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La Marca JE, Aubrey BJ, Yang B, Chang C, Wang Z, Kueh A, Tai L, Wilcox S, Milla L, Heinzel S, Vremec D, Whelan L, König C, Kaloni D, Voss AK, Strasser A, Diepstraten ST, Herold MJ, Kelly GL. Genome-wide CRISPR screening identifies a role for ARRDC3 in TRP53-mediated responses. Cell Death Differ 2024; 31:150-158. [PMID: 38097622 PMCID: PMC10850147 DOI: 10.1038/s41418-023-01249-3] [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: 08/31/2023] [Revised: 11/09/2023] [Accepted: 11/23/2023] [Indexed: 02/09/2024] Open
Abstract
Whole-genome screens using CRISPR technologies are powerful tools to identify novel tumour suppressors as well as factors that impact responses of malignant cells to anti-cancer agents. Applying this methodology to lymphoma cells, we conducted a genome-wide screen to identify novel inhibitors of tumour expansion that are induced by the tumour suppressor TRP53. We discovered that the absence of Arrestin domain containing 3 (ARRDC3) increases the survival and long-term competitiveness of MYC-driven lymphoma cells when treated with anti-cancer agents that activate TRP53. Deleting Arrdc3 in mice caused perinatal lethality due to various developmental abnormalities, including cardiac defects. Notably, the absence of ARRDC3 markedly accelerated MYC-driven lymphoma development. Thus, ARRDC3 is a new mediator of TRP53-mediated suppression of tumour expansion, and this discovery may open new avenues to harness this process for cancer therapy.
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Affiliation(s)
- John E La Marca
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Brandon J Aubrey
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Department of Medicine, Massachusetts General Hospital, Boston, USA
| | - Bruce Yang
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Catherine Chang
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Zilu Wang
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Kueh
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Lin Tai
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Liz Milla
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Environomics Future Science Platform, Centre for Australian National Biodiversity Research, CSIRO, Canberra, Australia
| | - Susanne Heinzel
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David Vremec
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Lauren Whelan
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Christina König
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Deeksha Kaloni
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Sarah T Diepstraten
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia.
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia.
| | - Gemma L Kelly
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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Barrington CL, Galindo G, Koch AL, Horton ER, Morrison EJ, Tisa S, Stasevich TJ, Rissland OS. Synonymous codon usage regulates translation initiation. Cell Rep 2023; 42:113413. [PMID: 38096059 PMCID: PMC10790568 DOI: 10.1016/j.celrep.2023.113413] [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: 05/13/2023] [Revised: 08/30/2023] [Accepted: 10/25/2023] [Indexed: 12/30/2023] Open
Abstract
Nonoptimal synonymous codons repress gene expression, but the underlying mechanisms are poorly understood. We and others have previously shown that nonoptimal codons slow translation elongation speeds and thereby trigger messenger RNA (mRNA) degradation. Nevertheless, transcript levels are often insufficient to explain protein levels, suggesting additional mechanisms by which codon usage regulates gene expression. Using reporters in human and Drosophila cells, we find that transcript levels account for less than half of the variation in protein abundance due to codon usage. This discrepancy is explained by translational differences whereby nonoptimal codons repress translation initiation. Nonoptimal transcripts are also less bound by the translation initiation factors eIF4E and eIF4G1, providing a mechanistic explanation for their reduced initiation rates. Importantly, translational repression can occur without mRNA decay and deadenylation, and it does not depend on the known nonoptimality sensor, CNOT3. Our results reveal a potent mechanism of regulation by codon usage where nonoptimal codons repress further rounds of translation.
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Affiliation(s)
- Chloe L Barrington
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gabriel Galindo
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Amanda L Koch
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Emma R Horton
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Evan J Morrison
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Samantha Tisa
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Timothy J Stasevich
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Olivia S Rissland
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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3
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Chen Q, Malki S, Xu X, Bennett B, Lackford BL, Kirsanov O, Geyer CB, Hu G. Cnot3 is required for male germ cell development and spermatogonial stem cell maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562256. [PMID: 37873304 PMCID: PMC10592795 DOI: 10.1101/2023.10.13.562256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The foundation of spermatogenesis and lifelong fertility is provided by spermatogonial stem cells (SSCs). SSCs divide asymmetrically to either replenish their numbers (self-renewal) or produce undifferentiated progenitors that proliferate before committing to differentiation. However, regulatory mechanisms governing SSC maintenance are poorly understood. Here, we show that the CCR4-NOT mRNA deadenylase complex subunit CNOT3 plays a critical role in maintaining spermatogonial populations in mice. Cnot3 is highly expressed in undifferentiated spermatogonia, and its deletion in spermatogonia resulted in germ cell loss and infertility. Single cell analyses revealed that Cnot3 deletion led to the de-repression of transcripts encoding factors involved in spermatogonial differentiation, including those in the glutathione redox pathway that are critical for SSC maintenance. Together, our study reveals that CNOT3 - likely via the CCR4-NOT complex - actively degrades transcripts encoding differentiation factors to sustain the spermatogonial pool and ensure the progression of spermatogenesis, highlighting the importance of CCR4-NOT-mediated post-transcriptional gene regulation during male germ cell development.
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Affiliation(s)
- Qing Chen
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
- Present address: Clinical Microbiome Unit (CMU), Laboratory of Host Immunity and Microbiome (LHIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Safia Malki
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Xiaojiang Xu
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
- Present address: Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Brian Bennett
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Brad L. Lackford
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Oleksandr Kirsanov
- Department of Anatomy & Cell Biology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Christopher B. Geyer
- Department of Anatomy & Cell Biology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute East Carolina University, Greenville, NC, USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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Kervadec A, Kezos J, Ni H, Yu M, Marchant J, Spiering S, Kannan S, Kwon C, Andersen P, Bodmer R, Grandi E, Ocorr K, Colas AR. Multiplatform modeling of atrial fibrillation identifies phospholamban as a central regulator of cardiac rhythm. Dis Model Mech 2023; 16:dmm049962. [PMID: 37293707 PMCID: PMC10387351 DOI: 10.1242/dmm.049962] [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: 10/25/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Atrial fibrillation (AF) is a common and genetically inheritable form of cardiac arrhythmia; however, it is currently not known how these genetic predispositions contribute to the initiation and/or maintenance of AF-associated phenotypes. One major barrier to progress is the lack of experimental systems to investigate the effects of gene function on rhythm parameters in models with human atrial and whole-organ relevance. Here, we assembled a multi-model platform enabling high-throughput characterization of the effects of gene function on action potential duration and rhythm parameters using human induced pluripotent stem cell-derived atrial-like cardiomyocytes and a Drosophila heart model, and validation of the findings using computational models of human adult atrial myocytes and tissue. As proof of concept, we screened 20 AF-associated genes and identified phospholamban loss of function as a top conserved hit that shortens action potential duration and increases the incidence of arrhythmia phenotypes upon stress. Mechanistically, our study reveals that phospholamban regulates rhythm homeostasis by functionally interacting with L-type Ca2+ channels and NCX. In summary, our study illustrates how a multi-model system approach paves the way for the discovery and molecular delineation of gene regulatory networks controlling atrial rhythm with application to AF.
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Affiliation(s)
- Anaïs Kervadec
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - James Kezos
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Haibo Ni
- Department of Pharmacology, UC Davis, Davis, CA 95616, USA
| | - Michael Yu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - James Marchant
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Sean Spiering
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Suraj Kannan
- Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chulan Kwon
- Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Rolf Bodmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Karen Ocorr
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alexandre R. Colas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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5
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Theusch E, Ting FY, Qin Y, Stevens K, Naidoo D, King SM, Yang N, Orr J, Han BY, Cyster JG, Chen YDI, Rotter JI, Krauss RM, Medina MW. Participant-derived cell line transcriptomic analyses and mouse studies reveal a role for ZNF335 in plasma cholesterol statin response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544860. [PMID: 37397985 PMCID: PMC10312755 DOI: 10.1101/2023.06.14.544860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background Statins lower circulating low-density lipoprotein cholesterol (LDLC) levels and reduce cardiovascular disease risk. Though highly efficacious in general, there is considerable inter-individual variation in statin efficacy that remains largely unexplained. Methods To identify novel genes that may modulate statin-induced LDLC lowering, we used RNA-sequencing data from 426 control- and 2 μM simvastatin-treated lymphoblastoid cell lines (LCLs) derived from European and African American ancestry participants of the Cholesterol and Pharmacogenetics (CAP) 40 mg/day 6-week simvastatin clinical trial (ClinicalTrials.gov Identifier: NCT00451828). We correlated statin-induced changes in LCL gene expression with plasma LDLC statin response in the corresponding CAP participants. For the most correlated gene identified (ZNF335), we followed up in vivo by comparing plasma cholesterol levels, lipoprotein profiles, and lipid statin response between wild-type mice and carriers of a hypomorphic (partial loss of function) missense mutation in Zfp335 (the mouse homolog of ZNF335). Results The statin-induced expression changes of 147 human LCL genes were significantly correlated to the plasma LDLC statin responses of the corresponding CAP participants in vivo (FDR=5%). The two genes with the strongest correlations were zinc finger protein 335 (ZNF335 aka NIF-1, rho=0.237, FDR-adj p=0.0085) and CCR4-NOT transcription complex subunit 3 (CNOT3, rho=0.233, FDR-adj p=0.0085). Chow-fed mice carrying a hypomorphic missense (R1092W; aka bloto) mutation in Zfp335 had significantly lower non-HDL cholesterol levels than wild type C57BL/6J mice in a sex combined model (p=0.04). Furthermore, male (but not female) mice carrying the Zfp335R1092W allele had significantly lower total and HDL cholesterol levels than wild-type mice. In a separate experiment, wild-type mice fed a control diet for 4 weeks and a matched simvastatin diet for an additional 4 weeks had significant statin-induced reductions in non-HDLC (-43±18% and -23±19% for males and females, respectively). Wild-type male (but not female) mice experienced significant reductions in plasma LDL particle concentrations, while male mice carrying Zfp335R1092W allele(s) exhibited a significantly blunted LDL statin response. Conclusions Our in vitro and in vivo studies identified ZNF335 as a novel modulator of plasma cholesterol levels and statin response, suggesting that variation in ZNF335 activity could contribute to inter-individual differences in statin clinical efficacy.
