1
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Banerji CRS, Greco A, Joosten LAB, van Engelen BGM, Zammit PS. The FSHD muscle-blood biomarker: a circulating transcriptomic biomarker for clinical severity in facioscapulohumeral muscular dystrophy. Brain Commun 2023; 5:fcad221. [PMID: 37731904 PMCID: PMC10507741 DOI: 10.1093/braincomms/fcad221] [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: 12/16/2022] [Revised: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable skeletal myopathy. Clinical trials for FSHD are hindered by heterogeneous biomarkers poorly associated with clinical severity, requiring invasive muscle biopsy. Macroscopically, FSHD presents with slow fatty replacement of muscle, rapidly accelerated by inflammation. Mis-expression of the transcription factor DUX4 is currently accepted to underlie pathogenesis, and mechanisms including PAX7 target gene repression have been proposed. Here, we performed RNA-sequencing on MRI-guided inflamed and isogenic non-inflamed muscle biopsies from the same clinically characterized FSHD patients (n = 24), alongside isogenic peripheral blood mononucleated cells from a subset of patients (n = 13) and unaffected controls (n = 11). Multivariate models were employed to evaluate the clinical associations of five published FSHD transcriptomic biomarkers. We demonstrated that PAX7 target gene repression can discriminate control, inflamed and non-inflamed FSHD muscle independently of age and sex (P < 0.013), while the discriminatory power of DUX4 target genes was limited to distinguishing FSHD muscle from control. Importantly, the level of PAX7 target gene repression in non-inflamed muscle associated with clinical assessments of FSHD severity (P = 0.04). DUX4 target gene biomarkers in FSHD muscle showed associations with lower limb fat fraction and D4Z4 array length but not clinical assessment. Lastly, PAX7 target gene repression in FSHD muscle correlated with the level in isogenic peripheral blood mononucleated cells (P = 0.002). A refined PAX7 target gene biomarker comprising 143/601 PAX7 target genes computed in peripheral blood (the FSHD muscle-blood biomarker) associated with clinical severity in FSHD patients (P < 0.036). Our new circulating biomarker validates as a classifier of clinical severity in an independent data set of 54 FSHD patient and 29 matched control blood samples, with improved power in older patients (P = 0.03). In summary, we present the minimally invasive FSHD muscle-blood biomarker of FSHD clinical severity valid in patient muscle and blood, of potential use in routine disease monitoring and clinical trials.
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Affiliation(s)
- Christopher R S Banerji
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- The Alan Turing Institute, The British Library, London NW1 2DB, UK
| | - Anna Greco
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen 6525, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen 6525, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Baziel G M van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Peter S Zammit
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
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2
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Wong CJ, Whiddon JL, Langford AT, Belleville AE, Tapscott SJ. Canine DUXC: Implications for DUX4 retrotransposition and preclinical models of FSHD. Hum Mol Genet 2021; 31:1694-1704. [PMID: 34888646 DOI: 10.1093/hmg/ddab352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 11/15/2022] Open
Abstract
Mis-expression of DUX4 in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). Human DUX4 and mouse Dux are retrogenes derived from retrotransposition of the mRNA from the parental DUXC gene. Primates and rodents have lost the parental DUXC gene and it is unknown whether DUXC had a similar role in driving an early pluripotent transcriptional program. Dogs and other Laurasiatherians have retained DUXC, providing an opportunity to determine the functional similarity to the retrotransposed DUX4 and Dux. Here we identify expression of two isoforms of DUXC mRNA in canine testis tissues, one encoding the canonical double homeodomain protein (DUXC), similar to DUX4/Dux, and a second that includes an in-frame alternative exon that disrupts the conserved amino-acid sequence of the first homeodomain (DUXC-ALT). Expression of DUXC in canine cells induces a pluripotent program similar to DUX4 and Dux, and induces expression of a similar set of retrotransposons of the ERV/MaLR and LINE-1 families, as well as pericentromeric satellite repeats; whereas DUXC-ALT did not robustly activate gene expression in these assays. Important for preclinical models of FSHD, human DUX4 and canine DUXC show higher conservation of their homeodomains and corresponding binding motifs compared to the conservation between human DUX4 and mouse Dux, and human DUX4 activates a highly similar transcriptional program in canine cells. Together, these findings show that retrotransposition resulted in the loss of an alternatively spliced isoform and that DUXC containing mammals might be good candidates for certain pre-clinical models of FSHD.
