem cells. Beyond production of paralogous protein-coding and microRNA genes, the regulatory program in the HOX clusters therefore also relies on paralogous lncRNAs acting in restricted spatial and temporal windows of embryonic development and cell differentiation.
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Affiliation(s)
- Neta Degani
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Lubelsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilites, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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21
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Yamada K, Maeno A, Araki S, Kikuchi M, Suzuki M, Ishizaka M, Satoh K, Akama K, Kawabe Y, Suzuki K, Kobayashi D, Hamano N, Kawamura A. An atlas of seven zebrafish hox cluster mutants provides insights into sub/neofunctionalization of vertebrate Hox clusters. Development 2021; 148:269044. [PMID: 34096572 DOI: 10.1242/dev.198325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Vertebrate Hox clusters are comprised of multiple Hox genes that control morphology and developmental timing along multiple body axes. Although results of genetic analyses using Hox-knockout mice have been accumulating, genetic studies in other vertebrates have not been sufficient for functional comparisons of vertebrate Hox genes. In this study, we isolated all of the seven hox cluster loss-of-function alleles in zebrafish using the CRISPR-Cas9 system. Comprehensive analysis of the embryonic phenotype and X-ray micro-computed tomography scan analysis of adult fish revealed several species-specific functional contributions of homologous Hox clusters along the appendicular axis, whereas important shared general principles were also confirmed, as exemplified by serial anterior vertebral transformations along the main body axis, observed in fish for the first time. Our results provide insights into discrete sub/neofunctionalization of vertebrate Hox clusters after quadruplication of the ancient Hox cluster. This set of seven complete hox cluster loss-of-function alleles provide a formidable resource for future developmental genetic analysis of the Hox patterning system in zebrafish.
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Affiliation(s)
- Kazuya Yamada
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Akiteru Maeno
- Plant Resource Development, Division of Genetic Resource Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Soh Araki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Morimichi Kikuchi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Masato Suzuki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Mizuki Ishizaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Koumi Satoh
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kagari Akama
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Yuki Kawabe
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kenya Suzuki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Daiki Kobayashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Nanami Hamano
- 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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22
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Delgado I, Giovinazzo G, Temiño S, Gauthier Y, Balsalobre A, Drouin J, Torres M. Control of mouse limb initiation and antero-posterior patterning by Meis transcription factors. Nat Commun 2021; 12:3086. [PMID: 34035267 PMCID: PMC8149412 DOI: 10.1038/s41467-021-23373-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 04/21/2021] [Indexed: 12/31/2022] Open
Abstract
Meis1 and Meis2 are homeodomain transcription factors that regulate organogenesis through cooperation with Hox proteins. Elimination of Meis genes after limb induction has shown their role in limb proximo-distal patterning; however, limb development in the complete absence of Meis function has not been studied. Here, we report that Meis1/2 inactivation in the lateral plate mesoderm of mouse embryos leads to limb agenesis. Meis and Tbx factors converge in this function, extensively co-binding with Tbx to genomic sites and co-regulating enhancers of Fgf10, a critical factor in limb initiation. Limbs with three deleted Meis alleles show proximal-specific skeletal hypoplasia and agenesis of posterior skeletal elements. This failure in posterior specification results from an early role of Meis factors in establishing the limb antero-posterior prepattern required for Shh activation. Our results demonstrate roles for Meis transcription factors in early limb development and identify their involvement in previously undescribed interaction networks that regulate organogenesis.
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Affiliation(s)
- Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Giovanna Giovinazzo
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Susana Temiño
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Yves Gauthier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Aurelio Balsalobre
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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23
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Castro J, Beviano V, Paço A, Leitão-Castro J, Cadete F, Francisco M, Freitas R. Hoxd13/Bmp2-mediated mechanism involved in zebrafish finfold design. Sci Rep 2021; 11:7165. [PMID: 33785799 PMCID: PMC8009906 DOI: 10.1038/s41598-021-86621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The overexpression of hoxd13a during zebrafish fin development causes distal endochondral expansion and simultaneous reduction of the finfold, mimicking the major events thought to have happened during the fin-to-limb transition in Vertebrates. We investigated the effect of hoxd13a overexpression on putative downstream targets and found it to cause downregulation of proximal fin identity markers (meis1 and emx2) and upregulation of genes involved in skeletogenesis/patterning (fbn1, dacha) and AER/Finfold maintenance (bmps). We then show that bmp2b overexpression leads to finfold reduction, recapitulating the phenotype observed in hoxd13a-overexpressing fins. In addition, we show that during the development of the long finfold in leot1/lofdt1 mutants, hoxd13a and bmp2b are downregulated. Our results suggest that modulation of the transcription factor Hoxd13 during evolution may have been involved in finfold reduction through regulation of the Bmp signalling that then activated apoptotic mechanisms impairing finfold elongation.
