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Wang X, Tang P, Yang K, Guo S, Tang Y, Zhang H, Wang Q. Regulation of bone homeostasis by traditional Chinese medicine active scaffolds and enhancement for the osteoporosis bone regeneration. JOURNAL OF ETHNOPHARMACOLOGY 2024; 329:118141. [PMID: 38570149 DOI: 10.1016/j.jep.2024.118141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/18/2024] [Accepted: 03/30/2024] [Indexed: 04/05/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The active ingredients of traditional Chinese medicine (TCM), such as naringin (NG), Eucommiol, isopsoralen, icariin, Astragalus polysaccharides, and chondroitin sulfate, contained in Drynariae Rhizoma, Eucommiae Cortex, Psoralea corylifolia, Herba Epimedii, Astragalus radix and deer antler, are considered promising candidates for enhancing the healing of osteoporotic defects due to their outstanding bone homeostasis regulating properties. They are commonly used to activate bone repair scaffolds. AIM OF THE REVIEW Bone repair scaffolds are inadequate to meet the demands of osteoporotic defect healing due to the lack of regulation of bone homeostasis. Therefore, selecting bone scaffolds activated with TCM to improve the therapeutic effect of repairing osteoporotic bone defects. MATERIALS AND METHODS To gather information on bone scaffold activated by traditional Chinese medicine, we conducted a thorough search of several scientific databases, including Google Scholar, Web of Science, Scifinder, Baidu Scholar, PubMed, and China National Knowledge Infrastructure (CNKI). RESULTS This review discusses the mechanism of TCM active ingredients in regulating bone homeostasis, including stimulating bone formation and inhibiting bone resorption process and the healing mechanism of traditional bone repair scaffolds activated by them for osteoporotic defect healing. CONCLUSION In general, the introduction of TCM active ingredients provides a novel therapeutic approach for modulating bone homeostasis and facilitating osteoporotic defect healing, and also offers a new strategy for design of other unconventional bone defect healing materials.
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Affiliation(s)
- Xi Wang
- School of Mechanical Engineering, Institute for Advanced Study, Chengdu University, Chengdu, 610106, China
| | - Pengfei Tang
- Failure Mechanics & Engineering Disaster Prevention and Mitigation, Key Laboratory of Sichuan Province, College of Architecture & Environment, Sichuan University, Chengdu, 610065, China
| | - Kun Yang
- School of Mechanical Engineering, Institute for Advanced Study, Chengdu University, Chengdu, 610106, China
| | - Shuangquan Guo
- Chengdu Holy (Group) Industry Co. Ltd., Chengdu, 610041, China
| | - Youhong Tang
- Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, South Australia 5042, Australia
| | - Hongping Zhang
- School of Mechanical Engineering, Institute for Advanced Study, Chengdu University, Chengdu, 610106, China.
| | - Qingyuan Wang
- School of Mechanical Engineering, Institute for Advanced Study, Chengdu University, Chengdu, 610106, China; Failure Mechanics & Engineering Disaster Prevention and Mitigation, Key Laboratory of Sichuan Province, College of Architecture & Environment, Sichuan University, Chengdu, 610065, China.
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2
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Brouze M, Czarnocka-Cieciura A, Gewartowska O, Kusio-Kobiałka M, Jachacy K, Szpila M, Tarkowski B, Gruchota J, Krawczyk P, Mroczek S, Borsuk E, Dziembowski A. TENT5-mediated polyadenylation of mRNAs encoding secreted proteins is essential for gametogenesis in mice. Nat Commun 2024; 15:5331. [PMID: 38909026 PMCID: PMC11193744 DOI: 10.1038/s41467-024-49479-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 05/31/2024] [Indexed: 06/24/2024] Open
Abstract
Cytoplasmic polyadenylation plays a vital role in gametogenesis; however, the participating enzymes and substrates in mammals remain unclear. Using knockout and knock-in mouse models, we describe the essential role of four TENT5 poly(A) polymerases in mouse fertility and gametogenesis. TENT5B and TENT5C play crucial yet redundant roles in oogenesis, with the double knockout of both genes leading to oocyte degeneration. Additionally, TENT5B-GFP knock-in females display a gain-of-function infertility effect, with multiple chromosomal aberrations in ovulated oocytes. TENT5C and TENT5D both regulate different stages of spermatogenesis, as shown by the sterility in males following the knockout of either gene. Finally, Tent5a knockout substantially lowers fertility, although the underlying mechanism is not directly related to gametogenesis. Through direct RNA sequencing, we discovered that TENT5s polyadenylate mRNAs encoding endoplasmic reticulum-targeted proteins essential for gametogenesis. Sequence motif analysis and reporter mRNA assays reveal that the presence of an endoplasmic reticulum-leader sequence represents the primary determinant of TENT5-mediated regulation.
