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Chen L, Duan Y, Wang P. Coffee intake leads to preeclampsia-like syndromes in susceptible pregnant rats. J Nutr Sci 2024; 13:e34. [PMID: 39314530 PMCID: PMC11418084 DOI: 10.1017/jns.2024.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/18/2024] [Accepted: 07/27/2024] [Indexed: 09/25/2024] Open
Abstract
Coffee is one of the most popular beverages worldwide, and there is an increasing concern of the health risk of coffee consumption in pregnancy. Preeclampsia (PE) is a serious pregnancy disease that causes elevated blood pressure and proteinuria in pregnant women and growth restriction of fetuses due to poorly developed placental vasculature. The aim of our study is to investigate the possible effect of coffee intake during pregnancy in rats with potential underlying vasculature conditions. The endothelial nitric oxide synthase inhibitor N(gamma)-nitro-L-arginine methyl ester (L-NAME) at a high dose (125 mg/kg/d) was used to induce PE in pregnant rats, which were used as the positive control group. In addition, low-dose L-NAME (10 mg/kg/d) was used to simulate the compromised placental vasculature function in pregnant rats. Coffee was given together with low-dose L-NAME to the pregnant rats from gestational day 10.5-18.5. Our results show that the pregnant rats treated with low-dose L-NAME + coffee, but not low-dose L-NAME alone, developed PE symptoms such as prominent fetal growth restriction, hypertension, and proteinuria. Therefore, our findings suggest that coffee intake during pregnancy may cause an increased risk of PE in susceptible women.
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Affiliation(s)
- Linyan Chen
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Yi Duan
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Pan Wang
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
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2
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Rochais F, Kelly RG. Fibroblast growth factor 10. Differentiation 2024; 139:100741. [PMID: 38040515 DOI: 10.1016/j.diff.2023.100741] [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: 07/26/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
Fibroblast growth factor 10 (FGF10) is a major morphoregulatory factor that plays essential signaling roles during vertebrate multiorgan development and homeostasis. FGF10 is predominantly expressed in mesenchymal cells and signals though FGFR2b in adjacent epithelia to regulate branching morphogenesis, stem cell fate, tissue differentiation and proliferation, in addition to autocrine roles. Genetic loss of function analyses have revealed critical requirements for FGF10 signaling during limb, lung, digestive system, ectodermal, nervous system, craniofacial and cardiac development. Heterozygous FGF10 mutations have been identified in human genetic syndromes associated with craniofacial anomalies, including lacrimal and salivary gland aplasia. Elevated Fgf10 expression is associated with poor prognosis in a range of cancers. In addition to developmental and disease roles, FGF10 regulates homeostasis and repair of diverse adult tissues and has been identified as a target for regenerative medicine.
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Affiliation(s)
| | - Robert G Kelly
- Aix-Marseille Université, CNRS UMR 7288, IBDM, Marseille, France.
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3
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Kawaguchi A, Wang J, Knapp D, Murawala P, Nowoshilow S, Masselink W, Taniguchi-Sugiura Y, Fei JF, Tanaka EM. A chromatin code for limb segment identity in axolotl limb regeneration. Dev Cell 2024; 59:2239-2253.e9. [PMID: 38788714 DOI: 10.1016/j.devcel.2024.05.002] [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: 01/15/2023] [Revised: 07/25/2023] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
The salamander limb correctly regenerates missing limb segments because connective tissue cells have segment-specific identities, termed "positional information". How positional information is molecularly encoded at the chromatin level has been unknown. Here, we performed genome-wide chromatin profiling in mature and regenerating axolotl limb connective tissue cells. We find segment-specific levels of histone H3K27me3 as the major positional mark, especially at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. In the hand, the permissive chromatin state of the homeoprotein gene HoxA13 engages with the regeneration program bypassing the upper limb program. Comparison of regeneration regulatory elements with those found in other regenerative animals identified a core shared set of transcription factors, supporting an ancient, conserved regeneration program.