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Affiliation(s)
- João Castro
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Vanessa Beviano
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Ana Paço
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Joana Leitão-Castro
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Francisco Cadete
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Miguel Francisco
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Renata Freitas
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal ,Cell Growth and Differentiation Group, IBMC/I3S, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
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24
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Beccari L, Jaquier G, Lopez-Delisle L, Rodriguez-Carballo E, Mascrez B, Gitto S, Woltering J, Duboule D. Dbx2 regulation in limbs suggests interTAD sharing of enhancers. Dev Dyn 2021; 250:1280-1299. [PMID: 33497014 PMCID: PMC8451760 DOI: 10.1002/dvdy.303] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND During tetrapod limb development, the HOXA13 and HOXD13 transcription factors are critical for the emergence and organization of the autopod, the most distal aspect where digits will develop. Since previous work had suggested that the Dbx2 gene is a target of these factors, we set up to analyze in detail this potential regulatory interaction. RESULTS We show that HOX13 proteins bind to mammalian-specific sequences at the vicinity of the Dbx2 locus that have enhancer activity in developing digits. However, the functional inactivation of the DBX2 protein did not elicit any particular phenotype related to Hox genes inactivation in digits, suggesting either redundant or compensatory mechanisms. We report that the neighboring Nell2 and Ano6 genes are also expressed in distal limb buds and are in part controlled by the same Dbx2 enhancers despite being localized into two different topologically associating domains (TADs) flanking the Dbx2 locus. CONCLUSIONS We conclude that Hoxa13 and Hoxd genes cooperatively activate Dbx2 expression in developing digits through binding to mammalian specific regulatory sequences in the Dbx2 neighborhood. Furthermore, these enhancers can overcome TAD boundaries in either direction to co-regulate a set of genes located in distinct chromatin domains.
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Affiliation(s)
- Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, University Claude Bernard Lyon1, Lyon, France
| | - Gabriel Jaquier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Eddie Rodriguez-Carballo
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Joost Woltering
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,School of Life Sciences, Federal School of Technology (EPFL), Lausanne, Switzerland.,Collège de France, Paris, France
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25
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Newton AH, Smith CA. Regulation of vertebrate forelimb development and wing reduction in the flightless emu. Dev Dyn 2021; 250:1248-1263. [PMID: 33368781 DOI: 10.1002/dvdy.288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
The vertebrate limb is a dynamic structure which has evolved into many diverse forms to facilitate complex behavioral adaptations. The principle molecular and cellular processes that underlie development of the vertebrate limb are well characterized. However, how these processes are altered to drive differential limb development between vertebrates is less well understood. Several vertebrate models are being utilized to determine the developmental basis of differential limb morphogenesis, though these typically focus on later patterning of the established limb bud and may not represent the complete developmental trajectory. Particularly, heterochronic limb development can occur prior to limb outgrowth and patterning but receives little attention. This review summarizes the genetic regulation of vertebrate forelimb diversity, with particular focus on wing reduction in the flightless emu as a model for examining limb heterochrony. These studies highlight that wing reduction is complex, with heterochronic cellular and genetic events influencing the major stages of limb development. Together, these studies provide a broader picture of how different limb morphologies may be established during development.
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Affiliation(s)
- Axel H Newton
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Craig A Smith
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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26
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Binversie EE, Baker LA, Engelman CD, Hao Z, Moran JJ, Piazza AM, Sample SJ, Muir P. Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture. PLoS One 2020; 15:e0244075. [PMID: 33382735 PMCID: PMC7774950 DOI: 10.1371/journal.pone.0244075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Anterior cruciate ligament (ACL) rupture is an important condition of the human knee. Second ruptures are common and societal costs are substantial. Canine cranial cruciate ligament (CCL) rupture closely models the human disease. CCL rupture is common in the Labrador Retriever (5.79% prevalence), ~100-fold more prevalent than in humans. Labrador Retriever CCL rupture is a polygenic complex disease, based on genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers. Dissection of genetic variation in complex traits can be enhanced by studying structural variation, including copy number variants (CNVs). Dogs are an ideal model for CNV research because of reduced genetic variability within breeds and extensive phenotypic diversity across breeds. We studied the genetic etiology of CCL rupture by association analysis of CNV regions (CNVRs) using 110 case and 164 control Labrador Retrievers. CNVs were called from SNPs using three different programs (PennCNV, CNVPartition, and QuantiSNP). After quality control, CNV calls were combined to create CNVRs using ParseCNV and an association analysis was performed. We found no strong effect CNVRs but found 46 small effect (max(T) permutation P<0.05) CCL rupture associated CNVRs in 22 autosomes; 25 were deletions and 21 were duplications. Of the 46 CCL rupture associated CNVRs, we identified 39 unique regions. Thirty four were identified by a single calling algorithm, 3 were identified by two calling algorithms, and 2 were identified by all three algorithms. For 42 of the associated CNVRs, frequency in the population was <10% while 4 occurred at a frequency in the population ranging from 10–25%. Average CNVR length was 198,872bp and CNVRs covered 0.11 to 0.15% of the genome. All CNVRs were associated with case status. CNVRs did not overlap previous canine CCL rupture risk loci identified by GWAS. Associated CNVRs contained 152 annotated genes; 12 CNVRs did not have genes mapped to CanFam3.1. Using pathway analysis, a cluster of 19 homeobox domain transcript regulator genes was associated with CCL rupture (P = 6.6E-13). This gene cluster influences cranial-caudal body pattern formation during embryonic limb development. Clustered genes were found in 3 CNVRs on chromosome 14 (HoxA), 28 (NKX6-2), and 36 (HoxD). When analysis was limited to deletion CNVRs, the association was strengthened (P = 8.7E-16). This study suggests a component of the polygenic risk of CCL rupture in Labrador Retrievers is associated with small effect CNVs and may include aspects of stifle morphology regulated by homeobox domain transcript regulator genes.