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Affiliation(s)
- Michał Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | | | - Olga Gewartowska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Genome Engineering Facility, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Monika Kusio-Kobiałka
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Kamil Jachacy
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Marcin Szpila
- Genome Engineering Facility, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Laboratory of Embryology, Institute of Developmental Biology and Biomedical Research, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Bartosz Tarkowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Jakub Gruchota
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Paweł Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Ewa Borsuk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Laboratory of Embryology, Institute of Developmental Biology and Biomedical Research, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland.
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland.
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland.
- Laboratory of Embryology, Institute of Developmental Biology and Biomedical Research, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland.
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3
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Lai G, De Grossi F, Catusi I, Pesce E, Manfrini N. Dissecting the Puzzling Roles of FAM46C: A Multifaceted Pan-Cancer Tumour Suppressor with Increasing Clinical Relevance. Cancers (Basel) 2024; 16:1706. [PMID: 38730656 PMCID: PMC11083040 DOI: 10.3390/cancers16091706] [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: 03/22/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
FAM46C is a well-established tumour suppressor with a role that is not completely defined or universally accepted. Although FAM46C expression is down-modulated in several tumours, significant mutations in the FAM46C gene are only found in multiple myeloma (MM). Consequently, its tumour suppressor activity has primarily been studied in the MM context. However, emerging evidence suggests that FAM46C is involved also in other cancer types, namely colorectal, prostate and gastric cancer and squamous cell and hepatocellular carcinoma, where FAM46C expression was found to be significantly reduced in tumoural versus non-tumoural tissues and where FAM46C was shown to possess anti-proliferative properties. Accordingly, FAM46C was recently proposed to function as a pan-cancer prognostic marker, bringing FAM46C under the spotlight and attracting growing interest from the scientific community in the pathways modulated by FAM46C and in its mechanistic activity. Here, we will provide the first comprehensive review regarding FAM46C by covering (1) the intracellular pathways regulated by FAM46C, namely the MAPK/ERK, PI3K/AKT, β-catenin and TGF-β/SMAD pathways; (2) the models regarding its mode of action, specifically the poly(A) polymerase, intracellular trafficking modulator and inhibitor of centriole duplication models, focusing on connections and interdependencies; (3) the regulation of FAM46C expression in different environments by interferons, IL-4, TLR engagement or transcriptional modulators; and, lastly, (4) how FAM46C expression levels associate with increased/decreased tumour cell sensitivity to anticancer agents, such as bortezomib, dexamethasone, lenalidomide, pomalidomide, doxorubicin, melphalan, SK1-I, docetaxel and norcantharidin.
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Affiliation(s)
- Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Federica De Grossi
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Ilaria Catusi
- SC Clinical Pathology, SS Medical Genetics Laboratory, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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4
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Spoutil F, Dlugosova S, Varga I, Aranaz-Novaliches G, Novosadova V, Prochazkova M, Sedlacek R, Prochazka J. Semi-Automated MicroCT Analysis of Bone Anatomy and Mineralization in Mouse Models. Curr Protoc 2024; 4:e980. [PMID: 38385868 DOI: 10.1002/cpz1.980] [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: 02/23/2024]
Abstract
The skeletal system mirrors several processes in the vertebrate body that impact developmental malfunctions, hormonal disbalance, malfunction of calcium metabolism and turn over, and inflammation processes such as arthrosis. X-ray micro computed tomography is a useful tool for 3D in situ evaluation of the skeletal system in a time-related manner, but results depend highly on resolution. Here, we provide the methodological background for a graduated evaluation from whole-body analysis of skeletal morphology and mineralization to high-resolution analysis of femoral and vertebral microstructure. We combine an expert-based evaluation with a machine-learning-based computational approach, including pre-setup analytical task lists. © 2024 Wiley Periodicals LLC. Basic Protocol 1: In vivo microCT scanning and skeletal analysis in mice Basic Protocol 2: Ex vivo high-resolution microCT scanning and microstructural analysis of the femur and L4 vertebra.
