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Shukla C, Datta B. G-quadruplexes in long non-coding RNAs and their interactions with proteins. Int J Biol Macromol 2024; 278:134946. [PMID: 39187110 DOI: 10.1016/j.ijbiomac.2024.134946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as crucial regulators of cellular processes, with their dysregulation linked to various disease states. Among the structural motifs in lncRNAs, RNA G-quadruplexes (rG4s) have gained increasing attention due to their diverse roles in cellular function and disease pathogenesis. This review provides an updated and comprehensive overview of rG4s in lncRNAs, elucidating their formation, interaction with proteins, and distinctive roles in cellular processes. We discuss current methodologies for experimentally probing RNA G4s, including the use of specific small molecules, biomolecular ligands and fluorescent probes. The commonly found RNA G4-interacting protein domains are summarised along with potential strategies for disrupting lncRNA G4-protein interactions from a therapeutic perspective.
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Affiliation(s)
- Chinmayee Shukla
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India
| | - Bhaskar Datta
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India; Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India.
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2
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Zanti M, O'Mahony DG, Parsons MT, Dorling L, Dennis J, Boddicker NJ, Chen W, Hu C, Naven M, Yiangou K, Ahearn TU, Ambrosone CB, Andrulis IL, Antoniou AC, Auer PL, Baynes C, Bodelon C, Bogdanova NV, Bojesen SE, Bolla MK, Brantley KD, Camp NJ, Campbell A, Castelao JE, Cessna MH, Chang-Claude J, Chen F, Chenevix-Trench G, Conroy DM, Czene K, De Nicolo A, Domchek SM, Dörk T, Dunning AM, Eliassen AH, Evans DG, Fasching PA, Figueroa JD, Flyger H, Gago-Dominguez M, García-Closas M, Glendon G, González-Neira A, Grassmann F, Hadjisavvas A, Haiman CA, Hamann U, Hart SN, Hartman MBA, Ho WK, Hodge JM, Hoppe R, Howell SJ, Jakubowska A, Khusnutdinova EK, Ko YD, Kraft P, Kristensen VN, Lacey JV, Li J, Lim GH, Lindström S, Lophatananon A, Luccarini C, Mannermaa A, Martinez ME, Mavroudis D, Milne RL, Muir K, Nathanson KL, Nuñez-Torres R, Obi N, Olson JE, Palmer JR, Panayiotidis MI, Patel AV, Pharoah PDP, Polley EC, Rashid MU, Ruddy KJ, Saloustros E, Sawyer EJ, Schmidt MK, Southey MC, Tan VKM, Teo SH, Teras LR, Torres D, Trentham-Dietz A, Truong T, Vachon CM, Wang Q, Weitzel JN, Yadav S, Yao S, Zirpoli GR, Cline MS, Devilee P, Tavtigian SV, Goldgar DE, Couch FJ, Easton DF, Spurdle AB, Michailidou K. Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.04.24313051. [PMID: 39281752 PMCID: PMC11398439 DOI: 10.1101/2024.09.04.24313051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
Clinical genetic testing identifies variants causal for hereditary cancer, information that is used for risk assessment and clinical management. Unfortunately, some variants identified are of uncertain clinical significance (VUS), complicating patient management. Case-control data is one evidence type used to classify VUS, and previous findings indicate that case-control likelihood ratios (LRs) outperform odds ratios for variant classification. As an initiative of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Analytical Working Group we analyzed germline sequencing data of BRCA1 and BRCA2 from 96,691 female breast cancer cases and 303,925 unaffected controls from three studies: the BRIDGES study of the Breast Cancer Association Consortium, the Cancer Risk Estimates Related to Susceptibility consortium, and the UK Biobank. We observed 11,227 BRCA1 and BRCA2 variants, with 6,921 being coding, covering 23.4% of BRCA1 and BRCA2 VUS in ClinVar and 19.2% of ClinVar curated (likely) benign or pathogenic variants. Case-control LR evidence was highly consistent with ClinVar assertions for (likely) benign or pathogenic variants; exhibiting 99.1% sensitivity and 95.4% specificity for BRCA1 and 92.2% sensitivity and 86.6% specificity for BRCA2. This approach provides case-control evidence for 785 unclassified variants, that can serve as a valuable element for clinical classification.
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Affiliation(s)
- Maria Zanti
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Denise G O'Mahony
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Michael T Parsons
- Public Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nicholas J Boddicker
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Wenan Chen
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Marc Naven
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kristia Yiangou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Institute, Buffalo, NY, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul L Auer
- Division of Biostatistics, Data Science Institute and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Clara Bodelon
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Natalia V Bogdanova
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kristen D Brantley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, UK
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS) Foundation, Complejo Hospitalario Universitario de Santiago, SERGAS, Vigo, Spain
| | - Melissa H Cessna
- Department of Pathology and Intermountatin Biorepository, Intermountain Health, Salt Lake City, UT, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fei Chen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Georgia Chenevix-Trench
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Don M Conroy
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Arcangela De Nicolo
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Manuela Gago-Dominguez
- Cancer Genetics and Epidemiology Group, Genomic Medicine Group, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Felix Grassmann
- Institute for Clinical Research, Health and Medical University, Potsdam, Germany
| | - Andreas Hadjisavvas
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steven N Hart
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mikael B A Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore City, Singapore
- Department of Surgery, National University Health System, Singapore City, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Weang-Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Selangor, Malaysia
| | - James M Hodge
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Sacha J Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Yon-Dschun Ko
- Department of Internal Medicine, Johanniter GmbH Bonn, Johanniter Krankenhaus, Bonn, Germany
| | - Peter Kraft
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Vessela N Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - James V Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Geok Hoon Lim
- Breast Department, KK Women's and Children's Hospital, Singapore City, Singapore
- Duke-NUS Medical School, Singapore City, Singapore
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Maria Elena Martinez
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Rocio Nuñez-Torres
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Nadia Obi
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute for Occupational and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Janet E Olson
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
- School of Medicine, Boston University, Boston, MA, USA
| | - Mihalis I Panayiotidis
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Paul D P Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Eric C Polley
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Muhammad U Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | | | - Emmanouil Saloustros
- Division of Oncology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Elinor J Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, King's College London, London, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Veronique Kiak-Mien Tan
- Duke-NUS Medical School, Singapore City, Singapore
- Department of Breast Surgery, Singapore General Hospital, Singapore City, Singapore
- Division of Surgery and Surgical Oncology, National Cancer Centre, Singapore City, Singapore
- SingHealth Duke-NUS Breast Centre, Singapore City, Singapore
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, UM Cancer Research Institute, Kuala Lumpur, Malaysia
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Amy Trentham-Dietz
- Carbone Cancer Center and Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Thérèse Truong
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | | | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Institute, Buffalo, NY, USA
| | - Gary R Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | | | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sean V Tavtigian
- Department of Oncological Services, University of Utah School of Medicine, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Amanda B Spurdle
- Public Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
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Boulgakoff L, Sturny R, Olejnickova V, Sedmera D, Kelly RG, Miquerol L. Participation of ventricular trabeculae in neonatal cardiac regeneration leads to ectopic recruitment of Purkinje-like cells. NATURE CARDIOVASCULAR RESEARCH 2024; 3:1140-1157. [PMID: 39198628 DOI: 10.1038/s44161-024-00530-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 07/30/2024] [Indexed: 09/01/2024]
Abstract
Unlike adult mammals, newborn mice can regenerate a functional heart after myocardial infarction; however, the precise origin of the newly formed cardiomyocytes and whether the distal part of the conduction system (the Purkinje fiber (PF) network) is properly formed in regenerated hearts remains unclear. PFs, as well as subendocardial contractile cardiomyocytes, are derived from trabeculae, transient myocardial ridges on the inner ventricular surface. Here, using connexin 40-driven genetic tracing, we uncover a substantial participation of the trabecular lineage in myocardial regeneration through dedifferentiation and proliferation. Concomitantly, regeneration disrupted PF network maturation, resulting in permanent PF hyperplasia and impaired ventricular conduction. Proliferation assays, genetic impairment of PF recruitment, lineage tracing and clonal analysis revealed that PF network hyperplasia results from excessive recruitment of PFs due to increased trabecular fate plasticity. These data indicate that PF network hyperplasia is a consequence of trabeculae participation in myocardial regeneration.
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Affiliation(s)
- Lucie Boulgakoff
- Aix-Marseille Université, CNRS UMR 7288, Developmental Biology Institute of Marseille, Marseille, France
| | - Rachel Sturny
- Aix-Marseille Université, CNRS UMR 7288, Developmental Biology Institute of Marseille, Marseille, France
| | - Veronika Olejnickova
- Charles University, First Faculty of Medicine, Institute of Anatomy, Prague, Czech Republic
| | - David Sedmera
- Charles University, First Faculty of Medicine, Institute of Anatomy, Prague, Czech Republic
| | - Robert G Kelly
- Aix-Marseille Université, CNRS UMR 7288, Developmental Biology Institute of Marseille, Marseille, France
| | - Lucile Miquerol
- Aix-Marseille Université, CNRS UMR 7288, Developmental Biology Institute of Marseille, Marseille, France.
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Chilton B, Roach RJ, Edwards PJB, Jameson GB, Hale TK, Filichev VV. Inverted strand polarity yields thermodynamically stable G-quadruplexes and prevents duplex formation within extended DNA. Chem Sci 2024:d3sc05432b. [PMID: 39246343 PMCID: PMC11376080 DOI: 10.1039/d3sc05432b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 08/26/2024] [Indexed: 09/10/2024] Open
Abstract
DNA G-quadruplexes (G4) formed in guanine-rich sequences play a key role in genome function and maintenance, interacting with multiple proteins. However, structural and functional studies of G4s within duplex DNA have been challenging because of the transient nature of G4s and thermodynamic preference of G-rich DNA to form duplexes with their complementary strand rather than G4s. To overcome these challenges, we have incorporated native nucleotides in G-rich sequences using commercially available inverted 3'-O-DMT-5'-O-phosphoramidites of native nucleosides, to give 3'-3' and 5'-5' linkages in the centre of the G-tract. Using circular dichroism and 1H nuclear magnetic resonance spectroscopies and native gel electrophoresis, we demonstrate that these polarity-inverted DNA sequences containing four telomeric repeats form G4s of parallel topology with one lateral or diagonal loop across the face of the quadruplex and two propeller loops across the edges of the quadruplex. These G4s were stable even in the presence of complementary C-rich DNA. As an example, G4 assemblies of inverted polarity were shown to bind to the hinge region of Heterochromatin Protein 1α (HP1α), a known G4-interacting domain. As such, internal polarity inversions in DNA provide a useful tool to control G4 topology while also disrupting the formation of other secondary structures, particularly the canonical duplex.
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Affiliation(s)
- Bruce Chilton
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Ruby J Roach
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Patrick J B Edwards
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Geoffrey B Jameson
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Tracy K Hale
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Vyacheslav V Filichev
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
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5
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Rachid Zaim S, Pebworth MP, McGrath I, Okada L, Weiss M, Reading J, Czartoski JL, Torgerson TR, McElrath MJ, Bumol TF, Skene PJ, Li XJ. MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts. Nat Commun 2024; 15:6828. [PMID: 39122670 PMCID: PMC11316085 DOI: 10.1038/s41467-024-50612-6] [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: 07/04/2023] [Accepted: 07/13/2024] [Indexed: 08/12/2024] Open
Abstract
Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) is being increasingly used to study gene regulation. However, major analytical gaps limit its utility in studying gene regulatory programs in complex diseases. In response, MOCHA (Model-based single cell Open CHromatin Analysis) presents major advances over existing analysis tools, including: 1) improving identification of sample-specific open chromatin, 2) statistical modeling of technical drop-out with zero-inflated methods, 3) mitigation of false positives in single cell analysis, 4) identification of alternative transcription-starting-site regulation, and 5) modules for inferring temporal gene regulatory networks from longitudinal data. These advances, in addition to open chromatin analyses, provide a robust framework after quality control and cell labeling to study gene regulatory programs in human disease. We benchmark MOCHA with four state-of-the-art tools to demonstrate its advances. We also construct cross-sectional and longitudinal gene regulatory networks, identifying potential mechanisms of COVID-19 response. MOCHA provides researchers with a robust analytical tool for functional genomic inference from scATAC-seq data.
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Affiliation(s)
| | | | | | - Lauren Okada
- Allen Institute for Immunology, Seattle, WA, USA
| | - Morgan Weiss
- Allen Institute for Immunology, Seattle, WA, USA
| | | | - Julie L Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Xiao-Jun Li
- Allen Institute for Immunology, Seattle, WA, USA.
