1
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Madè A, Bibi A, Garcia-Manteiga JM, Tascini AS, Piella SN, Tikhomirov R, Voellenkle C, Gaetano C, Leszek P, Castelvecchio S, Menicanti L, Martelli F, Greco S. circRNA-miRNA-mRNA Deregulated Network in Ischemic Heart Failure Patients. Cells 2023; 12:2578. [PMID: 37947656 PMCID: PMC10648415 DOI: 10.3390/cells12212578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Noncoding RNAs (ncRNAs), which include circular RNAs (circRNAs) and microRNAs (miRNAs), regulate the development of cardiovascular diseases (CVD). Notably, circRNAs can interact with miRNAs, influencing their specific mRNA targets' levels and shaping a competing endogenous RNAs (ceRNA) network. However, these interactions and their respective functions remain largely unexplored in ischemic heart failure (IHF). This study is aimed at identifying circRNA-centered ceRNA networks in non-end-stage IHF. Approximately 662 circRNA-miRNA-mRNA interactions were identified in the heart by combining state-of-the-art bioinformatics tools with experimental data. Importantly, KEGG terms of the enriched mRNA indicated CVD-related signaling pathways. A specific network centered on circBPTF was validated experimentally. The levels of let-7a-5p, miR-18a-3p, miR-146b-5p, and miR-196b-5p were enriched in circBPTF pull-down experiments, and circBPTF silencing inhibited the expression of HDAC9 and LRRC17, which are targets of miR-196b-5p. Furthermore, as suggested by the enriched pathway terms of the circBPTF ceRNA network, circBPTF inhibition elicited endothelial cell cycle arrest. circBPTF expression increased in endothelial cells exposed to hypoxia, and its upregulation was confirmed in cardiac samples of 36 end-stage IHF patients compared to healthy controls. In conclusion, circRNAs act as miRNA sponges, regulating the functions of multiple mRNA targets, thus providing a novel vision of HF pathogenesis and laying the theoretical foundation for further experimental studies.
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Affiliation(s)
- Alisia Madè
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Alessia Bibi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
- Department of Biosciences, University of Milan, 20122 Milan, Italy
| | - Jose Manuel Garcia-Manteiga
- Center for Omics Sciences COSR, BioInformatics Laboratory, San Raffaele Scientific Institute, 20132 Milan, Italy; (J.M.G.-M.); (A.S.T.)
| | - Anna Sofia Tascini
- Center for Omics Sciences COSR, BioInformatics Laboratory, San Raffaele Scientific Institute, 20132 Milan, Italy; (J.M.G.-M.); (A.S.T.)
- Università Vita-Salute San Raffaele, 20132 Milan, Italy
| | - Santiago Nicolas Piella
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Roman Tikhomirov
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Carlo Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy;
| | - Przemyslaw Leszek
- Department of Heart Failure and Transplantology, National Institute of Cardiology, 04-628 Warsaw, Poland;
| | - Serenella Castelvecchio
- Department of Adult Cardiac Surgery, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (S.C.); (L.M.)
| | - Lorenzo Menicanti
- Department of Adult Cardiac Surgery, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (S.C.); (L.M.)
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Simona Greco
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
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2
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Greco S, Piella SN, Made' A, Tascini AS, Garcia-Manteiga JM, Castelvecchio S, Menicanti L, Martelli F. LncRNA BACE1-AS: a link between heart failure and Alzheimer's disease. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
BACE1-antisense RNA (BACE1-AS) is a lncRNA antisense to the Beta-Secretase-1 (BACE1) gene encoding a key enzyme in the production of the β-amyloid peptide, associated to Alzheimer's disease (AD). In a previous study1, we showed that the BACE1-AS/BACE1 axis is activated in heart failure (HF) patients, leading to β-amyloid accumulation in failing hearts. Accordingly, BACE1-AS expression in different cultured cardiac cell types induced the expression of BACE1 and β-amyloid that, in turn, triggered apoptosis. The mechanisms underlying BACE1-AS action are not yet fully elucidated. Indeed, current models based on miRNA “sponging” or “masking” inducing BACE1 post-transcriptional stabilization may not recapitulate all BACE1-AS functions.
Purpose
Our aim is to investigate the molecular mechanisms regulated by BACE1-AS in heart failure disease.
Methods
BACE1-AS-pull-down, followed by RNA-Seq, was used to identify RNAs interacting with BACE1-AS in AC16 cardiomyocytes. Moreover, accessible chromatin sites induced by BACE1-AS overexpression were assayed by ATAC-Seq.
Results
BACE1-AS pull-down identified 698 BACE1-AS interacting RNAs. Among these enriched transcripts, 69 were mapping to genomic enhancer regions that have been found to be hypo-methylated in AD brains2. After qPCR validation of the interactions identified by RNA-seq, the modulation of SEMA4D, ABCG1, GFRA2 and RIMBP2, which were under the control of a subset of these enhancers, was assayed upon BACE1-AS overexpression in cardiomyocytes. It was found that their expression was induced, supporting the functional interaction between BACE1-AS and the identified enhancer loci.