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Affiliation(s)
- Chao-Jen Wong
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA
| | - Jennifer L Whiddon
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA
| | - Ashlee T Langford
- Comparative Medicine, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA
| | - Andrea E Belleville
- Divisions of Public Health Sciences and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA.,Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle WA USA
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3
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A SARS-CoV-2 host infection model network based on genomic human Transcription Factors (TFs) depletion. Heliyon 2020; 6:e05010. [PMID: 32984567 PMCID: PMC7501776 DOI: 10.1016/j.heliyon.2020.e05010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/30/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
In December 2019 a new beta-coronavirus was isolated and characterized by sequencing samples from pneumonia patients in Wuhan, Hubei Province, China. Coronaviruses are positive-sense RNA viruses widely distributed among different animal species and humans in which they cause respiratory, enteric, liver and neurological symptomatology. Six species of coronavirus have been described (HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1) that cause cold-like symptoms in immunocompetent or immunocompromised subjects and two strains of sometimes fatal zoonotic origin that cause severe acute respiratory syndrome (SARS-CoV and MERS-CoV). The SARS-CoV-2 strain is the emerging seventh member of the coronavirus family, which is actually determining a global emergency. In silico analysis is a promising approach for understanding biological events in complex diseases and due to serious worldwide emergency and serious threat to global health, it is extremely important to use bioinformatics methods able to study an emerging pathogen like SARS-CoV-2. Herein, we report on in silico comparative analysis between complete genome of SARS-CoV, MERS-CoV, HCoV-OC43 and SARS-CoV-2 strains, to identify the occurrence of specific conserved motifs on viral genomic sequences which should be able to bind and therefore induce a subtraction of host's Transcription Factors (TFs) which lead to a depletion, an effect comparable to haploinsufficiency (a genetic dominant condition in which a single copy of wild-type allele at a locus, in heterozygous combination with a variant allele, is insufficient to produce the correct quantity of transcript and, therefore, of protein, for a correct standard phenotypic expression). In this competitive scenario, virus versus host, the proposed in silico protocol identified the TFs same as the distribution of TFBSs (Transcription Factor Binding Sites) on analyzed viral strains, potentially able to influence genes and pathways with biological functions confirming that this approach could brings useful insights regarding SARS-CoV-2. According to our results obtained by this in silico approach it is possible to hypothesize that TF-binding motifs could be of help in the explanation of the complex and heterogeneous clinical presentation in SARS-CoV-2 and subsequently predict possible interactions regarding metabolic pathways, and drug or target relationships.
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4
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Eidahl JO, Giesige CR, Domire JS, Wallace LM, Fowler AM, Guckes SM, Garwick-Coppens SE, Labhart P, Harper SQ. Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4. Hum Mol Genet 2018; 25:4577-4589. [PMID: 28173143 PMCID: PMC5409219 DOI: 10.1093/hmg/ddw287] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 08/19/2016] [Accepted: 08/25/2016] [Indexed: 01/28/2023] Open
Abstract
D4Z4 repeats are present in at least 11 different mammalian species, including humans and mice. Each repeat contains an open reading frame encoding a double homeodomain (DUX) family transcription factor. Aberrant expression of the D4Z4 ORF called DUX4 is associated with the pathogenesis of Facioscapulohumeral muscular dystrophy (FSHD). DUX4 is toxic to numerous cell types of different species, and over-expression caused dysmorphism and developmental arrest in frogs and zebrafish, embryonic lethality in transgenic mice, and lesions in mouse muscle. Because DUX4 is a primate-specific gene, questions have been raised about the biological relevance of over-expressing it in non-primate models, as DUX4 toxicity could be related to non-specific cellular stress induced by over-expressing a DUX family transcription factor in organisms that did not co-evolve its regulated transcriptional networks. We assessed toxic phenotypes of DUX family genes, including DUX4, DUX1, DUX5, DUXA, DUX4-s, Dux-bl and mouse Dux. We found that DUX proteins were not universally toxic, and only the mouse Dux gene caused similar toxic phenotypes as human DUX4. Using RNA-seq, we found that 80% of genes upregulated by Dux were similarly increased in DUX4-expressing cells. Moreover, 43% of Dux-responsive genes contained ChIP-seq binding sites for both Dux and DUX4, and both proteins had similar consensus binding site sequences. These results suggested DUX4 and Dux may regulate some common pathways, and despite diverging from a common progenitor under different selective pressures for millions of years, the two genes maintain partial functional homology.