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Affiliation(s)
- Emily E. Binversie
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lauren A. Baker
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Corinne D. Engelman
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Zhengling Hao
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John J. Moran
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander M. Piazza
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susannah J. Sample
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter Muir
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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27
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Rodríguez-Carballo E, Lopez-Delisle L, Willemin A, Beccari L, Gitto S, Mascrez B, Duboule D. Chromatin topology and the timing of enhancer function at the HoxD locus. Proc Natl Acad Sci U S A 2020; 117:31231-31241. [PMID: 33229569 PMCID: PMC7733857 DOI: 10.1073/pnas.2015083117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different subgroups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate from two distinct topologically associating domains (TADs) flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory submodules. To understand the importance of this particular regulatory topology to control Hoxd gene transcription in time and space, we either deleted or inverted this sub-TAD boundary, eliminated the CTCF binding sites, or inverted the entire T-DOM to exchange the respective positions of the two sub-TADs. The effects of such perturbations on the transcriptional regulation of Hoxd genes illustrate the requirement of this regulatory topology for the precise timing of gene activation. However, the spatial distribution of transcripts was eventually resumed, showing that the presence of enhancer sequences, rather than either their exact topology or a particular chromatin architecture, is the key factor. We also show that the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border and an unfavorable orientation of CTCF sites.
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Affiliation(s)
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Andréa Willemin
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland;
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Collège de France, 75005 Paris, France
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28
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Desanlis I, Paul R, Kmita M. Transcriptional Trajectories in Mouse Limb Buds Reveal the Transition from Anterior-Posterior to Proximal-Distal Patterning at Early Limb Bud Stage. J Dev Biol 2020; 8:jdb8040031. [PMID: 33297480 PMCID: PMC7768367 DOI: 10.3390/jdb8040031] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/21/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022] Open
Abstract
Limb patterning relies in large part on the function of the Hox family of developmental genes. While the differential expression of Hox genes shifts from the anterior-posterior (A-P) to the proximal-distal (P-D) axis around embryonic day 11 (E11), whether this shift coincides with a more global change of A-P to P-D patterning program remains unclear. By performing and analyzing the transcriptome of the developing limb bud from E10.5 to E12.5, at single-cell resolution, we have uncovered transcriptional trajectories that revealed a general switch from A-P to P-D genetic program between E10.5 and E11.5. Interestingly, all the transcriptional trajectories at E10.5 end with cells expressing either proximal or distal markers suggesting a progressive acquisition of P-D identity. Moreover, we identified three categories of genes expressed in the distal limb mesenchyme characterized by distinct temporal expression dynamics. Among these are Hoxa13 and Hoxd13 (Hox13 hereafter), which start to be expressed around E10.5, and importantly the binding of the HOX13 factors was observed within or in the neighborhood of several of the distal limb genes. Our data are consistent with previous evidence suggesting that the transition from the early/proximal to the late/distal transcriptome of the limb mesenchyme largely relies on HOX13 function. Based on these results and the evidence that HOX13 factors restrict Hoxa11 expression to the proximal limb, in progenitor cells of the zeugopod, we propose that HOX13 act as a key determinant of P-D patterning.
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Affiliation(s)
- Ines Desanlis
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; (I.D.); (R.P.)
- Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Rachel Paul
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; (I.D.); (R.P.)
- Department of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; (I.D.); (R.P.)
- Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada
- Department of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-514-987-5749
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29
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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: 3.5] [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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30
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Gentile C, Kmita M. Polycomb Repressive Complexes in Hox Gene Regulation: Silencing and Beyond: The Functional Dynamics of Polycomb Repressive Complexes in Hox Gene Regulation. Bioessays 2020; 42:e1900249. [PMID: 32743818 DOI: 10.1002/bies.201900249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/17/2020] [Indexed: 11/10/2022]
Abstract
The coordinated expression of the Hox gene family encoding transcription factors is critical for proper embryonic development and patterning. Major efforts have thus been dedicated to understanding mechanisms controlling Hox expression. In addition to the temporal and spatial sequential activation of Hox genes, proper embryonic development requires that Hox genes get differentially silenced in a cell-type specific manner as development proceeds. Factors contributing to Hox silencing include the polycomb repressive complexes (PRCs), which control gene expression through epigenetic modifications. This review focuses on PRC-dependent regulation of the Hox genes and is aimed at integrating the growing complexity of PRC functional properties in the context of Hox regulation. In particular, mechanisms underlying PRC binding dynamics as well as a series of studies that have revealed the impact of PRC on the 3D organization of the genome is discussed, which has a significant role on Hox regulation during development.
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Affiliation(s)
- Claudia Gentile
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada.,Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada.,Département de Médecine, Université de Montréal, Montréal, Quebec, H3C 3J7, Canada
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31
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Roux M, Bouchard M, Kmita M. Multifaceted Hoxa13 function in urogenital development underlies the Hand-Foot-Genital Syndrome. Hum Mol Genet 2020; 28:1671-1681. [PMID: 30649340 DOI: 10.1093/hmg/ddz013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/14/2018] [Accepted: 01/08/2019] [Indexed: 02/05/2023] Open
Abstract
Hand-Foot-Genital syndrome is a rare condition caused by mutations in the HOXA13 gene and characterized by limb malformations and urogenital defects. While the role of Hoxa13 in limb development has been extensively studied, its function during the development of the urogenital system remains elusive mostly due to the embryonic lethality of Hoxa13 homozygous mutant mice. Using a conditional inactivation strategy, we show that mouse fetuses lacking Hoxa13 function develop megaureters, hydronephrosis and malformations of the uterus, reminiscent of the defects characterizing patients with Hand-Foot-Genital syndrome. Our analysis reveals that Hoxa13 plays a critical role in Müllerian ducts fusion and in ureter remodeling by regulating the elimination of the caudal common nephric duct, eventually preventing the separation from the nephric duct. Our data also reveal a specific role for Hoxa13 in the urogenital sinus, which is in part mediated by Gata3, as well as Hoxa13 requirement for the proper organization of the ureter. Finally, we provide evidence that Hoxa13 provides positional and temporal cues during the development of the lower urogenital system, a sine qua non condition for the proper function of the urinary system.