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Affiliation(s)
- Elizabeth Theusch
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Flora Y. Ting
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Yuanyuan Qin
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Kristen Stevens
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Devesh Naidoo
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Sarah M. King
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Neil Yang
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Joseph Orr
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Brenda Y. Han
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA USA
| | - Jason G. Cyster
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA USA
| | - Yii-Der I. Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Ronald M. Krauss
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
- Department of Medicine, University of California San Francisco, Oakland, CA USA
| | - Marisa W. Medina
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
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Migunova E, Rajamani S, Bonanni S, Wang F, Zhou C, Dubrovsky EB. Cardiac RNase Z edited via CRISPR-Cas9 drives heart hypertrophy in Drosophila. PLoS One 2023; 18:e0286214. [PMID: 37228086 PMCID: PMC10212119 DOI: 10.1371/journal.pone.0286214] [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: 02/03/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Cardiomyopathy (CM) is a group of diseases distinguished by morphological and functional abnormalities in the myocardium. It is etiologically heterogeneous and may develop via cell autonomous and/or non-autonomous mechanisms. One of the most severe forms of CM has been linked to the deficiency of the ubiquitously expressed RNase Z endoribonuclease. RNase Z cleaves off the 3'-trailer of both nuclear and mitochondrial primary tRNA (pre-tRNA) transcripts. Cells mutant for RNase Z accumulate unprocessed pre-tRNA molecules. Patients carrying RNase Z variants with reduced enzymatic activity display a plethora of symptoms including muscular hypotonia, microcephaly and severe heart hypertrophy; still, they die primarily due to acute heart decompensation. Determining whether the underlying mechanism of heart malfunction is cell autonomous or not will provide an opportunity to develop novel strategies of more efficient treatments for these patients. In this study, we used CRISPR-TRiM technology to create Drosophila models that carry cardiomyopathy-linked alleles of RNase Z only in the cardiomyocytes. We found that this modification is sufficient for flies to develop heart hypertrophy and systolic dysfunction. These observations support the idea that the RNase Z linked CM is driven by cell autonomous mechanisms.
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Affiliation(s)
- Ekaterina Migunova
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
| | - Saathvika Rajamani
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
| | - Stefania Bonanni
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
| | - Fei Wang
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Chao Zhou
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Edward B. Dubrovsky
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
- Center for Cancer, Genetic Diseases, and Gene Regulation, Fordham University, Bronx, NY, United States of America
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Tepe B, Macke EL, Niceta M, Weisz Hubshman M, Kanca O, Schultz-Rogers L, Zarate YA, Schaefer GB, Granadillo De Luque JL, Wegner DJ, Cogne B, Gilbert-Dussardier B, Le Guillou X, Wagner EJ, Pais LS, Neil JE, Mochida GH, Walsh CA, Magal N, Drasinover V, Shohat M, Schwab T, Schmitz C, Clark K, Fine A, Lanpher B, Gavrilova R, Blanc P, Burglen L, Afenjar A, Steel D, Kurian MA, Prabhakar P, Gößwein S, Di Donato N, Bertini ES, Wangler MF, Yamamoto S, Tartaglia M, Klee EW, Bellen HJ. Bi-allelic variants in INTS11 are associated with a complex neurological disorder. Am J Hum Genet 2023; 110:774-789. [PMID: 37054711 PMCID: PMC10183469 DOI: 10.1016/j.ajhg.2023.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/18/2023] [Indexed: 04/15/2023] Open
Abstract
The Integrator complex is a multi-subunit protein complex that regulates the processing of nascent RNAs transcribed by RNA polymerase II (RNAPII), including small nuclear RNAs, enhancer RNAs, telomeric RNAs, viral RNAs, and protein-coding mRNAs. Integrator subunit 11 (INTS11) is the catalytic subunit that cleaves nascent RNAs, but, to date, mutations in this subunit have not been linked to human disease. Here, we describe 15 individuals from 10 unrelated families with bi-allelic variants in INTS11 who present with global developmental and language delay, intellectual disability, impaired motor development, and brain atrophy. Consistent with human observations, we find that the fly ortholog of INTS11, dIntS11, is essential and expressed in the central nervous systems in a subset of neurons and most glia in larval and adult stages. Using Drosophila as a model, we investigated the effect of seven variants. We found that two (p.Arg17Leu and p.His414Tyr) fail to rescue the lethality of null mutants, indicating that they are strong loss-of-function variants. Furthermore, we found that five variants (p.Gly55Ser, p.Leu138Phe, p.Lys396Glu, p.Val517Met, and p.Ile553Glu) rescue lethality but cause a shortened lifespan and bang sensitivity and affect locomotor activity, indicating that they are partial loss-of-function variants. Altogether, our results provide compelling evidence that integrity of the Integrator RNA endonuclease is critical for brain development.
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Affiliation(s)
- Burak Tepe
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Monika Weisz Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Yuri A Zarate
- Division of Genetics and Metabolism, University of Kentucky, Lexington, KY, USA
| | - G Bradley Schaefer
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jorge Luis Granadillo De Luque
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel J Wegner
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine and St. Louis Children's Hospital, St. Louis, Missouri, USA
| | - Benjamin Cogne
- Laboratory of Molecular Genetics, CHU de Nantes, Nantes, France
| | | | | | - Eric J Wagner
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Lynn S Pais
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Nurit Magal
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Valerie Drasinover
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Mordechai Shohat
- Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel; Medical Genetics Institute of Maccabi HMO, Rechovot, Israel
| | - Tanya Schwab
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Chris Schmitz
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl Clark
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Anthony Fine
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Brendan Lanpher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Ralitza Gavrilova
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Pierre Blanc
- APHP, Département de génétique, Sorbonne Université, GRC n°19, ConCer-LD, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, 75012 Paris, France
| | - Lydie Burglen
- APHP, Département de génétique, Sorbonne Université, GRC n°19, ConCer-LD, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, 75012 Paris, France
| | - Alexandra Afenjar
- APHP. SU, Centre de Référence Malformations et maladies congénitales du cervelet, département de génétique et embryologie médicale, Hôpital Trousseau, 75012 Paris, France
| | - Dora Steel
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Prab Prabhakar
- Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Sophie Gößwein
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Nataliya Di Donato
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Enrico S Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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8
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Shan H, Fei T. CRISPR screening in cardiovascular research. Front Cell Dev Biol 2023; 11:1175849. [PMID: 37123412 PMCID: PMC10130668 DOI: 10.3389/fcell.2023.1175849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
The recent advent and widespread application of CRISPR-based genome editing tools have revolutionized biomedical research and beyond. Taking advantage of high perturbation efficiency and scalability, CRISPR screening has been regarded as one of the most powerful technologies in functional genomics which allows investigation of different genetic subjects at a large scale in parallel. Significant progress has been made using various CRISPR screening tools especially in cancer research, however, fewer attempts and less success are reported in other contexts. In this mini-review, we discuss how CRISPR screening has been implemented in studies on cardiovascular research and related metabolic disorders, highlight the scientific progress utilizing CRISPR screening, and further envision how to fully unleash the power of this technique to expedite scientific discoveries in these fields.
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Affiliation(s)
- Haihuan Shan
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, China
- Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, China
| | - Teng Fei
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, China
- Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, China
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9
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Zhao Y, van de Leemput J, Han Z. The opportunities and challenges of using Drosophila to model human cardiac diseases. Front Physiol 2023; 14:1182610. [PMID: 37123266 PMCID: PMC10130661 DOI: 10.3389/fphys.2023.1182610] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
The Drosophila heart tube seems simple, yet it has notable anatomic complexity and contains highly specialized structures. In fact, the development of the fly heart tube much resembles that of the earliest stages of mammalian heart development, and the molecular-genetic mechanisms driving these processes are highly conserved between flies and humans. Combined with the fly's unmatched genetic tools and a wide variety of techniques to assay both structure and function in the living fly heart, these attributes have made Drosophila a valuable model system for studying human heart development and disease. This perspective focuses on the functional and physiological similarities between fly and human hearts. Further, it discusses current limitations in using the fly, as well as promising prospects to expand the capabilities of Drosophila as a research model for studying human cardiac diseases.
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Affiliation(s)
- Yunpo Zhao
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
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10
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Zhao P, Meng Q, Wan C, Lei T, Zhang L, Zhang X, Tan L, Zhu H, He X. Clinical features of CNOT3-associated neurodevelopmental disorder in three Chinese patients. Neurogenetics 2023; 24:129-136. [PMID: 36802310 DOI: 10.1007/s10048-023-00713-z] [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: 11/29/2022] [Accepted: 01/25/2023] [Indexed: 02/23/2023]
Abstract
CNOT3 is the central component of the CCR4-NOT protein complex, which is a global regulator of RNA polymerase II transcription. Loss of function mutations in CNOT3 lead to intellectual developmental disorder with speech delay, autism, and dysmorphic facies (IDDSADF), which is very rare. Herein, we reported two novel heterozygous frameshift mutations (c.1058_1059insT and c.724delT) and one novel splice site variant (c.387 + 2 T > C) in CNOT3 (NM_014516.3) gene in three Chinese patients with dysmorphic features, developmental delay, and behavior anomalies. The functional study showed that the CNOT3 mRNA levels were significantly decreased in the peripheral blood of two patients with c.1058_1059insT and c.387 + 2 T > C variants, respectively, and minigene assay demonstrated that the splice variant (c.387 + 2 T > C) resulted in exon skipping. We also found that CNOT3 deficiency was linked to alterations of expression levels of other CCR4-NOT complex subunits in mRNA level in the peripheral blood. By analyzing the clinical manifestations of all these patients with CNOT3 variants, including our three cases and 22 patients previously reported, we did not observe a correlation between genotypes and phenotypes. In summary, this is the first time to report cases with IDDSADF in the Chinese population, and three novel CNOT3 variants in these patients expand its mutational spectrum.
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Affiliation(s)
- Peiwei Zhao
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, No. 100, Hongkong Rd, Wuhan, 430016, Jiangan, China
| | - Qingjie Meng
- Department of Clinical Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Chunhui Wan
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, No. 100, Hongkong Rd, Wuhan, 430016, Jiangan, China
| | - Tao Lei
- Rehabilitation Department, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, No. 100, Hongkong Rd, Wuhan, 430016, Jiangan, China
| | - Lei Zhang
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, No. 100, Hongkong Rd, Wuhan, 430016, Jiangan, China
| | - Xiankai Zhang
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, No. 100, Hongkong Rd, Wuhan, 430016, Jiangan, China
| | - Li Tan
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, No. 100, Hongkong Rd, Wuhan, 430016, Jiangan, China
| | - Hongmin Zhu
- Rehabilitation Department, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, No. 100, Hongkong Rd, Wuhan, 430016, Jiangan, China.
| | - Xuelian He
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, No. 100, Hongkong Rd, Wuhan, 430016, Jiangan, China.
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11
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Stanković D, Csordás G, Uhlirova M. Drosophila pVALIUM10 TRiP RNAi lines cause undesired silencing of Gateway-based transgenes. Life Sci Alliance 2023; 6:6/2/e202201801. [PMID: 36446522 PMCID: PMC9711858 DOI: 10.26508/lsa.202201801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022] Open
Abstract
Post-transcriptional gene silencing using double-stranded RNA has revolutionized the field of functional genetics, allowing fast and easy disruption of gene function in various organisms. In Drosophila, many transgenic RNAi lines have been generated in large-scale efforts, including the Drosophila Transgenic RNAi Project (TRiP), to facilitate in vivo knockdown of virtually any Drosophila gene with spatial and temporal resolution. The available transgenic RNAi lines represent a fundamental resource for the fly community, providing an unprecedented opportunity to address a vast range of biological questions relevant to basic and biomedical research fields. However, caution should be applied regarding the efficiency and specificity of the RNAi approach. Here, we demonstrate that pVALIUM10-based RNAi lines, representing ∼13% of the total TRiP collection (1,808 of 13,410 pVALIUM TRiP-based RNAi lines), cause unintended off-target silencing of transgenes expressed from Gateway destination vectors. The silencing is mediated by targeting attB1 and attB2 sequences generated via site-specific recombination and included in the transcribed mRNA. Deleting these attB sites from the Gateway expression vector prevents silencing and restores expected transgene expression.