To gain further insight into BACE1-AS function in cardiomyocytes, accessible chromatin sites induced by BACE1-AS overexpression were assayed by ATAC-Seq. Interestingly, 17 regions identified by this approach overlapped with enhancers that are hypo-methylated in AD brains. One of the accessible chromatin sites was the locus encompassing RNF214/BACE1/BACE1-AS that maps to active enhancer marks, indicating that BACE1-AS may regulate the expression of BACE1 transcriptionally.
Conclusion
Collectively, these data suggest BACE1-AS as a node of shared disease-mechanisms between heart failure and AD.
Funding Acknowledgement
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Italian Ministry of Health
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Affiliation(s)
- S Greco
- IRCCS Policlinico San Donato , San Donato Milanese , Italy
| | - S N Piella
- IRCCS Policlinico San Donato , San Donato Milanese , Italy
| | - A Made'
- IRCCS Policlinico San Donato , San Donato Milanese , Italy
| | - A S Tascini
- IRCCS Ospedale San Raffaele, Center for Omics Sciences , Milano , Italy
| | | | | | - L Menicanti
- IRCCS Policlinico San Donato , San Donato Milanese , Italy
| | - F Martelli
- IRCCS Policlinico San Donato , San Donato Milanese , Italy
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3
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Lenti E, Genovese L, Bianchessi S, Maurizio A, Sain SB, di Lillo A, Mattavelli G, Harel I, Bernassola F, Hehlgans T, Pfeffer K, Crosti M, Abrignani S, Evans SM, Sitia G, Guimarães-Camboa N, Russo V, van de Pavert SA, Garcia-Manteiga JM, Brendolan A. Fate mapping and scRNA sequencing reveal origin and diversity of lymph node stromal precursors. Immunity 2022; 55:606-622.e6. [PMID: 35358427 DOI: 10.1016/j.immuni.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/30/2021] [Accepted: 03/03/2022] [Indexed: 11/25/2022]
Abstract
Lymph node (LN) stromal cells play a crucial role in LN development and in supporting adaptive immune responses. However, their origin, differentiation pathways, and transcriptional programs are still elusive. Here, we used lineage-tracing approaches and single-cell transcriptome analyses to determine origin, transcriptional profile, and composition of LN stromal and endothelial progenitors. Our results showed that all major stromal cell subsets and a large proportion of blood endothelial cells originate from embryonic Hoxb6+ progenitors of the lateral plate mesoderm (LPM), whereas lymphatic endothelial cells arise from Pax3+ progenitors of the paraxial mesoderm (PXM). Single-cell RNA sequencing revealed the existence of different Cd34+ and Cxcl13+ stromal cell subsets and showed that embryonic LNs contain proliferating progenitors possibly representing the amplifying populations for terminally differentiated cells. Taken together, our work identifies the earliest embryonic sources of LN stromal and endothelial cells and demonstrates that stromal diversity begins already during LN development.
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Affiliation(s)
- Elisa Lenti
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Genovese
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Bianchessi
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Aurora Maurizio
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simona Baghai Sain
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessia di Lillo
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Greta Mattavelli
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Itamar Harel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Francesca Bernassola
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome 00133, Italy
| | - Thomas Hehlgans
- Leibniz Institute of Immunotherapy (LIT), Chair for Immunology, University of Regensburg, 93053 Regensburg, Germany
| | - Klaus Pfeffer
- Institute of Medical, Microbiology and Hospital Hygiene, University Hospital Düsseldorf, 40225 Düsseldorf, Germany
| | - Mariacristina Crosti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Sergio Abrignani
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy; Department of Clinical Science and Community Health (DISCCO), University of Milan, Milan, Italy
| | - Sylvia M Evans
- Skaggs School of Pharmacy, University of California at San Diego, La Jolla, CA 92093, USA
| | - Giovanni Sitia
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nuno Guimarães-Camboa
- Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt 60590, Germany; German Center for Cardiovascular Research, Berlin (partner site Frankfurt Rhine-Main), Germany
| | - Vincenzo Russo
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serge A van de Pavert
- Centre d'Immunologie de Marseille-Luminy (CIML), Aix Marseille Université, INSERM, CNRS, Marseille, France
| | | | - Andrea Brendolan
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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4
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Cardinali B, Provenzano C, Izzo M, Voellenkle C, Battistini J, Strimpakos G, Golini E, Mandillo S, Scavizzi F, Raspa M, Perfetti A, Baci D, Lazarevic D, Garcia-Manteiga JM, Gourdon G, Martelli F, Falcone G. Time-controlled and muscle-specific CRISPR/Cas9-mediated deletion of CTG-repeat expansion in the DMPK gene. Mol Ther Nucleic Acids 2022; 27:184-199. [PMID: 34976437 PMCID: PMC8693309 DOI: 10.1016/j.omtn.2021.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022]
Abstract
CRISPR/Cas9-mediated therapeutic gene editing is a promising technology for durable treatment of incurable monogenic diseases such as myotonic dystrophies. Gene-editing approaches have been recently applied to in vitro and in vivo models of myotonic dystrophy type 1 (DM1) to delete the pathogenic CTG-repeat expansion located in the 3′ untranslated region of the DMPK gene. In DM1-patient-derived cells removal of the expanded repeats induced beneficial effects on major hallmarks of the disease with reduction in DMPK transcript-containing ribonuclear foci and reversal of aberrant splicing patterns. Here, we set out to excise the triplet expansion in a time-restricted and cell-specific fashion to minimize the potential occurrence of unintended events in off-target genomic loci and select for the target cell type. To this aim, we employed either a ubiquitous promoter-driven or a muscle-specific promoter-driven Cas9 nuclease and tetracycline repressor-based guide RNAs. A dual-vector approach was used to deliver the CRISPR/Cas9 components into DM1 patient-derived cells and in skeletal muscle of a DM1 mouse model. In this way, we obtained efficient and inducible gene editing both in proliferating cells and differentiated post-mitotic myocytes in vitro as well as in skeletal muscle tissue in vivo.