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Affiliation(s)
- Marine Roux
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada
| | - Maxime Bouchard
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,Département de Médecine (Programme de Biologie Moléculaire), Université de Montréal, Montreal, Quebec, Canada
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32
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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: 0.5] [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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33
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The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13. Proc Natl Acad Sci U S A 2020; 117:1090-1096. [PMID: 31896583 DOI: 10.1073/pnas.1919470117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In the tetrapod limb, the digits (fingers or toes) are the elements most subject to morphological diversification in response to functional adaptations. However, despite their functional importance, the mechanisms controlling digit morphology remain poorly understood. Here we have focused on understanding the special morphology of the thumb (digit 1), the acquisition of which was an important adaptation of the human hand. To this end, we have studied the limbs of the Hoxa13 mouse mutant that specifically fail to form digit 1. We show that, consistent with the role of Hoxa13 in Hoxd transcriptional regulation, the expression of Hoxd13 in Hoxa13 mutant limbs does not extend into the presumptive digit 1 territory, which is therefore devoid of distal Hox transcripts, a circumstance that can explain its agenesis. The loss of Hoxd13 expression, exclusively in digit 1 territory, correlates with increased Gli3 repressor activity, a Hoxd negative regulator, resulting from increased Gli3 transcription that, in turn, is due to the release from the negative modulation exerted by Hox13 paralogs on Gli3 regulatory sequences. Our results indicate that Hoxa13 acts hierarchically to initiate the formation of digit 1 by reducing Gli3 transcription and by enabling expansion of the 5'Hoxd second expression phase, thereby establishing anterior-posterior asymmetry in the handplate. Our work uncovers a mutual antagonism between Gli3 and Hox13 paralogs that has important implications for Hox and Gli3 gene regulation in the context of development and evolution.
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34
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Dynamic and self-regulatory interactions among gene regulatory networks control vertebrate limb bud morphogenesis. Curr Top Dev Biol 2020; 139:61-88. [DOI: 10.1016/bs.ctdb.2020.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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35
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Pathways, Processes, and Candidate Drugs Associated with a Hoxa Cluster-Dependency Model of Leukemia. Cancers (Basel) 2019; 11:cancers11122036. [PMID: 31861091 PMCID: PMC6966468 DOI: 10.3390/cancers11122036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023] Open
Abstract
High expression of the HOXA cluster correlates with poor clinical outcome in acute myeloid leukemias, particularly those harboring rearrangements of the mixed-lineage-leukemia gene (MLLr). Whilst decreased HOXA expression acts as a readout for candidate experimental therapies, the necessity of the HOXA cluster for leukemia maintenance has not been fully explored. Primary leukemias were generated in hematopoietic stem/progenitor cells from Cre responsive transgenic mice for conditional deletion of the Hoxa locus. Hoxa deletion resulted in reduced proliferation and colony formation in which surviving leukemic cells retained at least one copy of the Hoxa cluster, indicating dependency. Comparative transcriptome analysis of Hoxa wild type and deleted leukemic cells identified a unique gene signature associated with key pathways including transcriptional mis-regulation in cancer, the Fanconi anemia pathway and cell cycle progression. Further bioinformatics analysis of the gene signature identified a number of candidate FDA-approved drugs for potential repurposing in high HOXA expressing cancers including MLLr leukemias. Together these findings support dependency for an MLLr leukemia on Hoxa expression and identified candidate drugs for further therapeutic evaluation.
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Le Caignec C, Pichon O, Briand A, de Courtivron B, Bonnard C, Lindenbaum P, Redon R, Schluth-Bolard C, Diguet F, Rollat-Farnier PA, Sanchez-Castro M, Vuillaume ML, Sanlaville D, Duboule D, Mégarbané A, Toutain A. Fryns type mesomelic dysplasia of the upper limbs caused by inverted duplications of the HOXD gene cluster. Eur J Hum Genet 2019; 28:324-332. [PMID: 31591517 DOI: 10.1038/s41431-019-0522-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 07/12/2019] [Accepted: 09/17/2019] [Indexed: 01/09/2023] Open
Abstract
The HoxD cluster is critical for vertebrate limb development. Enhancers located in both the telomeric and centromeric gene deserts flanking the cluster regulate the transcription of HoxD genes. In rare patients, duplications, balanced translocations or inversions misregulating HOXD genes are responsible for mesomelic dysplasia of the upper and lower limbs. By aCGH, whole-genome mate-pair sequencing, long-range PCR and fiber fluorescent in situ hybridization, we studied patients from two families displaying mesomelic dysplasia limited to the upper limbs. We identified microduplications including the HOXD cluster and showed that microduplications were in an inverted orientation and inserted between the HOXD cluster and the telomeric enhancers. Our results highlight the existence of an autosomal dominant condition consisting of isolated ulnar dysplasia caused by microduplications inserted between the HOXD cluster and the telomeric enhancers. The duplications likely disconnect the HOXD9 to HOXD11 genes from their regulatory sequences. This presumptive loss-of-function may have contributed to the phenotype. In both cases, however, these rearrangements brought HOXD13 closer to telomeric enhancers, suggesting that the alterations derive from the dominant-negative effect of this digit-specific protein when ectopically expressed during the early development of forearms, through the disruption of topologically associating domain structure at the HOXD locus.