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Affiliation(s)
- Dimitrije Stanković
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Gábor Csordás
- Institute of Genetics, Biological Research Centre of the Eötvös Loránd Research Network, Szeged, Hungary
| | - Mirka Uhlirova
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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12
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Yang D, Xiao F, Li J, Wang S, Fan X, Ni Q, Li Y, Zhang M, Yan T, Yang M, He Z. Age-related ceRNA networks in adult Drosophila ageing. Front Genet 2023; 14:1096902. [PMID: 36926584 PMCID: PMC10012872 DOI: 10.3389/fgene.2023.1096902] [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: 11/26/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
As Drosophila is an extensively used genetic model system, understanding of its regulatory networks has great significance in revealing the genetic mechanisms of ageing and human diseases. Competing endogenous RNA (ceRNA)-mediated regulation is an important mechanism by which circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) regulate ageing and age-related diseases. However, extensive analyses of the multiomics (circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA) characteristics of adult Drosophila during ageing have not been reported. Here, differentially expressed circRNAs and microRNAs (miRNAs) between 7 and 42-day-old flies were screened and identified. Then, the differentially expressed mRNAs, circRNAs, miRNAs, and lncRNAs between the 7- and 42-day old flies were analysed to identify age-related circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA networks in ageing Drosophila. Several key ceRNA networks were identified, such as the dme_circ_0009500/dme_miR-289-5p/CG31064, dme_circ_0009500/dme_miR-289-5p/frizzled, dme_circ_0009500/dme_miR-985-3p/Abl, and XLOC_027736/dme_miR-985-3p/Abl XLOC_189909/dme_miR-985-3p/Abl networks. Furthermore, real-time quantitative PCR (qPCR) was used to verify the expression level of those genes. Those results suggest that the discovery of these ceRNA networks in ageing adult Drosophila provide new information for research on human ageing and age-related diseases.
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Affiliation(s)
- Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Feng Xiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiamei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Siqi Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingyao Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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13
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Saha S, Spinelli L, Castro Mondragon JA, Kervadec A, Lynott M, Kremmer L, Roder L, Krifa S, Torres M, Brun C, Vogler G, Bodmer R, Colas AR, Ocorr K, Perrin L. Genetic architecture of natural variation of cardiac performance from flies to humans. eLife 2022; 11:82459. [DOI: 10.7554/elife.82459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
Deciphering the genetic architecture of human cardiac disorders is of fundamental importance but their underlying complexity is a major hurdle. We investigated the natural variation of cardiac performance in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP). Genome-wide associations studies (GWAS) identified genetic networks associated with natural variation of cardiac traits which were used to gain insights as to the molecular and cellular processes affected. Non-coding variants that we identified were used to map potential regulatory non-coding regions, which in turn were employed to predict transcription factors (TFs) binding sites. Cognate TFs, many of which themselves bear polymorphisms associated with variations of cardiac performance, were also validated by heart-specific knockdown. Additionally, we showed that the natural variations associated with variability in cardiac performance affect a set of genes overlapping those associated with average traits but through different variants in the same genes. Furthermore, we showed that phenotypic variability was also associated with natural variation of gene regulatory networks. More importantly, we documented correlations between genes associated with cardiac phenotypes in both flies and humans, which supports a conserved genetic architecture regulating adult cardiac function from arthropods to mammals. Specifically, roles for PAX9 and EGR2 in the regulation of the cardiac rhythm were established in both models, illustrating that the characteristics of natural variations in cardiac function identified in Drosophila can accelerate discovery in humans.
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Affiliation(s)
- Saswati Saha
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Lionel Spinelli
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | | | - Anaïs Kervadec
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Kremmer
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Laurence Roder
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Sallouha Krifa
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Magali Torres
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Christine Brun
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Perrin
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
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14
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Klinke N, Meyer H, Ratnavadivel S, Reinhardt M, Heinisch JJ, Malmendal A, Milting H, Paululat A. A Drosophila melanogaster model for TMEM43-related arrhythmogenic right ventricular cardiomyopathy type 5. Cell Mol Life Sci 2022; 79:444. [PMID: 35869176 PMCID: PMC9307560 DOI: 10.1007/s00018-022-04458-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2022]
Abstract
AbstractArrhythmogenic right ventricular cardiomyopathy (ARVC) is a severe cardiac disease that leads to heart failure or sudden cardiac death (SCD). For the pathogenesis of ARVC, various mutations in at least eight different genes have been identified. A rare form of ARVC is associated with the mutation TMEM43 p.S358L, which is a fully penetrant variant in male carriers. TMEM43 p.S358 is homologous to CG8111 p.S333 in Drosophila melanogaster. We established CRISPR/Cas9-mediated CG8111 knock-out mutants in Drosophila, as well as transgenic fly lines carrying an overexpression construct of the CG8111 p.S333L substitution. Knock-out flies developed normally, whereas the overexpression of CG8111 p.S333L caused growth defects, loss of body weight, cardiac arrhythmias, and premature death. An evaluation of a series of model mutants that replaced S333 by selected amino acids proved that the conserved serine is critical for the physiological function of CG8111. Metabolomic and proteomic analyses revealed that the S333 in CG8111 is essential to proper energy homeostasis and lipid metabolism in the fly. Of note, metabolic impairments were also found in the murine Tmem43 disease model, and fibrofatty replacement is a hallmark of human ARVC5. These findings contribute to a more comprehensive understanding of the molecular functions of CG8111 in Drosophila, and can represent a valuable basis to assess the aetiology of the human TMEM43 p.S358L variant in more detail.
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15
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Quan Y, Wang M, Xu C, Wang X, Wu Y, Qin D, Lin Y, Lu X, Lu F, Li L. Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition. Nucleic Acids Res 2022; 50:4414-4435. [PMID: 35390160 PMCID: PMC9071485 DOI: 10.1093/nar/gkac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 03/11/2022] [Accepted: 03/26/2022] [Indexed: 11/14/2022] Open
Abstract
Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
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Affiliation(s)
- Yujun Quan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meijiao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengpeng Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxuan Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Stoney PN, Yanagiya A, Nishijima S, Yamamoto T. CNOT7 outcompetes its paralog CNOT8 for integration into the CCR4-NOT complex. J Mol Biol 2022; 434:167523. [DOI: 10.1016/j.jmb.2022.167523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/08/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023]
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17
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Jiang ZY, Fan HY. Five questions toward mRNA degradation in oocytes and preimplantation embryos: When, who, to whom, how, and why? Biol Reprod 2022; 107:62-75. [DOI: 10.1093/biolre/ioac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
RNA, the primary product of the genome, is subject to various biological events during its lifetime. During mammalian gametogenesis and early embryogenesis, germ cells and preimplantation embryos undergo marked changes in the transcriptome, including mRNA turnover. Various factors, including specialized proteins, RNAs, and organelles, function in an intricate degradation system, and the degradation selectivity is determined by effectors and their target mRNAs. RNA homeostasis regulators and surveillance factors function in the global transcriptome of oocytes and somatic cells. Other factors, including BTG4, PABPN1L, the CCR4-NOT subunits, CNOT6L and CNOT7, and TUTs, are responsible for two maternal mRNA avalanches: M- and Z-decay. In this review, we discuss recent advances in mRNA degradation mechanisms in mammalian oocytes and preimplantation embryos. We focused on the studies in mice, as a model mammalian species, and on RNA turnover effectors and the cis-elements in targeting RNAs.
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Affiliation(s)
- Zhi-Yan Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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18
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Nim HT, Dang L, Thiyagarajah H, Bakopoulos D, See M, Charitakis N, Sibbritt T, Eichenlaub MP, Archer SK, Fossat N, Burke RE, Tam PPL, Warr CG, Johnson TK, Ramialison M. A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease. Genome Biol 2021; 22:335. [PMID: 34906219 PMCID: PMC8672579 DOI: 10.1186/s13059-021-02539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. RESULTS We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. CONCLUSIONS Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.
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Affiliation(s)
- Hieu T. Nim
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
| | - Louis Dang
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Harshini Thiyagarajah
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Daniel Bakopoulos
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Michael See
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Natalie Charitakis
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Tennille Sibbritt
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Michael P. Eichenlaub
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Stuart K. Archer
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Nicolas Fossat
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
- Present address: Copenhagen Hepatitis C Program, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Present address: Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Richard E. Burke
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Patrick P. L. Tam
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Coral G. Warr
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
- School of Molecular Sciences, La Trobe University, Bundoora, Victoria 3083 Australia
| | - Travis K. Johnson
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
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19
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Sarkar M, Martufi M, Roman-Trufero M, Wang YF, Whilding C, Dormann D, Sabbattini P, Dillon N. CNOT3 interacts with the Aurora B and MAPK/ERK kinases to promote survival of differentiating mesendodermal progenitor cells. Mol Biol Cell 2021; 32:ar40. [PMID: 34613789 PMCID: PMC8694085 DOI: 10.1091/mbc.e21-02-0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 09/23/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022] Open
Abstract
Mesendoderm cells are key intermediate progenitors that form at the early primitive streak (PrS) and give rise to mesoderm and endoderm in the gastrulating embryo. We have identified an interaction between CNOT3 and the cell cycle kinase Aurora B that requires sequences in the NOT box domain of CNOT3 and regulates MAPK/ERK signaling during mesendoderm differentiation. Aurora B phosphorylates CNOT3 at two sites located close to a nuclear localization signal and promotes localization of CNOT3 to the nuclei of mouse embryonic stem cells (ESCs) and metastatic lung cancer cells. ESCs that have both sites mutated give rise to embryoid bodies that are largely devoid of mesoderm and endoderm and are composed mainly of cells with ectodermal characteristics. The mutant ESCs are also compromised in their ability to differentiate into mesendoderm in response to FGF2, BMP4, and Wnt3 due to reduced survival and proliferation of differentiating mesendoderm cells. We also show that the double mutation alters the balance of interaction of CNOT3 with Aurora B and with ERK and reduces phosphorylation of ERK in response to FGF2. Our results identify a potential adaptor function for CNOT3 that regulates the Ras/MEK/ERK pathway during embryogenesis.
