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Utami KH, Yusof NABM, Garcia-Miralles M, Skotte NH, Nama S, Sampath P, Langley SR, Pouladi MA. Dysregulated COMT Expression in Fragile X Syndrome. Neuromolecular Med 2023; 25:644-649. [PMID: 37684514 DOI: 10.1007/s12017-023-08754-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/20/2023] [Indexed: 09/10/2023]
Abstract
Transcriptional and proteomics analyses in human fragile X syndrome (FXS) neurons identified markedly reduced expression of COMT, a key enzyme involved in the metabolism of catecholamines, including dopamine, epinephrine and norepinephrine. FXS is the most common genetic cause of intellectual disability and autism spectrum disorders. COMT encodes for catechol-o-methyltransferase and its association with neuropsychiatric disorders and cognitive function has been extensively studied. We observed a significantly reduced level of COMT in in FXS human neural progenitors and neurons, as well as hippocampal neurons from Fmr1 null mice. We show that deficits in COMT were associated with an altered response in an assay of dopaminergic activity in Fmr1 null mice. These findings demonstrate that loss of FMRP downregulates COMT expression and affects dopamine signaling in FXS, and supports the notion that targeting catecholamine metabolism may be useful in regulating certain neuropsychiatric aspects of FXS.
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Affiliation(s)
- Kagistia Hana Utami
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research, Singapore (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Nur Amirah Binte Muhammed Yusof
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research, Singapore (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
| | - Marta Garcia-Miralles
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research, Singapore (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
- Department of Molecular Embryology, Medical Faculty, Institute of Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Niels Henning Skotte
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Srikanth Nama
- Institute of Medical Biology, Agency for Science, Technology and Research, Singapore (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
| | - Prabha Sampath
- Agency for Science, Technology and Research, Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research, Singapore (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore.
- Department of Medical Genetics, Centre for Molecular Medicine & Therapeutics, Djavad Mowafaghian Centre for Brain Health, British Columbia Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
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2
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Zalivina I, Barwari T, Yin X, Langley SR, Barallobre-Barreiro J, Wakimoto H, Zampetaki A, Mayr M, Avkiran M, Eminaga S. Inhibition of miR-199a-3p in a murine hypertrophic cardiomyopathy (HCM) model attenuates fibrotic remodeling. J Mol Cell Cardiol Plus 2023; 6:100056. [PMID: 38143961 PMCID: PMC10739604 DOI: 10.1016/j.jmccpl.2023.100056] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023]
Abstract
Background Hypertrophic cardiomyopathy (HCM) is an autosomal dominant genetic disorder, characterized by cardiomyocyte hypertrophy, cardiomyocyte disarray and fibrosis, which has a prevalence of ∼1: 200-500 and predisposes individuals to heart failure and sudden death. The mechanisms through which diverse HCM-causing mutations cause cardiac dysfunction remain mostly unknown and their identification may reveal new therapeutic avenues. MicroRNAs (miRNAs) have emerged as critical regulators of gene expression and disease phenotype in various pathologies. We explored whether miRNAs could play a role in HCM pathogenesis and offer potential therapeutic targets. Methods and results Using high-throughput miRNA expression profiling and qPCR analysis in two distinct mouse models of HCM, we found that miR-199a-3p expression levels are upregulated in mutant mice compared to age- and treatment-matched wild-type mice. We also found that miR-199a-3p expression is enriched in cardiac non-myocytes compared to cardiomyocytes. When we expressed miR-199a-3p mimic in cultured murine primary cardiac fibroblasts and analyzed the conditioned media by proteomics, we found that several extracellular matrix (ECM) proteins (e.g., TSP2, FBLN3, COL11A1, LYOX) were differentially secreted (data are available via ProteomeXchange with identifier PXD042904). We confirmed our proteomics findings by qPCR analysis of selected mRNAs and demonstrated that miR-199a-3p mimic expression in cardiac fibroblasts drives upregulation of ECM gene expression, including Tsp2, Fbln3, Pcoc1, Col1a1 and Col3a1. To examine the role of miR-199a-3p in vivo, we inhibited its function using lock-nucleic acid (LNA)-based inhibitors (antimiR-199a-3p) in an HCM mouse model. Our results revealed that progression of cardiac fibrosis is attenuated when miR-199a-3p function is inhibited in mild-to-moderate HCM. Finally, guided by computational target prediction algorithms, we identified mRNAs Cd151 and Itga3 as direct targets of miR-199a-3p and have shown that miR-199a-3p mimic expression negatively regulates AKT activation in cardiac fibroblasts. Conclusions Altogether, our results suggest that miR-199a-3p may contribute to cardiac fibrosis in HCM through its actions in cardiac fibroblasts. Thus, inhibition of miR-199a-3p in mild-to-moderate HCM may offer therapeutic benefit in combination with complementary approaches that target the primary defect in cardiac myocytes.