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Affiliation(s)
- Jocelyn O Eidahl
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Carlee R Giesige
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Jacqueline S Domire
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Lindsay M Wallace
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Allison M Fowler
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Susan M Guckes
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Sara E Garwick-Coppens
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Scott Q Harper
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
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5
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Dmitriev P, Kiseleva E, Kharchenko O, Ivashkin E, Pichugin A, Dessen P, Robert T, Coppée F, Belayew A, Carnac G, Laoudj-Chenivesse D, Lipinski M, Vasiliev A, Vassetzky YS. Dux4 controls migration of mesenchymal stem cells through the Cxcr4-Sdf1 axis. Oncotarget 2018; 7:65090-65108. [PMID: 27556182 PMCID: PMC5323140 DOI: 10.18632/oncotarget.11368] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/10/2016] [Indexed: 12/13/2022] Open
Abstract
We performed transcriptome profiling of human immortalized myoblasts (MB) transiently expressing double homeobox transcription factor 4 (DUX4) and double homeobox transcription factor 4 centromeric (DUX4c) and identified 114 and 70 genes differentially expressed in DUX4- and DUX4c-transfected myoblasts, respectively. A significant number of differentially expressed genes were involved in inflammation, cellular migration and chemotaxis suggesting a role for DUX4 and DUX4c in these processes. DUX4 but not DUX4c overexpression resulted in upregulation of the CXCR4 (C-X-C motif Receptor 4) and CXCL12 (C-X-C motif ligand 12 also known as SDF1) expression in human immortalized myoblasts. In a Transwell cell migration assay, human bone marrow-derived mesenchymal stem cells (BMSCs) were migrating more efficiently towards human immortalized myoblasts overexpressing DUX4 as compared to controls; the migration efficiency of DUX4-transfected BMSCs was also increased. DUX4c overexpression in myoblasts or in BMSCs had no impact on the rate of BMSC migration. Antibodies against SDF1 and CXCR4 blocked the positive effect of DUX4 overexpression on BMSC migration. We propose that DUX4 controls the cellular migration of mesenchymal stem cells through the CXCR4 receptor.
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Affiliation(s)
- Petr Dmitriev
- UMR 8126, Univ. Paris-Sud, CNRS, Institut de Cancérologie Gustave-Roussy, Villejuif, France.,LIA1066 Laboratoire Franco-Russe de Recherches en Oncologie, Villejuif, France
| | - Ekaterina Kiseleva
- LIA1066 Laboratoire Franco-Russe de Recherches en Oncologie, Villejuif, France.,N.K. Koltzov Institute of Developmental Biology, RAS, Moscow, Russia
| | - Olga Kharchenko
- LIA1066 Laboratoire Franco-Russe de Recherches en Oncologie, Villejuif, France.,N.K. Koltzov Institute of Developmental Biology, RAS, Moscow, Russia
| | - Evgeny Ivashkin
- LIA1066 Laboratoire Franco-Russe de Recherches en Oncologie, Villejuif, France.,N.K. Koltzov Institute of Developmental Biology, RAS, Moscow, Russia
| | - Andrei Pichugin
- LIA1066 Laboratoire Franco-Russe de Recherches en Oncologie, Villejuif, France.,N.K. Koltzov Institute of Developmental Biology, RAS, Moscow, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Philippe Dessen
- Functional Genomics Unit, Institut de Cancérologie Gustave-Roussy, Villejuif, France
| | - Thomas Robert
- Functional Genomics Unit, Institut de Cancérologie Gustave-Roussy, Villejuif, France
| | - Frédérique Coppée
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Alexandra Belayew
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Gilles Carnac
- PhyMedExp, University of Montpellier, INSERM U1046, CNRS UMR 9214, Montpellier, France
| | | | - Marc Lipinski
- UMR 8126, Univ. Paris-Sud, CNRS, Institut de Cancérologie Gustave-Roussy, Villejuif, France.,LIA1066 Laboratoire Franco-Russe de Recherches en Oncologie, Villejuif, France
| | - Andrei Vasiliev
- N.K. Koltzov Institute of Developmental Biology, RAS, Moscow, Russia
| | - Yegor S Vassetzky
- UMR 8126, Univ. Paris-Sud, CNRS, Institut de Cancérologie Gustave-Roussy, Villejuif, France.,LIA1066 Laboratoire Franco-Russe de Recherches en Oncologie, Villejuif, France.,N.K. Koltzov Institute of Developmental Biology, RAS, Moscow, Russia
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6