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Affiliation(s)
- Moumita Sarkar
- Gene Regulation and Chromatin Group, Imperial College London, London W12 0NN, UK
| | - Matteo Martufi
- Gene Regulation and Chromatin Group, Imperial College London, London W12 0NN, UK
| | - Monica Roman-Trufero
- Gene Regulation and Chromatin Group, Imperial College London, London W12 0NN, UK
| | - Yi-Fang Wang
- Bioinformatics and Computing, Imperial College London, London W12 0NN, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Dirk Dormann
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | | | - Niall Dillon
- Gene Regulation and Chromatin Group, Imperial College London, London W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
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20
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Drosophila Heart as a Model for Cardiac Development and Diseases. Cells 2021; 10:cells10113078. [PMID: 34831301 PMCID: PMC8623483 DOI: 10.3390/cells10113078] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 01/26/2023] Open
Abstract
The Drosophila heart, also referred to as the dorsal vessel, pumps the insect blood, the hemolymph. The bilateral heart primordia develop from the most dorsally located mesodermal cells, migrate coordinately, and fuse to form the cardiac tube. Though much simpler, the fruit fly heart displays several developmental and functional similarities to the vertebrate heart and, as we discuss here, represents an attractive model system for dissecting mechanisms of cardiac aging and heart failure and identifying genes causing congenital heart diseases. Fast imaging technologies allow for the characterization of heartbeat parameters in the adult fly and there is growing evidence that cardiac dysfunction in human diseases could be reproduced and analyzed in Drosophila, as discussed here for heart defects associated with the myotonic dystrophy type 1. Overall, the power of genetics and unsuspected conservation of genes and pathways puts Drosophila at the heart of fundamental and applied cardiac research.
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21
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Migunova E, Theophilopoulos J, Mercadante M, Men J, Zhou C, Dubrovsky EB. ELAC2/RNaseZ-linked cardiac hypertrophy in Drosophila melanogaster. Dis Model Mech 2021; 14:271965. [PMID: 34338278 PMCID: PMC8419712 DOI: 10.1242/dmm.048931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022] Open
Abstract
A severe form of infantile cardiomyopathy (CM) has been linked to mutations in ELAC2, a highly conserved human gene. It encodes Zinc phosphodiesterase ELAC protein 2 (ELAC2), which plays an essential role in the production of mature tRNAs. To establish a causal connection between ELAC2 variants and CM, here we used the Drosophila melanogaster model organism, which carries the ELAC2 homolog RNaseZ. Even though RNaseZ and ELAC2 have diverged in some of their biological functions, our study demonstrates the use of the fly model to study the mechanism of ELAC2-related pathology. We established transgenic lines harboring RNaseZ with CM-linked mutations in the background of endogenous RNaseZ knockout. Importantly, we found that the phenotype of these flies is consistent with the pathological features in human patients. Specifically, expression of CM-linked variants in flies caused heart hypertrophy and led to reduction in cardiac contractility associated with a rare form of CM. This study provides first experimental evidence for the pathogenicity of CM-causing mutations in the ELAC2 protein, and the foundation to improve our understanding and diagnosis of this rare infantile disease. This article has an associated First Person interview with the first author of the paper. Summary: A newly established Drosophila model recapitulates key features of human heart pathology linked to mutations in ELAC2, thus providing experimental evidence of the pathogenicity of ELAC2 variants.
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Affiliation(s)
- Ekaterina Migunova
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
| | | | - Marisa Mercadante
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
| | - Jing Men
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO 63105, USA.,Department of Electrical and Computer Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Chao Zhou
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO 63105, USA
| | - Edward B Dubrovsky
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA.,Center for Cancer, Genetic diseases, and Gene Regulation, Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
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22
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Giri P, Mukhopadhyay A, Gupta M, Mohapatra B. Dilated cardiomyopathy: a new insight into the rare but common cause of heart failure. Heart Fail Rev 2021; 27:431-454. [PMID: 34245424 DOI: 10.1007/s10741-021-10125-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2021] [Indexed: 12/26/2022]
Abstract
Heart failure is a global health burden responsible for high morbidity and mortality with a prevalence of greater than 60 million individuals worldwide. One of the major causes of heart failure is dilated cardiomyopathy (DCM), characterized by associated systolic dysfunction. During the last few decades, there have been remarkable advances in our understanding about the genetics of dilated cardiomyopathy. The genetic causes were initially thought to be associated with mutations in genes encoding proteins that are localized to cytoskeleton and sarcomere only; however, with the advancement in mechanistic understanding, the roles of ion channels, Z-disc, mitochondria, nuclear proteins, cardiac transcription factors (e.g., NKX-2.5, TBX20, GATA4), and the factors involved in calcium homeostasis have also been identified and found to be implicated in both familial and sporadic DCM cases. During past few years, next-generation sequencing (NGS) has been established as a diagnostic tool for genetic analysis and it has added significantly to the existing candidate gene list for DCM. The animal models have also provided novel insights to develop a better treatment strategy based on phenotype-genotype correlation, epigenetic and phenomic profiling. Most of the DCM biomarkers that are used in routine genetic and clinical testing are structural proteins, but during the last few years, the role of mi-RNA has also emerged as a biomarker due to their accessibility through noninvasive methods. Our increasing genetic knowledge can improve the clinical management of DCM by bringing clinicians and geneticists on one platform, thereby influencing the individualized clinical decision making and leading to precision medicine.
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Affiliation(s)
- Prerna Giri
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi-5, India
| | - Amrita Mukhopadhyay
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi-5, India
| | - Mohini Gupta
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi-5, India
| | - Bhagyalaxmi Mohapatra
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi-5, India.
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23
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Priolo M, Radio FC, Pizzi S, Pintomalli L, Pantaleoni F, Mancini C, Cordeddu V, Africa E, Mammì C, Dallapiccola B, Tartaglia M. Co-Occurring Heterozygous CNOT3 and SMAD6 Truncating Variants: Unusual Presentation and Refinement of the IDDSADF Phenotype. Genes (Basel) 2021; 12:genes12071009. [PMID: 34208845 PMCID: PMC8303239 DOI: 10.3390/genes12071009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 11/29/2022] Open
Abstract
Objective, the application of genomic sequencing in clinical practice has allowed us to appreciate the contribution of co-occurring pathogenic variants to complex and unclassified clinical phenotypes. Besides the clinical relevance, these findings have provided evidence of previously unrecognized functional links between genes in the context of developmental processes and physiology. Patients and Methods, a 5-year-old patient showing an unclassified phenotype characterized by developmental delay, speech delay, peculiar behavioral features, facial dysmorphism and severe cardiopathy was analyzed by trio-based whole exome sequencing (WES) analysis to identify the genomic events underlying the condition. Results, two co-occurring heterozygous truncating variants in CNOT3 and SMAD6 were identified. Heterozygous loss-of-function variants in CNOT3, encoding a subunit of the CCR4-NOT protein complex, have recently been reported to cause a syndromic condition known as intellectual developmental disorder with speech delay, autism and dysmorphic facies (IDDSADF). Enrichment of rare/private variants in the SMAD6 gene, encoding a protein negatively controlling transforming growth factor β/bone morphogenetic protein (TGFB/BMP) signaling, has been described in association with a wide spectrum of congenital heart defects. We dissected the contribution of individual variants to the complex clinical manifestations and profiled a previously unappreciated set of facial features and signs characterizing IDDSADF. Conclusions, two concomitant truncating variants in CNOT3 and SMAD6 are the cause of the combination of features documented in the patient resulting in the unique multisystem neurodevelopmental condition. These findings provide evidence for a functional link between the CCR4-NOT complex and TGFB/BMP signaling in processes controlling cardiac development. Finally, the present revision provides evidence that IDDSADF is characterized by a distinctive facial gestalt.
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Affiliation(s)
- Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
| | - Francesca Clementina Radio
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Simone Pizzi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Letizia Pintomalli
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Francesca Pantaleoni
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Cecilia Mancini
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Viviana Cordeddu
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Emilio Africa
- UOC di Neuroradiologia, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy;
| | - Corrado Mammì
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Bruno Dallapiccola
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Marco Tartaglia
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
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24
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The CCR4-NOT deadenylase complex safeguards thymic positive selection by down-regulating aberrant pro-apoptotic gene expression. Nat Commun 2020; 11:6169. [PMID: 33268794 PMCID: PMC7710727 DOI: 10.1038/s41467-020-19975-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 11/05/2020] [Indexed: 12/25/2022] Open
Abstract
A repertoire of T cells with diverse antigen receptors is selected in the thymus. However, detailed mechanisms underlying this thymic positive selection are not clear. Here we show that the CCR4-NOT complex limits expression of specific genes through deadenylation of mRNA poly(A) tails, enabling positive selection. Specifically, the CCR4-NOT complex is up-regulated in thymocytes before initiation of positive selection, where in turn, it inhibits up-regulation of pro-apoptotic Bbc3 and Dab2ip. Elimination of the CCR4-NOT complex permits up-regulation of Bbc3 during a later stage of positive selection, inducing thymocyte apoptosis. In addition, CCR4-NOT elimination up-regulates Dab2ip at an early stage of positive selection. Thus, CCR4-NOT might control thymocyte survival during two-distinct stages of positive selection by suppressing expression levels of pro-apoptotic molecules. Taken together, we propose a link between CCR4-NOT-mediated mRNA decay and T cell selection in the thymus. The CCR4-NOT complex catalyzes mRNA deadenylation and hence regulates protein translation. Here the authors show that CNOT3 regulation of this complex is needed for positive selection of thymocytes via a mechanism involving inhibition of pro-apoptotic gene expression.
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25
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Xia J, Meng Z, Ruan H, Yin W, Xu Y, Zhang T. Heart Development and Regeneration in Non-mammalian Model Organisms. Front Cell Dev Biol 2020; 8:595488. [PMID: 33251221 PMCID: PMC7673453 DOI: 10.3389/fcell.2020.595488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular disease is a serious threat to human health and a leading cause of mortality worldwide. Recent years have witnessed exciting progress in the understanding of heart formation and development, enabling cardiac biologists to make significant advance in the field of therapeutic heart regeneration. Most of our understanding of heart development and regeneration, including the genes and signaling pathways, are driven by pioneering works in non-mammalian model organisms, such as fruit fly, fish, frog, and chicken. Compared to mammalian animal models, non-mammalian model organisms have special advantages in high-throughput applications such as disease modeling, drug discovery, and cardiotoxicity screening. Genetically engineered animals of cardiovascular diseases provide valuable tools to investigate the molecular and cellular mechanisms of pathogenesis and to evaluate therapeutic strategies. A large number of congenital heart diseases (CHDs) non-mammalian models have been established and tested for the genes and signaling pathways involved in the diseases. Here, we reviewed the mechanisms of heart development and regeneration revealed by these models, highlighting the advantages of non-mammalian models as tools for cardiac research. The knowledge from these animal models will facilitate therapeutic discoveries and ultimately serve to accelerate translational medicine.