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Affiliation(s)
- Beatrice Cardinali
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Claudia Provenzano
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Mariapaola Izzo
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Jonathan Battistini
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Georgios Strimpakos
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Elisabetta Golini
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Silvia Mandillo
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Ferdinando Scavizzi
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Marcello Raspa
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Alessandra Perfetti
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Denisa Baci
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | | | - Geneviève Gourdon
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Germana Falcone
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
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5
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Fan F, Malvestiti S, Vallet S, Lind J, Garcia-Manteiga JM, Morelli E, Jiang Q, Seckinger A, Hose D, Goldschmidt H, Stadlbauer A, Sun C, Mei H, Pecherstorfer M, Bakiri L, Wagner EF, Tonon G, Sattler M, Hu Y, Tassone P, Jaeger D, Podar K. Publisher Correction: JunB is a key regulator of multiple myeloma bone marrow angiogenesis. Leukemia 2021; 35:3628. [PMID: 34489554 DOI: 10.1038/s41375-021-01367-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fengjuan Fan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Stefano Malvestiti
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Sonia Vallet
- Department of Internal Medicine II, University Hospital Krems, Krems an der Donau, Austria.,Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Judith Lind
- Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | | | - Eugenio Morelli
- Department of Experimental and Clinical Medicine, University "Magna Græcia" of Catanzaro, Catanzaro, Italy.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Qinyue Jiang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Anja Seckinger
- University Hospital Heidelberg, Heidelberg, Germany.,Laboratory of Hematology and Immunology & Laboratory for Myeloma Research, Vrije Universiteit Brussel (VUB) Belgium, Brussels, Belgium
| | - Dirk Hose
- University Hospital Heidelberg, Heidelberg, Germany.,Laboratory of Hematology and Immunology & Laboratory for Myeloma Research, Vrije Universiteit Brussel (VUB) Belgium, Brussels, Belgium
| | - Hartmut Goldschmidt
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany.,University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas Stadlbauer
- Department of Neurosurgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Erlangen, Germany.,Institute of Medical Radiology, University Hospital St. Pölten, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Mei
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Martin Pecherstorfer
- Department of Internal Medicine II, University Hospital Krems, Krems an der Donau, Austria
| | - Latifa Bakiri
- Genes & Disease Group, Department of Dermatology, Medical University of Vienna (MUW), Vienna, Austria
| | - Erwin F Wagner
- Genes & Disease Group, Department of Dermatology, Medical University of Vienna (MUW), Vienna, Austria.,Genes & Disease Group, Department of Laboratory Medicine, Medical University of Vienna (MUW), Vienna, Austria
| | - Giovanni Tonon
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martin Sattler
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, University "Magna Græcia" of Catanzaro, Catanzaro, Italy
| | - Dirk Jaeger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Klaus Podar
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany. .,Department of Internal Medicine II, University Hospital Krems, Krems an der Donau, Austria. .,Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.
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6
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Garcia-Manteiga JM, Clarelli F, Bonfiglio S, Mascia E, Giannese F, Barbiera G, Guaschino C, Sorosina M, Santoro S, Protti A, Martinelli V, Cittaro D, Lazarevic D, Stupka E, Filippi M, Esposito F, Martinelli-Boneschi F. Identification of differential DNA methylation associated with multiple sclerosis: A family-based study. J Neuroimmunol 2021; 356:577600. [PMID: 33991750 DOI: 10.1016/j.jneuroim.2021.577600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 02/07/2023]
Abstract
Multiple Sclerosis (MS) is caused by a still unknown interplay between genetic and environmental factors. Epigenetics, including DNA methylation, represents a model for environmental factors to influence MS risk. Twenty-six affected and 26 unaffected relatives from 8 MS multiplex families were analysed in a multicentric Italian study using MeDIP-Seq, followed by technical validation and biological replication in two additional families of differentially methylated regions (DMRs) using SeqCap Epi Choice Enrichment kit (Roche®). Associations from MeDIP-Seq across families were combined with aggregation statistics, yielding 162 DMRs at FDR ≤ 0.1. Technical validation and biological replication led to 2 hypo-methylated regions, which point to NTM and BAI3 genes, and to 2 hyper-methylated regions in PIK3R1 and CAPN13. These 4 novel regions contain genes of potential interest that need to be tested in larger cohorts of patients.