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Affiliation(s)
- Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dunja Knapp
- DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Sergej Nowoshilow
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Wouter Masselink
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Yuka Taniguchi-Sugiura
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
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4
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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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5
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Chen KQ, Kawakami H, Anderson A, Corcoran D, Soni A, Nishinakamura R, Kawakami Y. Sall genes regulate hindlimb initiation in mouse embryos. Genetics 2024; 227:iyae029. [PMID: 38386912 PMCID: PMC11075541 DOI: 10.1093/genetics/iyae029] [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: 01/15/2024] [Revised: 01/15/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
Vertebrate limbs start to develop as paired protrusions from the lateral plate mesoderm at specific locations of the body with forelimb buds developing anteriorly and hindlimb buds posteriorly. During the initiation process, limb progenitor cells maintain active proliferation to form protrusions and start to express Fgf10, which triggers molecular processes for outgrowth and patterning. Although both processes occur in both types of limbs, forelimbs (Tbx5), and hindlimbs (Isl1) utilize distinct transcriptional systems to trigger their development. Here, we report that Sall1 and Sall4, zinc finger transcription factor genes, regulate hindlimb initiation in mouse embryos. Compared to the 100% frequency loss of hindlimb buds in TCre; Isl1 conditional knockouts, Hoxb6Cre; Isl1 conditional knockout causes a hypomorphic phenotype with only approximately 5% of mutants lacking the hindlimb. Our previous study of SALL4 ChIP-seq showed SALL4 enrichment in an Isl1 enhancer, suggesting that SALL4 acts upstream of Isl1. Removing 1 allele of Sall4 from the hypomorphic Hoxb6Cre; Isl1 mutant background caused loss of hindlimbs, but removing both alleles caused an even higher frequency of loss of hindlimbs, suggesting a genetic interaction between Sall4 and Isl1. Furthermore, TCre-mediated conditional double knockouts of Sall1 and Sall4 displayed a loss of expression of hindlimb progenitor markers (Isl1, Pitx1, Tbx4) and failed to develop hindlimbs, demonstrating functional redundancy between Sall1 and Sall4. Our data provides genetic evidence that Sall1 and Sall4 act as master regulators of hindlimb initiation.
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Affiliation(s)
- Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aaron Anderson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aditi Soni
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
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6
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McDonnell E, Orr SE, Barter MJ, Rux D, Brumwell A, Wrobel N, Murphy L, Overmann LM, Sorial AK, Young DA, Soul J, Rice SJ. Epigenetic mechanisms of osteoarthritis risk in human skeletal development. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.05.24306832. [PMID: 38766055 PMCID: PMC11100852 DOI: 10.1101/2024.05.05.24306832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The epigenome, including the methylation of cytosine bases at CG dinucleotides, is intrinsically linked to transcriptional regulation. The tight regulation of gene expression during skeletal development is essential, with ~1/500 individuals born with skeletal abnormalities. Furthermore, increasing evidence is emerging to link age-associated complex genetic musculoskeletal diseases, including osteoarthritis (OA), to developmental factors including joint shape. Multiple studies have shown a functional role for DNA methylation in the genetic mechanisms of OA risk using articular cartilage samples taken from aged patients. Despite this, our knowledge of temporal changes to the methylome during human cartilage development has been limited. We quantified DNA methylation at ~700,000 individual CpGs across the epigenome of developing human articular cartilage in 72 samples ranging from 7-21 post-conception weeks, a time period that includes cavitation of the developing knee joint. We identified significant changes in 8% of all CpGs, and >9400 developmental differentially methylated regions (dDMRs). The largest hypermethylated dDMRs mapped to transcriptional regulators of early skeletal patterning including MEIS1 and IRX1. Conversely, the largest hypomethylated dDMRs mapped to genes encoding extracellular matrix proteins including SPON2 and TNXB and were enriched in chondrocyte enhancers. Significant correlations were identified between the expression of these genes and methylation within the hypomethylated dDMRs. We further identified 811 CpGs at which significant dimorphism was present between the male and female samples, with the majority (68%) being hypermethylated in female samples. Following imputation, we captured the genotype of these samples at >5 million variants and performed epigenome-wide methylation quantitative trait locus (mQTL) analysis. Colocalization analysis identified 26 loci at which genetic variants exhibited shared impacts upon methylation and OA genetic risk. This included loci which have been previously reported to harbour OA-mQTLs (including GDF5 and ALDH1A2), yet the majority (73%) were novel (including those mapping to CHST3, FGF1 and TEAD1). To our knowledge, this is the first extensive study of DNA methylation across human articular cartilage development. We identify considerable methylomic plasticity within the development of knee cartilage and report active epigenomic mediators of OA risk operating in prenatal joint tissues.
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Affiliation(s)
- Euan McDonnell
- Computational Biology Facility, University of Liverpool, MerseyBio, Crown Street, United Kingdom
| | - Sarah E Orr
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Matthew J Barter
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Danielle Rux
- Orthopaedic Surgery, UConn Health, Farmington, Connecticut, USA
| | - Abby Brumwell
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Lynne M Overmann
- Human Developmental Biology Resource, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Antony K Sorial
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - David A Young
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Jamie Soul
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sarah J Rice
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
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7
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Dvoretskova E, Ho MC, Kittke V, Neuhaus F, Vitali I, Lam DD, Delgado I, Feng C, Torres M, Winkelmann J, Mayer C. Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development. Nat Neurosci 2024; 27:862-872. [PMID: 38528203 PMCID: PMC11088997 DOI: 10.1038/s41593-024-01611-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/23/2024] [Indexed: 03/27/2024]
Abstract
The mammalian telencephalon contains distinct GABAergic projection neuron and interneuron types, originating in the germinal zone of the embryonic basal ganglia. How genetic information in the germinal zone determines cell types is unclear. Here we use a combination of in vivo CRISPR perturbation, lineage tracing and ChIP-sequencing analyses and show that the transcription factor MEIS2 favors the development of projection neurons by binding enhancer regions in projection-neuron-specific genes during mouse embryonic development. MEIS2 requires the presence of the homeodomain transcription factor DLX5 to direct its functional activity toward the appropriate binding sites. In interneuron precursors, the transcription factor LHX6 represses the MEIS2-DLX5-dependent activation of projection-neuron-specific enhancers. Mutations of Meis2 result in decreased activation of regulatory enhancers, affecting GABAergic differentiation. We propose a differential binding model where the binding of transcription factors at cis-regulatory elements determines differential gene expression programs regulating cell fate specification in the mouse ganglionic eminence.