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Affiliation(s)
- Frantisek Spoutil
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sylvie Dlugosova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Igor Varga
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cybernetics, Czech Technical University in Prague, Prague, Czech Republic
| | - Goretti Aranaz-Novaliches
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michaela Prochazkova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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5
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Rogers JD, Leusch FD, Chambers B, Daniels KD, Everett LJ, Judson R, Maruya K, Mehinto AC, Neale PA, Paul-Friedman K, Thomas R, Snyder SA, Harrill J. High-Throughput Transcriptomics of Water Extracts Detects Reductions in Biological Activity with Water Treatment Processes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2027-2037. [PMID: 38235672 PMCID: PMC11003563 DOI: 10.1021/acs.est.3c07525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The presence of numerous chemical contaminants from industrial, agricultural, and pharmaceutical sources in water supplies poses a potential risk to human and ecological health. Current chemical analyses suffer from limitations, including chemical coverage and high cost, and broad-coverage in vitro assays such as transcriptomics may further improve water quality monitoring by assessing a large range of possible effects. Here, we used high-throughput transcriptomics to assess the activity induced by field-derived water extracts in MCF7 breast carcinoma cells. Wastewater and surface water extracts induced the largest changes in expression among cell proliferation-related genes and neurological, estrogenic, and antibiotic pathways, whereas drinking and reclaimed water extracts that underwent advanced treatment showed substantially reduced bioactivity on both gene and pathway levels. Importantly, reclaimed water extracts induced fewer changes in gene expression than laboratory blanks, which reinforces previous conclusions based on targeted assays and improves confidence in bioassay-based monitoring of water quality.
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Affiliation(s)
- Jesse D. Rogers
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
| | - Frederic D.L. Leusch
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport Qld 4222, Australia
| | - Bryant Chambers
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | | | - Logan J. Everett
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Richard Judson
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Keith Maruya
- Southern California Coastal Water Research Project Authority, 3535 Harbor Boulevard, Suite 110, Costa Mesa, CA 92626, USA
| | - Alvine C. Mehinto
- Southern California Coastal Water Research Project Authority, 3535 Harbor Boulevard, Suite 110, Costa Mesa, CA 92626, USA
| | - Peta A. Neale
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport Qld 4222, Australia
| | - Katie Paul-Friedman
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Russell Thomas
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Shane A. Snyder
- Nanyang Environment & Water Research Institute (NEWRI), Nanyang Technological University, 1 Cleantech Loop, CleanTech One, #06-08, 637141, Singapore
| | - Joshua Harrill
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
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6
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Krawczyk PS, Tudek A, Mroczek S, Dziembowski A. Transcriptome-Wide Analysis of mRNA Adenylation Status in Yeast Using Nanopore Sequencing. Methods Mol Biol 2024; 2723:193-214. [PMID: 37824072 DOI: 10.1007/978-1-0716-3481-3_12] [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: 10/13/2023]
Abstract
There are multiple methods for studying deadenylation, either in vitro or in vivo, which allow for observation of mRNA abundance or poly(A) tail dynamics. However, direct RNA sequencing using the Oxford Nanopore Technologies (ONT) platform makes it possible to conduct transcriptome-wide analyses at the single-molecule level without the PCR bias introduced by other methods. In this chapter, we provide a protocol to measure both RNA levels and poly(A)-tail lengths in the yeast Saccharomyces cerevisiae using ONT.
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Affiliation(s)
- Pawel S Krawczyk
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Seweryn Mroczek
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- International Institute of Molecular and Cell Biology, Warsaw, Poland.
- Faculty of Biology, University of Warsaw, Warsaw, Poland.
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7
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Nethander M, Movérare-Skrtic S, Kämpe A, Coward E, Reimann E, Grahnemo L, Borbély É, Helyes Z, Funck-Brentano T, Cohen-Solal M, Tuukkanen J, Koskela A, Wu J, Li L, Lu T, Gabrielsen ME, Mägi R, Hoff M, Lerner UH, Henning P, Ullum H, Erikstrup C, Brunak S, Langhammer A, Tuomi T, Oddsson A, Stefansson K, Pettersson-Kymmer U, Ostrowski SR, Pedersen OBV, Styrkarsdottir U, Mäkitie O, Hveem K, Richards JB, Ohlsson C. An atlas of genetic determinants of forearm fracture. Nat Genet 2023; 55:1820-1830. [PMID: 37919453 PMCID: PMC10632131 DOI: 10.1038/s41588-023-01527-3] [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: 01/27/2023] [Accepted: 09/13/2023] [Indexed: 11/04/2023]
Abstract
Osteoporotic fracture is among the most common and costly of diseases. While reasonably heritable, its genetic determinants have remained elusive. Forearm fractures are the most common clinically recognized osteoporotic fractures with a relatively high heritability. To establish an atlas of the genetic determinants of forearm fractures, we performed genome-wide association analyses including 100,026 forearm fracture cases. We identified 43 loci, including 26 new fracture loci. Although most fracture loci associated with bone mineral density, we also identified loci that primarily regulate bone quality parameters. Functional studies of one such locus, at TAC4, revealed that Tac4-/- mice have reduced mechanical bone strength. The strongest forearm fracture signal, at WNT16, displayed remarkable bone-site-specificity with no association with hip fractures. Tall stature and low body mass index were identified as new causal risk factors for fractures. The insights from this atlas may improve fracture prediction and enable therapeutic development to prevent fractures.