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Affiliation(s)
- J M Garcia-Manteiga
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - F Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy
| | - S Bonfiglio
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - E Mascia
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy
| | - F Giannese
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - G Barbiera
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - C Guaschino
- Department of Neurology, Sant'Antonio Abate Hospital, Gallarate, Italy
| | - M Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy
| | - S Santoro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy
| | - A Protti
- Ospedale Niguarda, Department of Neurology, Milan, Italy
| | - V Martinelli
- Neurology Unit, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - D Cittaro
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - D Lazarevic
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - E Stupka
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - M Filippi
- Neurology Unit, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy; Vita-Salute San Raffaele University, Via Olgettina 48, 20132 Milan, Italy; Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy; Neurophysiology Unit, IRCCS San Raffaele Scientific Institute, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - F Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy; Neurology Unit, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - F Martinelli-Boneschi
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy; Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy; Neurology Unit and MS Centre, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy.
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7
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Fan F, Malvestiti S, Vallet S, Lind J, Garcia-Manteiga JM, Morelli E, Jiang Q, Seckinger A, Hose D, Goldschmidt H, Stadlbauer A, Sun C, Mei H, Pecherstorfer M, Bakiri L, Wagner EF, Tonon G, Sattler M, Hu Y, Tassone P, Jaeger D, Podar K. JunB is a key regulator of multiple myeloma bone marrow angiogenesis. Leukemia 2021; 35:3509-3525. [PMID: 34007044 PMCID: PMC8632680 DOI: 10.1038/s41375-021-01271-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/14/2021] [Accepted: 04/28/2021] [Indexed: 02/04/2023]
Abstract
Bone marrow (BM) angiogenesis significantly influences disease progression in multiple myeloma (MM) patients and correlates with adverse prognosis. The present study shows a statistically significant correlation of the AP-1 family member JunB with VEGF, VEGFB, and IGF1 expression levels in MM. In contrast to the angiogenic master regulator Hif-1α, JunB protein levels were independent of hypoxia. Results in tumor-cell models that allow the induction of JunB knockdown or JunB activation, respectively, corroborated the functional role of JunB in the production and secretion of these angiogenic factors (AFs). Consequently, conditioned media derived from MM cells after JunB knockdown or JunB activation either inhibited or stimulated in vitro angiogenesis. The impact of JunB on MM BM angiogenesis was finally confirmed in a dynamic 3D model of the BM microenvironment, a xenograft mouse model as well as in patient-derived BM sections. In summary, in continuation of our previous study (Fan et al., 2017), the present report reveals for the first time that JunB is not only a mediator of MM cell survival, proliferation, and drug resistance, but also a promoter of AF transcription and consequently of MM BM angiogenesis. Our results thereby underscore worldwide efforts to target AP-1 transcription factors such as JunB as a promising strategy in MM therapy.
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Affiliation(s)
- Fengjuan Fan
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China ,grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Stefano Malvestiti
- grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Sonia Vallet
- grid.488547.2Department of Internal Medicine II, University Hospital Krems, Krems an der Donau, Austria ,grid.459693.4Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Judith Lind
- grid.459693.4Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Jose Manuel Garcia-Manteiga
- grid.18887.3e0000000417581884Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eugenio Morelli
- grid.411489.10000 0001 2168 2547Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Catanzaro, Italy ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Qinyue Jiang
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Anja Seckinger
- grid.5253.10000 0001 0328 4908University Hospital Heidelberg, Heidelberg, Germany ,grid.8767.e0000 0001 2290 8069Laboratory of Hematology and Immunology & Laboratory for Myeloma Research, Vrije Universiteit Brussel (VUB) Belgium, Brussels, Belgium
| | - Dirk Hose
- grid.5253.10000 0001 0328 4908University Hospital Heidelberg, Heidelberg, Germany ,grid.8767.e0000 0001 2290 8069Laboratory of Hematology and Immunology & Laboratory for Myeloma Research, Vrije Universiteit Brussel (VUB) Belgium, Brussels, Belgium
| | - Hartmut Goldschmidt
- grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas Stadlbauer
- grid.5330.50000 0001 2107 3311Department of Neurosurgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Erlangen, Germany ,grid.459693.4Institute of Medical Radiology, University Hospital St. Pölten, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Chunyan Sun
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Mei
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Martin Pecherstorfer
- grid.488547.2Department of Internal Medicine II, University Hospital Krems, Krems an der Donau, Austria
| | - Latifa Bakiri
- grid.22937.3d0000 0000 9259 8492Genes & Disease Group, Department of Dermatology, Medical University of Vienna (MUW), Vienna, Austria
| | - Erwin F. Wagner
- grid.22937.3d0000 0000 9259 8492Genes & Disease Group, Department of Dermatology, Medical University of Vienna (MUW), Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Genes & Disease Group, Department of Laboratory Medicine, Medical University of Vienna (MUW), Vienna, Austria
| | - Giovanni Tonon
- grid.18887.3e0000000417581884Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milan, Italy ,grid.18887.3e0000000417581884Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martin Sattler
- grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA ,grid.62560.370000 0004 0378 8294Department of Surgery, Brigham and Women’s Hospital, Boston, MA USA
| | - Yu Hu
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pierfrancesco Tassone
- grid.411489.10000 0001 2168 2547Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Dirk Jaeger
- grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Klaus Podar
- grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany ,grid.488547.2Department of Internal Medicine II, University Hospital Krems, Krems an der Donau, Austria ,grid.459693.4Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
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8
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Brambilla F, Garcia-Manteiga JM, Monteleone E, Hoelzen L, Zocchi A, Agresti A, Bianchi ME. Nucleosomes effectively shield DNA from radiation damage in living cells. Nucleic Acids Res 2020; 48:8993-9006. [PMID: 32710624 PMCID: PMC7498322 DOI: 10.1093/nar/gkaa613] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 06/22/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic DNA is organized in nucleosomes, which package DNA and regulate its accessibility to transcription, replication, recombination and repair. Here, we show that in living cells nucleosomes protect DNA from high-energy radiation and reactive oxygen species. We combined sequence-based methods (ATAC-seq and BLISS) to determine the position of both nucleosomes and double strand breaks (DSBs) in the genome of nucleosome-rich malignant mesothelioma cells, and of the same cells partially depleted of nucleosomes. The results were replicated in the human MCF-7 breast carcinoma cell line. We found that, for each genomic sequence, the probability of DSB formation is directly proportional to the fraction of time it is nucleosome-free; DSBs accumulate distal from the nucleosome dyad axis. Nucleosome free regions and promoters of actively transcribed genes are more sensitive to DSB formation, and consequently to mutation. We argue that this may be true for a variety of chemical and physical DNA damaging agents.