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Affiliation(s)
- Elena Dvoretskova
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - May C Ho
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Volker Kittke
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuhererg, Germany
- TUM School of Medicine and Health, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- DZPG (German Center for Mental Health), Munich, Germany
| | - Florian Neuhaus
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Ilaria Vitali
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Daniel D Lam
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuhererg, Germany
- TUM School of Medicine and Health, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Chao Feng
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuhererg, Germany
- TUM School of Medicine and Health, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- DZPG (German Center for Mental Health), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christian Mayer
- Max Planck Institute for Biological Intelligence, Martinsried, Germany.
- Max Planck Institute of Neurobiology, Martinsried, Germany.
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8
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Müller T, Reichlmeir M, Hau AC, Wittig I, Schulte D. The neuronal transcription factor MEIS2 is a calpain-2 protease target. J Cell Sci 2024; 137:jcs261482. [PMID: 38305737 PMCID: PMC10941658 DOI: 10.1242/jcs.261482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024] Open
Abstract
Tight control over transcription factor activity is necessary for a sensible balance between cellular proliferation and differentiation in the embryo and during tissue homeostasis by adult stem cells, but mechanistic details have remained incomplete. The homeodomain transcription factor MEIS2 is an important regulator of neurogenesis in the ventricular-subventricular zone (V-SVZ) adult stem cell niche in mice. We here identify MEIS2 as direct target of the intracellular protease calpain-2 (composed of the catalytic subunit CAPN2 and the regulatory subunit CAPNS1). Phosphorylation at conserved serine and/or threonine residues, or dimerization with PBX1, reduced the sensitivity of MEIS2 towards cleavage by calpain-2. In the adult V-SVZ, calpain-2 activity is high in stem and progenitor cells, but rapidly declines during neuronal differentiation, which is accompanied by increased stability of MEIS2 full-length protein. In accordance with this, blocking calpain-2 activity in stem and progenitor cells, or overexpression of a cleavage-insensitive form of MEIS2, increased the production of neurons, whereas overexpression of a catalytically active CAPN2 reduced it. Collectively, our results support a key role for calpain-2 in controlling the output of adult V-SVZ neural stem and progenitor cells through cleavage of the neuronal fate determinant MEIS2.
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Affiliation(s)
- Tanja Müller
- Goethe University, Faculty of Medicine, University Hospital Frankfurt, Institute of Neurology (Edinger Institute), 60528 Frankfurt, Germany
- Goethe University, University Hospital Frankfurt, Dr. Senckenberg Institute of Neurooncology and Institute of Neurology (Edinger Institute), Frankfurt Cancer Institute (FCI), University Cancer Center Frankfurt (UCT), MSNZ Junior Group Translational Neurooncology, 60528 Frankfurt, Germany
- Department of Cancer Research (DoCR), Luxembourg Institute of Health (LIH), Luxembourg Centre of Neuropathology (LCNP), 1445 Luxembourg, Luxembourg
| | - Marina Reichlmeir
- Goethe University, Faculty of Medicine, University Hospital Frankfurt, Institute of Neurology (Edinger Institute), 60528 Frankfurt, Germany
| | - Ann-Christin Hau
- Goethe University, University Hospital Frankfurt, Dr. Senckenberg Institute of Neurooncology and Institute of Neurology (Edinger Institute), Frankfurt Cancer Institute (FCI), University Cancer Center Frankfurt (UCT), MSNZ Junior Group Translational Neurooncology, 60528 Frankfurt, Germany
| | - Ilka Wittig
- Goethe University, Faculty of Medicine, Institute for Cardiovascular Physiology, Functional Proteomics, 60590, Frankfurt, Germany
| | - Dorothea Schulte
- Goethe University, Faculty of Medicine, University Hospital Frankfurt, Institute of Neurology (Edinger Institute), 60528 Frankfurt, Germany
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9
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Bobola N, Sagerström CG. TALE transcription factors: Cofactors no more. Semin Cell Dev Biol 2024; 152-153:76-84. [PMID: 36509674 DOI: 10.1016/j.semcdb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Exd/PBX, Hth/MEIS and PREP proteins belong to the TALE (three-amino-acid loop extension) superclass of transcription factors (TFs) with an atypical homedomain (HD). Originally discovered as "cofactors" to HOX proteins, revisiting their traditional role in light of genome-wide experiments reveals a strong and reproducible pattern of HOX and TALE co-occupancy across diverse embryonic tissues. While confirming that TALE increases HOX specificity and selectivity in vivo, this wider outlook also reveals novel aspects of HOX:TALE collaboration, namely that HOX TFs generally require pre-bound TALE factors to access their functional binding sites in vivo. In contrast to the restricted expression domains of HOX TFs, TALE factors are largely ubiquitous, and PBX and PREP are expressed at the earliest developmental stages. PBX and MEIS control development of many organs and tissues and their dysregulation is associated with congenital disease and cancer. Accordingly, many instances of TALE cooperation with non HOX TFs have been documented in various systems. The model that emerges from these studies is that TALE TFs create a permissive chromatin platform that is selected by tissue-restricted TFs for binding. In turn, HOX and other tissue-restricted TFs selectively convert a ubiquitous pool of low affinity TALE binding events into high confidence, tissue-restricted binding events associated with transcriptional activation. As a result, TALE:TF complexes are associated with active chromatin and domain/lineage-specific gene activity. TALE ubiquitous expression and broad genomic occupancy, as well as the increasing examples of TALE tissue-specific partners, reveal a universal and obligatory role for TALE in the control of tissue and lineage-specific transcriptional programs, beyond their initial discovery as HOX co-factors.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK.
