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Solovyeva EM, Utzinger S, Vissières A, Mitchelmore J, Ahrné E, Hermes E, Poetsch T, Ronco M, Bidinosti M, Merkl C, Serluca FC, Fessenden J, Naumann U, Voshol H, Meyer AS, Hoersch S. Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model. Mol Cell Proteomics 2024; 23:100683. [PMID: 37993104 PMCID: PMC10770608 DOI: 10.1016/j.mcpro.2023.100683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/02/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023] Open
Abstract
Dysregulated mRNA splicing is involved in the pathogenesis of many diseases including cancer, neurodegenerative diseases, and muscular dystrophies such as myotonic dystrophy type 1 (DM1). Comprehensive assessment of dysregulated splicing on the transcriptome and proteome level has been methodologically challenging, and thus investigations have often been targeting only few genes. Here, we performed a large-scale coordinated transcriptomic and proteomic analysis to characterize a DM1 mouse model (HSALR) in comparison to wild type. Our integrative proteogenomics approach comprised gene- and splicing-level assessments for mRNAs and proteins. It recapitulated many known instances of aberrant mRNA splicing in DM1 and identified new ones. It enabled the design and targeting of splicing-specific peptides and confirmed the translation of known instances of aberrantly spliced disease-related genes (e.g., Atp2a1, Bin1, Ryr1), complemented by novel findings (Flnc and Ywhae). Comparative analysis of large-scale mRNA and protein expression data showed quantitative agreement of differentially expressed genes and splicing patterns between disease and wild type. We hence propose this work as a suitable blueprint for a robust and scalable integrative proteogenomic strategy geared toward advancing our understanding of splicing-based disorders. With such a strategy, splicing-based biomarker candidates emerge as an attractive and accessible option, as they can be efficiently asserted on the mRNA and protein level in coordinated fashion.
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Affiliation(s)
- Elizaveta M Solovyeva
- Research Informatics, Biomedical Research at Novartis, Basel, Switzerland; V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.
| | - Stephan Utzinger
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | | | - Joanna Mitchelmore
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Erik Ahrné
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Erwin Hermes
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Tania Poetsch
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Marie Ronco
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Michael Bidinosti
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Claudia Merkl
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Fabrizio C Serluca
- Research Informatics, Biomedical Research at Novartis, Cambridge, Massachusetts, USA
| | - James Fessenden
- Neurodegenerative Diseases, Biomedical Research at Novartis, Cambridge, Massachusetts, USA
| | - Ulrike Naumann
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Hans Voshol
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Angelika S Meyer
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Sebastian Hoersch
- Research Informatics, Biomedical Research at Novartis, Basel, Switzerland.
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Cantara S, Chiofalo F, Ciuoli C, Marzocchi C, Dotti MT, Carla M, Castagna MG, Giannini F. RARE POMC MUTATION IN A PATIENT WITH MYOTONIC DYSTROPHY TYPE 1 AND ADRENOCORTICOTROPIN HYPERRESPONSE TO CORTICOTROPIN-RELEASING HORMONE. AACE Clin Case Rep 2018; 5:e132-e137. [PMID: 31967018 DOI: 10.4158/accr-2018-0382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/24/2018] [Indexed: 11/15/2022] Open
Abstract
Objective Myotonic dystrophy (DM) is a monogenic disorder. It is caused by expansion of a cytosine-thymineguanine triplet in the DMPK gene which encodes for myotonic dystrophy protein kinase (DMPK). Methods A 24-year-old man with DM and the DMPK mutation presented with elevated adrenocorticotropic hormone (ACTH) levels twice (152 and 185 pg/mL; normal value is 10 to 52 pg/mL) with normal cortisol levels (134.6 and 113.0 ng/mL, or 371.3 and 311.7 nmol/L; normal values are 67 to 226 ng/mL or 184.8 to 623.5 nmol/L). ACTH, corticotropin-releasing hormone (CRH) and insulin tolerance test (ITT) demonstrated normal cortisol response to ACTH and partial response to CRH and ITT tests, and ACTH hyperresponse to CRH and ITT. We suspected ACTH and/or ACTH receptor (ACTHR) mutations and evaluated the genetic profile for pro-opiomelanocortin (POMC), melanocortin 2 receptor (MC2R) and follicle-stimulating hormone receptor (FSHR) genes. Results No mutations were found in either the MC2R or FSHR genes. The patient was heterozygous for the c.614A>G mutation corresponding to a p.53D>G substitution with a glycine instead of an aspartate in position 53 in POMC gene. This mutation was outside the sequence for ACTH (which spans amino acids 138 to 176) but was included in the part originating the N-terminal peptide of pro-opiomelanocortin (also called pro-γ-melanocyte stimulating hormone) which spans amino acids 27 to 102 and is involved in the regulation of adrenal steroidogenesis. Conclusion The pathologic expansion of the cytosine-thymine-guanine triplet repeat in the 3' noncoding region of DMPK could explain the hyperresponse of ACTH typical of DM. The mutation of pro-γ-melanocyte-stimulating hormone could be associated with the abnormal response of cortisol, compatible with a partial adrenal insufficiency. Other studies are necessary to demonstrate this hypothesis.