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Affiliation(s)
- Jianhong Xia
- GMU-GIBH Joint School of Life Sciences, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Zhongxuan Meng
- GMU-GIBH Joint School of Life Sciences, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hongyue Ruan
- GMU-GIBH Joint School of Life Sciences, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wenguang Yin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yiming Xu
- School of Basic Medical Sciences, The Sixth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Tiejun Zhang
- GMU-GIBH Joint School of Life Sciences, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, China
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26
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The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
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27
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Chen H, Miller PW, Johnson DL, Laribee RN. The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity. PLoS Genet 2020; 16:e1009046. [PMID: 33064727 PMCID: PMC7592917 DOI: 10.1371/journal.pgen.1009046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 10/28/2020] [Accepted: 08/12/2020] [Indexed: 01/30/2023] Open
Abstract
The Ccr4-Not complex functions as an effector of multiple signaling pathways that control gene transcription and mRNA turnover. Consequently, Ccr4-Not contributes to a diverse array of processes, which includes a significant role in cell metabolism. Yet a mechanistic understanding of how it contributes to metabolism is lacking. Herein, we provide evidence that Ccr4-Not activates nutrient signaling through the essential target of rapamycin complex 1 (TORC1) pathway. Ccr4-Not disruption reduces global TORC1 signaling, and it also upregulates expression of the cell wall integrity (CWI) pathway terminal kinase Mpk1. Although CWI signaling represses TORC1 signaling, we find that Ccr4-Not loss inhibits TORC1 independently of CWI activation. Instead, we demonstrate that Ccr4-Not promotes the function of the vacuole V-ATPase, which interacts with the Gtr1 GTPase-containing EGO complex to stimulate TORC1 in response to nutrient sufficiency. Bypassing the V-ATPase requirement in TORC1 activation using a constitutively active Gtr1 mutant fully restores TORC1 signaling in Ccr4-Not deficient cells. Transcriptome analysis and functional studies revealed that loss of the Ccr4 subunit activates the TORC1 repressed retrograde signaling pathway to upregulate mitochondrial activity. Blocking this mitochondrial upregulation in Ccr4-Not deficient cells further represses TORC1 signaling, and it causes synergistic deficiencies in mitochondrial-dependent metabolism. These data support a model whereby Ccr4-Not loss impairs V-ATPase dependent TORC1 activation that forces cells to enhance mitochondrial metabolism to sustain a minimal level of TORC1 signaling necessary for cell growth and proliferation. Therefore, Ccr4-Not plays an integral role in nutrient signaling and cell metabolism by promoting V-ATPase dependent TORC1 activation.
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Affiliation(s)
- Hongfeng Chen
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - P. Winston Miller
- Molecular Bioinformatics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Daniel L. Johnson
- Molecular Bioinformatics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - R. Nicholas Laribee
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
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28
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The roles of multifunctional protein ErbB3 binding protein 1 (EBP1) isoforms from development to disease. Exp Mol Med 2020; 52:1039-1047. [PMID: 32719408 PMCID: PMC8080562 DOI: 10.1038/s12276-020-0476-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022] Open
Abstract
The roles of the two isoforms of ErbB3-binding protein 1 (Ebp1) in cellular function and its regulation in disease and development is a stimulating area in current fields of biology, such as neuroscience, cancer biology, and structural biology. Over the last two decades, a growing body of studies suggests have suggested different functions for the EBP1 isoforms in various cancers, along with their specific binding partners in the ubiquitin-proteasome system. Owing to the specific cellular context or spatial/temporal expression of the EBP1 isoforms, either transcriptional repression or the activation function of EBP1 has been proposed, and epigenetic regulation by p48 EBP1 has also been observed during in the embryo development, including in brain development and neurologic disorders, such as schizophrenia, in using an Ebp1 knockout mouse model. Here, we review recent findings that have shaped our current understanding of the emerging function of EBP1 isoforms in cellular events and gene expression, from development to disease. A pair of proteins that originate from a common gene exert strikingly different effects on embryonic development as well as tumor growth and progression. RNA transcripts generated from the PA2G4 gene can undergo enzymatic processing to yield two different protein products, p42 EB1 and p48 EB1. These proteins differ by the presence or absence of 54 amino acids at one end, and Jee-Yin Ahn at the Sungkyunkwan University School of Medicine, Suwon, South Korea, and colleagues have reviewed current insights into the functional consequences of this difference. The two proteins bind to distinct sets of molecular partners. The p48 form appears to regulate a host of genes involved in brain development, but also appears to drive cancerous growth in various tumors. In contrast, p42 is scarcer during development, and appears to inhibit tumor formation.
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29
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Elmén L, Volpato CB, Kervadec A, Pineda S, Kalvakuri S, Alayari NN, Foco L, Pramstaller PP, Ocorr K, Rossini A, Cammarato A, Colas AR, Hicks AA, Bodmer R. Silencing of CCR4-NOT complex subunits affects heart structure and function. Dis Model Mech 2020; 13:dmm044727. [PMID: 32471864 PMCID: PMC7390626 DOI: 10.1242/dmm.044727] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The identification of genetic variants that predispose individuals to cardiovascular disease and a better understanding of their targets would be highly advantageous. Genome-wide association studies have identified variants that associate with QT-interval length (a measure of myocardial repolarization). Three of the strongest associating variants (single-nucleotide polymorphisms) are located in the putative promotor region of CNOT1, a gene encoding the central CNOT1 subunit of CCR4-NOT: a multifunctional, conserved complex regulating gene expression and mRNA stability and turnover. We isolated the minimum fragment of the CNOT1 promoter containing all three variants from individuals homozygous for the QT risk alleles and demonstrated that the haplotype associating with longer QT interval caused reduced reporter expression in a cardiac cell line, suggesting that reduced CNOT1 expression might contribute to abnormal QT intervals. Systematic siRNA-mediated knockdown of CCR4-NOT components in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) revealed that silencing CNOT1 and other CCR4-NOT genes reduced their proliferative capacity. Silencing CNOT7 also shortened action potential duration. Furthermore, the cardiac-specific knockdown of Drosophila orthologs of CCR4-NOT genes in vivo (CNOT1/Not1 and CNOT7/8/Pop2) was either lethal or resulted in dilated cardiomyopathy, reduced contractility or a propensity for arrhythmia. Silencing CNOT2/Not2, CNOT4/Not4 and CNOT6/6L/twin also affected cardiac chamber size and contractility. Developmental studies suggested that CNOT1/Not1 and CNOT7/8/Pop2 are required during cardiac remodeling from larval to adult stages. To summarize, we have demonstrated how disease-associated genes identified by GWAS can be investigated by combining human cardiomyocyte cell-based and whole-organism in vivo heart models. Our results also suggest a potential link of CNOT1 and CNOT7/8 to QT alterations and further establish a crucial role of the CCR4-NOT complex in heart development and function.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Lisa Elmén
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Claudia B Volpato
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Anaïs Kervadec
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Santiago Pineda
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Sreehari Kalvakuri
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Nakissa N Alayari
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Luisa Foco
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Karen Ocorr
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Alessandra Rossini
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Anthony Cammarato
- Johns Hopkins University, Division of Cardiology, 720 Rutland Ave., Baltimore, MD 21205, USA
| | - Alexandre R Colas
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Rolf Bodmer
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
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30
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Tang TTL, Passmore LA. Recognition of Poly(A) RNA through Its Intrinsic Helical Structure. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:21-30. [PMID: 32295929 PMCID: PMC7116106 DOI: 10.1101/sqb.2019.84.039818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polyadenosine (poly(A)) tail, which is found on the 3’ end of almost all eukaryotic messenger RNAs (mRNAs), plays an important role in the posttranscriptional regulation of gene expression. Shortening of the poly(A) tail, a process known as deadenylation, is thought to be the first and rate-limiting step of mRNA turnover. Deadenylation is performed by the Pan2–Pan3 and Ccr4–Not complexes that contain highly conserved exonuclease enzymes Pan2, and Ccr4 and Caf1, respectively. These complexes have been extensively studied, but the mechanisms of how the deadenylase enzymes recognize the poly(A) tail were poorly understood until recently. Here, we summarize recent work from our laboratory demonstrating that the highly conserved Pan2 exonuclease recognizes the poly(A) tail, not through adenine-specific functional groups, but through the conformation of poly(A) RNA. Our biochemical, biophysical, and structural investigations suggest that poly(A) forms an intrinsic base-stacked, single-stranded helical conformation that is recognized by Pan2, and that disruption of this structure inhibits both Pan2 and Caf1. This intrinsic structure has been shown to be important in poly(A) recognition in other biological processes, further underlining the importance of the unique conformation of poly(A).
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Affiliation(s)
- Terence T L Tang
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Lori A Passmore
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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31
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Mostafa D, Takahashi A, Yanagiya A, Yamaguchi T, Abe T, Kureha T, Kuba K, Kanegae Y, Furuta Y, Yamamoto T, Suzuki T. Essential functions of the CNOT7/8 catalytic subunits of the CCR4-NOT complex in mRNA regulation and cell viability. RNA Biol 2020; 17:403-416. [PMID: 31924127 PMCID: PMC6999631 DOI: 10.1080/15476286.2019.1709747] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Shortening of mRNA poly(A) tails (deadenylation) to trigger their decay is mediated mainly by the CCR4-NOT deadenylase complex. While four catalytic subunits (CNOT6, 6L 7, and 8) have been identified in the mammalian CCR4-NOT complex, their individual biological roles are not fully understood. In this study, we addressed the contribution of CNOT7/8 to viability of primary mouse embryonic fibroblasts (MEFs). We found that MEFs lacking CNOT7/8 expression [Cnot7/8-double knockout (dKO) MEFs] undergo cell death, whereas MEFs lacking CNOT6/6L expression (Cnot6/6l-dKO MEFs) remain viable. Co-immunoprecipitation analyses showed that CNOT6/6L are also absent from the CCR4-NOT complex in Cnot7/8-dKO MEFs. In contrast, either CNOT7 or CNOT8 still interacts with other subunits in the CCR4-NOT complex in Cnot6/6l-dKO MEFs. Exogenous expression of a CNOT7 mutant lacking catalytic activity in Cnot7/8-dKO MEFs cannot recover cell viability, even though CNOT6/6L exists to some extent in the CCR4-NOT complex, confirming that CNOT7/8 is essential for viability. Bulk poly(A) tail analysis revealed that mRNAs with longer poly(A) tails are more numerous in Cnot7/8-dKO MEFs than in Cnot6/6l-dKO MEFs. Consistent with elongated poly(A) tails, more mRNAs are upregulated and stabilized in Cnot7/8-dKO MEFs than in Cnot6/6l-dKO MEFs. Importantly, Cnot6/6l-dKO mice are viable and grow normally to adulthood. Taken together, the CNOT7/8 catalytic subunits are essential for deadenylation, which is necessary to maintain cell viability, whereas CNOT6/6L are not.