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, Aurora, CO, USA.
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10
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Yang L, Liu M, Zhu Y, Li Y, Pan T, Li E, Wu X. Candidate Regulatory Genes for Hindlimb Development in the Embryos of the Chinese Alligator ( Alligator sinensis). Animals (Basel) 2023; 13:3126. [PMID: 37835732 PMCID: PMC10571561 DOI: 10.3390/ani13193126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/11/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Crocodilians, which are a kind of animal secondary adaptation to an aquatic environment, their hindlimb can provide the power needed to engage in various life activities, even in low-oxygen water environments. The development of limbs is an important aspect of animal growth and development, as it is closely linked to body movement, support, heat production, and other critical functions. For the Chinese alligator, the hindlimb is one of the main sources of power, and its development and differentiation will directly influence the survival ability in the wild. Furthermore, a better understanding of the hindlimb developmental process will provide data support for the comparative evolutionary and functional genomics of crocodilians. In this study, the expression levels of genes related to hindlimb development in the Chinese alligator embryos during fetal development (on days 29, 35, 41, and 46) were investigated through transcriptome analysis. A total of 1675 differentially expressed genes (DEGs) at different stages were identified by using limma software. These DEGs were then analyzed using weighted correlation network analysis (WGCNA), and 4 gene expression modules and 20 hub genes were identified that were associated with the development of hindlimbs in the Chinese alligator at different periods. The results of GO enrichment and hub gene expression showed that the hindlimb development of the Chinese alligator embryos involves the development of the embryonic structure, nervous system, and hindlimb muscle in the early stage (H29) and the development of metabolic capacity occurs in the later stage (H46). Additionally, the enrichment results showed that the AMPK signaling pathway, calcium signaling pathway, HIF-1 signaling pathway, and neuroactive ligand-receptor interaction are involved in the development of the hindlimb of the Chinese alligator. Among these, the HIF-1 signaling pathway and neuroactive ligand-receptor interaction may be related to the adaptation of Chinese alligators to low-oxygen environments. Additionally, five DEGs (CAV1, IRS2, LDHA, LDB3, and MYL3) were randomly selected for qRT-PCR to verify the transcriptome results. It is expected that further research on these genes will help us to better understand the process of embryonic hindlimb development in the Chinese alligator.
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Affiliation(s)
- Liuyang Yang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Mengqin Liu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Yunzhen Zhu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Yanan Li
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Tao Pan
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - En Li
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Xiaobing Wu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
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11
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Chen W, Wang Y, Gu H, Zhang Y, Chen C, Yu T, Chen T. Molecular characteristics, clinical significance, and immune landscape of extracellular matrix remodeling-associated genes in colorectal cancer. Front Oncol 2023; 13:1109181. [PMID: 37621680 PMCID: PMC10446763 DOI: 10.3389/fonc.2023.1109181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Background Extracellular matrix (ECM) remodeling is one of the hallmark events in cancer and has been shown to be closely related to tumor immunity. Immunotherapy has evolved as an important tool to treat various cancers and improve patient prognosis. The positive response to immunotherapy relies on the unique interaction between cancer and the tumor microenvironment (TME). However, the relationship between ECM remodeling and clinical outcomes, immune cell infiltration, and immunotherapy in colorectal cancer (CRC) remains unknown. Methods We systematically evaluated 69 ECM remodeling-associated genes (EAGs) and comprehensively identified interactions between ECM remodeling and prognosis and the immune microenvironment in CRC patients. The EAG_score was used to quantify the subtype of ECM remodeling in patients. We then assessed their value in predicting prognosis and responding to treatment in CRC. Results After elaborating the molecular characteristics of ECM remodeling-related genes in CRC patients, a model consisting of two ECM remodeling-related genes (MEIS2, SLC2A3) was developed for predicting the prognosis of CRC patients, Receiver Operating Characteristic (ROC) and Kaplan-Meier (K-M) analysis verified its reliable predictive ability. Furthermore, we created a highly reliable nomogram to enhance the clinical feasibility of the EAG_score. Significantly differences in TME and immune function, such as macrophages and CD8+ T cells, were observed between high- and low-risk CRC patients. In addition, drug sensitivity is also strongly related to EAG_score. Conclusion Overall, we developed a prognostic model associated with ECM remodeling, provided meaningful clinical implications for immunotherapy, and facilitated individualized treatment for CRC patients. Further studies are needed to reveal the underlying mechanisms of ECM remodeling in CRC.