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Affiliation(s)
| | - Jose Manuel Garcia-Manteiga
- IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Lena Hoelzen
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy
- Faculty of Biology, Albert-Ludwigs-University Freiburg, D79104 Freiburg, Germany
| | - Angelica Zocchi
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy
| | - Alessandra Agresti
- IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Marco E Bianchi
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy
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9
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Pedrotti S, Caccia R, Neguembor MV, Garcia-Manteiga JM, Ferri G, de Palma C, Canu T, Giovarelli M, Marra P, Fiocchi A, Molineris I, Raso M, Sanvito F, Doglioni C, Esposito A, Clementi E, Gabellini D. The Suv420h histone methyltransferases regulate PPAR-γ and energy expenditure in response to environmental stimuli. Sci Adv 2019; 5:eaav1472. [PMID: 31001581 PMCID: PMC6469946 DOI: 10.1126/sciadv.aav1472] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 02/28/2019] [Indexed: 05/10/2023]
Abstract
Obesity and its associated metabolic abnormalities have become a global emergency with considerable morbidity and mortality. Epidemiologic and animal model data suggest an epigenetic contribution to obesity. Nevertheless, the cellular and molecular mechanisms through which epigenetics contributes to the development of obesity remain to be elucidated. Suv420h1 and Suv420h2 are histone methyltransferases responsible for chromatin compaction and gene repression. Through in vivo, ex vivo, and in vitro studies, we found that Suv420h1 and Suv420h2 respond to environmental stimuli and regulate metabolism by down-regulating peroxisome proliferator-activated receptor gamma (PPAR-γ), a master transcriptional regulator of lipid storage and glucose metabolism. Accordingly, mice lacking Suv420h proteins activate PPAR-γ target genes in brown adipose tissue to increase mitochondria respiration, improve glucose tolerance, and reduce adipose tissue to fight obesity. We conclude that Suv420h proteins are key epigenetic regulators of PPAR-γ and the pathways controlling metabolism and weight balance in response to environmental stimuli.
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Affiliation(s)
- Simona Pedrotti
- IRCCS San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Milano, Italy
| | - Roberta Caccia
- IRCCS San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Milano, Italy
| | | | - Jose Manuel Garcia-Manteiga
- IRCCS San Raffaele Scientific Institute, Center for Translational Genomics and BioInformatics, Milano, Italy
| | - Giulia Ferri
- IRCCS San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Milano, Italy
| | - Clara de Palma
- Unit of Clinical Pharmacology, University Hospital “L. Sacco”-ASST Fatebenefratelli Sacco, Milano, Italy
| | - Tamara Canu
- IRCCS San Raffaele Scientific Institute, Preclinical Imaging Facility, Milano, Italy
| | - Matteo Giovarelli
- Department of Biomedical and Clinical Sciences “L. Sacco”, Università degli Studi di Milano, Milano, Italy
| | - Paolo Marra
- IRCCS San Raffaele Scientific Institute, Preclinical Imaging Facility, Milano, Italy
| | - Amleto Fiocchi
- IRCCS San Raffaele Scientific Institute, Mouse Clinic, Milano, Italy
| | - Ivan Molineris
- IRCCS San Raffaele Scientific Institute, Center for Translational Genomics and BioInformatics, Milano, Italy
| | - Michele Raso
- IRCCS San Raffaele Scientific Institute, Mouse Clinic, Milano, Italy
| | - Francesca Sanvito
- IRCCS San Raffaele Scientific Institute, Division of Experimental Oncology, Milano, Italy
| | - Claudio Doglioni
- IRCCS San Raffaele Scientific Institute, Division of Experimental Oncology, Milano, Italy
| | - Antonio Esposito
- IRCCS San Raffaele Scientific Institute, Preclinical Imaging Facility, Milano, Italy
| | - Emilio Clementi
- Department of Biomedical and Clinical Sciences “L. Sacco”, Università degli Studi di Milano, Milano, Italy
- Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Davide Gabellini
- IRCCS San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Milano, Italy
- Corresponding author.