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6
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Zhang X, Tseo Y, Bai Y, Chen F, Uhler C. Prediction of protein subcellular localization in single cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605178. [PMID: 39091825 PMCID: PMC11291118 DOI: 10.1101/2024.07.25.605178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The subcellular localization of a protein is important for its function and interaction with other molecules, and its mislocalization is linked to numerous diseases. While atlas-scale efforts have been made to profile protein localization across various cell lines, existing datasets only contain limited pairs of proteins and cell lines which do not cover all human proteins. We present a method that uses both protein sequences and cellular landmark images to perform P redictions of U nseen P roteins' S ubcellular localization ( PUPS ), which can generalize to both proteins and cell lines not used for model training. PUPS combines a protein language model and an image inpainting model to utilize both protein sequence and cellular images for protein localization prediction. The protein sequence input enables generalization to unseen proteins and the cellular image input enables cell type specific prediction that captures single-cell variability. PUPS' ability to generalize to unseen proteins and cell lines enables us to assess the variability in protein localization across cell lines as well as across single cells within a cell line and to identify the biological processes associated with the proteins that have variable localization. Experimental validation shows that PUPS can be used to predict protein localization in newly performed experiments outside of the Human Protein Atlas used for training. Collectively, PUPS utilizes both protein sequences and cellular images to predict protein localization in unseen proteins and cell lines with the ability to capture single-cell variability.
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Chen Q, Zhang JL, Yang JS, Jin Q, Yang J, Xue Q, Guang XF. Novel Diagnostic Biomarkers Related to Necroptosis and Immune Infiltration in Coronary Heart Disease. J Inflamm Res 2024; 17:4525-4548. [PMID: 39006493 PMCID: PMC11246668 DOI: 10.2147/jir.s457469] [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: 02/20/2024] [Accepted: 06/11/2024] [Indexed: 07/16/2024] Open
Abstract
Purpose Necroptosis, a monitored form of inflammatory cell death, contributes to coronary heart disease (CHD) progression. This study examined the potential of using necroptosis genes as diagnostic markers for CHD and sought to elucidate the underlying roles. Methods Through bioinformatic analysis of GSE20680 and GSE20681, we first identified the differentially expressed genes (DEGs) related to necroptosis in CHD. Hub genes were identified using least absolute shrinkage and selection operator (LASSO) regression and random forest analysis after studying immune infiltration and transcription factor-miRNA interaction networks according to the DEGs. Quantitative polymerase chain reaction and immunohistochemistry were used to further investigate hub gene expression in vivo, for which a diagnostic model was constructed and the predictive efficacy was validated. Finally, the CHD group was categorized into high- and low-score groups in accordance with the single-sample gene set enrichment analysis (ssGSEA) score of the necroptosis genes. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, GSEA, and further immune infiltration analyses were performed on the two groups to explore the possible roles of hub genes. Results Based on the results of the LASSO regression and random forest analyses, four genes were used to construct a diagnostic model to establish a nomogram. Additionally, an extensive analysis of all seventeen necroptosis genes revealed notable distinctions in expression between high-risk and low-risk groups. Evaluation of immune infiltration revealed that neutrophils, monocytes, B cells, and activated dendritic cells were highly distributed in the peripheral blood of patients with CHD. Specifically, the high CHD score group exhibited greater neutrophil and monocyte infiltration. Conversely, the high-score group showed lower infiltration of M0 and M2 macrophages, CD8+ T, plasma, and resting mast cells. Conclusion TLR3, MLKL, HMGB1, and NDRG2 may be prospective biomarkers for CHD diagnosis. These findings offer plausible explanations for the role of necroptosis in CHD progression through immune infiltration and inflammatory response.
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Affiliation(s)
- Qiu Chen
- Department of Cardiology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, People's Republic of China
| | - Ji-Lei Zhang
- Department of Cardiology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, People's Republic of China
| | - Jie-Shun Yang
- Department of Pathology, The Second Affiliated Hospital of Kunming Medical University, Kunming, People's Republic of China
| | - Qing Jin
- Department of Cardiology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, People's Republic of China
| | - Jun Yang
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, People's Republic of China
| | - Qiang Xue
- Department of Cardiology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, People's Republic of China
| | - Xue-Feng Guang
- Department of Cardiology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, People's Republic of China
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8
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Dobrzyn K, Kopij G, Kiezun M, Zaobidna E, Gudelska M, Zarzecka B, Paukszto L, Rak A, Smolinska N, Kaminski T. Visfatin (NAMPT) affects global gene expression in porcine anterior pituitary cells during the mid-luteal phase of the oestrous cycle. J Anim Sci Biotechnol 2024; 15:96. [PMID: 38978053 PMCID: PMC11232246 DOI: 10.1186/s40104-024-01054-z] [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: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND The pituitary belongs to the most important endocrine glands involved in regulating reproductive functions. The proper functioning of this gland ensures the undisturbed course of the oestrous cycle and affects the female's reproductive potential. It is believed that visfatin, a hormone belonging to the adipokine family, may regulate reproductive functions in response to the female's metabolic state. Herein we verified the hypothesis that suggests a modulatory effect of visfatin on the anterior pituitary transcriptome during the mid-luteal phase of the oestrous cycle. RESULTS RNA-seq analysis of the porcine anterior pituitary cells revealed changes in the expression of 202 genes (95 up-regulated and 107 down-regulated in the presence of visfatin, when compared to the non-treated controls), assigned to 318 gene ontology terms. We revealed changes in the frequency of alternative splicing events (235 cases), as well as long noncoding RNA expression (79 cases) in the presence of the adipokine. The identified genes were associated, among others, with reproductive system development, epithelial cell proliferation, positive regulation of cell development, gland morphogenesis and cell chemotaxis. CONCLUSIONS The obtained results indicate a modulatory influence of visfatin on the regulation of the porcine transcriptome and, in consequence, pituitary physiology during the mid-luteal phase of the oestrous cycle.
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Affiliation(s)
- Kamil Dobrzyn
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
| | - Grzegorz Kopij
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marta Kiezun
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Ewa Zaobidna
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marlena Gudelska
- School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Barbara Zarzecka
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Lukasz Paukszto
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Agnieszka Rak
- Institute of Zoology and Biomedical Research, Jagiellonian University, Krakow, Poland
| | - Nina Smolinska
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tadeusz Kaminski
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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9
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Schwarz JE, Mrčela A, Lahens NF, Li Y, Hsu CT, Grant G, Skarke C, Zhang SL, Sehgal A. Evidence for a role of human blood-borne factors in mediating age-associated changes in molecular circadian rhythms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.19.537477. [PMID: 37808824 PMCID: PMC10557775 DOI: 10.1101/2023.04.19.537477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Aging is associated with a number of physiologic changes including perturbed circadian rhythms; however, mechanisms by which rhythms are altered remain unknown. To test the idea that circulating factors mediate age-dependent changes in peripheral rhythms, we compared the ability of human serum from young and old individuals to synchronize circadian rhythms in culture. We collected blood from apparently healthy young (age 25-30) and old (age 70-76) individuals at 14:00 and used the serum to synchronize cultured fibroblasts. We found that young and old sera are equally competent at initiating robust ~24h oscillations of a luciferase reporter driven by clock gene promoter. However, cyclic gene expression is affected, such that young and old sera promote cycling of different sets of genes. Genes that lose rhythmicity with old serum entrainment are associated with oxidative phosphorylation and Alzheimer's Disease as identified by STRING and IPA analyses. Conversely, the expression of cycling genes associated with cholesterol biosynthesis increased in the cells entrained with old serum. Genes involved in the cell cycle and transcription/translation remain rhythmic in both conditions. We did not observe a global difference in the distribution of phase between groups, but found that peak expression of several clock-controlled genes (PER3, NR1D1, NR1D2, CRY1, CRY2, and TEF) lagged in the cells synchronized ex vivo with old serum. Taken together, these findings demonstrate that age-dependent blood-borne factors affect circadian rhythms in peripheral cells and have the potential to impact health and disease via maintaining or disrupting rhythms respectively.
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Affiliation(s)
- Jessica E. Schwarz
- Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Nicholas F. Lahens
- Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Yongjun Li
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Cynthia T. Hsu
- Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Gregory Grant
- Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Carsten Skarke
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Shirley L. Zhang
- Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Current Institution: Department of Cell Biology, Emory University School of Medicine; Atlanta, GA 30323, United States
| | - Amita Sehgal
- Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
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10
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Low ZS, Chua D, Cheng HS, Tee R, Tan WR, Ball C, Sahib NBE, Ng SS, Qu J, Liu Y, Hong H, Cai C, Rao NCL, Wee A, Muthiah MD, Bichler Z, Mickelson B, Kong MS, Tay VS, Yan Z, Chen J, Ng AS, Yip YS, Vos MIG, Tan NA, Lim DL, Lim DXE, Chittezhath M, Yaligar J, Verma SK, Poptani H, Guan XL, Velan SS, Ali Y, Li L, Tan NS, Wahli W. The LIDPAD Mouse Model Captures the Multisystem Interactions and Extrahepatic Complications in MASLD. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404326. [PMID: 38952069 DOI: 10.1002/advs.202404326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/22/2024] [Indexed: 07/03/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) represents an impending global health challenge. Current management strategies often face setbacks, emphasizing the need for preclinical models that faithfully mimic the human disease and its comorbidities. The liver disease progression aggravation diet (LIDPAD), a diet-induced murine model, extensively characterized under thermoneutral conditions and refined diets is introduced to ensure reproducibility and minimize species differences. LIDPAD recapitulates key phenotypic, genetic, and metabolic hallmarks of human MASLD, including multiorgan communications, and disease progression within 4 to 16 weeks. These findings reveal gut-liver dysregulation as an early event and compensatory pancreatic islet hyperplasia, underscoring the gut-pancreas axis in MASLD pathogenesis. A robust computational pipeline is also detailed for transcriptomic-guided disease staging, validated against multiple harmonized human hepatic transcriptomic datasets, thereby enabling comparative studies between human and mouse models. This approach underscores the remarkable similarity of the LIDPAD model to human MASLD. The LIDPAD model fidelity to human MASLD is further confirmed by its responsiveness to dietary interventions, with improvements in metabolic profiles, liver histopathology, hepatic transcriptomes, and gut microbial diversity. These results, alongside the closely aligned changing disease-associated molecular signatures between the human MASLD and LIDPAD model, affirm the model's relevance and potential for driving therapeutic development.
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Affiliation(s)
- Zun Siong Low
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Damien Chua
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Hong Sheng Cheng
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Rachel Tee
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Wei Ren Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Christopher Ball
- Metabolic Imaging Group, Institute of Bioengineering and Bioimaging, Agency for Science Technology and Research (A*STAR), 11 Biopolis Way, Singapore, 138667, Singapore
| | - Norliza Binte Esmail Sahib
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Ser Sue Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Jing Qu
- Department of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yingzi Liu
- Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Haiyu Hong
- Department of Otolaryngology Head and Neck Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Mei Hua East Road, Zhuhai, 519000, China
| | - Chaonong Cai
- Department of Otolaryngology Head and Neck Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Mei Hua East Road, Zhuhai, 519000, China
| | | | - Aileen Wee
- Department of Pathology, National University Hospital, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Mark Dhinesh Muthiah
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Division of Gastroenterology and Hepatology, Department of Medicine, National University Hospital, Singapore, 119074, Singapore
- National University Centre for Organ Transplantation, National University Health System, Singapore, 119074, Singapore
| | - Zoë Bichler
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | | | - Mei Suen Kong
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Vanessa Shiyun Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Zhuang Yan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Jiapeng Chen
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Aik Seng Ng
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Yun Sheng Yip
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Marcus Ivan Gerard Vos
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Nicole Ashley Tan
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Dao Liang Lim
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Debbie Xiu En Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Manesh Chittezhath
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Jadegoud Yaligar
- Metabolic Imaging Group, Institute of Bioengineering and Bioimaging, Agency for Science Technology and Research (A*STAR), 11 Biopolis Way, Singapore, 138667, Singapore
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Sanjay Kumar Verma
- Metabolic Imaging Group, Institute of Bioengineering and Bioimaging, Agency for Science Technology and Research (A*STAR), 11 Biopolis Way, Singapore, 138667, Singapore
| | - Harish Poptani
- Centre for Preclinical Imaging, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Sambasivam Sendhil Velan
- Metabolic Imaging Group, Institute of Bioengineering and Bioimaging, Agency for Science Technology and Research (A*STAR), 11 Biopolis Way, Singapore, 138667, Singapore
- Division of Gastroenterology and Hepatology, Department of Medicine, National University Hospital, Singapore, 119074, Singapore
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Yusuf Ali
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, 168751, Singapore
| | - Liang Li
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Walter Wahli
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
- Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Toxalim (Research Centre in Food Toxicology), 180 Chemin de Tournefeuille, Toulouse, 1331, France
- Center for Integrative Genomics, Université de Lausanne, Le Génopode, Lausanne, 1015, Switzerland
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11
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Zhang M, Sjöström M, Cui X, Foye A, Farh K, Shrestha R, Lundberg A, Dang HX, Li H, Febbo PG, Aggarwal R, Alumkal JJ, Small EJ, Maher CA, Feng FY, Quigley DA. Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression. Nat Cell Biol 2024; 26:1176-1186. [PMID: 38871824 DOI: 10.1038/s41556-024-01438-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/11/2024] [Indexed: 06/15/2024]
Abstract
Transcription factor (TF) proteins regulate gene activity by binding to regulatory regions, most importantly at gene promoters. Many genes have alternative promoters (APs) bound by distinct TFs. The role of differential TF activity at APs during tumour development is poorly understood. Here we show, using deep RNA sequencing in 274 biopsies of benign prostate tissue, localized prostate tumours and metastatic castration-resistant prostate cancer, that AP usage increases as tumours progress and APs are responsible for a disproportionate amount of tumour transcriptional activity. Expression of the androgen receptor (AR), the key driver of prostate tumour activity, is correlated with elevated AP usage. We identified AR, FOXA1 and MYC as potential drivers of AP activation. DNA methylation is a likely mechanism for AP activation during tumour progression and lineage plasticity. Our data suggest that prostate tumours activate APs to magnify the transcriptional impact of tumour drivers, including AR and MYC.