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Affiliation(s)
- Dina Mostafa
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Akiko Yanagiya
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Taku Kureha
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | - Yumi Kanegae
- Research Center for Medical Science, Jikei University School of Medicine, Tokyo, Japan
| | - Yasuhide Furuta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Laboratory for Immunogenetics, Riken Center of Integrative Medical Sciences, Yokohama, Japan
| | - Toru Suzuki
- Laboratory for Immunogenetics, Riken Center of Integrative Medical Sciences, Yokohama, Japan
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Wang L, Ren A, Tian T, Li N, Cao X, Zhang P, Jin L, Li Z, Shen Y, Zhang B, Finnell RH, Lei Y. Whole-Exome Sequencing Identifies Damaging de novo Variants in Anencephalic Cases. Front Neurosci 2019; 13:1285. [PMID: 31849593 PMCID: PMC6896715 DOI: 10.3389/fnins.2019.01285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Anencephaly is a lethal neural tube defect (NTD). Although variants in several genes have been implicated in the development of anencephaly, a more complete picture of variants in the genome, especially de novo variants (DNVs), remains unresolved. We aim to identify DNVs that play an important role in the development of anencephaly by performing whole-exome DNA sequencing (WES) of proband-parent trios. RESULTS A total of 13 DNVs were identified in 8 anencephaly trios by WES, including two loss of function (LoF) variants detected in pLI > 0.9 genes (SPHKAP, c.2629_2633del, and NCOR1, p.Y1907X). Damaging DNVs were identified in 61.5% (8/13) of the anencephalic cases. Independent validation was conducted in an additional 502 NTD cases. Gene inactivation using targeted morpholino antisense oligomers and rescue assays were conducted in zebrafish, and transfection expression in HEK293T cells. Four DNVs in four cases were identified and predicted to alter protein function, including p.R328Q in WD repeat domain phosphoinositide-interacting 1 (WIPI1). Three variants, p.G313R, p.T418M, and p.L406P, in the WIPI1 gene were identified from the independent replication cohort consisting of 502 cases. Functional analysis suggested that the wipi1 p.L406P and p.R328Q variants most likely displayed loss-of-function effects during embryonic development. CONCLUSION De novo damaging variants are the main culprit for majority of anencephalic cases. Missense variants in WIPI1 may play a role in the genetic etiology of anencephaly, and LoF variants in SPHKAP and NCOR1 may also contribute to anencephaly. These findings add to our existing understanding of the genetic mechanisms of NTD formation.
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Affiliation(s)
- Linlin Wang
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Aiguo Ren
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Tian Tian
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Nan Li
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Xuanye Cao
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Peng Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lei Jin
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Zhiwen Li
- Institute of Reproductive and Child Health, National Health Commission Health Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Yan Shen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Richard H. Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
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33
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Pinard A, Guey S, Guo D, Cecchi AC, Kharas N, Wallace S, Regalado ES, Hostetler EM, Sharrief AZ, Bergametti F, Kossorotoff M, Hervé D, Kraemer M, Bamshad MJ, Nickerson DA, Smith ER, Tournier-Lasserve E, Milewicz DM. The pleiotropy associated with de novo variants in CHD4, CNOT3, and SETD5 extends to moyamoya angiopathy. Genet Med 2019; 22:427-431. [PMID: 31474762 DOI: 10.1038/s41436-019-0639-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/13/2019] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Moyamoya angiopathy (MMA) is a cerebrovascular disease characterized by occlusion of large arteries, which leads to strokes starting in childhood. Twelve altered genes predispose to MMA but the majority of cases of European descent do not have an identified genetic trigger. METHODS Exome sequencing from 39 trios were analyzed. RESULTS We identified four de novo variants in three genes not previously associated with MMA: CHD4, CNOT3, and SETD5. Identification of additional rare variants in these genes in 158 unrelated MMA probands provided further support that rare pathogenic variants in CHD4 and CNOT3 predispose to MMA. Previous studies identified de novo variants in these genes in children with developmental disorders (DD), intellectual disability, and congenital heart disease. CONCLUSION These genes encode proteins involved in chromatin remodeling, and taken together with previously reported genes leading to MMA-like cerebrovascular occlusive disease (YY1AP1, SMARCAL1), implicate disrupted chromatin remodeling as a molecular pathway predisposing to early onset, large artery occlusive cerebrovascular disease. Furthermore, these data expand the spectrum of phenotypic pleiotropy due to alterations of CHD4, CNOT3, and SETD5 beyond DD to later onset disease in the cerebrovascular arteries and emphasize the need to assess clinical complications into adulthood for genes associated with DD.
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Affiliation(s)
- Amélie Pinard
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Stéphanie Guey
- INSERM UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Dongchuan Guo
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alana C Cecchi
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Natasha Kharas
- Department of Neurobiology and Anatomy, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Stephanie Wallace
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ellen S Regalado
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ellen M Hostetler
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Anjail Z Sharrief
- Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Françoise Bergametti
- INSERM UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Manoelle Kossorotoff
- AP-HP, French Center for Pediatric Stroke and Pediatric Neurology Department, University Hospital Necker-Enfants Malades, Paris, France
| | - Dominique Hervé
- AP-HP, Service de neurologie, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de L'œil, Groupe Hospitalier Lariboisière Saint Louis, Paris, France
| | - Markus Kraemer
- Department of Neurology Alfried Krupp-Hospital, Essen and Department of Neurology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Michael J Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Edward R Smith
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elisabeth Tournier-Lasserve
- INSERM UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l'œil, Groupe Hospitalier Saint-Louis Lariboisière, Paris, France
| | - Dianna M Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
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34
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Abstract
The Ccr4-Not complex is an essential multi-subunit protein complex that plays a fundamental role in eukaryotic mRNA metabolism and has a multitude of different roles that impact eukaryotic gene expression . It has a conserved core of three Not proteins, the Ccr4 protein, and two Ccr4 associated factors, Caf1 and Caf40. A fourth Not protein, Not4, is conserved, but is only a stable subunit of the complex in yeast. Certain subunits have been duplicated during evolution, with functional divergence, such as Not3 in yeast, and Ccr4 or Caf1 in human. However the complex includes only one homolog for each protein. In addition, species-specific subunits are part of the complex, such as Caf130 in yeast or Not10 and Not11 in human. Two conserved catalytic functions are associated with the complex, deadenylation and ubiquitination . The complex adopts an L-shaped structure, in which different modules are bound to a large Not1 scaffold protein. In this chapter we will summarize our current knowledge of the architecture of the complex and of the structure of its constituents.
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Affiliation(s)
- Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, Geneva, Switzerland.
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, Geneva, Switzerland
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35
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Walters R, Manion J, Neely GG. Dissecting Motor Neuron Disease With Drosophila melanogaster. Front Neurosci 2019; 13:331. [PMID: 31031583 PMCID: PMC6473072 DOI: 10.3389/fnins.2019.00331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/21/2019] [Indexed: 12/13/2022] Open
Abstract
Motor Neuron Disease (MND) typically affects patients during the later stages of life, and thus, MND is having an increasingly devastating impact on diagnosed individuals, their families and society. The umbrella term MND refers to diseases which cause the progressive loss of upper and/or lower motor neurons and a subsequent decrease in motor ability such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). The study of these diseases is complex and has recently involved the use of genome-wide association studies (GWAS). However, in the case of MND, it has been difficult to identify the complex genetics involved in subtypes, and functional investigation of new candidate disease genes is warranted. Drosophila is a powerful model for addressing these complex diseases. The UAS/Gal4/Gal80 system allows for the upregulation of Drosophila genes, the “knockdown” of genes and the ectopic expression of human genes or mutations in a tissue-specific manner; often resulting in Drosophila models which exhibit typical MND disease pathologies. These can then be further interrogated to identify disease-modifying genes or mutations and disease pathways. This review will discuss two common MNDs and the current Drosophila models which are being used to research their genetic basis and the different pathologies of MND.
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Affiliation(s)
- Rachel Walters
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - John Manion
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - G Gregory Neely
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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Hepatic posttranscriptional network comprised of CCR4-NOT deadenylase and FGF21 maintains systemic metabolic homeostasis. Proc Natl Acad Sci U S A 2019; 116:7973-7981. [PMID: 30926667 DOI: 10.1073/pnas.1816023116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Whole-body metabolic homeostasis is tightly controlled by hormone-like factors with systemic or paracrine effects that are derived from nonendocrine organs, including adipose tissue (adipokines) and liver (hepatokines). Fibroblast growth factor 21 (FGF21) is a hormone-like protein, which is emerging as a major regulator of whole-body metabolism and has therapeutic potential for treating metabolic syndrome. However, the mechanisms that control FGF21 levels are not fully understood. Herein, we demonstrate that FGF21 production in the liver is regulated via a posttranscriptional network consisting of the CCR4-NOT deadenylase complex and RNA-binding protein tristetraprolin (TTP). In response to nutrient uptake, CCR4-NOT cooperates with TTP to degrade AU-rich mRNAs that encode pivotal metabolic regulators, including FGF21. Disruption of CCR4-NOT activity in the liver, by deletion of the catalytic subunit CNOT6L, increases serum FGF21 levels, which ameliorates diet-induced metabolic disorders and enhances energy expenditure without disrupting bone homeostasis. Taken together, our study describes a hepatic CCR4-NOT/FGF21 axis as a hitherto unrecognized systemic regulator of metabolism and suggests that hepatic CCR4-NOT may serve as a target for devising therapeutic strategies in metabolic syndrome and related morbidities.
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Suzuki T, Kikuguchi C, Nishijima S, Nagashima T, Takahashi A, Okada M, Yamamoto T. Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes. Development 2019; 146:dev.168146. [PMID: 30733279 PMCID: PMC6398447 DOI: 10.1242/dev.168146] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 01/21/2019] [Indexed: 12/22/2022]
Abstract
Liver development involves dramatic gene expression changes mediated by transcriptional and post-transcriptional control. Here, we show that the Cnot deadenylase complex plays a crucial role in liver functional maturation. The Cnot3 gene encodes an essential subunit of the Cnot complex. Mice lacking Cnot3 in liver have reduced body and liver masses, and they display anemia and severe liver damage. Histological analyses indicate that Cnot3-deficient (Cnot3−/−) hepatocytes are irregular in size and morphology, resulting in formation of abnormal sinusoids. We observe hepatocyte death, increased abundance of mitotic and mononucleate hepatocytes, and inflammation. Cnot3−/− livers show increased expression of immune response-related, cell cycle-regulating and immature liver genes, while many genes relevant to liver functions, such as oxidation-reduction, lipid metabolism and mitochondrial function, decrease, indicating impaired liver functional maturation. Highly expressed mRNAs possess elongated poly(A) tails and are stabilized in Cnot3−/− livers, concomitant with an increase of the proteins they encode. In contrast, transcription of liver function-related mRNAs was lower in Cnot3−/− livers. We detect efficient suppression of Cnot3 protein postnatally, demonstrating the crucial contribution of mRNA decay to postnatal liver functional maturation. Summary: Regulation of both mRNA transcription and stability plays a crucial role in postnatal liver development; in particular, Cnot complex-mediated mRNA decay is essential for postnatal liver functional maturation.