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Fuller HR, Graham LC, Llavero Hurtado M, Wishart TM. Understanding the molecular consequences of inherited muscular dystrophies: advancements through proteomic experimentation. Expert Rev Proteomics 2016; 13:659-71. [PMID: 27329572 DOI: 10.1080/14789450.2016.1202768] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/14/2016] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Proteomic techniques offer insights into the molecular perturbations occurring in muscular-dystrophies (MD). Revisiting published datasets can highlight conserved downstream molecular alterations, which may be worth re-assessing to determine whether their experimental manipulation is capable of modulating disease severity. AREAS COVERED Here, we review the MD literature, highlighting conserved molecular insights warranting mechanistic investigation for therapeutic potential. We also describe a workflow currently proving effective for efficient identification of biomarkers & therapeutic targets in other neurodegenerative conditions, upon which future MD proteomic investigations could be modelled. Expert commentary: Studying disease models can be useful for identifying biomarkers and model specific degenerative cascades, but rarely offer translatable mechanistic insights into disease pathology. Conversely, direct analysis of human samples undergoing degeneration presents challenges derived from complex chronic degenerative molecular processes. This requires a carefully planed & reproducible experimental paradigm accounting for patient selection through to grouping by disease severity and ending with proteomic data filtering and processing.
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Affiliation(s)
- Heidi R Fuller
- a Wolfson Centre for Inherited Neuromuscular Disease , RJAH Orthopaedic Hospital , Oswestry , UK
- b Institute for Science and Technology in Medicine , Keele University , Staffordshire , UK
| | - Laura C Graham
- c Euan MacDonald Centre for Motor Neurone Disease Research , University of Edinburgh , Edinburgh , UK
- d Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Studies , University of Edinburgh , Edinburgh , UK
| | - Maica Llavero Hurtado
- c Euan MacDonald Centre for Motor Neurone Disease Research , University of Edinburgh , Edinburgh , UK
- d Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Studies , University of Edinburgh , Edinburgh , UK
| | - Thomas M Wishart
- c Euan MacDonald Centre for Motor Neurone Disease Research , University of Edinburgh , Edinburgh , UK
- d Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Studies , University of Edinburgh , Edinburgh , UK
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Pantic B, Trevisan E, Citta A, Rigobello MP, Marin O, Bernardi P, Salvatori S, Rasola A. Myotonic dystrophy protein kinase (DMPK) prevents ROS-induced cell death by assembling a hexokinase II-Src complex on the mitochondrial surface. Cell Death Dis 2013; 4:e858. [PMID: 24136222 PMCID: PMC3920960 DOI: 10.1038/cddis.2013.385] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/30/2013] [Accepted: 09/04/2013] [Indexed: 11/19/2022]
Abstract
The biological functions of myotonic dystrophy protein kinase (DMPK), a serine/threonine kinase whose gene mutations cause myotonic dystrophy type 1 (DM1), remain poorly understood. Several DMPK isoforms exist, and the long ones (DMPK-A/B/C/D) are associated with the mitochondria, where they exert unknown activities. We have studied the isoform A of DMPK, which we have found to be prevalently associated to the outer mitochondrial membrane. The kinase activity of mitochondrial DMPK protects cells from oxidative stress and from the ensuing opening of the mitochondrial permeability transition pore (PTP), which would otherwise irreversibly commit cells to death. We observe that DMPK (i) increases the mitochondrial localization of hexokinase II (HK II), (ii) forms a multimeric complex with HK II and with the active form of the tyrosine kinase Src, binding its SH3 domain and (iii) it is tyrosine-phosphorylated by Src. Both interaction among these proteins and tyrosine phosphorylation of DMPK are increased under oxidative stress, and Src inhibition selectively enhances death in DMPK-expressing cells after HK II detachment from the mitochondria. Down-modulation of DMPK abolishes the appearance of muscle markers in in vitro myogenesis, which is rescued by oxidant scavenging. Our data indicate that, together with HK II and Src, mitochondrial DMPK is part of a multimolecular complex endowed with antioxidant and pro-survival properties that could be relevant during the function and differentiation of muscle fibers.