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Affiliation(s)
- Meng Zhang
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Xiekui Cui
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California at San Francisco, San Francisco, CA, USA
| | - Adam Foye
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | | | - Raunak Shrestha
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Arian Lundberg
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Bristol Myers Squibb, San Diego, CA, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | | | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California at San Francisco, San Francisco, CA, USA.
- Department of Epidemiology & Biostatistics, University of California at San Francisco, San Francisco, CA, USA.
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12
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Eirin A, Thaler R, Glasstetter LM, Xing L, Zhu XY, Osborne AC, Mondesir R, Bhagwate AV, Lerman A, van Wijnen AJ, Lerman LO. Obesity-driven mitochondrial dysfunction in human adipose tissue-derived mesenchymal stem/stromal cells involves epigenetic changes. Cell Death Dis 2024; 15:387. [PMID: 38824145 PMCID: PMC11144257 DOI: 10.1038/s41419-024-06774-8] [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: 08/30/2023] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
Obesity exacerbates tissue degeneration and compromises the integrity and reparative potential of mesenchymal stem/stromal cells (MSCs), but the underlying mechanisms have not been sufficiently elucidated. Mitochondria modulate the viability, plasticity, proliferative capacity, and differentiation potential of MSCs. We hypothesized that alterations in the 5-hydroxymethylcytosine (5hmC) profile of mitochondria-related genes may mediate obesity-driven dysfunction of human adipose-derived MSCs. MSCs were harvested from abdominal subcutaneous fat of obese and age/sex-matched non-obese subjects (n = 5 each). The 5hmC profile and expression of nuclear-encoded mitochondrial genes were examined by hydroxymethylated DNA immunoprecipitation sequencing (h MeDIP-seq) and mRNA-seq, respectively. MSC mitochondrial structure (electron microscopy) and function, metabolomics, proliferation, and neurogenic differentiation were evaluated in vitro, before and after epigenetic modulation. hMeDIP-seq identified 99 peaks of hyper-hydroxymethylation and 150 peaks of hypo-hydroxymethylation in nuclear-encoded mitochondrial genes from Obese- versus Non-obese-MSCs. Integrated hMeDIP-seq/mRNA-seq analysis identified a select group of overlapping (altered levels of both 5hmC and mRNA) nuclear-encoded mitochondrial genes involved in ATP production, redox activity, cell proliferation, migration, fatty acid metabolism, and neuronal development. Furthermore, Obese-MSCs exhibited decreased mitochondrial matrix density, membrane potential, and levels of fatty acid metabolites, increased superoxide production, and impaired neuronal differentiation, which improved with epigenetic modulation. Obesity elicits epigenetic changes in mitochondria-related genes in human adipose-derived MSCs, accompanied by structural and functional changes in their mitochondria and impaired fatty acid metabolism and neurogenic differentiation capacity. These observations may assist in developing novel therapies to preserve the potential of MSCs for tissue repair and regeneration in obese individuals.
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Grants
- AG062104 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- DK122734 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R56 DK129240 NIDDK NIH HHS
- DK129240 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 DK129240 NIDDK NIH HHS
- HL158691 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- DK120292 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
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Affiliation(s)
- Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Li Xing
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Department of Urology, The Affiliated Zhongda Hospital, Southeast University, Nanjing, China
| | - Xiang-Yang Zhu
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Andrew C Osborne
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ronscardy Mondesir
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Aditya V Bhagwate
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Amir Lerman
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Lilach O Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.
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13
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Stahr MN, Parada-Rojas C, Childs KL, Alfenas RF, Fernandes FM, Avila K, Quesada-Ocampo LM. Long-Read Sequencing Genome Assembly of Ceratocystis fimbriata Enables Development of Molecular Diagnostics for Sweetpotato Black Rot. PHYTOPATHOLOGY 2024; 114:1411-1420. [PMID: 38264989 DOI: 10.1094/phyto-09-23-0341-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Ceratocystis fimbriata is a destructive fungal pathogen of sweetpotato (Ipomoea batatas) that leads to losses at all stages of sweetpotato production. Accurate detection of C. fimbriata would allow for more efficient deployment of management tactics in sweetpotato production. To develop a diagnostic assay, a hybrid genome assembly of C. fimbriata isolate AS236 was generated. The resulting 31.7-MB assembly was near-chromosome level, with 18 contigs, 6,481 predicted genes, and a BUSCO completion score of 98.4% when compared with the fungus-specific lineage database. Additional Illumina DNA reads from C. manginecans, C. platani, and a second C. fimbriata isolate (C1421) were then mapped to the assembled genome using BOWTIE2 and counted using HTSeq, which identified 148 genes present only within C. fimbriata as molecular diagnostic candidates; 6 single-copy and 35 highly multi-copy (>40 BLAST hits), as determined through a self-BLAST-P alignment. Primers for PCR were designed in the 200-bp flanking region of the first exon for each candidate, and the candidates were validated against a diverse DNA panel containing Ceratocystis species, sweetpotato pathogens, and plants. After validation, two diagnostic candidates amplified only C. fimbriata DNA and were considered to be highly specific to the species. These genetic markers will serve as valuable diagnostic tools with multiple applications including the detection of C. fimbriata in seed, soil, and wash water in sweetpotato production.
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Affiliation(s)
- M N Stahr
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695-7825, U.S.A
| | - C Parada-Rojas
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695-7825, U.S.A
| | - K L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
| | - R F Alfenas
- Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - F M Fernandes
- Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - K Avila
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695-7825, U.S.A
| | - L M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695-7825, U.S.A
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14
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MacDonald N, Raven N, Diep W, Evans S, Pannipitiya S, Bramwell G, Vanbeek C, Thomas F, Russell T, Dujon AM, Telonis-Scott M, Ujvari B. The molecular evolution of cancer associated genes in mammals. Sci Rep 2024; 14:11650. [PMID: 38773187 PMCID: PMC11109183 DOI: 10.1038/s41598-024-62425-0] [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: 11/16/2023] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
Cancer is a disease that many multicellular organisms have faced for millions of years, and species have evolved various tumour suppression mechanisms to control oncogenesis. Although cancer occurs across the tree of life, cancer related mortality risks vary across mammalian orders, with Carnivorans particularly affected. Evolutionary theory predicts different selection pressures on genes associated with cancer progression and suppression, including oncogenes, tumour suppressor genes and immune genes. Therefore, we investigated the evolutionary history of cancer associated gene sequences across 384 mammalian taxa, to detect signatures of selection across categories of oncogenes (GRB2, FGL2 and CDC42), tumour suppressors (LITAF, Casp8 and BRCA2) and immune genes (IL2, CD274 and B2M). This approach allowed us to conduct a fine scale analysis of gene wide and site-specific signatures of selection across mammalian lineages under the lens of cancer susceptibility. Phylogenetic analyses revealed that for most species the evolution of cancer associated genes follows the species' evolution. The gene wide selection analyses revealed oncogenes being the most conserved, tumour suppressor and immune genes having similar amounts of episodic diversifying selection. Despite BRCA2's status as a key caretaker gene, episodic diversifying selection was detected across mammals. The site-specific selection analyses revealed that the two apoptosis associated domains of the Casp8 gene of bats (Chiroptera) are under opposing forces of selection (positive and negative respectively), highlighting the importance of site-specific selection analyses to understand the evolution of highly complex gene families. Our results highlighted the need to critically assess different types of selection pressure on cancer associated genes when investigating evolutionary adaptations to cancer across the tree of life. This study provides an extensive assessment of cancer associated genes in mammals with highly representative, and substantially large sample size for a comparative genomic analysis in the field and identifies various avenues for future research into the mechanisms of cancer resistance and susceptibility in mammals.
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Affiliation(s)
- Nick MacDonald
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Nynke Raven
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Wendy Diep
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Samantha Evans
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Senuri Pannipitiya
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Georgina Bramwell
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Caitlin Vanbeek
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
- MIVEGEC, IRD, CNRS, Université Montpellier, Montpellier, France
| | - Tracey Russell
- Faculty of Science, School of Life and Environmental Sciences, Sydney, NSW, Australia
| | - Antoine M Dujon
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Marina Telonis-Scott
- School of Life and Environmental Sciences, Deakin University, Burwood, Burwood, VIC, 3125, Australia
| | - Beata Ujvari
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia.
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15
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Miliotis C, Ma Y, Katopodi XL, Karagkouni D, Kanata E, Mattioli K, Kalavros N, Pita-Juárez YH, Batalini F, Ramnarine VR, Nanda S, Slack FJ, Vlachos IS. Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci. Nat Commun 2024; 15:4319. [PMID: 38773080 PMCID: PMC11109163 DOI: 10.1038/s41467-024-48436-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/01/2024] [Indexed: 05/23/2024] Open
Abstract
The landscape of non-coding mutations in cancer progression and immune evasion is largely unexplored. Here, we identify transcrptome-wide somatic and germline 3' untranslated region (3'-UTR) variants from 375 gastric cancer patients from The Cancer Genome Atlas. By performing gene expression quantitative trait loci (eQTL) and immune landscape QTL (ilQTL) analysis, we discover 3'-UTR variants with cis effects on expression and immune landscape phenotypes, such as immune cell infiltration and T cell receptor diversity. Using a massively parallel reporter assay, we distinguish between causal and correlative effects of 3'-UTR eQTLs in immune-related genes. Our approach identifies numerous 3'-UTR eQTLs and ilQTLs, providing a unique resource for the identification of immunotherapeutic targets and biomarkers. A prioritized ilQTL variant signature predicts response to immunotherapy better than standard-of-care PD-L1 expression in independent patient cohorts, showcasing the untapped potential of non-coding mutations in cancer.
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Affiliation(s)
- Christos Miliotis
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Program in Virology, Harvard University Graduate School of Arts and Sciences, Boston, MA, USA
| | - Yuling Ma
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xanthi-Lida Katopodi
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Dimitra Karagkouni
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Eleni Kanata
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kaia Mattioli
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nikolas Kalavros
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Yered H Pita-Juárez
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Felipe Batalini
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Division of Oncology, Department of Medicine, Mayo Clinic, Phoenix, AZ, USA
| | - Varune R Ramnarine
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shivani Nanda
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Ioannis S Vlachos
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Spatial Technologies Unit, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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16
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Chen CK, Chang YM, Jiang TX, Yue Z, Liu TY, Lu J, Yu Z, Lin JJ, Vu TD, Huang TY, Harn HIC, Ng CS, Wu P, Chuong CM, Li WH. Conserved regulatory switches for the transition from natal down to juvenile feather in birds. Nat Commun 2024; 15:4174. [PMID: 38755126 PMCID: PMC11099144 DOI: 10.1038/s41467-024-48303-3] [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: 09/24/2023] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Abstract
The transition from natal downs for heat conservation to juvenile feathers for simple flight is a remarkable environmental adaptation process in avian evolution. However, the underlying epigenetic mechanism for this primary feather transition is mostly unknown. Here we conducted time-ordered gene co-expression network construction, epigenetic analysis, and functional perturbations in developing feather follicles to elucidate four downy-juvenile feather transition events. We report that extracellular matrix reorganization leads to peripheral pulp formation, which mediates epithelial-mesenchymal interactions for branching morphogenesis. α-SMA (ACTA2) compartmentalizes dermal papilla stem cells for feather renewal cycling. LEF1 works as a key hub of Wnt signaling to build rachis and converts radial downy to bilateral symmetry. Novel usage of scale keratins strengthens feather sheath with SOX14 as the epigenetic regulator. We show that this primary feather transition is largely conserved in chicken (precocial) and zebra finch (altricial) and discuss the possibility that this evolutionary adaptation process started in feathered dinosaurs.
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Affiliation(s)
- Chih-Kuan Chen
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ting-Xin Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - ZhiCao Yue
- Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen, Guangdong, China
- International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Tzu-Yu Liu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Jiayi Lu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zhou Yu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jinn-Jy Lin
- National Applied Research Laboratories, National Center for High-performance Computing, Hsinchu, Taiwan
| | - Trieu-Duc Vu
- Michigan Neuroscience Institute, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Tao-Yu Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans I-Chen Harn
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chen Siang Ng
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- Bioresource Conservation Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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17
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Fishman L, Modak A, Nechooshtan G, Razin T, Erhard F, Regev A, Farrell JA, Rabani M. Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nat Commun 2024; 15:3104. [PMID: 38600066 PMCID: PMC11006943 DOI: 10.1038/s41467-024-47290-9] [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: 04/12/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Avani Modak
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Talya Razin
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
- Chair of Computational Immunology, University of Regensburg, Regensburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge, MA, 02139, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, 02142, USA
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA.