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Affiliation(s)
- Toru Suzuki
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan
| | - Chisato Kikuguchi
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan
| | - Saori Nishijima
- Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Takeshi Nagashima
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Mariko Okada
- Laboratory for Integrated Cellular Systems, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan.,Laboratory for Cell Systems, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tadashi Yamamoto
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan .,Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
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38
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Kopp Z, Park Y. Longer lifespan in the Rpd3 and Loco signaling results from the reduced catabolism in young age with noncoding RNA. Aging (Albany NY) 2019; 11:230-239. [PMID: 30620723 PMCID: PMC6339784 DOI: 10.18632/aging.101744] [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: 09/02/2018] [Accepted: 12/22/2018] [Indexed: 11/25/2022]
Abstract
Downregulation of Rpd3 (histone deacetylase) or Loco (regulator of G-protein signaling protein) extends Drosophila lifespan with higher stress resistance. We found rpd3-downregulated long-lived flies genetically interact with loco-upregulated short-lived flies in stress resistance and lifespan. Gene expression profiles between those flies revealed that they regulate common target genes in metabolic enzymes and signaling pathways, showing an opposite expression pattern in their contrasting lifespans. Functional analyses of more significantly changed genes indicated that the activities of catabolic enzymes and uptake/storage proteins are reduced in long-lived flies with Rpd3 downregulation. This reduced catabolism exhibited from a young age is considered to be necessary for the resultant longer lifespan of the Rpd3- and Loco-downregulated old flies, which mimics the dietary restriction (DR) effect that extends lifespan in the several species. Inversely, those catabolic activities that break down carbohydrates, lipids, and peptides were high in the short lifespan of Loco-upregulated flies. Long noncoding gene, dntRL (CR45923), was also found as a putative target modulated by Rpd3 and Loco for the longevity. Interestingly, this dntRL could affect stress resistance and lifespan, suggesting that the dntRL lncRNA may be involved in the metabolic mechanism of Rpd3 and Loco signaling.
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Affiliation(s)
- Zachary Kopp
- Department of Cell Biology and Molecular Medicine, Rutgers-New Jersey Medical School, Newark, NJ 07103, USA
| | - Yongkyu Park
- Department of Cell Biology and Molecular Medicine, Rutgers-New Jersey Medical School, Newark, NJ 07103, USA
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39
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CNOT3 targets negative cell cycle regulators in non-small cell lung cancer development. Oncogene 2018; 38:2580-2594. [DOI: 10.1038/s41388-018-0603-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/13/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022]
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40
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Vicente C, Stirparo R, Demeyer S, de Bock CE, Gielen O, Atkins M, Yan J, Halder G, Hassan BA, Cools J. The CCR4-NOT complex is a tumor suppressor in Drosophila melanogaster eye cancer models. J Hematol Oncol 2018; 11:108. [PMID: 30144809 PMCID: PMC6109294 DOI: 10.1186/s13045-018-0650-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CNOT3 protein is a subunit of the CCR4-NOT complex, which is involved in mRNA degradation. We recently identified CNOT3 loss-of-function mutations in patients with T-cell acute lymphoblastic leukemia (T-ALL). METHODS Here, we use different Drosophila melanogaster eye cancer models to study the potential tumor suppressor function of Not3, the CNOT3 orthologue, and other members of the CCR4-NOT complex. RESULTS Our data show that knockdown of Not3, the structural components Not1/Not2, and the deadenylases twin/Pop2 all result in increased tumor formation. In addition, overexpression of Not3 could reduce tumor formation. Not3 downregulation has a mild but broad effect on gene expression and leads to increased levels of genes involved in DNA replication and ribosome biogenesis. CycB upregulation also contributes to the Not3 tumor phenotype. Similar findings were obtained in human T-ALL cell lines, pointing out the conserved function of Not3. CONCLUSIONS Together, our data establish a critical role for Not3 and the entire CCR4-NOT complex as tumor suppressor.
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Affiliation(s)
- Carmen Vicente
- Center for Cancer Biology, VIB, Leuven, Belgium. .,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium. .,Centro de Investigación Médica Aplicada, Av. de Pío XII, 55, 31008, Pamplona, Spain.
| | - Rocco Stirparo
- Center for Cancer Biology, VIB, Leuven, Belgium.,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium
| | - Sofie Demeyer
- Center for Cancer Biology, VIB, Leuven, Belgium.,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium
| | - Charles E de Bock
- Center for Cancer Biology, VIB, Leuven, Belgium.,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium
| | - Olga Gielen
- Center for Cancer Biology, VIB, Leuven, Belgium.,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium
| | - Mardelle Atkins
- Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jiekun Yan
- Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium.,Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - Georg Halder
- Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Bassem A Hassan
- Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium.,Center for Brain & Disease Research, VIB, Leuven, Belgium.,Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, UPMC, Sorbonne Universités, Inserm, CNRS, Paris, France
| | - Jan Cools
- Center for Cancer Biology, VIB, Leuven, Belgium. .,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium.
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41
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Weaver LN, Drummond-Barbosa D. Maintenance of Proper Germline Stem Cell Number Requires Adipocyte Collagen in Adult Drosophila Females. Genetics 2018; 209:1155-1166. [PMID: 29884747 PMCID: PMC6063239 DOI: 10.1534/genetics.118.301137] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
Stem cells reside in specialized niches and are regulated by a variety of physiological inputs. Adipocytes influence whole-body physiology and stem cell lineages; however, the molecular mechanisms linking adipocytes to stem cells are poorly understood. Here, we report that collagen IV produced in adipocytes is transported to the ovary to maintain proper germline stem cell (GSC) number in adult Drosophila females. Adipocyte-derived collagen IV acts through β-integrin signaling to maintain normal levels of E-cadherin at the niche, thereby ensuring proper adhesion to GSCs. These findings demonstrate that extracellular matrix components produced in adipocytes can be transported to and incorporated into an established adult tissue to influence stem cell number.
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Affiliation(s)
- Lesley N Weaver
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Daniela Drummond-Barbosa
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
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42
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The Drosophila homologue of MEGF8 is essential for early development. Sci Rep 2018; 8:8790. [PMID: 29884872 PMCID: PMC5993795 DOI: 10.1038/s41598-018-27076-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/23/2018] [Indexed: 12/15/2022] Open
Abstract
Mutations of the gene MEGF8 cause Carpenter syndrome in humans, and the mouse orthologue has been functionally associated with Nodal and Bmp4 signalling. Here, we have investigated the phenotype associated with loss-of-function of CG7466, a gene that encodes the Drosophila homologue of MEGF8. We generated three different frame-shift null mutations in CG7466 using CRISPR/Cas9 gene editing. Heterozygous flies appeared normal, but homozygous animals had disorganised denticle belts and died as 2nd or 3rd instar larvae. Larvae were delayed in transition to 3rd instars and showed arrested growth, which was associated with abnormal feeding behaviour and prolonged survival when yeast food was supplemented with sucrose. RNAi-mediated knockdown using the Gal4-UAS system resulted in lethality with ubiquitous and tissue-specific Gal4 drivers, and growth defects including abnormal bristle number and orientation in a subset of escapers. We conclude that CG7466 is essential for larval development and that diminished function perturbs denticle and bristle formation.
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43
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Limpitikul WB, Viswanathan MC, O'Rourke B, Yue DT, Cammarato A. Conservation of cardiac L-type Ca 2+ channels and their regulation in Drosophila: A novel genetically-pliable channelopathic model. J Mol Cell Cardiol 2018; 119:64-74. [PMID: 29684406 DOI: 10.1016/j.yjmcc.2018.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/08/2018] [Accepted: 04/11/2018] [Indexed: 01/28/2023]
Abstract
Dysregulation of L-type Ca2+ channels (LTCCs) underlies numerous cardiac pathologies. Understanding their modulation with high fidelity relies on investigating LTCCs in their native environment with intact interacting proteins. Such studies benefit from genetic manipulation of endogenous channels in cardiomyocytes, which often proves cumbersome in mammalian models. Drosophila melanogaster, however, offers a potentially efficient alternative as it possesses a relatively simple heart, is genetically pliable, and expresses well-conserved genes. Fluorescence in situ hybridization confirmed an abundance of Ca-α1D and Ca-α1T mRNA in fly myocardium, which encode subunits that specify hetero-oligomeric channels homologous to mammalian LTCCs and T-type Ca2+ channels, respectively. Cardiac-specific knockdown of Ca-α1D via interfering RNA abolished cardiac contraction, suggesting Ca-α1D (i.e. A1D) represents the primary functioning Ca2+ channel in Drosophila hearts. Moreover, we successfully isolated viable single cardiomyocytes and recorded Ca2+ currents via patch clamping, a feat never before accomplished with the fly model. The profile of Ca2+ currents recorded in individual cells when Ca2+ channels were hypomorphic, absent, or under selective LTCC blockage by nifedipine, additionally confirmed the predominance of A1D current across all activation voltages. T-type current, activated at more negative voltages, was also detected. Lastly, A1D channels displayed Ca2+-dependent inactivation, a critical negative feedback mechanism of LTCCs, and the current through them was augmented by forskolin, an activator of the protein kinase A pathway. In sum, the Drosophila heart possesses a conserved compendium of Ca2+ channels, suggesting that the fly may serve as a robust and effective platform for studying cardiac channelopathies.
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Affiliation(s)
- Worawan B Limpitikul
- Calcium Signals Laboratory, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Baltimore, MD 21205, United States
| | - Meera C Viswanathan
- Institute of CardioScience, Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Baltimore, MD 21205, United States
| | - Brian O'Rourke
- Institute of CardioScience, Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Baltimore, MD 21205, United States
| | - David T Yue
- Calcium Signals Laboratory, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Baltimore, MD 21205, United States
| | - Anthony Cammarato
- Institute of CardioScience, Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Baltimore, MD 21205, United States; Department of Physiology, The Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Baltimore, MD 21205, United States.
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44
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Abstract
The extracellular matrix (ECM) has central roles in tissue integrity and remodeling throughout the life span of animals. While collagens are the most abundant structural components of ECM in most tissues, tissue-specific molecular complexity is contributed by ECM glycoproteins. The matricellular glycoproteins are categorized primarily according to functional criteria and represented predominantly by the thrombospondin, tenascin, SPARC/osteonectin, and CCN families. These proteins do not self-assemble into ECM fibrils; nevertheless, they shape ECM properties through interactions with structural ECM proteins, growth factors, and cells. Matricellular proteins also promote cell migration or morphological changes through adhesion-modulating or counter-adhesive actions on cell-ECM adhesions, intracellular signaling, and the actin cytoskeleton. Typically, matricellular proteins are most highly expressed during embryonic development. In adult tissues, expression is more limited unless activated by cues for dynamic tissue remodeling and cell motility, such as occur during inflammatory response and wound repair. Many insights in the complex roles of matricellular proteins have been obtained from studies of gene knockout mice. However, with the exception of chordate-specific tenascins, these are highly conserved proteins that are encoded in many animal phyla. This review will consider the increasing body of research on matricellular proteins in nonmammalian animal models. These models provide better access to the very earliest stages of embryonic development and opportunities to study biological processes such as limb and organ regeneration. In aggregate, this research is expanding concepts of the functions and mechanisms of action of matricellular proteins.
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Affiliation(s)
- Josephine C Adams
- School of Biochemistry, University of Bristol, Bristol, United Kingdom.