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Affiliation(s)
- Cédric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Nantes, France. .,Universite de Nantes, Nantes, France.
| | - Olivier Pichon
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Annaig Briand
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | | | - Christian Bonnard
- Service de Chirurgie Orthopédique Pédiatrique, CHRU de Tours, Tours, France.,Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France
| | - Pierre Lindenbaum
- INSERM, UMR_S1087, l'institut du thorax, Nantes, France.,CNRS, UMR 6291, Nantes, France
| | - Richard Redon
- INSERM, UMR_S1087, l'institut du thorax, Nantes, France.,CNRS, UMR 6291, Nantes, France
| | - Caroline Schluth-Bolard
- Department of Genetics, Lyon University Hospital, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Flavie Diguet
- Department of Genetics, Lyon University Hospital, Lyon, France
| | | | | | - Marie-Laure Vuillaume
- Service de Génétique, Hôpital Bretonneau, CHU, Tours, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Damien Sanlaville
- Department of Genetics, Lyon University Hospital, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Denis Duboule
- University of Geneva and Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | | | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, CHU, Tours, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
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Rodríguez-Carballo E, Lopez-Delisle L, Yakushiji-Kaminatsui N, Ullate-Agote A, Duboule D. Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes. BMC Biol 2019; 17:55. [PMID: 31299961 PMCID: PMC6626364 DOI: 10.1186/s12915-019-0677-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/28/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The spatial organization of the mammalian genome relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). These domains often contain ranges of enhancers displaying similar or related tissue specificity, suggesting that in some cases, such domains may act as coherent regulatory units, with a global on or off state. By using the HoxD gene cluster, which specifies the topology of the developing limbs via highly orchestrated regulation of gene expression, as a paradigm, we investigated how the arrangement of regulatory domains determines their activity and function. RESULTS Proximal and distal cells in the developing limb express different levels of Hoxd genes, regulated by flanking 3' and 5' TADs, respectively. We characterized the effect of large genomic rearrangements affecting these two TADs, including their fusion into a single chromatin domain. We show that, within a single hybrid TAD, the activation of both proximal and distal limb enhancers globally occurred as when both TADs are intact. However, the activity of the 3' TAD in distal cells is generally increased in the fused TAD, when compared to wild type where it is silenced. Also, target gene activity in distal cells depends on whether or not these genes had previously responded to proximal enhancers, which determines the presence or absence of H3K27me3 marks. We also show that the polycomb repressive complex 2 is mainly recruited at the Hox gene cluster and can extend its coverage to far-cis regulatory sequences as long as confined to the neighboring TAD structure. CONCLUSIONS We conclude that antagonistic limb proximal and distal enhancers can exert their specific effects when positioned into the same TAD and in the absence of their genuine target genes. We also conclude that removing these target genes reduced the coverage of a regulatory landscape by chromatin marks associated with silencing, which correlates with its prolonged activity in time.
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Affiliation(s)
- Eddie Rodríguez-Carballo
- Laboratory of Developmental Genomics, Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015, Lausanne, Switzerland
| | - Nayuta Yakushiji-Kaminatsui
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015, Lausanne, Switzerland
- Present Address: Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohoma, Kanagawa, 230-0045, Japan
| | - Asier Ullate-Agote
- Laboratory of Artificial and Natural Evolution, Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
| | - Denis Duboule
- Laboratory of Developmental Genomics, Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland.
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015, Lausanne, Switzerland.
- Collège de France, 75005, Paris, France.
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Yamamoto S, Uchida Y, Ohtani T, Nozaki E, Yin C, Gotoh Y, Yakushiji-Kaminatsui N, Higashiyama T, Suzuki T, Takemoto T, Shiraishi YI, Kuroiwa A. Hoxa13 regulates expression of common Hox target genes involved in cartilage development to coordinate the expansion of the autopodal anlage. Dev Growth Differ 2019; 61:228-251. [PMID: 30895612 PMCID: PMC6850407 DOI: 10.1111/dgd.12601] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 02/04/2023]
Abstract
To elucidate the role of Hox genes in limb cartilage development, we identified the target genes of HOXA11 and HOXA13 by ChIP‐Seq. The ChIP DNA fragment contained evolutionarily conserved sequences and multiple highly conserved HOX binding sites. A substantial portion of the HOXA11 ChIP fragment overlapped with the HOXA13 ChIP fragment indicating that both factors share common targets. Deletion of the target regions neighboring Bmp2 or Tshz2 reduced their expression in the autopod suggesting that they function as the limb bud‐specific enhancers. We identified the Hox downstream genes as exhibiting expression changes in the Hoxa13 knock out (KO) and Hoxd11‐13 deletion double mutant (Hox13 dKO) autopod by Genechip analysis. The Hox downstream genes neighboring the ChIP fragment were defined as the direct targets of Hox. We analyzed the spatial expression pattern of the Hox target genes that encode two different categories of transcription factors during autopod development and Hox13dKO limb bud. (a) Bcl11a, encoding a repressor of cartilage differentiation, was expressed in the E11.5 autopod and was substantially reduced in the Hox13dKO. (b) The transcription factors Aff3, Bnc2, Nfib and Runx1t1 were expressed in the zeugopodal cartilage but not in the autopod due to the repressive or relatively weak transcriptional activity of Hox13 at E11.5. Interestingly, the expression of these genes was later observed in the autopodal cartilage at E12.5. These results indicate that Hox13 transiently suspends the cartilage differentiation in the autopodal anlage via multiple pathways until establishing the paddle‐shaped structure required to generate five digits.