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel.
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18
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Mah CK, Ahmed N, Lopez NA, Lam DC, Pong A, Monell A, Kern C, Han Y, Prasad G, Cesnik AJ, Lundberg E, Zhu Q, Carter H, Yeo GW. Bento: a toolkit for subcellular analysis of spatial transcriptomics data. Genome Biol 2024; 25:82. [PMID: 38566187 PMCID: PMC11289963 DOI: 10.1186/s13059-024-03217-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit that takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. We demonstrate MERFISH, seqFISH + , Molecular Cartography, and Xenium datasets. Bento is part of the open-source Scverse ecosystem, enabling integration with other single-cell analysis tools.
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Affiliation(s)
- Clarence K Mah
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA
| | - Noorsher Ahmed
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA
| | - Nicole A Lopez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Dylan C Lam
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Avery Pong
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alexander Monell
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Colin Kern
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Yuanyuan Han
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Gino Prasad
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Anthony J Cesnik
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Emma Lundberg
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Quan Zhu
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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19
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Reid SE, Pantaleo J, Bolivar P, Bocci M, Sjölund J, Morsing M, Cordero E, Larsson S, Malmberg M, Seashore-Ludlow B, Pietras K. Cancer-associated fibroblasts rewire the estrogen receptor response in luminal breast cancer, enabling estrogen independence. Oncogene 2024; 43:1113-1126. [PMID: 38388711 PMCID: PMC10997519 DOI: 10.1038/s41388-024-02973-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]
Abstract
Advanced breast cancers represent a major therapeutic challenge due to their refractoriness to treatment. Cancer-associated fibroblasts (CAFs) are the most abundant constituents of the tumor microenvironment and have been linked to most hallmarks of cancer. However, the influence of CAFs on therapeutic outcome remains largely unchartered. Here, we reveal that spatial coincidence of abundant CAF infiltration with malignant cells was associated with reduced estrogen receptor (ER)-α expression and activity in luminal breast tumors. Notably, CAFs mediated estrogen-independent tumor growth by selectively regulating ER-α signaling. Whereas most prototypical estrogen-responsive genes were suppressed, CAFs maintained gene expression related to therapeutic resistance, basal-like differentiation, and invasion. A functional drug screen in co-cultures identified effector pathways involved in the CAF-induced regulation of ER-α signaling. Among these, the Transforming Growth Factor-β and the Janus kinase signaling cascades were validated as actionable targets to counteract the CAF-induced modulation of ER-α activity. Finally, genes that were downregulated in cancer cells by CAFs were predictive of poor response to endocrine treatment. In conclusion, our work reveals that CAFs directly control the luminal breast cancer phenotype by selectively modulating ER-α expression and transcriptional function, and further proposes novel targets to disrupt the crosstalk between CAFs and tumor cells to reinstate treatment response to endocrine therapy in patients.
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Affiliation(s)
- Steven E Reid
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Jessica Pantaleo
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Paulina Bolivar
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Matteo Bocci
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Jonas Sjölund
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Mikkel Morsing
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Eugenia Cordero
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Sara Larsson
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Maria Malmberg
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Brinton Seashore-Ludlow
- Department of Oncology-Pathology, SciLifeLab, Stockholm, Sweden
- Chemical Biology Consortium Sweden (CBCS), Karolinska Institute, Stockholm, Sweden
| | - Kristian Pietras
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden.
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20
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Kuang R, Xu Z, Zhou H, Zhang Z, Peng H, Wang D, Xu X, Zhao S, Zhao Y, Zhu M. H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig. Anim Genet 2024; 55:217-229. [PMID: 38296601 DOI: 10.1111/age.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 12/25/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
The establishment of high-quality pork breeds for improving meat quality in the pig industry is needed. The Chuxiang Black (CX) pig is a new breed developed from Chinese local pigs and Western lean pigs that has a high proportion of lean meat and excellent meat quality. However, the characteristics of cis-regulatory elements in CX pigs are still unknown. In this study, cis-regulatory elements of muscle and adipose tissues in CX pigs were investigated using ChIP-seq and RNA sequencing. Compared with the reported cis-regulatory elements of muscle and adipose tissues, 1768 and 1012 highly activated enhancers and 433 and 275 highly activated promoters in CX muscle and adipose tissues were identified, respectively. Motif analysis showed that transcription factors, such as MEF2A and MEF2C, were core regulators of highly activated enhancers and promoters in muscle. Similarly, the transcription factors JUNB and CUX1 were identified as essential for highly activated enhancers and promoters in CX adipose tissue. These results enrich the resources for the analysis of cis-regulatory elements in the pig genome and provide new basic data for further meat quality improvement through breeding in pigs.
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Affiliation(s)
- Renzhuo Kuang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Zhixiang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Honghong Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Zhao Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Hao Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Daoyuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yunxia Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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21
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Khoa LTP, Yang W, Shan M, Zhang L, Mao F, Zhou B, Li Q, Malcore R, Harris C, Zhao L, Rao RC, Iwase S, Kalantry S, Bielas SL, Lyssiotis CA, Dou Y. Quiescence enables unrestricted cell fate in naive embryonic stem cells. Nat Commun 2024; 15:1721. [PMID: 38409226 PMCID: PMC10897426 DOI: 10.1038/s41467-024-46121-1] [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: 12/08/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Quiescence in stem cells is traditionally considered as a state of inactive dormancy or with poised potential. Naive mouse embryonic stem cells (ESCs) can enter quiescence spontaneously or upon inhibition of MYC or fatty acid oxidation, mimicking embryonic diapause in vivo. The molecular underpinning and developmental potential of quiescent ESCs (qESCs) are relatively unexplored. Here we show that qESCs possess an expanded or unrestricted cell fate, capable of generating both embryonic and extraembryonic cell types (e.g., trophoblast stem cells). These cells have a divergent metabolic landscape comparing to the cycling ESCs, with a notable decrease of the one-carbon metabolite S-adenosylmethionine. The metabolic changes are accompanied by a global reduction of H3K27me3, an increase of chromatin accessibility, as well as the de-repression of endogenous retrovirus MERVL and trophoblast master regulators. Depletion of methionine adenosyltransferase Mat2a or deletion of Eed in the polycomb repressive complex 2 results in removal of the developmental constraints towards the extraembryonic lineages. Our findings suggest that quiescent ESCs are not dormant but rather undergo an active transition towards an unrestricted cell fate.
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Affiliation(s)
- Le Tran Phuc Khoa
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Wentao Yang
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Mengrou Shan
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Bo Zhou
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Qiang Li
- Department of Ophthalmology & Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA
| | - Rebecca Malcore
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Lili Zhao
- Beaumont Hospital, Wayne, 33155 Annapolis St., Wayne, MI, 48184, USA
| | - Rajesh C Rao
- Department of Ophthalmology & Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yali Dou
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA.
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22
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Willemin A, Szabó D, Pombo A. Epigenetic regulatory layers in the 3D nucleus. Mol Cell 2024; 84:415-428. [PMID: 38242127 PMCID: PMC10872226 DOI: 10.1016/j.molcel.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of sequence information transfer from DNA to RNAs and proteins. We have since learned that gene expression is finely tuned in time and space, due to the activities of RNAs and proteins on regulatory DNA elements, and through cell-type-specific three-dimensional conformations of the genome. Here, we review major advances in genome biology and discuss a set of ideas on gene regulation and highlight how various biomolecular assemblies lead to the formation of structural and regulatory features within the nucleus, with roles in transcriptional control. We conclude by suggesting further developments that will help capture the complex, dynamic, and often spatially restricted events that govern gene expression in mammalian cells.
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Affiliation(s)
- Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
| | - Dominik Szabó
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
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23
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Zhu QM, Hsu YHH, Lassen FH, MacDonald BT, Stead S, Malolepsza E, Kim A, Li T, Mizoguchi T, Schenone M, Guzman G, Tanenbaum B, Fornelos N, Carr SA, Gupta RM, Ellinor PT, Lage K. Protein interaction networks in the vasculature prioritize genes and pathways underlying coronary artery disease. Commun Biol 2024; 7:87. [PMID: 38216744 PMCID: PMC10786878 DOI: 10.1038/s42003-023-05705-1] [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: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
Population-based association studies have identified many genetic risk loci for coronary artery disease (CAD), but it is often unclear how genes within these loci are linked to CAD. Here, we perform interaction proteomics for 11 CAD-risk genes to map their protein-protein interactions (PPIs) in human vascular cells and elucidate their roles in CAD. The resulting PPI networks contain interactions that are outside of known biology in the vasculature and are enriched for genes involved in immunity-related and arterial-wall-specific mechanisms. Several PPI networks derived from smooth muscle cells are significantly enriched for genetic variants associated with CAD and related vascular phenotypes. Furthermore, the networks identify 61 genes that are found in genetic loci associated with risk of CAD, prioritizing them as the causal candidates within these loci. These findings indicate that the PPI networks we have generated are a rich resource for guiding future research into the molecular pathogenesis of CAD.
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Affiliation(s)
- Qiuyu Martin Zhu
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yu-Han H Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Frederik H Lassen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bryan T MacDonald
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie Stead
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edyta Malolepsza
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - April Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Taibo Li
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Taiji Mizoguchi
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Monica Schenone
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gaelen Guzman
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Tanenbaum
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nadine Fornelos
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajat M Gupta
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
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24
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Olivares-Costa M, Oyarzún GM, Verbel-Vergara D, González MP, Arancibia D, Andrés ME, Opazo JC. Evolution of lysine-specific demethylase 1 and REST corepressor gene families and their molecular interaction. Commun Biol 2023; 6:1267. [PMID: 38097664 PMCID: PMC10721905 DOI: 10.1038/s42003-023-05652-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Lysine-specific demethylase 1A (LSD1) binds to the REST corepressor (RCOR) protein family of corepressors to erase transcriptionally active marks on histones. Functional diversity in these complexes depends on the type of RCOR included, which modulates the catalytic activity of the complex. Here, we studied the duplicative history of the RCOR and LSD gene families and analyzed the evolution of their interaction. We found that RCOR genes are the product of the two rounds of whole-genome duplications that occurred early in vertebrate evolution. In contrast, the origin of the LSD genes traces back before to the divergence of animals and plants. Using bioinformatics tools, we show that the RCOR and LSD1 interaction precedes the RCOR repertoire expansion that occurred in the last common ancestor of jawed vertebrates. Overall, we trace LSD1-RCOR complex evolution and propose that animal non-model species offer advantages in addressing questions about the molecular biology of this epigenetic complex.
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Affiliation(s)
- Montserrat Olivares-Costa
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Ciencias Biomédica, Facultad de Medicina, Universidad Católica del Norte, Coquimbo, Chile
| | - Gianluca Merello Oyarzún
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Daniel Verbel-Vergara
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela P González
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Duxan Arancibia
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile
| | - María E Andrés
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Juan C Opazo
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile.
- Integrative Biology Group, Valdivia, Chile.
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile.
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25
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Vanickova K, Milosevic M, Ribeiro Bas I, Burocziova M, Yokota A, Danek P, Grusanovic S, Chiliński M, Plewczynski D, Rohlena J, Hirai H, Rohlenova K, Alberich‐Jorda M. Hematopoietic stem cells undergo a lymphoid to myeloid switch in early stages of emergency granulopoiesis. EMBO J 2023; 42:e113527. [PMID: 37846891 PMCID: PMC10690458 DOI: 10.15252/embj.2023113527] [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: 01/16/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/18/2023] Open
Abstract
Emergency granulopoiesis is the enhanced and accelerated production of granulocytes that occurs during acute infection. The contribution of hematopoietic stem cells (HSCs) to this process was reported; however, how HSCs participate in emergency granulopoiesis remains elusive. Here, using a mouse model of emergency granulopoiesis we observe transcriptional changes in HSCs as early as 4 h after lipopolysaccharide (LPS) administration. We observe that the HSC identity is changed towards a myeloid-biased HSC and show that CD201 is enriched in lymphoid-biased HSCs. While CD201 expression under steady-state conditions reveals a lymphoid bias, under emergency granulopoiesis loss of CD201 marks the lymphoid-to-myeloid transcriptional switch. Mechanistically, we determine that lymphoid-biased CD201+ HSCs act as a first response during emergency granulopoiesis due to direct sensing of LPS by TLR4 and downstream activation of NF-κΒ signaling. The myeloid-biased CD201- HSC population responds indirectly during an acute infection by sensing G-CSF, increasing STAT3 phosphorylation, and upregulating LAP/LAP* C/EBPβ isoforms. In conclusion, HSC subpopulations support early phases of emergency granulopoiesis due to their transcriptional rewiring from a lymphoid-biased to myeloid-biased population and thus establishing alternative paths to supply elevated numbers of granulocytes.