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10
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Castiglioni I, Caccia R, Garcia-Manteiga JM, Ferri G, Caretti G, Molineris I, Nishioka K, Gabellini D. The Trithorax protein Ash1L promotes myoblast fusion by activating Cdon expression. Nat Commun 2018; 9:5026. [PMID: 30487570 PMCID: PMC6262021 DOI: 10.1038/s41467-018-07313-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 10/24/2018] [Indexed: 12/17/2022] Open
Abstract
Myoblast fusion (MF) is required for muscle growth and repair, and its alteration contributes to muscle diseases. The mechanisms governing this process are incompletely understood, and no epigenetic regulator has been previously described. Ash1L is an epigenetic activator belonging to the Trithorax group of proteins and is involved in FSHD muscular dystrophy, autism and cancer. Its physiological role in skeletal muscle is unknown. Here we report that Ash1L expression is positively correlated with MF and reduced in Duchenne muscular dystrophy. In vivo, ex vivo and in vitro experiments support a selective and evolutionary conserved requirement for Ash1L in MF. RNA- and ChIP-sequencing indicate that Ash1L is required to counteract Polycomb repressive activity to allow activation of selected myogenesis genes, in particular the key MF gene Cdon. Our results promote Ash1L as an important epigenetic regulator of MF and suggest that its activity could be targeted to improve cell therapy for muscle diseases. Myoblast fusion in skeletal muscle is a complex process but how this is regulated is unclear. Here, the authors identify Ash1L, a histone methyltransferase, as modulating myoblast fusion via activation of the myogenesis gene Cdon, and observe decreased Ash1L expression in Duchenne muscular dystrophy.
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Affiliation(s)
- Ilaria Castiglioni
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Roberta Caccia
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Jose Manuel Garcia-Manteiga
- Center for Translational Genomics and BioInformatics, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Giulia Ferri
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Giuseppina Caretti
- Department of Biosciences, University of Milan, via Celoria 26, Milano, 20133, Italy
| | - Ivan Molineris
- Center for Translational Genomics and BioInformatics, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Kenichi Nishioka
- Department of Biomolecular Sciences, Division of Molecular Genetics and Epigenetics, Faculty of Medicine, Saga University, Saga, Japan.,Laboratory for Developmental Genetics, RIKEN IMS, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Davide Gabellini
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy.
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11
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Cappella M, Perfetti A, Cardinali B, Garcia-Manteiga JM, Carrara M, Provenzano C, Fuschi P, Cardani R, Renna LV, Meola G, Falcone G, Martelli F. High-throughput analysis of the RNA-induced silencing complex in myotonic dystrophy type 1 patients identifies the dysregulation of miR-29c and its target ASB2. Cell Death Dis 2018; 9:729. [PMID: 29955039 PMCID: PMC6023919 DOI: 10.1038/s41419-018-0769-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/01/2018] [Accepted: 06/08/2018] [Indexed: 01/06/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a multi-systemic disorder caused by abnormally expanded stretches of CTG DNA triplets in the DMPK gene, leading to mutated-transcript RNA-toxicity. MicroRNAs (miRNAs) are short non-coding RNAs that, after maturation, are loaded onto the RISC effector complex that destabilizes target mRNAs and represses their translation. In DM1 muscle biopsies not only the expression, but also the intracellular localization of specific miRNAs is disrupted, leading to the dysregulation of the relevant mRNA targets. To investigate the functional alterations of the miRNA/target interactions in DM1, we analyzed by RNA-sequencing the RISC-associated RNAs in skeletal muscle biopsies derived from DM1 patients and matched controls. The mRNAs found deregulated in DM1 biopsies were involved in pathways and functions relevant for the disease, such as energetic metabolism, calcium signaling, muscle contraction and p53-dependent apoptosis. Bioinformatic analysis of the miRNA/mRNA interactions based on the RISC enrichment profiles, identified 24 miRNA/mRNA correlations. Following validation in 21 independent samples, we focused on the couple miR-29c/ASB2 because of the role of miR-29c in fibrosis (a feature of late-stage DM1 patients) and of ASB2 in the regulation of muscle mass. Luciferase reporter assay confirmed the direct interaction between miR-29c and ASB2. Moreover, decreased miR-29c and increased ASB2 levels were verified also in immortalized myogenic cells and primary fibroblasts, derived from biopsies of DM1 patients and controls. CRISPR/Cas9-mediated deletion of CTG expansions rescued normal miR-29c and ASB2 levels, indicating a direct link between the mutant repeats and the miRNA/target expression. In conclusion, functionally relevant miRNA/mRNA interactions were identified in skeletal muscles of DM1 patients, highlighting the dysfunction of miR-29c and ASB2.