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Affiliation(s)
- Shiori Yamamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Yuji Uchida
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Tomomi Ohtani
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Erina Nozaki
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Chunyang Yin
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Yoshihiro Gotoh
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | | | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai-shi, Aichi-ken, Japan
| | - Tatsuya Takemoto
- Laboratory for Embryology, Institute for Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Yo-Ichi Shiraishi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya-shi, Aichi-ken, Japan
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Wymeersch FJ, Skylaki S, Huang Y, Watson JA, Economou C, Marek-Johnston C, Tomlinson SR, Wilson V. Transcriptionally dynamic progenitor populations organised around a stable niche drive axial patterning. Development 2019; 146:dev168161. [PMID: 30559277 PMCID: PMC6340148 DOI: 10.1242/dev.168161] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022]
Abstract
The elongating mouse anteroposterior axis is supplied by progenitors with distinct tissue fates. It is not known whether these progenitors confer anteroposterior pattern to the embryo. We have analysed the progenitor population transcriptomes in the mouse primitive streak and tail bud throughout axial elongation. Transcriptomic signatures distinguish three known progenitor types (neuromesodermal, lateral/paraxial mesoderm and notochord progenitors; NMPs, LPMPs and NotoPs). Both NMP and LPMP transcriptomes change extensively over time. In particular, NMPs upregulate Wnt, Fgf and Notch signalling components, and many Hox genes as progenitors transit from production of the trunk to the tail and expand in number. In contrast, the transcriptome of NotoPs is stable throughout axial elongation and they are required for normal axis elongation. These results suggest that NotoPs act as a progenitor niche whereas anteroposterior patterning originates within NMPs and LPMPs.
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Affiliation(s)
- Filip J Wymeersch
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Stavroula Skylaki
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Yali Huang
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Julia A Watson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Constantinos Economou
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Carylyn Marek-Johnston
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Simon R Tomlinson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Valerie Wilson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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40
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Young JJ, Grayson P, Tabin CJ. Developmental Biology: Hox Timing Determines Limb Placement. Curr Biol 2019; 29:R52-R54. [DOI: 10.1016/j.cub.2018.11.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Reassessing the Role of Hox Genes during Vertebrate Development and Evolution. Trends Genet 2018; 34:209-217. [PMID: 29269261 DOI: 10.1016/j.tig.2017.11.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/21/2017] [Accepted: 11/29/2017] [Indexed: 12/13/2022]
Abstract
Since their discovery Hox genes have been at the core of the established models explaining the development and evolution of the vertebrate body plan as well as its paired appendages. Recent work brought new light to their role in the patterning processes along the main body axis. These studies show that Hox genes do not control the basic layout of the vertebrate body plan but carry out region-specific patterning instructions loaded on the derivatives of axial progenitors by Hox-independent processes. Furthermore, the finding that Hox clusters are embedded in functional chromatin domains, which critically impacts their expression, has significantly altered our understanding of the mechanisms of Hox gene regulation. This new conceptual framework has broadened our understanding of both limb development and the evolution of vertebrate paired appendages.
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42
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Swenson JD, Klomp J, Fisher RA, Crow KD. How the Devil Ray Got Its Horns: The Evolution and Development of Cephalic Lobes in Myliobatid Stingrays (Batoidea: Myliobatidae). Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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43
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Plein A, Fantin A, Denti L, Pollard JW, Ruhrberg C. Erythro-myeloid progenitors contribute endothelial cells to blood vessels. Nature 2018; 562:223-228. [PMID: 30258231 PMCID: PMC6289247 DOI: 10.1038/s41586-018-0552-x] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 08/17/2018] [Indexed: 12/16/2022]
Abstract
The earliest blood vessels in mammalian embryos are formed when endothelial cells differentiate from angioblasts and coalesce into tubular networks. Thereafter, the endothelium is thought to expand solely by proliferation of pre-existing endothelial cells. Here we show that a complementary source of endothelial cells is recruited into pre-existing vasculature after differentiation from the earliest precursors of erythrocytes, megakaryocytes and macrophages, the erythro-myeloid progenitors (EMPs) that are born in the yolk sac. A first wave of EMPs contributes endothelial cells to the yolk sac endothelium, and a second wave of EMPs colonizes the embryo and contributes endothelial cells to intraembryonic endothelium in multiple organs, where they persist into adulthood. By demonstrating that EMPs constitute a hitherto unrecognized source of endothelial cells, we reveal that embryonic blood vascular endothelium expands in a dual mechanism that involves both the proliferation of pre-existing endothelial cells and the incorporation of endothelial cells derived from haematopoietic precursors.