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Affiliation(s)
- Karolina Vanickova
- Laboratory of Hemato‐oncologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
- Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Mirko Milosevic
- Institute of Biotechnology of the Czech Academy of SciencesPragueCzech Republic
| | - Irina Ribeiro Bas
- Laboratory of Hemato‐oncologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
- Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Monika Burocziova
- Laboratory of Hemato‐oncologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Asumi Yokota
- Laboratory of Stem Cell Regulation, School of Life SciencesTokyo University of Pharmacy and Life SciencesTokyoJapan
| | - Petr Danek
- Laboratory of Hemato‐oncologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Srdjan Grusanovic
- Laboratory of Hemato‐oncologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Mateusz Chiliński
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information ScienceWarsaw University of TechnologyWarsawPoland
- Laboratory of Functional and Structural Genomics, Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information ScienceWarsaw University of TechnologyWarsawPoland
- Laboratory of Functional and Structural Genomics, Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Jakub Rohlena
- Institute of Biotechnology of the Czech Academy of SciencesPragueCzech Republic
| | - Hideyo Hirai
- Laboratory of Stem Cell Regulation, School of Life SciencesTokyo University of Pharmacy and Life SciencesTokyoJapan
| | - Katerina Rohlenova
- Institute of Biotechnology of the Czech Academy of SciencesPragueCzech Republic
| | - Meritxell Alberich‐Jorda
- Laboratory of Hemato‐oncologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
- Childhood Leukaemia Investigation Prague, Department of Pediatric Haematology and Oncology, 2 Faculty of Medicine, University Hospital MotolCharles University in PraguePrahaCzech Republic
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26
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Brasher MS, Mize TJ, Thomas AL, Hoeffer CA, Ehringer MA, Evans LM. Testing associations between human anxiety and genes previously implicated by mouse anxiety models. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12851. [PMID: 37259642 PMCID: PMC10733569 DOI: 10.1111/gbb.12851] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
Anxiety disorders are common and can be debilitating, with effective treatments remaining hampered by an incomplete understanding of the underlying genetic etiology. Improvements have been made in understanding the genetic influences on mouse behavioral models of anxiety, yet it is unclear the extent to which genes identified in these experimental systems contribute to genetic variation in human anxiety phenotypes. Leveraging new and existing large-scale human genome-wide association studies, we tested whether sets of genes previously identified in mouse anxiety-like behavior studies contribute to a range of human anxiety disorders. When tested as individual genes, 13 mouse-identified genes were associated with human anxiety phenotypes, suggesting an overlap of individual genes contributing to both mouse models of anxiety-like behaviors and human anxiety traits. When genes were tested as sets, we did identify 14 significant associations between mouse gene sets and human anxiety, but the majority of gene sets showed no significant association with human anxiety phenotypes. These few significant associations indicate a need to identify and develop more translatable mouse models by identifying sets of genes that "match" between model systems and specific human phenotypes of interest. We suggest that continuing to develop improved behavioral paradigms and finer-scale experimental data, for instance from individual neuronal subtypes or cell-type-specific expression data, is likely to improve our understanding of the genetic etiology and underlying functional changes in anxiety disorders.
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Affiliation(s)
- Maizy S. Brasher
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
- Institute for Behavioral GeneticsBoulderColoradoUSA
| | - Travis J. Mize
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
- Institute for Behavioral GeneticsBoulderColoradoUSA
| | | | - Charles A. Hoeffer
- Institute for Behavioral GeneticsBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Marissa A. Ehringer
- Institute for Behavioral GeneticsBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Luke M. Evans
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
- Institute for Behavioral GeneticsBoulderColoradoUSA
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27
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Wang M, He B, Hao Y, Srinivasan D, Shrinet J, Fraser P. Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions. BMC Biol 2023; 21:264. [PMID: 37981682 PMCID: PMC10658794 DOI: 10.1186/s12915-023-01766-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Long-range interactions between promoters and cis-regulatory elements, such as enhancers, play critical roles in gene regulation. However, the role of three-dimensional (3D) chromatin structure in orchestrating changes in transcriptional regulation during direct cell reprogramming is not fully understood. RESULTS Here, we performed integrated analyses of chromosomal architecture, epigenetics, and gene expression using Hi-C, promoter Capture Hi-C (PCHi-C), ChIP-seq, and RNA-seq during trans-differentiation of Pre-B cells into macrophages with a β-estradiol inducible C/EBPαER transgene. Within 1h of β-estradiol induction, C/EBPα translocated from the cytoplasm to the nucleus, binding to thousands of promoters and putative regulatory elements, resulting in the downregulation of Pre-B cell-specific genes and induction of macrophage-specific genes. Hi-C results were remarkably consistent throughout trans-differentiation, revealing only a small number of TAD boundary location changes, and A/B compartment switches despite significant changes in the expression of thousands of genes. PCHi-C revealed widespread changes in promoter-anchored loops with decreased interactions in parallel with decreased gene expression, and new and increased promoter-anchored interactions in parallel with increased expression of macrophage-specific genes. CONCLUSIONS Overall, our data demonstrate that C/EBPα-induced trans-differentiation involves few changes in genome architecture at the level of TADs and A/B compartments, in contrast with widespread reorganization of thousands of promoter-anchored loops in association with changes in gene expression and cell identity.
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Affiliation(s)
- Miao Wang
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Bing He
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Yueling Hao
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Divyaa Srinivasan
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
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28
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Brown JL, Zhang L, Rocha PP, Kassis JA, Sun MA. Polycomb protein binding and looping mediated by Polycomb Response Elements in the ON transcriptional state. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565256. [PMID: 38076900 PMCID: PMC10705551 DOI: 10.1101/2023.11.02.565256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Polycomb group proteins (PcG) mediate epigenetic silencing of important developmental genes and other targets. In Drosophila, canonical PcG-target genes contain Polycomb Response Elements (PREs) that recruit PcG protein complexes including PRC2 that trimethylates H3K27 forming large H3K27me3 domains. In the OFF transcriptional state, PREs loop with each other and this looping strengthens silencing. Here we address the question of what PcG proteins bind to PREs when canonical PcG target genes are expressed, and whether PREs loop when these genes are ON. Our data show that the answer to this question is PRE-specific but general conclusions can be made. First, within a PcG-target gene, some regulatory DNA can remain covered with H3K27me3 and PcG proteins remain bound to PREs in these regions. Second, when PREs are within H3K27ac domains, PcG-binding decreases, however, this depends on the protein and PRE. The DNA binding protein GAF, and the PcG protein Ph remain at PREs even when other PcG proteins are greatly depleted. In the ON state, PREs can still loop with each other, but also form loops with presumptive enhancers. These data support the model that, in addition to their role in PcG silencing, PREs can act as "promoter-tethering elements" mediating interactions between promoter proximal PREs and distant enhancers.
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Affiliation(s)
- J. Lesley Brown
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liangliang Zhang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Pedro P Rocha
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Judith A. Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Important Animal Infectious Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
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29
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Chen M, Wang N, Yang H, Liu D, Gao Y, Duo L, Cui X, Hao F, Ye J, Gao F, Tu Q, Gui Y. Single-cell transcriptome analysis of the germ cells and somatic cells during mitotic quiescence stage in goats. FASEB J 2023; 37:e23244. [PMID: 37823602 DOI: 10.1096/fj.202301278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
The mitotic quiescence of prospermatogonia is the event known to occur during genesis of the male germline and is tied to the development of the spermatogenic lineage. The regulatory mechanisms and the functional importance of this process have been demonstrated in mice; however, regulation of this process in human and domestic animal is still largely unknown. In this study, we employed single-cell RNA sequencing to identify transcriptional signatures of prospermatogonia and major somatic cell types in testes of goats at E85, E105, and E125. We identified both common and specific Gene Ontology categories, transcription factor regulatory networks, and cell-cell interactions in cell types from goat testis. We also analyzed the transcriptional dynamic changes in prospermatogonia, Sertoli cells, Leydig cells, and interstitial cells. Our datasets provide a useful resource for the study of domestic animal germline development.
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Affiliation(s)
- Min Chen
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Nan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hang Yang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dongjun Liu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Yuan Gao
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Lei Duo
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Xiuhong Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Fei Hao
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Jing Ye
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Fei Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Tu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yaoting Gui
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
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30
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Lagger C, Ursu E, Equey A, Avelar RA, Pisco AO, Tacutu R, de Magalhães JP. scDiffCom: a tool for differential analysis of cell-cell interactions provides a mouse atlas of aging changes in intercellular communication. NATURE AGING 2023; 3:1446-1461. [PMID: 37919434 PMCID: PMC10645595 DOI: 10.1038/s43587-023-00514-x] [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] [Received: 11/08/2021] [Accepted: 09/27/2023] [Indexed: 11/04/2023]
Abstract
Dysregulation of intercellular communication is a hallmark of aging. To better quantify and explore changes in intercellular communication, we present scDiffCom and scAgeCom. scDiffCom is an R package, relying on approximately 5,000 curated ligand-receptor interactions, that performs differential intercellular communication analysis between two conditions from single-cell transcriptomics data. Built upon scDiffCom, scAgeCom is an atlas of age-related cell-cell communication changes covering 23 mouse tissues from 58 single-cell RNA sequencing datasets from Tabula Muris Senis and the Calico murine aging cell atlas. It offers a comprehensive resource of tissue-specific and sex-specific aging dysregulations and highlights age-related intercellular communication changes widespread across the whole body, such as the upregulation of immune system processes and inflammation, the downregulation of developmental processes, angiogenesis and extracellular matrix organization and the deregulation of lipid metabolism. Our analysis emphasizes the relevance of the specific ligands, receptors and cell types regulating these processes. The atlas is available online ( https://scagecom.org ).
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Affiliation(s)
- Cyril Lagger
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
- Altos Labs, San Diego, CA, USA
| | - Eugen Ursu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Anaïs Equey
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Roberto A Avelar
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Angela Oliveira Pisco
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Insitro, Inc., South San Francisco, USA
| | - Robi Tacutu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK.
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK.
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31
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Dézé O, Ordanoska D, Rossille D, Miglierina E, Laffleur B, Cogné M. Unique repetitive nucleic acid structures mirror switch regions in the human IgH locus. Biochimie 2023; 214:167-175. [PMID: 37678746 DOI: 10.1016/j.biochi.2023.08.017] [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: 07/06/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
Immunoglobulin (Ig) genes carry the unique ability to be reshaped in peripheral B lymphocytes after these cells encounter a specific antigen. B cells can then further improve their affinity, acquire new functions as memory cells and eventually end up as antibody-secreting cells. Ig class switching is an important change that occurs in this context, thanks to local DNA lesions initiated by the enzyme activation-induced deaminase (AID). Several cis-acting elements of the Ig heavy (IgH) chain locus make it accessible to the AID-mediated lesions that promote class switch recombination (CSR). DNA repeats, with a non-template strand rich in G-quadruplexes (G4)-DNA, are prominent cis-targets of AID and define the so-called "switch" (S) regions specifically targeted for CSR. By analyzing the structure of the human IgH locus, we uncover that abundant DNA repeats, some with a putative G4-rich template strand, are additionally present in downstream portions of the IgH coding genes. These like-S (LS) regions stand as 3' mirror-images of S regions and also show analogies to some previously reported repeats associated with the IgH locus 3' super-enhancer. A regulatory role of LS repeats is strongly suggested by their specific localization close to exons encoding the membrane form of Ig molecules, and by their conservation during mammalian evolution.
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Affiliation(s)
- Ophélie Dézé
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France
| | - Delfina Ordanoska
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France
| | - Delphine Rossille
- Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, F-35033, Rennes, France
| | - Emma Miglierina
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France
| | - Brice Laffleur
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France
| | - Michel Cogné
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France; Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, F-35033, Rennes, France.
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32
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Lo JW, Cozzetto D, Alexander JL, Danckert NP, Madgwick M, Knox N, Sieh JYX, Olbei M, Liu Z, Ibraheim H, Blanco JM, Kudo H, Seoane RC, Possamai LA, Goldin R, Marchesi J, Korcsmaros T, Lord GM, Powell N. Immune checkpoint inhibitor-induced colitis is mediated by polyfunctional lymphocytes and is dependent on an IL23/IFNγ axis. Nat Commun 2023; 14:6719. [PMID: 37872166 PMCID: PMC10593820 DOI: 10.1038/s41467-023-41798-2] [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: 01/11/2022] [Accepted: 09/18/2023] [Indexed: 10/25/2023] Open
Abstract
Immune checkpoint inhibitors (CPIs) are a relatively newly licenced cancer treatment, which make a once previously untreatable disease now amenable to a potential cure. Combination regimens of anti-CTLA4 and anti-PD-1 show enhanced efficacy but are prone to off-target immune-mediated tissue injury, particularly at the barrier surfaces. To probe the impact of immune checkpoints on intestinal homoeostasis, mice are challenged with anti-CTLA4 and anti-PD-1 immunotherapy and manipulation of the intestinal microbiota. The immune profile of the colon of these mice with CPI-colitis is analysed using bulk RNA sequencing, single-cell RNA sequencing and flow cytometry. CPI-colitis in mice is dependent on the composition of the intestinal microbiota and by the induction of lymphocytes expressing interferon-γ (IFNγ), cytotoxicity molecules and other pro-inflammatory cytokines/chemokines. This pre-clinical model of CPI-colitis could be attenuated following blockade of the IL23/IFNγ axis. Therapeutic targeting of IFNγ-producing lymphocytes or regulatory networks, may hold the key to reversing CPI-colitis.