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Affiliation(s)
- Wenlong Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yiwen Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haitao Gu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cong Chen
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tingting Yu
- Department of Medical Genetics, School of Basic Medical Science, Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, China
| | - Tao Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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12
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Kun E, Javan EM, Smith O, Gulamali F, de la Fuente J, Flynn BI, Vajrala K, Trutner Z, Jayakumar P, Tucker-Drob EM, Sohail M, Singh T, Narasimhan VM. The genetic architecture and evolution of the human skeletal form. Science 2023; 381:eadf8009. [PMID: 37471560 PMCID: PMC11075689 DOI: 10.1126/science.adf8009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
The human skeletal form underlies bipedalism, but the genetic basis of skeletal proportions (SPs) is not well characterized. We applied deep-learning models to 31,221 x-rays from the UK Biobank to extract a comprehensive set of SPs, which were associated with 145 independent loci genome-wide. Structural equation modeling suggested that limb proportions exhibited strong genetic sharing but were independent of width and torso proportions. Polygenic score analysis identified specific associations between osteoarthritis and hip and knee SPs. In contrast to other traits, SP loci were enriched in human accelerated regions and in regulatory elements of genes that are differentially expressed between humans and great apes. Combined, our work identifies specific genetic variants that affect the skeletal form and ties a major evolutionary facet of human anatomical change to pathogenesis.
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Affiliation(s)
- Eucharist Kun
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Emily M. Javan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Olivia Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Faris Gulamali
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Javier de la Fuente
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
| | - Brianna I. Flynn
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kushal Vajrala
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Zoe Trutner
- Department of Surgery and Perioperative Care, The University of Texas at Austin, Austin, TX, USA
| | - Prakash Jayakumar
- Department of Surgery and Perioperative Care, The University of Texas at Austin, Austin, TX, USA
| | | | - Mashaal Sohail
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), 62209 Cuernavaca, Mexico
| | - Tarjinder Singh
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- The New York Genome Center, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University, New York, NY, USA
| | - Vagheesh M. Narasimhan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Statistics and Data Science, The University of Texas at Austin, Austin, TX, USA
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13
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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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14
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Zhai J, Xu Y, Wan H, Yan R, Guo J, Skory R, Yan L, Wu X, Sun F, Chen G, Zhao W, Yu K, Li W, Guo F, Plachta N, Wang H. Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture. Cell 2023; 186:2078-2091.e18. [PMID: 37172562 DOI: 10.1016/j.cell.2023.04.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/15/2022] [Accepted: 04/12/2023] [Indexed: 05/15/2023]
Abstract
Neural tube (NT) defects arise from abnormal neurulation and result in the most common birth defects worldwide. Yet, mechanisms of primate neurulation remain largely unknown due to prohibitions on human embryo research and limitations of available model systems. Here, we establish a three-dimensional (3D) prolonged in vitro culture (pIVC) system supporting cynomolgus monkey embryo development from 7 to 25 days post-fertilization. Through single-cell multi-omics analyses, we demonstrate that pIVC embryos form three germ layers, including primordial germ cells, and establish proper DNA methylation and chromatin accessibility through advanced gastrulation stages. In addition, pIVC embryo immunofluorescence confirms neural crest formation, NT closure, and neural progenitor regionalization. Finally, we demonstrate that the transcriptional profiles and morphogenetics of pIVC embryos resemble key features of similarly staged in vivo cynomolgus and human embryos. This work therefore describes a system to study non-human primate embryogenesis through advanced gastrulation and early neurulation.