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Affiliation(s)
- Irina Zalivina
- King's College London, British Heart Foundation Centre of Research Excellence, London, United Kingdom
| | - Temo Barwari
- King's College London, British Heart Foundation Centre of Research Excellence, London, United Kingdom
| | - Xiaoke Yin
- King's College London, British Heart Foundation Centre of Research Excellence, London, United Kingdom
| | - Sarah R. Langley
- King's College London, British Heart Foundation Centre of Research Excellence, London, United Kingdom
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Zampetaki
- King's College London, British Heart Foundation Centre of Research Excellence, London, United Kingdom
| | - Manuel Mayr
- King's College London, British Heart Foundation Centre of Research Excellence, London, United Kingdom
| | - Metin Avkiran
- King's College London, British Heart Foundation Centre of Research Excellence, London, United Kingdom
| | - Seda Eminaga
- King's College London, British Heart Foundation Centre of Research Excellence, London, United Kingdom
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Tano V, Utami KH, Yusof NABM, Bégin J, Tan WWL, Pouladi MA, Langley SR. Widespread dysregulation of mRNA splicing implicates RNA processing in the development and progression of Huntington's disease. EBioMedicine 2023; 94:104720. [PMID: 37481821 PMCID: PMC10393612 DOI: 10.1016/j.ebiom.2023.104720] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND In Huntington's disease (HD), a CAG repeat expansion mutation in the Huntingtin (HTT) gene drives a gain-of-function toxicity that disrupts mRNA processing. Although dysregulation of gene splicing has been shown in human HD post-mortem brain tissue, post-mortem analyses are likely confounded by cell type composition changes in late-stage HD, limiting the ability to identify dysregulation related to early pathogenesis. METHODS To investigate gene splicing changes in early HD, we performed alternative splicing analyses coupled with a proteogenomics approach to identify early CAG length-associated splicing changes in an established isogenic HD cell model. FINDINGS We report widespread neuronal differentiation stage- and CAG length-dependent splicing changes, and find an enrichment of RNA processing, neuronal function, and epigenetic modification-related genes with mutant HTT-associated splicing. When integrated with a proteomics dataset, we identified several of these differential splicing events at the protein level. By comparing with human post-mortem and mouse model data, we identified common patterns of altered splicing from embryonic stem cells through to post-mortem striatal tissue. INTERPRETATION We show that widespread splicing dysregulation in HD occurs in an early cell model of neuronal development. Importantly, we observe HD-associated splicing changes in our HD cell model that were also identified in human HD striatum and mouse model HD striatum, suggesting that splicing-associated pathogenesis possibly occurs early in neuronal development and persists to later stages of disease. Together, our results highlight splicing dysregulation in HD which may lead to disrupted neuronal function and neuropathology. FUNDING This research is supported by the Lee Kong Chian School of Medicine, Nanyang Technological University Singapore Nanyang Assistant Professorship Start-Up Grant, the Singapore Ministry of Education under its Singapore Ministry of Education Academic Research Fund Tier 1 (RG23/22), the BC Children's Hospital Research Institute Investigator Grant Award (IGAP), and a Scholar Award from the Michael Smith Health Research BC.
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Affiliation(s)
- Vincent Tano
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Kagistia Hana Utami
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore; Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Nur Amirah Binte Mohammad Yusof
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Jocelyn Bégin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Willy Wei Li Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore; Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore.