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Affiliation(s)
- Jonathan W Lo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Domenico Cozzetto
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - James L Alexander
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nathan P Danckert
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Matthew Madgwick
- Organisms and Ecosystems, Earlham Institute, NR4 7UZ, Norwich, UK
- Gut Microbes and Health Programme, Quadram Institute Bioscience, NR4 7UQ, Norwich, UK
| | - Naomi Knox
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Jillian Yong Xin Sieh
- School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
| | - Marton Olbei
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Organisms and Ecosystems, Earlham Institute, NR4 7UZ, Norwich, UK
- Gut Microbes and Health Programme, Quadram Institute Bioscience, NR4 7UQ, Norwich, UK
| | - Zhigang Liu
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Hajir Ibraheim
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Jesus Miguens Blanco
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Hiromi Kudo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Rocio Castro Seoane
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Lucia A Possamai
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Robert Goldin
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Julian Marchesi
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Tamas Korcsmaros
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Organisms and Ecosystems, Earlham Institute, NR4 7UZ, Norwich, UK
- Gut Microbes and Health Programme, Quadram Institute Bioscience, NR4 7UQ, Norwich, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9NT, UK
| | - Nick Powell
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
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Lv Q, Chen G, He H, Yang Z, Zhao L, Chen HY, Chen CYC. TCMBank: bridges between the largest herbal medicines, chemical ingredients, target proteins, and associated diseases with intelligence text mining. Chem Sci 2023; 14:10684-10701. [PMID: 37829020 PMCID: PMC10566508 DOI: 10.1039/d3sc02139d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/30/2023] [Indexed: 10/14/2023] Open
Abstract
Traditional Chinese Medicine (TCM) has long been viewed as a precious source of modern drug discovery. AI-assisted drug discovery (AIDD) has been investigated extensively. However, there are still two challenges in applying AIDD to guide TCM drug discovery: the lack of a large amount of standardized TCM-related information and AIDD is prone to pathological failures in out-of-domain data. We have released TCM Database@Taiwan in 2011, and it has been widely disseminated and used. Now, we developed TCMBank, the largest systematic free TCM database, which is an extension of TCM Database@Taiwan. TCMBank contains 9192 herbs, 61 966 ingredients (unduplicated), 15 179 targets, 32 529 diseases, and their pairwise relationships. By integrating multiple data sources, TCMBank provides 3D structure information of ingredients and provides a standard list and detailed information on herbs, ingredients, targets and diseases. TCMBank has an intelligent document identification module that continuously adds TCM-related information retrieved from the literature in PubChem. In addition, driven by TCMBank big data, we developed an ensemble learning-based drug discovery protocol for identifying potential leads and drug repurposing. We take colorectal cancer and Alzheimer's disease as examples to demonstrate how to accelerate drug discovery by artificial intelligence. Using TCMBank, researchers can view literature-driven relationship mapping between herbs/ingredients and genes/diseases, allowing the understanding of molecular action mechanisms for ingredients and identification of new potentially effective treatments. TCMBank is available at https://TCMBank.CN/.
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Affiliation(s)
- Qiujie Lv
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University Shenzhen Guangdong 518107 P. R. China
| | - Guanxing Chen
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University Shenzhen Guangdong 518107 P. R. China
| | - Haohuai He
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University Shenzhen Guangdong 518107 P. R. China
| | - Ziduo Yang
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University Shenzhen Guangdong 518107 P. R. China
| | - Lu Zhao
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University Guangzhou Guangdong 510655 P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University Guangzhou Guangdong 510655 P. R. China
| | - Hsin-Yi Chen
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University Shenzhen Guangdong 518107 P. R. China
| | - Calvin Yu-Chian Chen
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University Shenzhen Guangdong 518107 P. R. China
- Department of Medical Research, China Medical University Hospital Taichung 40447 Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University Taichung 41354 Taiwan
- Guangdong L-Med Medicine Biotechnology Co., Ltd Meizhou Guangdong 514699 P. R. China
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Ruth KS, Beaumont RN, Locke JM, Tyrrell J, Crandall CJ, Hawkes G, Frayling TM, Prague JK, Patel KA, Wood AR, Weedon MN, Murray A. Insights into the genetics of menopausal vasomotor symptoms: genome-wide analyses of routinely-collected primary care health records. BMC Med Genomics 2023; 16:231. [PMID: 37784116 PMCID: PMC10546673 DOI: 10.1186/s12920-023-01658-w] [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: 12/14/2022] [Accepted: 09/08/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Vasomotor symptoms (VMS) can often significantly impact women's quality of life at menopause. In vivo studies have shown that increased neurokinin B (NKB) / neurokinin 3 receptor (NK3R) signalling contributes to VMS, with previous genetic studies implicating the TACR3 gene locus that encodes NK3R. Large-scale genomic analyses offer the possibility of biological insights but few such studies have collected data on VMS, while proxy phenotypes such as hormone replacement therapy (HRT) use are likely to be affected by changes in clinical practice. We investigated the genetic basis of VMS by analysing routinely-collected health records. METHODS We performed a GWAS of VMS derived from linked primary-care records and cross-sectional self-reported HRT use in up to 153,152 women from UK Biobank, a population-based cohort. In a subset of this cohort (n = 39,356), we analysed exome-sequencing data to test the association with VMS of rare deleterious genetic variants. Finally, we used Mendelian randomisation analysis to investigate the reasons for HRT use over time. RESULTS Our GWAS of health-records derived VMS identified a genetic signal near TACR3 associated with a lower risk of VMS (OR=0.76 (95% CI 0.72,0.80) per A allele, P=3.7x10-27), which was consistent with previous studies, validating this approach. Conditional analyses demonstrated independence of genetic signals for puberty timing and VMS at the TACR3 locus, including a rare variant predicted to reduce functional NK3R levels that was associated with later menarche (P = 5 × 10-9) but showed no association with VMS (P = 0.6). Younger menopause age was causally-associated with greater HRT use before 2002 but not after. CONCLUSIONS We provide support for TACR3 in the genetic basis of VMS but unexpectedly find that rare genomic variants predicted to lower NK3R levels did not modify VMS, despite the proven efficacy of NK3R antagonists. Using genomics we demonstrate changes in genetic associations with HRT use over time, arising from a change in clinical practice since the early 2000s, which is likely to reflect a switch from preventing post-menopausal complications in women with earlier menopause to primarily treating VMS. Our study demonstrates that integrating routinely-collected primary care health records and genomic data offers great potential for exploring the genetic basis of symptoms.
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Affiliation(s)
- Katherine S Ruth
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK.
| | - Robin N Beaumont
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Jonathan M Locke
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Jessica Tyrrell
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Carolyn J Crandall
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine at University of California, Los Angeles, CA, 90024, USA
| | - Gareth Hawkes
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Julia K Prague
- Exeter Centre of Excellence for Diabetes Research, University of Exeter, Exeter, EX2 5DW, UK
- Macleod Diabetes and Endocrinology Centre, Royal Devon and Exeter National Health Service Foundation Trust, Exeter, EX2 5DW, UK
| | - Kashyap A Patel
- Exeter Centre of Excellence for Diabetes Research, University of Exeter, Exeter, EX2 5DW, UK
- Macleod Diabetes and Endocrinology Centre, Royal Devon and Exeter National Health Service Foundation Trust, Exeter, EX2 5DW, UK
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Michael N Weedon
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Anna Murray
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
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35
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Lamanna F, Hervas-Sotomayor F, Oel AP, Jandzik D, Sobrido-Cameán D, Santos-Durán GN, Martik ML, Stundl J, Green SA, Brüning T, Mößinger K, Schmidt J, Schneider C, Sepp M, Murat F, Smith JJ, Bronner ME, Rodicio MC, Barreiro-Iglesias A, Medeiros DM, Arendt D, Kaessmann H. A lamprey neural cell type atlas illuminates the origins of the vertebrate brain. Nat Ecol Evol 2023; 7:1714-1728. [PMID: 37710042 PMCID: PMC10555824 DOI: 10.1038/s41559-023-02170-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
The vertebrate brain emerged more than ~500 million years ago in common evolutionary ancestors. To systematically trace its cellular and molecular origins, we established a spatially resolved cell type atlas of the entire brain of the sea lamprey-a jawless species whose phylogenetic position affords the reconstruction of ancestral vertebrate traits-based on extensive single-cell RNA-seq and in situ sequencing data. Comparisons of this atlas to neural data from the mouse and other jawed vertebrates unveiled various shared features that enabled the reconstruction of cell types, tissue structures and gene expression programs of the ancestral vertebrate brain. However, our analyses also revealed key tissues and cell types that arose later in evolution. For example, the ancestral brain was probably devoid of cerebellar cell types and oligodendrocytes (myelinating cells); our data suggest that the latter emerged from astrocyte-like evolutionary precursors in the jawed vertebrate lineage. Altogether, our work illuminates the cellular and molecular architecture of the ancestral vertebrate brain and provides a foundation for exploring its diversification during evolution.
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Affiliation(s)
- Francesco Lamanna
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | | | - A Phillip Oel
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
- Department of Zoology, Comenius University, Bratislava, Slovakia
| | - Daniel Sobrido-Cameán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Gabriel N Santos-Durán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Megan L Martik
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jan Stundl
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stephen A Green
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thoomke Brüning
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - María Celina Rodicio
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antón Barreiro-Iglesias
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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36
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Nikolatou K, Sandilands E, Román‐Fernández A, Cumming EM, Freckmann E, Lilla S, Buetow L, McGarry L, Neilson M, Shaw R, Strachan D, Miller C, Huang DT, McNeish IA, Norman JC, Zanivan S, Bryant DM. PTEN deficiency exposes a requirement for an ARF GTPase module for integrin-dependent invasion in ovarian cancer. EMBO J 2023; 42:e113987. [PMID: 37577760 PMCID: PMC10505920 DOI: 10.15252/embj.2023113987] [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: 03/09/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023] Open
Abstract
Dysregulation of the PI3K/AKT pathway is a common occurrence in high-grade serous ovarian carcinoma (HGSOC), with the loss of the tumour suppressor PTEN in HGSOC being associated with poor prognosis. The cellular mechanisms of how PTEN loss contributes to HGSOC are largely unknown. We here utilise time-lapse imaging of HGSOC spheroids coupled to a machine learning approach to classify the phenotype of PTEN loss. PTEN deficiency induces PI(3,4,5)P3 -rich and -dependent membrane protrusions into the extracellular matrix (ECM), resulting in a collective invasion phenotype. We identify the small GTPase ARF6 as a crucial vulnerability of HGSOC cells upon PTEN loss. Through a functional proteomic CRISPR screen of ARF6 interactors, we identify the ARF GTPase-activating protein (GAP) AGAP1 and the ECM receptor β1-integrin (ITGB1) as key ARF6 interactors in HGSOC regulating PTEN loss-associated invasion. ARF6 functions to promote invasion by controlling the recycling of internalised, active β1-integrin to maintain invasive activity into the ECM. The expression of the CYTH2-ARF6-AGAP1 complex in HGSOC patients is inversely associated with outcome, allowing the identification of patient groups with improved versus poor outcome. ARF6 may represent a therapeutic vulnerability in PTEN-depleted HGSOC.
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Affiliation(s)
- Konstantina Nikolatou
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Emma Sandilands
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Alvaro Román‐Fernández
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Erin M Cumming
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Eva Freckmann
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | | | | | | | | | | | | | | | - Danny T Huang
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Iain A McNeish
- Department of Surgery and Cancer, Ovarian Cancer Action Research CentreImperial College LondonLondonUK
| | - James C Norman
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Sara Zanivan
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - David M Bryant
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
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37
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Dubois‐Chevalier J, Gheeraert C, Berthier A, Boulet C, Dubois V, Guille L, Fourcot M, Marot G, Gauthier K, Dubuquoy L, Staels B, Lefebvre P, Eeckhoute J. An extended transcription factor regulatory network controls hepatocyte identity. EMBO Rep 2023; 24:e57020. [PMID: 37424431 PMCID: PMC10481658 DOI: 10.15252/embr.202357020] [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: 02/16/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/11/2023] Open
Abstract
Cell identity is specified by a core transcriptional regulatory circuitry (CoRC), typically limited to a small set of interconnected cell-specific transcription factors (TFs). By mining global hepatic TF regulons, we reveal a more complex organization of the transcriptional regulatory network controlling hepatocyte identity. We show that tight functional interconnections controlling hepatocyte identity extend to non-cell-specific TFs beyond the CoRC, which we call hepatocyte identity (Hep-ID)CONNECT TFs. Besides controlling identity effector genes, Hep-IDCONNECT TFs also engage in reciprocal transcriptional regulation with TFs of the CoRC. In homeostatic basal conditions, this translates into Hep-IDCONNECT TFs being involved in fine tuning CoRC TF expression including their rhythmic expression patterns. Moreover, a role for Hep-IDCONNECT TFs in the control of hepatocyte identity is revealed in dedifferentiated hepatocytes where Hep-IDCONNECT TFs are able to reset CoRC TF expression. This is observed upon activation of NR1H3 or THRB in hepatocarcinoma or in hepatocytes subjected to inflammation-induced loss of identity. Our study establishes that hepatocyte identity is controlled by an extended array of TFs beyond the CoRC.