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Moyle LA, Blanc E, Jaka O, Prueller J, Banerji CR, Tedesco FS, Harridge SD, Knight RD, Zammit PS. Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral muscular dystrophy. eLife 2016; 5. [PMID: 27841748 PMCID: PMC5108591 DOI: 10.7554/elife.11405] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 09/01/2016] [Indexed: 12/16/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) involves sporadic expression of DUX4, which inhibits myogenesis and is pro-apoptotic. To identify target genes, we over-expressed DUX4 in myoblasts and found that the receptor tyrosine kinase Ret was significantly up-regulated, suggesting a role in FSHD. RET is dynamically expressed during myogenic progression in mouse and human myoblasts. Constitutive expression of either RET9 or RET51 increased myoblast proliferation, whereas siRNA-mediated knockdown of Ret induced myogenic differentiation. Suppressing RET activity using Sunitinib, a clinically-approved tyrosine kinase inhibitor, rescued differentiation in both DUX4-expressing murine myoblasts and in FSHD patient-derived myoblasts. Importantly, Sunitinib also increased engraftment and differentiation of FSHD myoblasts in regenerating mouse muscle. Thus, DUX4-mediated activation of Ret prevents myogenic differentiation and could contribute to FSHD pathology by preventing satellite cell-mediated repair. Rescue of DUX4-induced pathology by Sunitinib highlights the therapeutic potential of tyrosine kinase inhibitors for treatment of FSHD. DOI:http://dx.doi.org/10.7554/eLife.11405.001
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Affiliation(s)
- Louise A Moyle
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.,Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Eric Blanc
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.,Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany.,Institute of Pathology, Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Oihane Jaka
- Centre of Human and Aerospace Physiological Sciences, King's College London, London, United Kingdom
| | - Johanna Prueller
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Christopher Rs Banerji
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | | | - Stephen Dr Harridge
- Centre of Human and Aerospace Physiological Sciences, King's College London, London, United Kingdom
| | - Robert D Knight
- Craniofacial Development and Stem Cell Biology, King's College London, London, United Kingdom
| | - Peter S Zammit
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
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7
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Zhang Y, Lee JK, Toso EA, Lee JS, Choi SH, Slattery M, Aihara H, Kyba M. DNA-binding sequence specificity of DUX4. Skelet Muscle 2016; 6:8. [PMID: 26823969 PMCID: PMC4730607 DOI: 10.1186/s13395-016-0080-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/08/2016] [Indexed: 11/10/2022] Open
Abstract
Background Misexpression of the double homeodomain transcription factor DUX4 results in facioscapulohumeral muscular dystrophy (FSHD). A DNA-binding consensus with two tandem TAAT motifs based on chromatin IP peaks has been discovered; however, the consensus has multiple variations (flavors) of unknown relative activity. In addition, not all peaks have this consensus, and the Pitx1 promoter, the first DUX4 target sequence mooted, has a different TAAT-rich sequence. Furthermore, it is not known whether and to what extent deviations from the consensus affect DNA-binding affinity and transcriptional activation potential. Results Here, we take both unbiased and consensus sequence-driven approaches to determine the DNA-binding specificity of DUX4 and its tolerance to mismatches at each site within its consensus sequence. We discover that the best binding and the greatest transcriptional activation are observed when the two TAAT motifs are separated by a C residue. The second TAAT motif in the consensus sequence is actually (T/C)AAT. We find that a T is preferred here. DUX4 has no transcriptional activity on “half-sites”, i.e., those bearing only a single TAAT motif. We further find that DUX4 does not bind to the TAATTA motif in the Pitx1 promoter, that Pitx1 sequences have no competitive band shift activity, and that the Pitx1 sequence is transcriptionally inactive, calling into question PITX1 as a DUX4 target gene. Finally, by multimerizing binding sites, we find that DUX4 transcriptional activation demonstrates tremendous synergy and that at low DNA concentrations, at least two motifs are necessary to detect a transcriptional response. Conclusions These studies illuminate the DNA-binding sequence preferences of DUX4. Electronic supplementary material The online version of this article (doi:10.1186/s13395-016-0080-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Zhang
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455 USA ; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455 USA
| | - John K Lee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Erik A Toso
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455 USA ; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Joslynn S Lee
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812 USA
| | - Si Ho Choi
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455 USA ; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455 USA ; Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan, South Korea
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812 USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455 USA ; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455 USA
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8