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Affiliation(s)
- Marisa Cappella
- Institute of Cell Biology and Neurobiology, National Research Council-Monterotondo, Rome, Italy
| | - Alessandra Perfetti
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Beatrice Cardinali
- Institute of Cell Biology and Neurobiology, National Research Council-Monterotondo, Rome, Italy
| | | | - Matteo Carrara
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Claudia Provenzano
- Institute of Cell Biology and Neurobiology, National Research Council-Monterotondo, Rome, Italy
| | - Paola Fuschi
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Rosanna Cardani
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Laura Valentina Renna
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Giovanni Meola
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
- Department of Neurology, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Germana Falcone
- Institute of Cell Biology and Neurobiology, National Research Council-Monterotondo, Rome, Italy.
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy.
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12
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Conte I, Merella S, Garcia-Manteiga JM, Migliore C, Lazarevic D, Carrella S, Marco-Ferreres R, Avellino R, Davidson NP, Emmett W, Sanges R, Bockett N, Van Heel D, Meroni G, Bovolenta P, Stupka E, Banfi S. The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance. Nucleic Acids Res 2014; 42:7793-806. [PMID: 24895435 PMCID: PMC4081098 DOI: 10.1093/nar/gku498] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Vertebrate organogenesis is critically sensitive to gene dosage and even subtle variations in the expression levels of key genes may result in a variety of tissue anomalies. MicroRNAs (miRNAs) are fundamental regulators of gene expression and their role in vertebrate tissue patterning is just beginning to be elucidated. To gain further insight into this issue, we analysed the transcriptomic consequences of manipulating the expression of miR-204 in the Medaka fish model system. We used RNA-Seq and an innovative bioinformatics approach, which combines conventional differential expression analysis with the behavior expected by miR-204 targets after its overexpression and knockdown. With this approach combined with a correlative analysis of the putative targets, we identified a wider set of miR-204 target genes belonging to different pathways. Together, these approaches confirmed that miR-204 has a key role in eye development and further highlighted its putative function in neural differentiation processes, including axon guidance as supported by in vivo functional studies. Together, our results demonstrate the advantage of integrating next-generation sequencing and bioinformatics approaches to investigate miRNA biology and provide new important information on the role of miRNAs in the control of axon guidance and more broadly in nervous system development.
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Affiliation(s)
- Ivan Conte
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Stefania Merella
- Center For Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina, 58, 20132 Milan, Italy
| | - Jose Manuel Garcia-Manteiga
- Center For Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina, 58, 20132 Milan, Italy
| | - Chiara Migliore
- CBM Scrl, c/o Area Science Park, Basovizza, 30143 Trieste, Italy
| | - Dejan Lazarevic
- Center For Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina, 58, 20132 Milan, Italy
| | - Sabrina Carrella
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Raquel Marco-Ferreres
- Centro de Biología Molecular 'Severo Ochoa', CSIC-UAM, c/Nicolas Cabrera 1, Madrid 28049, Spain CIBER de Enfermedades Raras (CIBERER), c/ Nicolas Cabrera 1, Madrid 28049, Spain
| | - Raffaella Avellino
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Nathan Paul Davidson
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Warren Emmett
- UCL Cancer Institute, Huntley Street, University College London, London WC1E 6BT, UK
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Nicholas Bockett
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - David Van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Germana Meroni
- CBM Scrl, c/o Area Science Park, Basovizza, 30143 Trieste, Italy
| | - Paola Bovolenta
- Centro de Biología Molecular 'Severo Ochoa', CSIC-UAM, c/Nicolas Cabrera 1, Madrid 28049, Spain CIBER de Enfermedades Raras (CIBERER), c/ Nicolas Cabrera 1, Madrid 28049, Spain
| | - Elia Stupka
- Center For Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina, 58, 20132 Milan, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy
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13
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Oliveira G, Toffalori C, Garcia-Manteiga JM, Camisa B, Crucitti L, Lazarevic D, Peccatori J, Bernardi M, Bordignon C, Bondanza A, Stupka E, Ciceri F, Fleischhauer K, Bonini C, Vago L. Modeling leukemia immunoediting in mouse-human chimeras (P2169). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.170.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Acute Myeloid Leukemia (AML) can be recognized and eliminated by the immune system, as demonstrated by the clinical efficacy of allogeneic hematopoietic stem cell transplantation. Still, immune-resistant variants of AML can outgrow upon the selective pressure of the transplanted immune system and determine clinical relapse, in a process called “leukemia immunoediting”, the biological bases of which remain largely unknown. To unravel novel mechanisms of immunoediting, we engrafted primary human AML in immunocompromised NOD/SCID γ-chainnull mice and modeled immune pressure by serial infusions of human T cells, either autologous or allogeneic to the leukemic cells. HLA-mismatched allogeneic T cells eradicated AML from 6/6 treated mice, whereas HLA-identical T cells granted only temporary control in 3/3 mice and autologous T cells were completely inefficacious in 3/3 mice. To fine-tune immune pressure from HLA-mismatched T cells, and thus model a phase of equilibrium before leukemia immune escape, we genetically modified allogeneic T cells to express the HSV-Tk suicide gene. The activation of the suicidal machinery abated circulating T cell counts in 3/3 mice, halted the ongoing antileukemic response and resulted in leukemia outgrowth. Gene expression profiling of the AML blasts purified from the mice upon escape from immune pressure demonstrated the selective and significant deregulation of genes involved in immune processes, including antigen processing and presentation.