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Affiliation(s)
- Jinglei Zhai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yanhong Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Haifeng Wan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Rui Yan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jing Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Robin Skory
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Long Yan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Xulun Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Fengyuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Gang Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Wentao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Kunyuan Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Fan Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Nicolas Plachta
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
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15
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Bandler RC, Mayer C. Deciphering inhibitory neuron development: The paths to diversity. Curr Opin Neurobiol 2023; 79:102691. [PMID: 36805715 DOI: 10.1016/j.conb.2023.102691] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/29/2022] [Accepted: 01/10/2023] [Indexed: 02/19/2023]
Abstract
The regulation of fate decisions in progenitor cells lays the foundation for the generation of neuronal diversity and the formation of specialized circuits with remarkable processing capacity. Since the discovery more than 20 years ago that inhibitory (GABAergic) neurons originate from progenitors in the ventral part of the embryonic brain, numerous details about their development and function have been unveiled. GABAergic neurons are an extremely heterogeneous group, comprising many specialized subtypes of local interneurons and long-range projection neurons. Clearly distinguishable types emerge during postmitotic maturation, at a time when precursors migrate, morphologically mature, and establish synaptic connections. Yet, differentiation begins at an earlier stage within their progenitor domains, where a combination of birthdate and place of origin are key drivers. This review explains how new insights from single-cell sequencing inform our current understanding of how GABAergic neuron diversity emerges.
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Affiliation(s)
- Rachel C Bandler
- Yale University, Department of Psychiatry, New Haven, CT 06510, USA; Max Planck Institute for Biological Intelligence, Martinsried, 82152, Germany. https://twitter.com/Rachel_Bandler
| | - Christian Mayer
- Max Planck Institute for Biological Intelligence, Martinsried, 82152, Germany.
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16
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Wang S, Sun Y, Liu X, Guo Y, Huang Y, Zhang S, Tian Q. Meis1 Controls the Differentiation of Eye Progenitor Cells and the Formation of Posterior Poles during Planarian Regeneration. Int J Mol Sci 2023; 24:ijms24043505. [PMID: 36834910 PMCID: PMC9961902 DOI: 10.3390/ijms24043505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/21/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
As a member of TALE family, Meis1 has been proven to regulate cell proliferation and differentiation during cell fate commitment; however, the mechanism is still not fully understood. The planarian, which has an abundance of stem cells (neoblasts) responsible for regenerating any organ after injury, is an ideal model for studying the mechanisms of tissue identity determination. Here, we characterized a planarian homolog of Meis1 from the planarian Dugesia japonica. Importantly, we found that knockdown of DjMeis1 inhibits the differentiation of neoblasts into eye progenitor cells and results in an eyeless phenotype with normal central nervous system. Furthermore, we observed that DjMeis1 is required for the activation of Wnt signaling pathway by promoting the Djwnt1 expression during posterior regeneration. The silencing of DjMeis1 suppresses the expression of Djwnt1 and results in the inability to reconstruct posterior poles. In general, our findings indicated that DjMeis1 acts as a trigger for the activation of eye and tail regeneration by regulating the differentiation of eye progenitor cells and the formation of posterior poles, respectively.
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Affiliation(s)
- Shaocong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yujia Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaomai Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yajun Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yongding Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shoutao Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou 450046, China
- Correspondence: (S.Z.); (Q.T.)
| | - Qingnan Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (S.Z.); (Q.T.)
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17
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Abstract
Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.
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Affiliation(s)
- Katharine A. Hubert
- Program in Genetics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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18
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Zhao S, Zhang B, Yuan H, Yin Y, Qi S, Li W, Wu X, Yaling F. IGF2BP2 promotes the progression of ovarian endometriosis by regulating m6A-modified MEIS2 and GATA6. Int J Biochem Cell Biol 2022; 152:106296. [PMID: 36113831 DOI: 10.1016/j.biocel.2022.106296] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/25/2022] [Accepted: 09/11/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND m6A-RNA modification mediated by the N6-methyladenosine RNA methylation-related molecule methyltransferase-like 3 has been implicated in the progression of endometriosis. However, the functions of other m6A regulators, especially in ovarian endometriosis, remain unknown. METHODS Three datasets (GSE7305, GSE7307, and GSE37837) with diagnosed ovarian endometriosis were extracted from the Gene Expression Omnibus database. Using bioinformatics methods such as Weighted Gene Co-expression Network Analysis, Gene Ontology analysis, protein-protein interaction, and correlation, hub genes were identified. Using dot blot and N6-methyladenosine-IP-qPCR, the total and individual N6-methyladenosine gene levels were quantified. On clinical ovarian ectopic and eutopic endometrium tissues, N6-methyladenosine RNA methylation sequencing was performed. To authenticate protein localization and expression level, immunohistochemical staining and western blot were conducted, respectively. The database Connectivity Map was used to predict small molecules with potential therapeutic effects. RESULTS In ovarian endometriosis, the N6-methyladenosine "reader" molecule IGF2BP2 and related target genes MEIS2 and GATA6 were highly expressed. IGF2BP2 promoted the proliferation, migration, and invasion of ectopic endometrial stromal cells by stabilizing the mRNA of MEIS2 and GATA6. Synergistically, METTL3 and IGF2BP2 increased the N6-methyladenosine methylation of MEIS2 and GATA6. We developed five molecules (Mercaptopurine, MK-886, CP-863187, Canadine, and Securinine) that could be used to treat ovarian endometriosis based on IGF2BP2. CONCLUSION Our findings provided additional support for a systematized understanding of the role of N6-methyladenosine RNA methylation in endometriosis and confirmed for the first time the mechanism of IGF2BP2 in promoting ovarian endometriosis. This provides the molecular foundation for potential future therapies for ovarian endometriosis. DATA AVAILABILITY The data used to support the findings of this study are available from the corresponding author upon request.