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Fairley LH, Lai KO, Wong JH, Chong WJ, Vincent AS, D’Agostino G, Wu X, Naik RR, Jayaraman A, Langley SR, Ruedl C, Barron AM. Mitochondrial control of microglial phagocytosis by the translocator protein and hexokinase 2 in Alzheimer's disease. Proc Natl Acad Sci U S A 2023; 120:e2209177120. [PMID: 36787364 PMCID: PMC9974442 DOI: 10.1073/pnas.2209177120] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 05/30/2022] [Accepted: 12/17/2022] [Indexed: 02/15/2023] Open
Abstract
Microglial phagocytosis is an energetically demanding process that plays a critical role in the removal of toxic protein aggregates in Alzheimer's disease (AD). Recent evidence indicates that a switch in energy production from mitochondrial respiration to glycolysis disrupts this important protective microglial function and may provide therapeutic targets for AD. Here, we demonstrate that the translocator protein (TSPO) and a member of its mitochondrial complex, hexokinase-2 (HK), play critical roles in microglial respiratory-glycolytic metabolism and phagocytosis. Pharmacological and genetic loss-of-function experiments showed that TSPO is critical for microglial respiratory metabolism and energy supply for phagocytosis, and its expression is enriched in phagocytic microglia of AD mice. Meanwhile, HK controlled glycolytic metabolism and phagocytosis via mitochondrial binding or displacement. In cultured microglia, TSPO deletion impaired mitochondrial respiration and increased mitochondrial recruitment of HK, inducing a switch to glycolysis and reducing phagocytosis. To determine the functional significance of mitochondrial HK recruitment, we developed an optogenetic tool for reversible control of HK localization. Displacement of mitochondrial HK inhibited glycolysis and improved phagocytosis in TSPO-knockout microglia. Mitochondrial HK recruitment also coordinated the inflammatory switch to glycolysis that occurs in response to lipopolysaccharide in normal microglia. Interestingly, cytosolic HK increased phagocytosis independent of its metabolic activity, indicating an immune signaling function. Alzheimer's beta amyloid drastically stimulated mitochondrial HK recruitment in cultured microglia, which may contribute to microglial dysfunction in AD. Thus, targeting mitochondrial HK may offer an immunotherapeutic approach to promote phagocytic microglial function in AD.
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Affiliation(s)
- Lauren H. Fairley
- Neurobiology of Aging and Disease Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
| | - Kei Onn Lai
- Neurobiology of Aging and Disease Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
| | - Jia Hui Wong
- Neurobiology of Aging and Disease Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
| | - Wei Jing Chong
- Neurobiology of Aging and Disease Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
| | - Anselm Salvatore Vincent
- Neurobiology of Aging and Disease Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
| | - Giuseppe D’Agostino
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
| | - Xiaoting Wu
- School of Biological Sciences, Nanyang Technological University Singapore, 637551, Singapore
| | - Roshan R. Naik
- Neurobiology of Aging and Disease Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
| | - Anusha Jayaraman
- Center for Molecular Neuropathology, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
| | - Sarah R. Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
| | - Christiane Ruedl
- School of Biological Sciences, Nanyang Technological University Singapore, 637551, Singapore
| | - Anna M. Barron
- Neurobiology of Aging and Disease Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 308232, Singapore
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5
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Chothani SP, Adami E, Widjaja AA, Langley SR, Viswanathan S, Pua CJ, Zhihao NT, Harmston N, D'Agostino G, Whiffin N, Mao W, Ouyang JF, Lim WW, Lim S, Lee CQE, Grubman A, Chen J, Kovalik JP, Tryggvason K, Polo JM, Ho L, Cook SA, Rackham OJL, Schafer S. A high-resolution map of human RNA translation. Mol Cell 2022; 82:2885-2899.e8. [PMID: 35841888 DOI: 10.1016/j.molcel.2022.06.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 09/19/2021] [Revised: 03/10/2022] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
Translated small open reading frames (smORFs) can have important regulatory roles and encode microproteins, yet their genome-wide identification has been challenging. We determined the ribosome locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. Integration with 456 mass-spectrometry datasets confirms the presence of 603 small peptides at the protein level in humans and provides insights into the subcellular localization of these small proteins. This study provides a comprehensive atlas of high-confidence translated smORFs derived from primary human cells and tissues in order to provide a more complete understanding of the translated human genome.
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Affiliation(s)
- Sonia P Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anissa A Widjaja
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Chee Jian Pua
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Nevin Tham Zhihao
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Science Division, Yale-NUS College, Singapore 138527, Singapore
| | - Giuseppe D'Agostino
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nicola Whiffin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Wang Mao
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Wei Wen Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Shiqi Lim
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Cheryl Q E Lee
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - J P Kovalik
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Lena Ho
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore; London Institute of Medical Sciences, London W12 ONN, UK
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; School of Biological Sciences, University of Southampton, Southampton, UK.
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore.