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Ansseau E, Eidahl JO, Lancelot C, Tassin A, Matteotti C, Yip C, Liu J, Leroy B, Hubeau C, Gerbaux C, Cloet S, Wauters A, Zorbo S, Meyer P, Pirson I, Laoudj-Chenivesse D, Wattiez R, Harper SQ, Belayew A, Coppée F. Homologous Transcription Factors DUX4 and DUX4c Associate with Cytoplasmic Proteins during Muscle Differentiation. PLoS One 2016; 11:e0146893. [PMID: 26816005 PMCID: PMC4729438 DOI: 10.1371/journal.pone.0146893] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022] Open
Abstract
Hundreds of double homeobox (DUX) genes map within 3.3-kb repeated elements dispersed in the human genome and encode DNA-binding proteins. Among these, we identified DUX4, a potent transcription factor that causes facioscapulohumeral muscular dystrophy (FSHD). In the present study, we performed yeast two-hybrid screens and protein co-purifications with HaloTag-DUX fusions or GST-DUX4 pull-down to identify protein partners of DUX4, DUX4c (which is identical to DUX4 except for the end of the carboxyl terminal domain) and DUX1 (which is limited to the double homeodomain). Unexpectedly, we identified and validated (by co-immunoprecipitation, GST pull-down, co-immunofluorescence and in situ Proximal Ligation Assay) the interaction of DUX4, DUX4c and DUX1 with type III intermediate filament protein desmin in the cytoplasm and at the nuclear periphery. Desmin filaments link adjacent sarcomere at the Z-discs, connect them to sarcolemma proteins and interact with mitochondria. These intermediate filament also contact the nuclear lamina and contribute to positioning of the nuclei. Another Z-disc protein, LMCD1 that contains a LIM domain was also validated as a DUX4 partner. The functionality of DUX4 or DUX4c interactions with cytoplasmic proteins is underscored by the cytoplasmic detection of DUX4/DUX4c upon myoblast fusion. In addition, we identified and validated (by co-immunoprecipitation, co-immunofluorescence and in situ Proximal Ligation Assay) as DUX4/4c partners several RNA-binding proteins such as C1QBP, SRSF9, RBM3, FUS/TLS and SFPQ that are involved in mRNA splicing and translation. FUS and SFPQ are nuclear proteins, however their cytoplasmic translocation was reported in neuronal cells where they associated with ribonucleoparticles (RNPs). Several other validated or identified DUX4/DUX4c partners are also contained in mRNP granules, and the co-localizations with cytoplasmic DAPI-positive spots is in keeping with such an association. Large muscle RNPs were recently shown to exit the nucleus via a novel mechanism of nuclear envelope budding. Following DUX4 or DUX4c overexpression in muscle cell cultures, we observed their association with similar nuclear buds. In conclusion, our study demonstrated unexpected interactions of DUX4/4c with cytoplasmic proteins playing major roles during muscle differentiation. Further investigations are on-going to evaluate whether these interactions play roles during muscle regeneration as previously suggested for DUX4c.
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Affiliation(s)
- Eugénie Ansseau
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Jocelyn O. Eidahl
- Center for Gene Therapy, Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
| | - Céline Lancelot
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Alexandra Tassin
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Christel Matteotti
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Cassandre Yip
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Jian Liu
- Center for Gene Therapy, Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
| | - Baptiste Leroy
- Laboratory of Proteomic and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Céline Hubeau
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Cécile Gerbaux
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Samuel Cloet
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Armelle Wauters
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Sabrina Zorbo
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Pierre Meyer
- Pediatric Department, CHRU Montpellier, Montpellier, France
| | - Isabelle Pirson
- I.R.I.B.H.M., Free University of Brussels, Brussels, Belgium
| | | | - Ruddy Wattiez
- Laboratory of Proteomic and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Scott Q. Harper
- Center for Gene Therapy, Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
- Department of Pediatrics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Alexandra Belayew
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Frédérique Coppée
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
- * E-mail:
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9