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Affiliation(s)
- B Pantic
- 1] CNR Institute of Neuroscience, University of Padova, Padova 35121, Italy [2] Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
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Johnson R, Noble W, Tartaglia GG, Buckley NJ. Neurodegeneration as an RNA disorder. Prog Neurobiol 2012; 99:293-315. [PMID: 23063563 PMCID: PMC7116994 DOI: 10.1016/j.pneurobio.2012.09.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/14/2012] [Accepted: 09/26/2012] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases constitute one of the single most important public health challenges of the coming decades, and yet we presently have only a limited understanding of the underlying genetic, cellular and molecular causes. As a result, no effective disease-modifying therapies are currently available, and no method exists to allow detection at early disease stages, and as a result diagnoses are only made decades after disease pathogenesis, by which time the majority of physical damage has already occurred. Since the sequencing of the human genome, we have come to appreciate that the transcriptional output of the human genome is extremely rich in non-protein coding RNAs (ncRNAs). This heterogeneous class of transcripts is widely expressed in the nervous system, and is likely to play many crucial roles in the development and functioning of this organ. Most exciting, evidence has recently been presented that ncRNAs play central, but hitherto unappreciated roles in neurodegenerative processes. Here, we review the diverse available evidence demonstrating involvement of ncRNAs in neurodegenerative diseases, and discuss their possible implications in the development of therapies and biomarkers for these conditions.
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Key Words
- neurodegeneration
- neurodegenerative disease
- non-coding rna
- alzheimer's disease
- parkinson's disease
- huntington's disease
- trinucleotide repeat disorder
- bace1
- rest
- long non-coding rna
- microrna
- har1
- sox2ot
- mir-9
- mir-132
- mir-124
- ndds, neurodegenerative disorders
- ad, alzheimer's disease
- hd, huntington's disease
- pd, parkinson's disease
- als, amyotrophic lateral sclerosis
- app, amyloid precursor protein
- cftr, cystic fibrosis
- csf, cerebrospinal fluid
- sod1, superoxide dismutase 1
- tardbp, tar dna binding protein
- psen-1, presenilin 1
- psen-2, presenilin 1
- mapt, microtubule-associated protein tau
- snca, α-synuclein
- ups, ubiquitin-proteasome system
- aββ, -amyloid
- er, endoplasmic reticulum
- ber, base excision repair
- parp-1, poly-adp ribose polymerase-1
- lncrnas, long non-coding rnas
- mirnas, microrna
- ncrna, non-coding rnas
- ngs, next generation sequencing
- pcr, polymerase chain reaction
- sars, severe acute respiratory disorder
- sca, spinal cerebellar ataxia
- dm, myotonic dystrophy
- hdl2, huntington's disease-like 2
- tnds, trinucleotide repeat disorders
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Affiliation(s)
- Rory Johnson
- Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader, 88, 08003 Barcelona, Catalunya, Spain
| | - Wendy Noble
- Kings College London, Institute of Psychiatry, London, UK
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader, 88, 08003 Barcelona, Catalunya, Spain
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Agnetti G, Husberg C, Van Eyk JE. Divide and conquer: the application of organelle proteomics to heart failure. Circ Res 2011; 108:512-26. [PMID: 21335433 PMCID: PMC3936251 DOI: 10.1161/circresaha.110.226910] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 11/19/2010] [Indexed: 01/16/2023]
Abstract
Chronic heart failure is a worldwide cause of mortality and morbidity and is the final outcome of a number of different etiologies. This reflects both the complexity of the disease and our incomplete understanding of its underlying molecular mechanisms. One experimental approach to address this is to study subcellular organelles and how their functions are activated and synchronized under physiological and pathological conditions. In this review, we discuss the application of proteomic technologies to organelles and how this has deepened our perception of the cellular proteome and its alterations with heart failure. The use of proteomics to monitor protein quantity and posttranslational modifications has revealed a highly intricate and sophisticated level of protein regulation. Posttranslational modifications have the potential to regulate organelle function and interplay most likely by targeting both structural and signaling proteins throughout the cell, ultimately coordinating their responses. The potentials and limitations of existing proteomic technologies are also discussed emphasizing that the development of novel methods will enhance our ability to further investigate organelles and decode intracellular communication.
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Affiliation(s)
- Giulio Agnetti
- The Johns Hopkins Bayview Proteomics Center, Johns Hopkins University, Baltimore, US
- INRC, Dept. of Biochemistry, University of Bologna, Italy
| | - Cathrine Husberg
- The Johns Hopkins Bayview Proteomics Center, Johns Hopkins University, Baltimore, US
- Institute for Experimental Medical Research, Oslo University Hospital - Ullevaal, Norway
| | - Jennifer E. Van Eyk
- The Johns Hopkins Bayview Proteomics Center, Johns Hopkins University, Baltimore, US
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