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Grants
- Wellcome Trust
- IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)
- Novo Nordisk Fonden (Novo Nordisk Foundation)
- Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)
- the Swedish state under the agreement between the Swedish government and the county councils, the ALF-agreement (ALFGBG-720331 and ALFGBG-965235)
- the Hungarian Brain research Program 3.0, Hungarian National Research, Development and Innovation Office (OTKA K- 138046, OTKA FK-137951, TKP2021-EGA-16), New National Excellence Program of the Ministry for Innovation and Technology (ÚNKP-22-5-PTE-1447), János Bolyai János Scholarship (BO/00496/21/5) of the Hungarian Academy of Sciences, Eotvos Lorad Research Network, National Laboratory for Drug Research and Development.
- Vetenskapsrådet (Swedish Research Council)
- Svenska Läkaresällskapet (Swedish Society of Medicine)
- Kempestiftelserna (Kempe Foundations)
- the Swedish Sports Research Council (87/06) the Medical Faculty of Umeå University (ALFVLL:968:22-2005, ALFVLL: 937-2006, ALFVLL:223:11-2007, ALFVLL:78151-2009) the county council of Västerbotten (Spjutspetsanslag VLL:159:33-2007)
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Affiliation(s)
- Maria Nethander
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sofia Movérare-Skrtic
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Kämpe
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Eivind Coward
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ene Reimann
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Louise Grahnemo
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Éva Borbély
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
- Eotvos Lorand Research Network, Chronic Pain Research Group, University of Pécs, Pécs, Hungary
| | - Thomas Funck-Brentano
- BIOSCAR UMRS 1132, Université Paris Diderot, Sorbonne Paris Cité, INSERM, Paris, France
| | - Martine Cohen-Solal
- BIOSCAR UMRS 1132, Université Paris Diderot, Sorbonne Paris Cité, INSERM, Paris, France
| | - Juha Tuukkanen
- Department of Anatomy and Cell Biology, Faculty of Medicine, Institute of Cancer Research and Translational Medicine, University of Oulu, Oulu, Finland
| | - Antti Koskela
- Department of Anatomy and Cell Biology, Faculty of Medicine, Institute of Cancer Research and Translational Medicine, University of Oulu, Oulu, Finland
| | - Jianyao Wu
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lei Li
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mari Hoff
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Rheumatology, St Olavs Hospital, Trondheim, Norway
| | - Ulf H Lerner
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Petra Henning
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
- Department of Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Kari Stefansson
- deCODE genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Sisse Rye Ostrowski
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen Hospital Biobank Unit, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Ole Birger Vesterager Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Koege, Denmark
| | | | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Children's Hospital and Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, and Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Drug Treatment, Gothenburg, Sweden.
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8
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Devos H, Zoidakis J, Roubelakis MG, Latosinska A, Vlahou A. Reviewing the Regulators of COL1A1. Int J Mol Sci 2023; 24:10004. [PMID: 37373151 DOI: 10.3390/ijms241210004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/28/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The collagen family contains 28 proteins, predominantly expressed in the extracellular matrix (ECM) and characterized by a triple-helix structure. Collagens undergo several maturation steps, including post-translational modifications (PTMs) and cross-linking. These proteins are associated with multiple diseases, the most pronounced of which are fibrosis and bone diseases. This review focuses on the most abundant ECM protein highly implicated in disease, type I collagen (collagen I), in particular on its predominant chain collagen type I alpha 1 (COLα1 (I)). An overview of the regulators of COLα1 (I) and COLα1 (I) interactors is presented. Manuscripts were retrieved searching PubMed, using specific keywords related to COLα1 (I). COL1A1 regulators at the epigenetic, transcriptional, post-transcriptional and post-translational levels include DNA Methyl Transferases (DNMTs), Tumour Growth Factor β (TGFβ), Terminal Nucleotidyltransferase 5A (TENT5A) and Bone Morphogenic Protein 1 (BMP1), respectively. COLα1 (I) interacts with a variety of cell receptors including integrinβ, Endo180 and Discoidin Domain Receptors (DDRs). Collectively, even though multiple factors have been identified in association to COLα1 (I) function, the implicated pathways frequently remain unclear, underscoring the need for a more spherical analysis considering all molecular levels simultaneously.