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de la Kethulle de Ryhove L, Ansseau E, Nachtegael C, Pieters K, Vanderplanck C, Geens M, Sermon K, Wilton SD, Coppée F, Lagneaux L, Belayew A. The Role of D4Z4-Encoded Proteins in the Osteogenic Differentiation of Mesenchymal Stromal Cells Isolated from Bone Marrow. Stem Cells Dev 2015; 24:2674-86. [PMID: 26192274 DOI: 10.1089/scd.2014.0575] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is associated with an activation of the double homeobox 4 (DUX4) gene, which we previously identified within the D4Z4 repeated elements in the 4q35 subtelomeric region. The pathological DUX4 mRNA is derived from the most distal D4Z4 unit and extends unexpectedly within the flanking pLAM region, which provides an intron and polyadenylation signal. The conditions that are required to develop FSHD are a permissive allele providing the polyadenylation signal and hypomethylation of the D4Z4 repeat array compared with the healthy muscle. The DUX4 protein is a 52-kDa transcription factor that initiates a large gene deregulation cascade leading to muscle atrophy, inflammation, differentiation defects, and oxidative stress, which are the key features of FSHD. DUX4 is a retrogene that is normally expressed in germline cells and is submitted to repeat-induced silencing in adult tissues. Since DUX4 mRNAs have been detected in human embryonic and induced pluripotent stem cells, we investigated whether they could also be expressed in human mesenchymal stromal cells (hMSCs). We found that DUX4 mRNAs were induced during the differentiation of hMSCs into osteoblasts and that this process involved DUX4 and new longer protein forms (58 and 70 kDa). A DUX4 mRNA with a more distant 5' start site was characterized that presented a 60-codon reading frame extension and encoded the 58-kDa protein. Transfections of hMSCs with an antisense oligonucleotide targeting DUX4 mRNAs decreased both the 52- and 58-kDa protein levels and confirmed their identity. Gain- and loss-of-function experiments in hMSCs suggested these DUX4 proteins had opposite roles in osteogenic differentiation as evidenced by the alkaline phosphatase activity and calcium deposition. Differentiation was delayed by the 58-kDa DUX4 expression and it was increased by 52-kDa DUX4. These data indicate a role for DUX4 protein forms in the osteogenic differentiation of hMSCs.
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Affiliation(s)
| | - Eugénie Ansseau
- 1 Laboratory of Molecular Biology, University of Mons , Mons, Belgium
| | | | - Karlien Pieters
- 2 Laboratory of Clinical Cell Therapy, Institut Jules Bordet, Université Libre de Bruxelles , Brussels, Belgium
| | | | - Mieke Geens
- 3 Department of Embryology and Genetics, Vrije Universiteit Brussel , Jette, Belgium
| | - Karen Sermon
- 3 Department of Embryology and Genetics, Vrije Universiteit Brussel , Jette, Belgium
| | - Steve D Wilton
- 4 Centre for Comparative Genomics, Murdoch University , Murdoch, and The University of Western Australia, Crawley, and Western Australian Neuroscience Institute, Nedlands, Western Australia, Australia
| | - Frédérique Coppée
- 1 Laboratory of Molecular Biology, University of Mons , Mons, Belgium
| | - Laurence Lagneaux
- 2 Laboratory of Clinical Cell Therapy, Institut Jules Bordet, Université Libre de Bruxelles , Brussels, Belgium
| | - Alexandra Belayew
- 1 Laboratory of Molecular Biology, University of Mons , Mons, Belgium
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10
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Tawil R, van der Maarel SM, Tapscott SJ. Facioscapulohumeral dystrophy: the path to consensus on pathophysiology. Skelet Muscle 2014; 4:12. [PMID: 24940479 PMCID: PMC4060068 DOI: 10.1186/2044-5040-4-12] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/13/2014] [Indexed: 01/07/2023] Open
Abstract
Although the pathophysiology of facioscapulohumeral dystrophy (FSHD) has been controversial over the last decades, progress in recent years has led to a model that incorporates these decades of findings and is gaining general acceptance in the FSHD research community. Here we review how the contributions from many labs over many years led to an understanding of a fundamentally new mechanism of human disease. FSHD is caused by inefficient repeat-mediated epigenetic repression of the D4Z4 macrosatellite repeat array on chromosome 4, resulting in the variegated expression of the DUX4 retrogene, encoding a double-homeobox transcription factor, in skeletal muscle. Normally expressed in the testis and epigenetically repressed in somatic tissues, DUX4 expression in skeletal muscle induces expression of many germline, stem cell, and other genes that might account for the pathophysiology of FSHD. Although some disagreements regarding the details of mechanisms remain in the field, the coalescing agreement on a central model of pathophysiology represents a pivot-point in FSHD research, transitioning the field from discovery-oriented studies to translational studies aimed at developing therapies based on a sound model of disease pathophysiology.
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Affiliation(s)
- Rabi Tawil
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Stephen J Tapscott
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Neurology, University of Washington, Seattle, WA 98105, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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