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Affiliation(s)
| | - Céline Gheeraert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Alexandre Berthier
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Clémence Boulet
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Vanessa Dubois
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
- Basic and Translational Endocrinology (BaTE), Department of Basic and Applied Medical SciencesGhent UniversityGhentBelgium
| | - Loïc Guille
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Marie Fourcot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 – UAR 2014 – PLBSLilleFrance
| | - Guillemette Marot
- Univ. Lille, Inria, CHU Lille, ULR 2694 – METRICS: Évaluation des technologies de santé et des pratiques médicalesLilleFrance
| | - Karine Gauthier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, INRAE USC 1370, École Normale Supérieure de LyonLyonFrance
| | - Laurent Dubuquoy
- Univ. Lille, Inserm, CHU Lille, U1286 – INFINITE – Institute for Translational Research in InflammationLilleFrance
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Jérôme Eeckhoute
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
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38
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Aromolaran OT, Isewon I, Adedeji E, Oswald M, Adebiyi E, Koenig R, Oyelade J. Heuristic-enabled active machine learning: A case study of predicting essential developmental stage and immune response genes in Drosophila melanogaster. PLoS One 2023; 18:e0288023. [PMID: 37556452 PMCID: PMC10411809 DOI: 10.1371/journal.pone.0288023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/18/2023] [Indexed: 08/11/2023] Open
Abstract
Computational prediction of absolute essential genes using machine learning has gained wide attention in recent years. However, essential genes are mostly conditional and not absolute. Experimental techniques provide a reliable approach of identifying conditionally essential genes; however, experimental methods are laborious, time and resource consuming, hence computational techniques have been used to complement the experimental methods. Computational techniques such as supervised machine learning, or flux balance analysis are grossly limited due to the unavailability of required data for training the model or simulating the conditions for gene essentiality. This study developed a heuristic-enabled active machine learning method based on a light gradient boosting model to predict essential immune response and embryonic developmental genes in Drosophila melanogaster. We proposed a new sampling selection technique and introduced a heuristic function which replaces the human component in traditional active learning models. The heuristic function dynamically selects the unlabelled samples to improve the performance of the classifier in the next iteration. Testing the proposed model with four benchmark datasets, the proposed model showed superior performance when compared to traditional active learning models (random sampling and uncertainty sampling). Applying the model to identify conditionally essential genes, four novel essential immune response genes and a list of 48 novel genes that are essential in embryonic developmental condition were identified. We performed functional enrichment analysis of the predicted genes to elucidate their biological processes and the result evidence our predictions. Immune response and embryonic development related processes were significantly enriched in the essential immune response and embryonic developmental genes, respectively. Finally, we propose the predicted essential genes for future experimental studies and use of the developed tool accessible at http://heal.covenantuniversity.edu.ng for conditional essentiality predictions.
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Affiliation(s)
- Olufemi Tony Aromolaran
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Itunu Isewon
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Eunice Adedeji
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum, Jena, Germany
| | - Ezekiel Adebiyi
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Rainer Koenig
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum, Jena, Germany
| | - Jelili Oyelade
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
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39
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Javaid H, Barberis A, Chervova O, Nassiri I, Voloshin V, Sato Y, Ogawa S, Fairfax B, Buffa F, Humphrey TC. A role for SETD2 loss in tumorigenesis through DNA methylation dysregulation. BMC Cancer 2023; 23:721. [PMID: 37528416 PMCID: PMC10394884 DOI: 10.1186/s12885-023-11162-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
SETD2-dependent H3 Lysine-36 trimethylation (H3K36me3) has been recently linked to the deposition of de-novo DNA methylation. SETD2 is frequently mutated in cancer, however, the functional impact of SETD2 loss and depletion on DNA methylation across cancer types and tumorigenesis is currently unknown. Here, we perform a pan-cancer analysis and show that both SETD2 mutation and reduced expression are associated with DNA methylation dysregulation across 21 out of the 24 cancer types tested. In renal cancer, these DNA methylation changes are associated with altered gene expression of oncogenes, tumour suppressors, and genes involved in neoplasm invasiveness, including TP53, FOXO1, and CDK4. This suggests a new role for SETD2 loss in tumorigenesis and cancer aggressiveness through DNA methylation dysregulation. Moreover, using a robust machine learning methodology, we develop and validate a 3-CpG methylation signature which is sufficient to predict SETD2 mutation status with high accuracy and correlates with patient prognosis.
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Affiliation(s)
- Hira Javaid
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Alessandro Barberis
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Olga Chervova
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Isar Nassiri
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Vitaly Voloshin
- Royal Botanic Gardens Kew, Kew Green, Richmond, TW9 3AE, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Benjamin Fairfax
- The MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital/Headley Way, OX3 9DS, Oxford, UK
| | - Francesca Buffa
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Timothy C Humphrey
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BN1 9RQ, Brighton, UK.
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40
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Pistek M, Kahlig CI, Hackl M, Unterthurner S, Kraus B, Grabherr R, Grillari J, Hernandez Bort JA. Comprehensive mRNA-sequencing-based characterization of three HEK-293 cell lines during an rAAV production process for gene therapy applications. Biotechnol J 2023; 18:e2200513. [PMID: 37191240 DOI: 10.1002/biot.202200513] [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: 10/11/2022] [Revised: 04/20/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Human embryonal kidney cells (HEK-293) are the most common host cells used for transient recombinant adeno-associated virus (rAAV) production in pharmaceutical industry. To better cover the expected gene therapy product demands in the future, different traditional strategies such as cell line sub-cloning and/or addition of chemical substances to the fermentation media have been used to maximize titers and improve product quality. A more effective and advanced approach to boost yield can be envisaged by characterizing the transcriptome of different HEK-293 cell line pedigrees with distinct rAAV productivity patterns to subsequently identify potential gene targets for cell engineering. In this work, the mRNA expression profile of three HEK-293 cell lines, resulting in various yields during a fermentation batch process for rAAV production, was investigated to gain basic insight into cell variability and eventually to identify genes that correlate with productivity. Mock runs using only transfection reagents were performed in parallel as a control. It finds significant differences in gene regulatory behaviors between the three cell lines at different growth and production stages. The evaluation of these transcriptomics profiles combined with collected in-process control parameters and titers shed some light on potential cell engineering targets to maximize transient production of rAAV in HEK-293 cells.
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Affiliation(s)
- Martina Pistek
- Biotherapeutics Process Development, Baxalta Innovations GmbH, a part of Takeda companies, Orth an der Donau, Austria
| | - Carolin-Isabel Kahlig
- Biotherapeutics Process Development, Baxalta Innovations GmbH, a part of Takeda companies, Orth an der Donau, Austria
| | | | - Sabine Unterthurner
- Biotherapeutics Process Development, Baxalta Innovations GmbH, a part of Takeda companies, Orth an der Donau, Austria
| | - Barbara Kraus
- Biotherapeutics Process Development, Baxalta Innovations GmbH, a part of Takeda companies, Orth an der Donau, Austria
| | - Reingard Grabherr
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johannes Grillari
- TAmiRNA, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Collaboration with AUVA, Vienna, Austria
| | - Juan A Hernandez Bort
- Biotherapeutics Process Development, Baxalta Innovations GmbH, a part of Takeda companies, Orth an der Donau, Austria
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41
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Mas AM, Goñi E, Ruiz de Los Mozos I, Arcas A, Statello L, González J, Blázquez L, Lee WTC, Gupta D, Sejas Á, Hoshina S, Armaos A, Tartaglia GG, Waga S, Ule J, Rothenberg E, Gómez M, Huarte M. ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins. Nat Commun 2023; 14:4447. [PMID: 37488096 PMCID: PMC10366126 DOI: 10.1038/s41467-023-40105-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in this process remains unclear. We show that the ORC1 subunit of the human Origin Recognition Complex interacts with RNAs transcribed from genes with origins in their transcription start sites (TSSs), displaying a positive correlation between RNA binding and origin activity. RNA depletion, or the use of ORC1 RNA-binding mutant, result in inefficient activation of proximal origins, linked to impaired ORC1 chromatin release. ORC1 RNA binding activity resides in its intrinsically disordered region, involved in intra- and inter-molecular interactions, regulation by phosphorylation, and phase-separation. We show that RNA binding favors ORC1 chromatin release, by regulating its phosphorylation and subsequent degradation. Our results unveil a non-coding function of RNA as a dynamic component of the chromatin, orchestrating the activation of replication origins.
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Affiliation(s)
- Aina Maria Mas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Enrique Goñi
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Igor Ruiz de Los Mozos
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Aida Arcas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Luisa Statello
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Jovanna González
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Lorea Blázquez
- RNA Networks Lab, The Francis Crick Institute, NW11BF, London, UK
- Neurosciences Area, Biodonostia Health Research Institute, 20014, San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
| | - Wei Ting Chelsea Lee
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Álvaro Sejas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Shoko Hoshina
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, 112-8681, Japan
| | - Alexandros Armaos
- Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Biology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Shou Waga
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, 112-8681, Japan
| | - Jernej Ule
- RNA Networks Lab, The Francis Crick Institute, NW11BF, London, UK
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - María Gómez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049, Madrid, Spain
| | - Maite Huarte
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain.
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain.
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42
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Sasaki S, Ma Y, Hirokawa T, Ikebukuro K, Tera M, Nagasawa K. Regulation of thrombin activity by ligand-induced topological alteration in a thrombin-binding aptamer. Chem Commun (Camb) 2023. [PMID: 37377065 DOI: 10.1039/d3cc02308g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Thrombin-binding aptamer (TBA), which forms a G-quadruplex (G4) structure with anti-parallel topology, interacts with thrombin to inhibit its enzymatic activity. Here we show that the G4-topology-altering ligand L2H2-2M2EA-6LCO (6LCO) changes the anti-parallel topology of TBA G4 to the parallel topology, thereby abrogating the thrombin-inhibitory activity of TBA. This finding suggests that G4 ligands that alter topology may be promising drug candidates for diseases involving G4-binding proteins.
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Affiliation(s)
- Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yue Ma
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
- Research Core Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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43
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Xiao CD, Jia MH, Zhong MQ, Xu Y, Yu ZT, He ZY, Lu X, Zhang Y, Zhou X, Fu LY, Shen XC. Unveiling the role of G-quadruplex structure in promoter region: Regulation of ABCA1 expression in macrophages possibly via NONO protein recruitment. Int J Biol Macromol 2023:125443. [PMID: 37353131 DOI: 10.1016/j.ijbiomac.2023.125443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/25/2023]
Abstract
ABCA1 has been found to be critical for cholesterol efflux in macrophages. Understanding the mechanism regulating ABCA1 expression is important for the prevention and treatment of atherosclerosis. In the present study, a G-quadruplex (G4) structure was identified in the ABCA1 promoter region. This G4 was shown to be essential for ABCA1 transcription. Stabilizing the G4 by ligands surprisingly upregulated ABCA1 expression in macrophages. Knocking out the G4 remarkably reduced ABCA1 expression, and abolished the increase of ABCA1 expression induced by the G4 ligand. By pull-down assays, the protein NONO was identified as an ABCA1 G4 binder. Overexpression or repression of NONO significantly induced upregulation and downregulation of ABCA1 expression, respectively. ChIP and EMSA experiments showed that the G4 ligand promoted the binding between the ABCA1 G4 and NONO, which led to more recruitment of NONO to the promoter region and enhanced ABCA1 transcription. Finally, the G4 ligand was shown to significantly reduce the accumulation of cholesterol in macrophages. This study showed a new insight into the regulation of gene expression by G4, and provided a new molecular mechanism regulating ABCA1 expression in macrophages. Furthermore, the study showed a possible novel application of the G4 ligand: preventing and treating atherosclerosis.
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Affiliation(s)
- Chao-Da Xiao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China.
| | - Meng-Hao Jia
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China.
| | - Ming-Qing Zhong
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Zu-Tao Yu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Zhi-Yong He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Xu Lu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Yan Zhang
- Department of Radiology, Affiliated Hospital of Guizhou Medical University, Guiyang 550001, China
| | - Xue Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Lin-Yun Fu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Xiang-Chun Shen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China.