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Affiliation(s)
- Hanne Devos
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Jerome Zoidakis
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Maria G Roubelakis
- Laboratory of Biology, University of Athens School of Medicine, 11527 Athens, Greece
- Laboratory of Cell and Gene Therapy, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | | | - Antonia Vlahou
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
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9
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Bina M. Defining Candidate Imprinted loci in Bos taurus. Genes (Basel) 2023; 14:1036. [PMID: 37239396 PMCID: PMC10217866 DOI: 10.3390/genes14051036] [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: 03/31/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Using a whole-genome assembly of Bos taurus, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: CNNM1 and CNR1. I also give examples of candidate ICRs in loci that influence muscle development: SIX1 and BCL6. By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the SIX1 promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of BCL6 locus to regulatory proteins in mouse ESCs and examined tissues.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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10
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Liu S, Chen H, Yin Y, Lu D, Gao G, Li J, Bai XC, Zhang X. Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold. SCIENCE ADVANCES 2023; 9:eadf5583. [PMID: 37018411 PMCID: PMC10075960 DOI: 10.1126/sciadv.adf5583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPβ, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPβ. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The β sheets in BCCIPα and FAM46 pack side by side to form an extended β sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46.
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Affiliation(s)
- Shun Liu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Yin
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guoming Gao
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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11
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3D osteogenic differentiation of human iPSCs reveals the role of TGFβ signal in the transition from progenitors to osteoblasts and osteoblasts to osteocytes. Sci Rep 2023; 13:1094. [PMID: 36658197 PMCID: PMC9852429 DOI: 10.1038/s41598-023-27556-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Although the formation of bone-like nodules is regarded as the differentiation process from stem cells to osteogenic cells, including osteoblasts and osteocytes, the precise biological events during nodule formation are unknown. Here we performed the osteogenic induction of human induced pluripotent stem cells using a three-dimensional (3D) culture system using type I collagen gel and a rapid induction method with retinoic acid. Confocal and time-lapse imaging revealed the osteogenic differentiation was initiated with vigorous focal proliferation followed by aggregation, from which cells invaded the gel. Invading cells changed their morphology and expressed osteocyte marker genes, suggesting the transition from osteoblasts to osteocytes. Single-cell RNA sequencing analysis revealed that 3D culture-induced cells with features of periosteal skeletal stem cells, some of which expressed TGFβ-regulated osteoblast-related molecules. The role of TGFβ signal was further analyzed in the transition from osteoblasts to osteocytes, which revealed that modulation of the TGFβ signal changed the morphology and motility of cells isolated from the 3D culture, suggesting that the TGFβ signal maintains the osteoblastic phenotype and the transition into osteocytes requires down-regulation of the TGFβ signal.
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12
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Brouze A, Krawczyk PS, Dziembowski A, Mroczek S. Measuring the tail: Methods for poly(A) tail profiling. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1737. [PMID: 35617484 PMCID: PMC10078590 DOI: 10.1002/wrna.1737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/31/2023]
Abstract
The 3'-end poly(A) tail is an important and potent feature of most mRNA molecules that affects mRNA fate and translation efficiency. Polyadenylation is a posttranscriptional process that occurs in the nucleus by canonical poly(A) polymerases (PAPs). In some specific instances, the poly(A) tail can also be extended in the cytoplasm by noncanonical poly(A) polymerases (ncPAPs). This epitranscriptomic regulation of mRNA recently became one of the most interesting aspects in the field. Advances in RNA sequencing technologies and software development have allowed the precise measurement of poly(A) tails, identification of new ncPAPs, expansion of the function of known enzymes, discovery and a better understanding of the physiological role of tail heterogeneity, and recognition of a correlation between tail length and RNA translatability. Here, we summarize the development of polyadenylation research methods, including classic low-throughput approaches, Illumina-based genome-wide analysis, and advanced state-of-art techniques that utilize long-read third-generation sequencing with Pacific Biosciences and Oxford Nanopore Technologies platforms. A boost in technical opportunities over recent decades has allowed a better understanding of the regulation of gene expression at the mRNA level. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Aleksandra Brouze