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Affiliation(s)
- Giacomo Oliveira
- 1Experimental Hematology Unit, San Raffaele Scientific Inst., Milan, Italy
- 2Vita-Salute San Raffaele University, Milan, Italy
| | - Cristina Toffalori
- 2Vita-Salute San Raffaele University, Milan, Italy
- 3Unit of Molecular and Functional Immunogenetics, San Raffaele Scientific Inst., Milan, Italy
| | | | - Barbara Camisa
- 1Experimental Hematology Unit, San Raffaele Scientific Inst., Milan, Italy
| | - Lara Crucitti
- 5Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Inst., Milan, Italy
| | - Dejan Lazarevic
- 4Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Inst., Milan, Italy
| | - Jacopo Peccatori
- 5Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Inst., Milan, Italy
| | - Massimo Bernardi
- 5Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Inst., Milan, Italy
| | - Claudio Bordignon
- 2Vita-Salute San Raffaele University, Milan, Italy
- 6MolMed SpA, Milan, Italy
| | - Attilio Bondanza
- 1Experimental Hematology Unit, San Raffaele Scientific Inst., Milan, Italy
| | - Elia Stupka
- 4Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Inst., Milan, Italy
| | - Fabio Ciceri
- 5Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Inst., Milan, Italy
| | - Katharina Fleischhauer
- 3Unit of Molecular and Functional Immunogenetics, San Raffaele Scientific Inst., Milan, Italy
| | - Chiara Bonini
- 1Experimental Hematology Unit, San Raffaele Scientific Inst., Milan, Italy
| | - Luca Vago
- 5Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Inst., Milan, Italy
- 1Experimental Hematology Unit, San Raffaele Scientific Inst., Milan, Italy
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14
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Margittai É, Löw P, Stiller I, Greco A, Garcia-Manteiga JM, Pengo N, Benedetti A, Sitia R, Bánhegyi G. Production of H₂O₂ in the endoplasmic reticulum promotes in vivo disulfide bond formation. Antioxid Redox Signal 2012; 16:1088-99. [PMID: 22369093 DOI: 10.1089/ars.2011.4221] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIMS Oxidative protein folding in the luminal compartment of endoplasmic reticulum (ER) is thought to be accompanied by the generation of H₂O₂, as side-product of disulfide bond formation. We aimed to examine the role of H₂O₂ produced in the lumen, which on one hand can lead to redox imbalance and hence can contribute to ER stress caused by overproduction of secretory proteins; on the other hand, as an excellent electron acceptor, H₂O₂ might serve as an additional pro-oxidant in physiological oxidative folding. RESULTS Stimulation of H₂O₂ production in the hepatic ER resulted in a decrease in microsomal GSH and protein-thiol contents and in a redox shift of certain luminal oxidoreductases in mice. The oxidative effect, accompanied by moderate signs of ER stress and reversible dilation of ER cisternae, was prevented by concomitant reducing treatment. The imbalance also affected the redox state of pyridine nucleotides in the ER. Antibody producing cells artificially engineered with powerful luminal H₂O₂ eliminating system showed diminished secretion of mature antibody polymers, while incomplete antibody monomers/dimers were accumulated and/or secreted. INNOVATION Evidence are provided by using in vivo models that hydrogen peroxide can promote disulfide bond formation in the ER. CONCLUSION The results indicate that local H₂O₂ production promotes, while quenching of H₂O₂ impairs disulfide formation. The contribution of H₂O₂ to disulfide bond formation previously observed in vitro can be also shown in cellular and in vivo systems.
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Affiliation(s)
- Éva Margittai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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Garcia-Manteiga JM, Mari S, Godejohann M, Spraul M, Napoli C, Cenci S, Musco G, Sitia R. Metabolomics of B to plasma cell differentiation. J Proteome Res 2011; 10:4165-76. [PMID: 21744784 DOI: 10.1021/pr200328f] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
When small B lymphocytes bind antigen in the context of suitable signals, a profound geno-proteomic metamorphosis is activated that generates antibody-secreting cells. To study the metabolic changes associated with this differentiation program, we compared the exometabolome of differentiating murine B lymphoma cells and primary B cells by monodimensional proton nuclear magnetic resonance spectroscopy and mass spectrometry coupled to liquid chromatography. Principal component analysis, a multivariate statistical analysis, highlighted metabolic hallmarks of the sequential differentiation phases discriminating between the proliferation and antibody secreting phases and revealing novel metabolic pathways. During proliferation, lactate production increased together with consumption of essential amino acids; massive Ig secretion was paralleled by alanine and glutamate production, glutamine being used as carbon and energy sources. Notably, ethanol and 5'-methylthioadenosine were produced during the last phase of protein secretion and the proliferative burst, respectively. Our metabolomics results are in agreement with previous genoproteomics studies. Thus, metabolic profiling of extracellular medium is a useful tool to characterize the functional state of differentiating B cells and to identify novel underlying metabolic pathways.
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