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45
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Abstract
Heart failure places an enormous burden on health and economic systems worldwide. It is a complex disease that is profoundly influenced by both genetic and environmental factors. Neither the molecular mechanisms underlying heart failure nor effective prevention strategies are fully understood. Fortunately, relevant aspects of human heart failure can be experimentally studied in tractable model animals, including the fruit fly, Drosophila, allowing the in vivo application of powerful and sophisticated molecular genetic and physiological approaches. Heart failure in Drosophila, as in humans, can be classified into dilated cardiomyopathies and hypertrophic cardiomyopathies. Critically, many genes and cellular pathways directing heart development and function are evolutionarily conserved from Drosophila to humans. Studies of molecular mechanisms linking aging with heart failure have revealed that genes involved in aging-associated energy homeostasis and oxidative stress resistance influence cardiac dysfunction through perturbation of IGF and TOR pathways. Importantly, ion channel proteins, cytoskeletal proteins, and integrins implicated in aging of the mammalian heart have been shown to play significant roles in heart failure. A number of genes previously described having roles in development of the Drosophila heart, such as genes involved in Wnt signaling pathways, have recently been shown to play important roles in the adult fly heart. Moreover, the fly model presents opportunities for innovative studies that cannot currently be pursued in the mammalian heart because of technical limitations. In this review, we discuss progress in our understanding of genes, proteins, and molecular mechanisms that affect the Drosophila adult heart and heart failure.
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Affiliation(s)
- Shasha Zhu
- The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Zhe Han
- Center for Cancer and Immunology Research, Children's National Medical Center, 111 Michigan Ave. NW, Washington, DC, 20010, USA
| | - Yan Luo
- The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Yulin Chen
- The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Qun Zeng
- The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Xiushan Wu
- The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China.
| | - Wuzhou Yuan
- The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China.
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46
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Heigwer F, Port F, Boutros M. RNA Interference (RNAi) Screening in Drosophila. Genetics 2018; 208:853-874. [PMID: 29487145 PMCID: PMC5844339 DOI: 10.1534/genetics.117.300077] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
In the last decade, RNA interference (RNAi), a cellular mechanism that uses RNA-guided degradation of messenger RNA transcripts, has had an important impact on identifying and characterizing gene function. First discovered in Caenorhabditis elegans, RNAi can be used to silence the expression of genes through introduction of exogenous double-stranded RNA into cells. In Drosophila, RNAi has been applied in cultured cells or in vivo to perturb the function of single genes or to systematically probe gene function on a genome-wide scale. In this review, we will describe the use of RNAi to study gene function in Drosophila with a particular focus on high-throughput screening methods applied in cultured cells. We will discuss available reagent libraries and cell lines, methodological approaches for cell-based assays, and computational methods for the analysis of high-throughput screens. Furthermore, we will review the generation and use of genome-scale RNAi libraries for tissue-specific knockdown analysis in vivo and discuss the differences and similarities with the use of genome-engineering methods such as CRISPR/Cas9 for functional analysis.
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Affiliation(s)
- Florian Heigwer
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, Medical Faculty Mannheim, D-69120, Germany
| | - Fillip Port
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, Medical Faculty Mannheim, D-69120, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, Medical Faculty Mannheim, D-69120, Germany
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47
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Abstract
Autophagy plays a context-dependent role in cardiac homeostasis. In this issue of Science Signaling, Yamaguchi et al delineate a role for CCR4-NOT-mediated mRNA deadenylation in preventing the autophagy factor Atg7 from coactivating p53-mediated transcription of cell death genes in the heart.
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Affiliation(s)
- Saumya Das
- Cardiology Division, Department of Medicine and Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Charles River Plaza, Boston, MA 02114, USA.
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48
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Yamaguchi T, Suzuki T, Sato T, Takahashi A, Watanabe H, Kadowaki A, Natsui M, Inagaki H, Arakawa S, Nakaoka S, Koizumi Y, Seki S, Adachi S, Fukao A, Fujiwara T, Natsume T, Kimura A, Komatsu M, Shimizu S, Ito H, Suzuki Y, Penninger JM, Yamamoto T, Imai Y, Kuba K. The CCR4-NOT deadenylase complex controls Atg7-dependent cell death and heart function. Sci Signal 2018; 11:11/516/eaan3638. [PMID: 29438013 DOI: 10.1126/scisignal.aan3638] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Shortening and removal of the polyadenylate [poly(A)] tail of mRNA, a process called deadenylation, is a key step in mRNA decay that is mediated through the CCR4-NOT (carbon catabolite repression 4-negative on TATA-less) complex. In our investigation of the regulation of mRNA deadenylation in the heart, we found that this complex was required to prevent cell death. Conditional deletion of the CCR4-NOT complex components Cnot1 or Cnot3 resulted in the formation of autophagic vacuoles and cardiomyocyte death, leading to lethal heart failure accompanied by long QT intervals. Cnot3 bound to and shortened the poly(A) tail of the mRNA encoding the key autophagy regulator Atg7. In Cnot3-depleted hearts, Atg7 expression was posttranscriptionally increased. Genetic ablation of Atg7, but not Atg5, increased survival and partially restored cardiac function of Cnot1 or Cnot3 knockout mice. We further showed that in Cnot3-depleted hearts, Atg7 interacted with p53 and modulated p53 activity to induce the expression of genes encoding cell death-promoting factors in cardiomyocytes, indicating that defects in deadenylation in the heart aberrantly activated Atg7 and p53 to promote cell death. Thus, mRNA deadenylation mediated by the CCR4-NOT complex is crucial to prevent Atg7-induced cell death and heart failure, suggesting a role for mRNA deadenylation in targeting autophagy genes to maintain normal cardiac homeostasis.
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Affiliation(s)
- Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Takashi Suzuki
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Teruki Sato
- Department of Cardiovascular and Respiratory Medicine, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Akinori Takahashi
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Hiroyuki Watanabe
- Department of Cardiovascular and Respiratory Medicine, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Ayumi Kadowaki
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Miyuki Natsui
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Hideaki Inagaki
- Bioscience Education and Research Support Center, Akita University, Akita 010-8543, Japan
| | - Satoko Arakawa
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Shinji Nakaoka
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan.,Laboratory for Regulation of Intractable Infectious Diseases, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Yukio Koizumi
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Shinsuke Seki
- Bioscience Education and Research Support Center, Akita University, Akita 010-8543, Japan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Akira Fukao
- Molecular Laboratory of Biochemistry, Department of Pharmacy, Kindai University, Higashi-Osaka 577-8502, Japan
| | - Toshinobu Fujiwara
- Molecular Laboratory of Biochemistry, Department of Pharmacy, Kindai University, Higashi-Osaka 577-8502, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Akinori Kimura
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masaaki Komatsu
- Department of Biochemistry, School of Medicine, Niigata University, Niigata 951-8510, Japan
| | - Shigeomi Shimizu
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroshi Ito
- Department of Cardiovascular and Respiratory Medicine, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Campus Vienna BioCenter, Vienna 1030, Austria
| | - Tadashi Yamamoto
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Yumiko Imai
- Laboratory for Regulation of Intractable Infectious Diseases, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan. .,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Tokyo 102-0076, Japan
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49
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The Impact of CRISPR/Cas9 Technology on Cardiac Research: From Disease Modelling to Therapeutic Approaches. Stem Cells Int 2017; 2017:8960236. [PMID: 29434642 PMCID: PMC5757142 DOI: 10.1155/2017/8960236] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/16/2017] [Indexed: 12/19/2022] Open
Abstract
Genome-editing technology has emerged as a powerful method that enables the generation of genetically modified cells and organisms necessary to elucidate gene function and mechanisms of human diseases. The clustered regularly interspaced short palindromic repeats- (CRISPR-) associated 9 (Cas9) system has rapidly become one of the most popular approaches for genome editing in basic biomedical research over recent years because of its simplicity and adaptability. CRISPR/Cas9 genome editing has been used to correct DNA mutations ranging from a single base pair to large deletions in both in vitro and in vivo model systems. CRISPR/Cas9 has been used to increase the understanding of many aspects of cardiovascular disorders, including lipid metabolism, electrophysiology and genetic inheritance. The CRISPR/Cas9 technology has been proven to be effective in creating gene knockout (KO) or knockin in human cells and is particularly useful for editing induced pluripotent stem cells (iPSCs). Despite these progresses, some biological, technical, and ethical issues are limiting the therapeutic potential of genome editing in cardiovascular diseases. This review will focus on various applications of CRISPR/Cas9 genome editing in the cardiovascular field, for both disease research and the prospect of in vivo genome-editing therapies in the future.
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50
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Mönck H, Toppe D, Michael E, Sigrist S, Richter V, Hilpert D, Raccuglia D, Efetova M, Schwärzel M. A new method to characterize function of the Drosophila heart by means of optical flow. J Exp Biol 2017; 220:4644-4653. [DOI: 10.1242/jeb.164343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/09/2017] [Indexed: 01/05/2023]
Abstract
ABSTRACT
The minuteness of Drosophila poses a challenge to quantify performance of its tubular heart and computer-aided analysis of its beating heart has evolved as a resilient compromise between instrumental costs and data robustness. Here, we introduce an optical flow algorithm (OFA) that continuously registers coherent movement within videos of the beating Drosophila heart and uses this information to subscribe the time course of observation with characteristic phases of cardiac contraction or relaxation. We report that the OFA combines high discriminatory power with robustness to characterize the performance of the Drosophila tubular heart using indicators from human cardiology. We provide proof of this concept using the test bed of established cardiac conditions that include the effects of ageing, knockdown of the slow repolarizing potassium channel subunit KCNQ and ras-mediated hypertrophy of the heart tube. Together, this establishes the analysis of coherent movement as a suitable indicator of qualitative changes of the heart's beating characteristics, which improves the usefulness of Drosophila as a model of cardiac diseases.
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Affiliation(s)
- Hauke Mönck
- Freie Universität Berlin, Department of Biology/Neurobiology, Königin-Luise Strasse 28-30, D-14195 Berlin, Germany
| | - David Toppe
- Freie Universität Berlin, Department of Biology/Neurobiology, Königin-Luise Strasse 28-30, D-14195 Berlin, Germany
| | - Eva Michael
- Freie Universität Berlin, Department of Biology/Neurogenetics, Takustrasse 6, D-14195 Berlin, Germany
| | - Stephan Sigrist
- Freie Universität Berlin, Department of Biology/Neurogenetics, Takustrasse 6, D-14195 Berlin, Germany
| | - Vincent Richter
- Freie Universität Berlin, Department of Biology/Neurobiology, Königin-Luise Strasse 28-30, D-14195 Berlin, Germany
| | - Diana Hilpert
- Freie Universität Berlin, Department of Biology/Neurobiology, Königin-Luise Strasse 28-30, D-14195 Berlin, Germany
| | - Davide Raccuglia
- Institute of Neurophysiology, Charité - Universitätsmedizin, 10117 Berlin, Germany
| | - Marina Efetova
- Freie Universität Berlin, Department of Biology/Neurobiology, Königin-Luise Strasse 28-30, D-14195 Berlin, Germany
| | - Martin Schwärzel
- Freie Universität Berlin, Department of Biology/Neurobiology, Königin-Luise Strasse 28-30, D-14195 Berlin, Germany
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