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Szczepan Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Seweryn Mroczek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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13
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Alcorta-Sevillano N, Infante A, Macías I, Rodríguez CI. Murine Animal Models in Osteogenesis Imperfecta: The Quest for Improving the Quality of Life. Int J Mol Sci 2022; 24:ijms24010184. [PMID: 36613624 PMCID: PMC9820162 DOI: 10.3390/ijms24010184] [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: 11/24/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Osteogenesis imperfecta is a rare genetic disorder characterized by bone fragility, due to alterations in the type I collagen molecule. It is a very heterogeneous disease, both genetically and phenotypically, with a high variability of clinical phenotypes, ranging from mild to severe forms, the most extreme cases being perinatal lethal. There is no curative treatment for OI, and so great efforts are being made in order to develop effective therapies. In these attempts, the in vivo preclinical studies are of paramount importance; therefore, serious analysis is required to choose the right murine OI model able to emulate as closely as possible the disease of the target OI population. In this review, we summarize the features of OI murine models that have been used for preclinical studies until today, together with recently developed new murine models. The bone parameters that are usually evaluated in order to determine the relevance of new developing therapies are exposed, and finally, current and innovative therapeutic strategies attempts considered in murine OI models, along with their mechanism of action, are reviewed. This review aims to summarize the in vivo studies developed in murine models available in the field of OI to date, in order to help the scientific community choose the most accurate OI murine model when developing new therapeutic strategies capable of improving the quality of life.
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Affiliation(s)
- Natividad Alcorta-Sevillano
- Stem Cells and Cell Therapy Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Plaza de Cruces S/N, 48903 Barakaldo, Spain
- Department of Cell Biology and Histology, University of Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Arantza Infante
- Stem Cells and Cell Therapy Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Plaza de Cruces S/N, 48903 Barakaldo, Spain
| | - Iratxe Macías
- Stem Cells and Cell Therapy Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Plaza de Cruces S/N, 48903 Barakaldo, Spain
| | - Clara I. Rodríguez
- Stem Cells and Cell Therapy Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Plaza de Cruces S/N, 48903 Barakaldo, Spain
- Correspondence:
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14
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Nadimpalli HP, Guitart T, Coll O, Gebauer F. Ataxin-2, Twenty-four, and Dicer-2 are components of a noncanonical cytoplasmic polyadenylation complex. Life Sci Alliance 2022; 5:5/12/e202201417. [PMID: 36114004 PMCID: PMC9481931 DOI: 10.26508/lsa.202201417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022] Open
Abstract
Identification of components of a noncanonical cytoplasmic polyadenylation machinery in Drosophila expands the diversity of RNA-binding proteins involved in poly(A) tail length control. Cytoplasmic polyadenylation is a mechanism to promote mRNA translation in a wide variety of biological contexts. A canonical complex centered around the conserved RNA-binding protein family CPEB has been shown to be responsible for this process. We have previously reported evidence for an alternative noncanonical, CPEB-independent complex in Drosophila, of which the RNA-interference factor Dicer-2 is a component. Here, we investigate Dicer-2 mRNA targets and protein cofactors in cytoplasmic polyadenylation. Using RIP-Seq analysis, we identify hundreds of potential Dicer-2 target transcripts, ∼60% of which were previously found as targets of the cytoplasmic poly(A) polymerase Wispy, suggesting widespread roles of Dicer-2 in cytoplasmic polyadenylation. Large-scale immunoprecipitation revealed Ataxin-2 and Twenty-four among the high-confidence interactors of Dicer-2. Complex analyses indicated that both factors form an RNA-independent complex with Dicer-2 and mediate interactions of Dicer-2 with Wispy. Functional poly(A)-test analyses showed that Twenty-four and Ataxin-2 are required for cytoplasmic polyadenylation of a subset of Dicer-2 targets. Our results reveal components of a novel cytoplasmic polyadenylation complex that operates during Drosophila early embryogenesis.