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44
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Wang Z, Zhang C, Guo J, Wang W, Si Q, Chen C, Luo Y, Duan Z. Exosomal miRNA-223-3p derived from tumor associated macrophages promotes pulmonary metastasis of breast cancer 4T1 cells. Transl Oncol 2023; 35:101715. [PMID: 37329828 PMCID: PMC10366638 DOI: 10.1016/j.tranon.2023.101715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023] Open
Abstract
Research about the effect of exosomes derived from tumor associated macrophages (TAM-exos) in the distant organ metastasis of breast cancer is limited. In this study, we found that TAM-exos could promote the migration of 4T1 cells. Through comparing the expression of microRNAs in 4T1 cells, TAM-exos, and exosomes from bone marrow derived macrophages (BMDM-exos) by sequencing, miR-223-3p and miR-379-5p were screened out as two noteworthy differentially expressed microRNAs. Furthermore, miR-223-3p was confirmed to be the reason for the improved migration and metastasis of 4T1 cells. The expression of miR-223-3p was also increased in 4T1 cells isolated from the lung of tumor-bearing mice. Cbx5, which has been reported to be closely related with metastasis of breast cancer, was identified to be the target of miR-223-3p. Based on the information of breast cancer patients from online databases, miR-223-3p had a negative correlation with the overall survival rate of breast cancer patients within a three-year follow-up, while Cbx5 showed an opposite relationship. Taken together, miR-223-3p in TAM-exos can be delivered into 4T1 cells and exosomal miR-223-3p promotes pulmonary metastasis of 4T1 cells by targeting Cbx5.
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Affiliation(s)
- Ziyuan Wang
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China
| | - Chen Zhang
- Department of Immunology, Nankai University, Tianjin 300071, China
| | - Jian Guo
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China
| | - Wei Wang
- BioMetas(Shanghai) Limited, 201203, China
| | - Qin Si
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China
| | - Chong Chen
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China
| | - Yunping Luo
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China.
| | - Zhaojun Duan
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China.
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45
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Wall JD, Sathirapongsasuti JF, Gupta R, Rasheed A, Venkatesan R, Belsare S, Menon R, Phalke S, Mittal A, Fang J, Tanneeru D, Deshmukh M, Bassi A, Robinson J, Chaudhary R, Murugan S, Ul-Asar Z, Saleem I, Ishtiaq U, Fatima A, Sheikh SS, Hameed S, Ishaq M, Rasheed SZ, Memon FUR, Jalal A, Abbas S, Frossard P, Fuchsberger C, Forer L, Schoenherr S, Bei Q, Bhangale T, Tom J, Gadde SGK, B V P, Naik NK, Wang M, Kwok PY, Khera AV, Lakshmi BR, Butterworth AS, Chowdhury R, Danesh J, di Angelantonio E, Naheed A, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Wadia PM, Yadav R, Desai S, Kumar N, Biswas A, Pal PK, Muthane UB, Das SK, Ramprasad VL, Kukkle PL, Seshagiri S, Kathiresan S, Ghosh A, Mohan V, Saleheen D, Stawiski EW, Peterson AS. South Asian medical cohorts reveal strong founder effects and high rates of homozygosity. Nat Commun 2023; 14:3377. [PMID: 37291107 PMCID: PMC10250394 DOI: 10.1038/s41467-023-38766-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.
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Affiliation(s)
- Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.
- Dept of Ornithology and Mammology, California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - J Fah Sathirapongsasuti
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
| | - Ravi Gupta
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Asif Rasheed
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Radha Venkatesan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Saurabh Belsare
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | - Ramesh Menon
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Sameer Phalke
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - John Fang
- Thermo Fisher Scientific, Santa Clara, CA, 95051, USA
| | - Deepak Tanneeru
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - Akshi Bassi
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | | | | | - Zameer Ul-Asar
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Imran Saleem
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Unzila Ishtiaq
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Areej Fatima
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | | | | | | | | | | | - Anjum Jalal
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Shahid Abbas
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Philippe Frossard
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Qixin Bei
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA, 94080, USA
| | - Jennifer Tom
- Product Development Data Sciences, Genentech, South San Francisco, CA, 94080, USA
| | | | - Priya B V
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | | | - Minxian Wang
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
- Cardiovascular Research Institute and Department of Dermatology, University of California San Francisco, San Francisco, CA, 94143, USA
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Amit V Khera
- Harvard Medical School, Boston, MA, 02115, USA
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, MA, 02115, Boston, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
| | - B R Lakshmi
- MDCRC, Royal Care Super Speciality Hospital 1/520, Neelambur, Coimbatore, Tamil Nadu, 641062, India
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Rajiv Chowdhury
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Emanuele di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Aliya Naheed
- Initiative for Non Communicable Diseases, Health Systems and Population Studies Division, icddr,b, Dhaka, Bangladesh
| | - Vinay Goyal
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Medanta Hospital, New Delhi, India
- Medanta, The Medicity, Gurgaon, India
| | | | | | - Rupam Borgohain
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
| | - Adreesh Mukherjee
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Ravi Yadav
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Soaham Desai
- Shree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Karamsad, Gujarat, India
| | - Niraj Kumar
- All India Institute of Medical Sciences, Rishikesh, India
| | - Atanu Biswas
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Pramod Kumar Pal
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Uday B Muthane
- Parkinson and Ageing Research Foundation, Bengaluru, India
| | - Shymal K Das
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Prashanth L Kukkle
- All India Institute of Medical Sciences, Rishikesh, India
- Manipal Hospital, Miller Road, Bengaluru, India
- Parkinson's Disease and Movement Disorders Clinic, Bengaluru, India
| | - Somasekar Seshagiri
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Arkasubhra Ghosh
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | - V Mohan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Danish Saleheen
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
- Seymour, Paul and Gloria Milstein Division of Cardiology at Columbia University, New York, NY, 10032, USA
| | - Eric W Stawiski
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
- Caribou Biosciences, Berkeley, CA, 94710, USA
| | - Andrew S Peterson
- MedGenome Inc., Foster City, CA, 94404, USA.
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA.
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA.
- Broadwing Bio, South San Francisco, CA, 94080, USA.
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46
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Viborg N, Pavlidis MA, Barrio-Calvo M, Friis S, Trolle T, Sørensen AB, Thygesen CB, Kofoed SV, Kleine-Kohlbrecher D, Hadrup SR, Rønø B. DNA based neoepitope vaccination induces tumor control in syngeneic mouse models. NPJ Vaccines 2023; 8:77. [PMID: 37244905 DOI: 10.1038/s41541-023-00671-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Recent findings have positioned tumor mutation-derived neoepitopes as attractive targets for cancer immunotherapy. Cancer vaccines that deliver neoepitopes via various vaccine formulations have demonstrated promising preliminary results in patients and animal models. In the presented work, we assessed the ability of plasmid DNA to confer neoepitope immunogenicity and anti-tumor effect in two murine syngeneic cancer models. We demonstrated that neoepitope DNA vaccination led to anti-tumor immunity in the CT26 and B16F10 tumor models, with the long-lasting presence of neoepitope-specific T-cell responses in blood, spleen, and tumors after immunization. We further observed that engagement of both the CD4+ and CD8+ T cell compartments was essential to hamper tumor growth. Additionally, combination therapy with immune checkpoint inhibition provided an additive effect, superior to either monotherapy. DNA vaccination offers a versatile platform that allows the encoding of multiple neoepitopes in a single formulation and is thus a feasible strategy for personalized immunotherapy via neoepitope vaccination.
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Affiliation(s)
- Nadia Viborg
- Evaxion Biotech, Hørsholm, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | | | | | | | | | | | | | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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47
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Pavlova I, Iudin M, Surdina A, Severov V, Varizhuk A. G-Quadruplexes in Nuclear Biomolecular Condensates. Genes (Basel) 2023; 14:genes14051076. [PMID: 37239436 DOI: 10.3390/genes14051076] [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: 04/21/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
G-quadruplexes (G4s) have long been implicated in the regulation of chromatin packaging and gene expression. These processes require or are accelerated by the separation of related proteins into liquid condensates on DNA/RNA matrices. While cytoplasmic G4s are acknowledged scaffolds of potentially pathogenic condensates, the possible contribution of G4s to phase transitions in the nucleus has only recently come to light. In this review, we summarize the growing evidence for the G4-dependent assembly of biomolecular condensates at telomeres and transcription initiation sites, as well as nucleoli, speckles, and paraspeckles. The limitations of the underlying assays and the remaining open questions are outlined. We also discuss the molecular basis for the apparent permissive role of G4s in the in vitro condensate assembly based on the interactome data. To highlight the prospects and risks of G4-targeting therapies with respect to the phase transitions, we also touch upon the reported effects of G4-stabilizing small molecules on nuclear biomolecular condensates.
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Affiliation(s)
- Iuliia Pavlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Mikhail Iudin
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Anastasiya Surdina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Vjacheslav Severov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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48
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Wagner N, Çelik MH, Hölzlwimmer FR, Mertes C, Prokisch H, Yépez VA, Gagneur J. Aberrant splicing prediction across human tissues. Nat Genet 2023; 55:861-870. [PMID: 37142848 DOI: 10.1038/s41588-023-01373-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
Aberrant splicing is a major cause of genetic disorders but its direct detection in transcriptomes is limited to clinically accessible tissues such as skin or body fluids. While DNA-based machine learning models can prioritize rare variants for affecting splicing, their performance in predicting tissue-specific aberrant splicing remains unassessed. Here we generated an aberrant splicing benchmark dataset, spanning over 8.8 million rare variants in 49 human tissues from the Genotype-Tissue Expression (GTEx) dataset. At 20% recall, state-of-the-art DNA-based models achieve maximum 12% precision. By mapping and quantifying tissue-specific splice site usage transcriptome-wide and modeling isoform competition, we increased precision by threefold at the same recall. Integrating RNA-sequencing data of clinically accessible tissues into our model, AbSplice, brought precision to 60%. These results, replicated in two independent cohorts, substantially contribute to noncoding loss-of-function variant identification and to genetic diagnostics design and analytics.
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Affiliation(s)
- Nils Wagner
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany
| | - Muhammed H Çelik
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Florian R Hölzlwimmer
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Christian Mertes
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Data Science Institute, Technical University of Munich, Garching, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Vicente A Yépez
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany.
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
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49
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Tsang MJ, Cheeseman IM. Alternative CDC20 translational isoforms tune mitotic arrest duration. Nature 2023; 617:154-161. [PMID: 37100900 PMCID: PMC10461078 DOI: 10.1038/s41586-023-05943-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/13/2023] [Indexed: 04/28/2023]
Abstract
Mitotic defects activate the spindle-assembly checkpoint, which inhibits the anaphase-promoting complex co-activator CDC20 to induce a prolonged cell cycle arrest1,2. Once errors are corrected, the spindle-assembly checkpoint is silenced, allowing anaphase onset to occur. However, in the presence of persistent unresolvable errors, cells can undergo 'mitotic slippage', exiting mitosis into a tetraploid G1 state and escaping the cell death that results from a prolonged arrest. The molecular logic that enables cells to balance these duelling mitotic arrest and slippage behaviours remains unclear. Here we demonstrate that human cells modulate the duration of their mitotic arrest through the presence of conserved, alternative CDC20 translational isoforms. Downstream translation initiation results in a truncated CDC20 isoform that is resistant to spindle-assembly-checkpoint-mediated inhibition and promotes mitotic exit even in the presence of mitotic perturbations. Our study supports a model in which the relative levels of CDC20 translational isoforms control the duration of mitotic arrest. During a prolonged mitotic arrest, new protein synthesis and differential CDC20 isoform turnover create a timer, with mitotic exit occurring once the truncated Met43 isoform achieves sufficient levels. Targeted molecular changes or naturally occurring cancer mutations that alter CDC20 isoform ratios or its translational control modulate mitotic arrest duration and anti-mitotic drug sensitivity, with potential implications for the diagnosis and treatment of human cancers.
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Affiliation(s)
- Mary-Jane Tsang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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50
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Fishman L, Nechooshtan G, Erhard F, Regev A, Farrell JA, Rabani M. Single-cell temporal dynamics reveals the relative contributions of transcription and degradation to cell-type specific gene expression in zebrafish embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537620. [PMID: 37131717 PMCID: PMC10153228 DOI: 10.1101/2023.04.20.537620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the underlying regulation of mRNA transcription and degradation remains a challenge, especially within whole embryos with diverse cellular identities. Here, we collect temporal cellular transcriptomes of zebrafish embryos, and decompose them into their newly-transcribed (zygotic) and pre-existing (maternal) mRNA components by combining single-cell RNA-Seq and metabolic labeling. We introduce kinetic models capable of quantifying regulatory rates of mRNA transcription and degradation within individual cell types during their specification. These reveal different regulatory rates between thousands of genes, and sometimes between cell types, that shape spatio-temporal expression patterns. Transcription drives most cell-type restricted gene expression. However, selective retention of maternal transcripts helps to define the gene expression profiles of germ cells and enveloping layer cells, two of the earliest specified cell-types. Coordination between transcription and degradation restricts expression of maternal-zygotic genes to specific cell types or times, and allows the emergence of spatio-temporal patterns when overall mRNA levels are held relatively constant. Sequence-based analysis links differences in degradation to specific sequence motifs. Our study reveals mRNA transcription and degradation events that control embryonic gene expression, and provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jeffrey A. Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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