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Affiliation(s)
- Shaojie Zhao
- Department of Gynaecology, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu Province 214002, PR China
| | - Bing Zhang
- Department of Gynaecology, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu Province 214002, PR China
| | - Hua Yuan
- Department of Gynaecology, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu Province 214002, PR China
| | - Yongxiang Yin
- Department of Pathology, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu Province 214002, PR China
| | - Suwan Qi
- Department of Women Health Care, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu Province 214002, PR China
| | - Wenjuan Li
- Department of Women Health Care, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu Province 214002, PR China
| | - Xiadi Wu
- Department of Women Health Care, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu Province 214002, PR China
| | - Feng Yaling
- Department of Women Health Care, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu Province 214002, PR China.
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19
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Cao Z, Huang C, Lu F, Jiang X, Hu Y, Cao C, Liu Z. Meis1 Regulates Nociceptor Development and Behavioral Response to Tactile Stimuli. Front Mol Neurosci 2022; 15:901466. [PMID: 35875660 PMCID: PMC9301487 DOI: 10.3389/fnmol.2022.901466] [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: 03/22/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Nociceptors in the dorsal root ganglia (DRG) and trigeminal ganglia (TG) are necessary for transmitting pain and itch signals. However, the molecular mechanism regulating nociceptor development remains largely unknown. This study identifies that the transcription factor Meis1 is generally expressed in two groups of sensory neurons in the developing DRG. During prenatal and neonatal stages, approximately 2/3 of Meis1+ neurons are Runx1+ nociceptors, while 1/3 of Meis1+ neurons are NF200+ myelinated neurons. At postnatal stages, Meis1 expression in nociceptors is gradually reduced. Here, we constructed a Meis1 conditional knockout mouse line to selectively delete Meis1 in Nav1.8 lineage nociceptors. Microarray analyses showed that differentially expressed genes in the Meis1 mutant DRG were enriched in pathways related to sensory perception of pain and nervous system development. In addition, Meis1 regulates the expression of some marker genes of Nppb+ neurons and C-LTMRs. Furthermore, Meis1 mutant mice exhibit behavioral deficits in response to light mechanical pain, static touch and chemical itch. Therefore, this study reveals that Meis1 is required to regulate the development of nociceptors.
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Affiliation(s)
- Zheng Cao
- Beijing Institute of Biotechnology, Beijing, China.,School of Biological Engineering and Food Science, Hubei University of Technology, Wuhan, China
| | - Chengcheng Huang
- Beijing Institute of Biotechnology, Beijing, China.,General Hospital of Central Theater Command, Wuhan, China
| | - Fumin Lu
- Beijing Institute of Biotechnology, Beijing, China
| | - Xuequan Jiang
- Beijing Institute of Biotechnology, Beijing, China.,School of Biological Engineering and Food Science, Hubei University of Technology, Wuhan, China
| | - Yong Hu
- Beijing Institute of Biotechnology, Beijing, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, Beijing, China
| | - Zijing Liu
- Beijing Institute of Biotechnology, Beijing, China
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Ishihara T, Hickford D, Fenelon JC, Griffith OW, Suzuki S, Renfree MB. Evolution of the short form of DNMT3A, DNMT3A2, occurred in the common ancestor of mammals. Genome Biol Evol 2022; 14:6615359. [PMID: 35749276 PMCID: PMC9254654 DOI: 10.1093/gbe/evac094] [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] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is found in marsupial and eutherian mammals, but not in monotremes. While the primary regulator of genomic imprinting in eutherians is differential DNA methylation between parental alleles, conserved imprinted genes in marsupials tend to lack DNA methylation at their promoters. DNA methylation at eutherian imprinted genes is mainly catalysed by a DNA methyltransferase (DNMT) enzyme, DNMT3A. There are two isoforms of eutherian DNMT3A: DNMT3A and DNMT3A2. DNMT3A2 is the primary isoform for establishing DNA methylation at eutherian imprinted genes and is essential for eutherian genomic imprinting. In this study, we investigated whether DNMT3A2 is also present in the two other mammalian lineages, marsupials and monotremes. We identified DNMT3A2 in both marsupials and monotremes, although imprinting has not been identified in monotremes. By analysing genomic sequences and transcriptome data across vertebrates, we concluded that the evolution of DNMT3A2 occurred in the common ancestor of mammals. In addition, DNMT3A/3A2 gene and protein expression during gametogenesis showed distinct sexual dimorphisms in a marsupial, the tammar wallaby, and this pattern coincided with the sex-specific DNA methylation reprogramming in this species as it does in mice. Our results show that DNMT3A2 is present in all mammalian groups and suggests that the basic DNMT3A/3A2-based DNA methylation mechanism is conserved at least in therian mammals.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Danielle Hickford
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jane C Fenelon
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Oliver W Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Shinshu University, Nagano, Japan
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
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21
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Swank S, Sanger TJ, Stuart YE. (Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss. Ecol Evol 2021; 11:15484-15497. [PMID: 34824770 PMCID: PMC8601893 DOI: 10.1002/ece3.8226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/31/2021] [Accepted: 09/21/2021] [Indexed: 01/16/2023] Open
Abstract
Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. The multiple routes to appendage reduction and loss suggest that adaptive loss of function phenotypes might arise routinely through changes in expression of key developmental genes.