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Affiliation(s)
- Hima Priyanka Nadimpalli
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Olga Coll
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- University of Pompeu Fabra (UPF), Barcelona, Spain
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15
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Liudkovska V, Krawczyk PS, Brouze A, Gumińska N, Wegierski T, Cysewski D, Mackiewicz Z, Ewbank JJ, Drabikowski K, Mroczek S, Dziembowski A. TENT5 cytoplasmic noncanonical poly(A) polymerases regulate the innate immune response in animals. SCIENCE ADVANCES 2022; 8:eadd9468. [PMID: 36383655 PMCID: PMC9668313 DOI: 10.1126/sciadv.add9468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Innate immunity is the first line of host defense against pathogens. Here, through global transcriptome and proteome analyses, we uncover that newly described cytoplasmic poly(A) polymerase TENT-5 (terminal nucleotidyltransferase 5) enhances the expression of secreted innate immunity effector proteins in Caenorhabditis elegans. Direct RNA sequencing revealed that multiple mRNAs with signal peptide-encoding sequences have shorter poly(A) tails in tent-5-deficient worms. Those mRNAs are translated at the endoplasmic reticulum where a fraction of TENT-5 is present, implying that they represent its direct substrates. Loss of tent-5 makes worms more susceptible to bacterial infection. Notably, the role of TENT-5 in innate immunity is evolutionarily conserved. Its orthologs, TENT5A and TENT5C, are expressed in macrophages and induced during their activation. Analysis of macrophages devoid of TENT5A/C revealed their role in the regulation of secreted proteins involved in defense response. In summary, our study reveals cytoplasmic polyadenylation to be a previously unknown component of the posttranscriptional regulation of innate immunity in animals.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aleksandra Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Natalia Gumińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz Wegierski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Zuzanna Mackiewicz
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jonathan J Ewbank
- Aix Marseille University, INSERM, CNRS, CIML, Turing Centre for Living Systems, Marseille, France
| | - Krzysztof Drabikowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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16
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Matsumura T, Totani H, Gunji Y, Fukuda M, Yokomori R, Deng J, Rethnam M, Yang C, Tan TK, Karasawa T, Kario K, Takahashi M, Osato M, Sanda T, Suda T. A Myb enhancer-guided analysis of basophil and mast cell differentiation. Nat Commun 2022; 13:7064. [PMID: 36400777 PMCID: PMC9674656 DOI: 10.1038/s41467-022-34906-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
The transcription factor MYB is a crucial regulator of hematopoietic stem and progenitor cells. However, the nature of lineage-specific enhancer usage of the Myb gene is largely unknown. We identify the Myb -68 enhancer, a regulatory element which marks basophils and mast cells. Using the Myb -68 enhancer activity, we show a population of granulocyte-macrophage progenitors with higher potential to differentiate into basophils and mast cells. Single cell RNA-seq demonstrates the differentiation trajectory is continuous from progenitors to mature basophils in vivo, characterizes bone marrow cells with a gene signature of mast cells, and identifies LILRB4 as a surface marker of basophil maturation. Together, our study leads to a better understanding of how MYB expression is regulated in a lineage-associated manner, and also shows how a combination of lineage-related reporter mice and single-cell transcriptomics can overcome the rarity of target cells and enhance our understanding of gene expression programs that control cell differentiation in vivo.
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Affiliation(s)
- Takayoshi Matsumura
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan ,grid.410804.90000000123090000Division of Cardiovascular Medicine, Department of Medicine, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Haruhito Totani
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yoshitaka Gunji
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Masahiro Fukuda
- grid.428397.30000 0004 0385 0924Signature Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore ,grid.274841.c0000 0001 0660 6749International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Rui Yokomori
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jianwen Deng
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Malini Rethnam
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chong Yang
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tze King Tan
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tadayoshi Karasawa
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Kazuomi Kario
- grid.410804.90000000123090000Division of Cardiovascular Medicine, Department of Medicine, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Masafumi Takahashi
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Motomi Osato
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Takaomi Sanda
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Toshio Suda
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.274841.c0000 0001 0660 6749International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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17
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Luo M, Yang H, Wu D, You X, Huang S, Song Y. Tent5a modulates muscle fiber formation in adolescent idiopathic scoliosis via maintenance of myogenin expression. Cell Prolif 2022; 55:e13183. [PMID: 35137485 PMCID: PMC8891553 DOI: 10.1111/cpr.13183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/04/2021] [Accepted: 01/02/2022] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Paravertebral muscle asymmetry may be involved in the pathogenesis of adolescent idiopathic scoliosis (AIS), and the Tent5a protein was recently identified as a novel active noncanonical poly(A) polymerase. We, therefore, explored the function of the AIS susceptibility gene Tent5a in myoblasts. MATERIALS AND METHODS RNA-seq of AIS paravertebral muscle was performed, and the molecular differences in paravertebral muscle were investigated. Twenty-four AIS susceptibility genes were screened, and differential expression of Tent5a in paravertebral muscles was confirmed with qPCR and Western blot. After the knockdown of Tent5a, the functional effects of Tent5a on C2C12 cell proliferation, migration, and apoptosis were detected by Cell Counting Kit-8 assay, wound-healing assay, and TUNEL assay, respectively. Myogenic differentiation markers were tested with immunofluorescence and qPCR in vitro, and muscle fiber formation was compared in vivo. RESULTS The AIS susceptibility gene Tent5a was differentially expressed in AIS paravertebral muscles. Tent5a knockdown inhibited the proliferation and migration of C2C12 cells and inhibited the maturation of type I muscle fibers in vitro and in vivo. Mechanistically, the expression of myogenin was decreased along with the suppression of Tent5a. CONCLUSIONS Tent5a plays an important role in the proliferation and migration of myoblasts, and it regulates muscle fiber maturation by maintaining the stability of myogenin. Tent5a may be involved in the pathogenesis of AIS by regulating the formation of muscle fiber type I.