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Affiliation(s)
- Alice Plein
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Alessandro Fantin
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Laura Denti
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Jeffrey W Pollard
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
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44
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Fabre PJ, Leleu M, Mascrez B, Lo Giudice Q, Cobb J, Duboule D. Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development. BMC Biol 2018; 16:101. [PMID: 30223853 PMCID: PMC6142630 DOI: 10.1186/s12915-018-0570-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Global analyses of gene expression during development reveal specific transcription patterns associated with the emergence of various cell types, tissues, and organs. These heterogeneous patterns are instrumental to ensure the proper formation of the different parts of our body, as shown by the phenotypic effects generated by functional genetic approaches. However, variations at the cellular level can be observed within each structure or organ. In the developing mammalian limbs, expression of Hox genes from the HoxD cluster is differentially controlled in space and time, in cells that will pattern the digits and the forearms. While the Hoxd genes broadly share a common regulatory landscape and large-scale analyses have suggested a homogenous Hox gene transcriptional program, it has not previously been clear whether Hoxd genes are expressed together at the same levels in the same cells. RESULTS We report a high degree of heterogeneity in the expression of the Hoxd11 and Hoxd13 genes. We analyzed single-limb bud cell transcriptomes and show that Hox genes are expressed in specific combinations that appear to match particular cell types. In cells giving rise to digits, we find that the expression of the five relevant Hoxd genes (Hoxd9 to Hoxd13) is unbalanced, despite their control by known global enhancers. We also report that specific combinatorial expression follows a pseudo-time sequence, which is established based on the transcriptional diversity of limb progenitors. CONCLUSIONS Our observations reveal the existence of distinct combinations of Hoxd genes at the single-cell level during limb development. In addition, we document that the increasing combinatorial expression of Hoxd genes in this developing structure is associated with specific transcriptional signatures and that these signatures illustrate a temporal progression in the differentiation of these cells.
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Affiliation(s)
- P J Fabre
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015, Lausanne, Switzerland. .,Department of Basic Neurosciences, University of Geneva, 1211, Geneva, Switzerland.
| | - M Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015, Lausanne, Switzerland
| | - B Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
| | - Q Lo Giudice
- Department of Basic Neurosciences, University of Geneva, 1211, Geneva, Switzerland
| | - J Cobb
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - D Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015, Lausanne, Switzerland. .,Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland.
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45
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Wan J, Liu H, Feng Q, Liu J, Ming L. HOXB9 promotes endometrial cancer progression by targeting E2F3. Cell Death Dis 2018; 9:509. [PMID: 29724991 PMCID: PMC5938704 DOI: 10.1038/s41419-018-0556-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 12/30/2022]
Abstract
HOXB9, as a HOX family transcription factor, playing a significant role in embryonic development and cancer progression. However, the function of HOXB9 and its precise mechanism in regulating endometrial cancer progression remains unknown. Here, we demonstrated that the expression of HOXB9 was increased in endometrial cancer, and associated with histological grade and lymph node metastasis. In addition, elevated HOXB9 predicts a poor prognosis in endometrial cancer patients. Interestingly, bioinformatics analysis of TCGA cancer database showed that HOXB9 expression is positively correlated with E2F3 expression. Moreover, HOXB9 promoted E2F3 expression by directly targeting to its promoter. Furthermore, we found that knocking down E2F3 abolished the ability of HOXB9 in enhancing cell migration. Taken together, for the first, we demonstrated the function and mechanism of HOXB9 in regulating endometrial cancer progression, and indicated HOXB9 may be a novel prognostic marker of endometrial cancer.
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Affiliation(s)
- Junhu Wan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
| | - Hongyang Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Quanling Feng
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Jun Liu
- Department of General Surgery, Zhecheng People's Hospital, 476000, Shangqiu, Henan, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
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46
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Lalonde RL, Akimenko MA. Effects of fin fold mesenchyme ablation on fin development in zebrafish. PLoS One 2018; 13:e0192500. [PMID: 29420592 PMCID: PMC5805328 DOI: 10.1371/journal.pone.0192500] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/24/2018] [Indexed: 11/19/2022] Open
Abstract
The evolution of the tetrapod limb involved an expansion and elaboration of the endoskeletal elements, while the fish fin rays were lost. Loss of fin-specific genes, and regulatory changes in key appendicular patterning genes have been identified as mechanisms of limb evolution, however their contributions to cellular organization and tissue differences between fins and limbs remains poorly understood. During early larval fin development, hoxa13a/hoxd13a-expressing fin fold mesenchyme migrate through the median and pectoral fin along actinotrichia fibrils, non-calcified skeletal elements crucial for supporting the fin fold. Fin fold mesenchyme migration defects have previously been proposed as a mechanism of fin dermal bone loss during tetrapod evolution as it has been shown they contribute directly to the fin ray osteoblast population. Using the nitroreductase/metronidazole system, we genetically ablated a subset of hoxa13a/hoxd13a-expressing fin fold mesenchyme to assess its contributions to fin development. Following the ablation of fin fold mesenchyme in larvae, the actinotrichia are unable to remain rigid and the median and pectoral fin folds collapse, resulting in a reduced fin fold size. The remaining cells following ablation are unable to migrate and show decreased actinodin1 mesenchymal reporter activity. Actinodin proteins are crucial structural component of the actinotrichia. Additionally, we show a decrease in hoxa13a, hoxd13a, fgf10a and altered shha, and ptch2 expression during larval fin development. A continuous treatment of metronidazole leads to fin ray defects at 30dpf. Fewer rays are present compared to stage-matched control larvae, and these rays are shorter and less defined. These results suggest the targeted hoxa13a/hoxd13a-expressing mesenchyme contribute to their own successful migration through their contributions to actinotrichia. Furthermore, due to their fate as fin ray osteoblasts, we propose their initial ablation, and subsequent disorganization produces truncated fin dermal bone elements during late larval stages.