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Affiliation(s)
- Samantha Swank
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Thomas J. Sanger
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Yoel E. Stuart
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
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22
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Weldon SA, Münsterberg AE. Somite development and regionalisation of the vertebral axial skeleton. Semin Cell Dev Biol 2021; 127:10-16. [PMID: 34690064 DOI: 10.1016/j.semcdb.2021.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/27/2021] [Accepted: 10/06/2021] [Indexed: 11/25/2022]
Abstract
A critical stage in the development of all vertebrate embryos is the generation of the body plan and its subsequent patterning and regionalisation along the main anterior-posterior axis. This includes the formation of the vertebral axial skeleton. Its organisation begins during early embryonic development with the periodic formation of paired blocks of mesoderm tissue called somites. Here, we review axial patterning of somites, with a focus on studies using amniote model systems - avian and mouse. We summarise the molecular and cellular mechanisms that generate paraxial mesoderm and review how the different anatomical regions of the vertebral column acquire their specific identity and thus shape the body plan. We also discuss the generation of organoids and embryo-like structures from embryonic stem cells, which provide insights regarding axis formation and promise to be useful for disease modelling.
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Affiliation(s)
- Shannon A Weldon
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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23
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Blasi F, Bruckmann C. MEIS1 in Hematopoiesis and Cancer. How MEIS1-PBX Interaction Can Be Used in Therapy. J Dev Biol 2021; 9:jdb9040044. [PMID: 34698191 PMCID: PMC8544432 DOI: 10.3390/jdb9040044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022] Open
Abstract
Recently MEIS1 emerged as a major determinant of the MLL-r leukemic phenotype. The latest and most efficient drugs effectively decrease the levels of MEIS1 in cancer cells. Together with an overview of the latest drugs developed to target MEIS1 in MLL-r leukemia, we review, in detail, the role of MEIS1 in embryonic and adult hematopoiesis and suggest how a more profound knowledge of MEIS1 biochemistry can be used to design potent and effective drugs against MLL-r leukemia. In addition, we present data showing that the interaction between MEIS1 and PBX1 can be blocked efficiently and might represent a new avenue in anti-MLL-r and anti-leukemic therapy.
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Abstract
The postnatal kidney is predominantly composed of nephron epithelia with the interstitial components representing a small proportion of the final organ, except in the diseased state. This is in stark contrast to the developing organ, which arises from the mesoderm and comprises an expansive stromal population with distinct regional gene expression. In many organs, the identity and ultimate function of an epithelium is tightly regulated by the surrounding stroma during development. However, although the presence of a renal stromal stem cell population has been demonstrated, the focus has been on understanding the process of nephrogenesis whereas the role of distinct stromal components during kidney morphogenesis is less clear. In this Review, we consider what is known about the role of the stroma of the developing kidney in nephrogenesis, where these cells come from as well as their heterogeneity, and reflect on how this information may improve human kidney organoid models.
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Affiliation(s)
- Sean B. Wilson
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Melissa H. Little
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3000, Australia
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25
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Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development. Nat Commun 2021; 12:5685. [PMID: 34584102 PMCID: PMC8479071 DOI: 10.1038/s41467-021-25935-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
Chromatin remodeling and genomic alterations impact spatio-temporal regulation of gene expression, which is central to embryonic development. The analysis of mouse and chicken limb development provides important insights into the morphoregulatory mechanisms, however little is known about the regulatory differences underlying their morphological divergence. Here, we identify the underlying shared and species-specific epigenomic and genomic variations. In mouse forelimb buds, we observe striking synchrony between the temporal dynamics of chromatin accessibility and gene expression, while their divergence in chicken wing buds uncovers species-specific regulatory heterochrony. In silico mapping of transcription factor binding sites and computational footprinting establishes the developmental time-restricted transcription factor-DNA interactions. Finally, the construction of target gene networks for HAND2 and GLI3 transcriptional regulators reveals both conserved and species-specific interactions. Our analysis reveals the impact of genome evolution on the regulatory interactions orchestrating vertebrate limb bud morphogenesis and provides a molecular framework for comparative Evo-Devo studies. The vertebrate limb bud is a paradigm to uncover the fundamental mechanisms that govern embryogenesis and evolutionary diversification. Here the authors compare mouse and chicken limb bud development to study the impact of genome evolution on conserved and divergent gene regulatory interactions.
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