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Affiliation(s)
- Ming Luo
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China.,Department of Orthopedics, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Huiliang Yang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Diwei Wu
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Xuanhe You
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Shishu Huang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Yueming Song
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
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18
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Mukamel RE, Handsaker RE, Sherman MA, Barton AR, Zheng Y, McCarroll SA, Loh PR. Protein-coding repeat polymorphisms strongly shape diverse human phenotypes. Science 2021; 373:1499-1505. [PMID: 34554798 PMCID: PMC8549062 DOI: 10.1126/science.abg8289] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Many human proteins contain domains that vary in size or copy number because of variable numbers of tandem repeats (VNTRs) in protein-coding exons. However, the relationships of VNTRs to most phenotypes are unknown because of difficulties in measuring such repetitive elements. We developed methods to estimate VNTR lengths from whole-exome sequencing data and impute VNTR alleles into single-nucleotide polymorphism haplotypes. Analyzing 118 protein-altering VNTRs in 415,280 UK Biobank participants for association with 786 phenotypes identified some of the strongest associations of common variants with human phenotypes, including height, hair morphology, and biomarkers of health. Accounting for large-effect VNTRs further enabled fine-mapping of associations to many more protein-coding mutations in the same genes. These results point to cryptic effects of highly polymorphic common structural variants that have eluded molecular analyses to date.
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Affiliation(s)
- Ronen E Mukamel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maxwell A Sherman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Boston, MA, USA
| | - Alison R Barton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Bioinformatics and Integrative Genomics Program, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yiming Zheng
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Boston, MA, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
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19
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Marini F, Giusti F, Iantomasi T, Brandi ML. Congenital Metabolic Bone Disorders as a Cause of Bone Fragility. Int J Mol Sci 2021; 22:10281. [PMID: 34638624 PMCID: PMC8509040 DOI: 10.3390/ijms221910281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Bone fragility is a pathological condition caused by altered homeostasis of the mineralized bone mass with deterioration of the microarchitecture of the bone tissue, which results in a reduction of bone strength and an increased risk of fracture, even in the absence of high-impact trauma. The most common cause of bone fragility is primary osteoporosis in the elderly. However, bone fragility can manifest at any age, within the context of a wide spectrum of congenital rare bone metabolic diseases in which the inherited genetic defect alters correct bone modeling and remodeling at different points and aspects of bone synthesis and/or bone resorption, leading to defective bone tissue highly prone to long bone bowing, stress fractures and pseudofractures, and/or fragility fractures. To date, over 100 different Mendelian-inherited metabolic bone disorders have been identified and included in the OMIM database, associated with germinal heterozygote, compound heterozygote, or homozygote mutations, affecting over 80 different genes involved in the regulation of bone and mineral metabolism. This manuscript reviews clinical bone phenotypes, and the associated bone fragility in rare congenital metabolic bone disorders, following a disease taxonomic classification based on deranged bone metabolic activity.
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Affiliation(s)
- Francesca Marini
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50139 Florence, Italy; (F.M.); (F.G.); (T.I.)
- F.I.R.M.O. Fondazione Italiana per la Ricerca sulle Malattie dell’Osso, Italian Foundation for the Research on Bone Diseases, 50141 Florence, Italy
| | - Francesca Giusti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50139 Florence, Italy; (F.M.); (F.G.); (T.I.)
| | - Teresa Iantomasi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50139 Florence, Italy; (F.M.); (F.G.); (T.I.)
| | - Maria Luisa Brandi
- F.I.R.M.O. Fondazione Italiana per la Ricerca sulle Malattie dell’Osso, Italian Foundation for the Research on Bone Diseases, 50141 Florence, Italy
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