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Affiliation(s)
- Robert L. Lalonde
- Department of Biology, University of Ottawa, 20 Marie-Curie, Ottawa, Ontario, Canada
| | - Marie-Andrée Akimenko
- Department of Biology, University of Ottawa, 20 Marie-Curie, Ottawa, Ontario, Canada
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47
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Darbellay F, Duboule D. Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci. Curr Top Dev Biol 2017; 116:299-314. [PMID: 26970625 DOI: 10.1016/bs.ctdb.2015.11.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hox gene clusters of jaw vertebrates display a tight genomic organization, which has no equivalent in any other bilateria genomes sequenced thus far. It was previously argued that such a topological consolidation toward a condensed, metagenic structure was due to the accumulation of long-range regulations flanking Hox loci, a phenomenon made possible by the successive genome duplications that occurred at the root of the vertebrate lineage, similar to gene neofunctionalization but applied to a coordinated multigenic system. Here, we propose that the emergence of such large vertebrate regulatory landscapes containing a range of global enhancers was greatly facilitated by the presence of topologically associating domains (TADs). These chromatin domains, mostly constitutive, may have been used as genomic niches where novel regulations could evolve due to both the preexistence of a structural backbone poised to integrate novel regulatory inputs, and a highly adaptive transcriptional readout. We propose a scenario for the coevolution of such TADs and the emergence of pleiotropy at ancestral vertebrate Hox loci.
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Affiliation(s)
- Fabrice Darbellay
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland
| | - Denis Duboule
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland; Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
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Tanaka M. Alterations in anterior-posterior patterning and its accompanying changes along the proximal-distal axis during the fin-to-limb transition. Genesis 2017; 56. [PMID: 28834131 DOI: 10.1002/dvg.23053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 11/07/2022]
Abstract
The evolution from fins to limbs was one of the most successful innovations for vertebrates, allowing them to vastly expand their behaviors and habitats. Fossil records suggest that morphological changes occurred not only along the proximal-distal axis included appearance of the autopod, but also occurred along the anterior-posterior axis included reductions in the size and number of basal bones and digits. This review focuses on recent progress in developmental and genetic studies aimed at elucidating the mechanisms underlying alteration of anterior-posterior patterning and its accompanying changes along the proximal-distal axis during the fin-to-limb transition.
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Affiliation(s)
- Mikiko Tanaka
- Department of Life Science and Technology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
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Kherdjemil Y, Kmita M. Insights on the role of hox genes in the emergence of the pentadactyl ground state. Genesis 2017; 56. [DOI: 10.1002/dvg.23046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/19/2017] [Accepted: 06/22/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Yacine Kherdjemil
- Laboratory of Genetics and Development; Institut de Recherches Cliniques de Montréal (IRCM); 110 avenue des Pins Ouest, Montréal, QC H2W1R7 Canada
- Département de Médecine (Programme de Biologie Moléculaire); Université de Montréal; Montréal QC H3T 1J4 Canada
| | - Marie Kmita
- Laboratory of Genetics and Development; Institut de Recherches Cliniques de Montréal (IRCM); 110 avenue des Pins Ouest, Montréal, QC H2W1R7 Canada
- Département de Médecine (Programme de Biologie Moléculaire); Université de Montréal; Montréal QC H3T 1J4 Canada
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Wang K, Jin J, Ma T, Zhai H. MiR-139-5p inhibits the tumorigenesis and progression of oral squamous carcinoma cells by targeting HOXA9. J Cell Mol Med 2017; 21:3730-3740. [PMID: 28780773 PMCID: PMC5706525 DOI: 10.1111/jcmm.13282] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Our study sought to clarify the effects of microRNA-139-5p (miR-139-5p) in the tumorigenesis and progression of oral squamous cell carcinoma (OSCC) by regulating HOXA9. MiR-139-5p and HOXA9 expression in OSCC tissues, tumour adjacent tissues, OSCC cells and normal cells were tested by qRT-PCR. SAS and CAL-27 cell lines were selected in among four OSCC cell lines and then transfected with miR-139-5p mimics, pEGFP-HOXA9 and cotransfected with miR-139-5p mimics + pEGFP-HOXA9. We used MTT, colony formation, transwell and wound healing assays to analyse cell viability, proliferation, invasion and migration. The target relationship between miR-139-5p and HOXA9 was verified by luciferase reporter assay and Western blot, respectively. MiR-139-5p was down-regulated, whereas HOXA9 was up-regulated in OSCC tissues and cells. The proliferation, invasion and migration ability of SAS and CAL-27 cells in miR-139-5p mimics group were significantly weaker than those in the control group and the miR-NC group (P < 0.01). MiR-139-5p can negatively regulate HOXA9. The proliferation, invasion and migration of SAS and CAL-27 cells in the miR-139-5p mimics + pEGFP-HOXA9 group were not significantly different from those in the blank control and negative control groups (P > 0.05). Our results indicated that miR-139-5p could directly inhibit HOXA9, which might be a potential mechanism in inhibiting the proliferation, invasiveness and migration of OSCC cells.
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Affiliation(s)
- Kai Wang
- Department of Plastic Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Jun Jin
- Department of Plastic Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Tengxiao Ma
- Department of Plastic Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hongfeng Zhai
- Department of Plastic Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan, China
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