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6
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Ziaei A, Garcia-Miralles M, Radulescu CI, Sidik H, Silvin A, Bae HG, Bonnard C, Yusof NABM, Ferrari Bardile C, Tan LJ, Ng AYJ, Tohari S, Dehghani L, Henry L, Yeo XY, Lee S, Venkatesh B, Langley SR, Shaygannejad V, Reversade B, Jung S, Ginhoux F, Pouladi MA. Ermin deficiency leads to compromised myelin, inflammatory milieu, and susceptibility to demyelinating insult. Brain Pathol 2022; 32:e13064. [PMID: 35285112 PMCID: PMC9425013 DOI: 10.1111/bpa.13064] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/09/2022] [Accepted: 02/10/2022] [Indexed: 11/28/2022] Open
Abstract
Ermin is an actin-binding protein found almost exclusively in the central nervous system (CNS) as a component of myelin sheaths. Although Ermin has been predicted to play a role in the formation and stability of myelin sheaths, this has not been directly examined in vivo. Here, we show that Ermin is essential for myelin sheath integrity and normal saltatory conduction. Loss of Ermin in mice caused de-compacted and fragmented myelin sheaths and led to slower conduction along with progressive neurological deficits. RNA sequencing of the corpus callosum, the largest white matter structure in the CNS, pointed to inflammatory activation in aged Ermin-deficient mice, which was corroborated by increased levels of microgliosis and astrogliosis. The inflammatory milieu and myelin abnormalities were further associated with increased susceptibility to immune-mediated demyelination insult in Ermin knockout mice. Supporting a possible role of Ermin deficiency in inflammatory white matter disorders, a rare inactivating mutation in the ERMN gene was identified in multiple sclerosis patients. Our findings demonstrate a critical role for Ermin in maintaining myelin integrity. Given its near-exclusive expression in myelinating oligodendrocytes, Ermin deficiency represents a compelling "inside-out" model of inflammatory dysmyelination and may offer a new paradigm for the development of myelin stability-targeted therapies.
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Affiliation(s)
- Amin Ziaei
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore.,UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
| | - Marta Garcia-Miralles
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Carola I Radulescu
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Harwin Sidik
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Aymeric Silvin
- Singapore Immunology Network (SIgN), A*STAR, Singapore, Singapore
| | - Han-Gyu Bae
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore.,Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Carine Bonnard
- Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Nur Amirah Binte Mohammad Yusof
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Costanza Ferrari Bardile
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore.,Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liang Juin Tan
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Alvin Yu Jin Ng
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Leila Dehghani
- Department of Neurology, Isfahan Neurosciences Research Centre, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Lily Henry
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Xin Yi Yeo
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Sejin Lee
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Vahid Shaygannejad
- Department of Neurology, Isfahan Neurosciences Research Centre, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Sangyong Jung
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore.,Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, Singapore, Singapore.,Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai, China.,Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore.,Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
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7
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Trott J, Alpagu Y, Tan EK, Shboul M, Dawood Y, Elsy M, Wollmann H, Tano V, Bonnard C, Eng S, Narayanan G, Junnarkar S, Wearne S, Strutt J, Kumar A, Tomaz LB, Goy PA, Mzoughi S, Jennings R, Hagoort J, Eskin A, Lee H, Nelson SF, Al-Kazaleh F, El-Khateeb M, Fathallah R, Shah H, Goeke J, Langley SR, Guccione E, Hanley N, De Bakker BS, Reversade B, Dunn NR. Mitchell-Riley syndrome iPSCs exhibit reduced pancreatic endoderm differentiation due to a mutation in RFX6. Development 2020; 147:dev194878. [PMID: 33033118 DOI: 10.1242/dev.194878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/14/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022]
Abstract
Mitchell-Riley syndrome (MRS) is caused by recessive mutations in the regulatory factor X6 gene (RFX6) and is characterised by pancreatic hypoplasia and neonatal diabetes. To determine why individuals with MRS specifically lack pancreatic endocrine cells, we micro-CT imaged a 12-week-old foetus homozygous for the nonsense mutation RFX6 c.1129C>T, which revealed loss of the pancreas body and tail. From this foetus, we derived iPSCs and show that differentiation of these cells in vitro proceeds normally until generation of pancreatic endoderm, which is significantly reduced. We additionally generated an RFX6HA reporter allele by gene targeting in wild-type H9 cells to precisely define RFX6 expression and in parallel performed in situ hybridisation for RFX6 in the dorsal pancreatic bud of a Carnegie stage 14 human embryo. Both in vitro and in vivo, we find that RFX6 specifically labels a subset of PDX1-expressing pancreatic endoderm. In summary, RFX6 is essential for efficient differentiation of pancreatic endoderm, and its absence in individuals with MRS specifically impairs formation of endocrine cells of the pancreas head and tail.
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Affiliation(s)
- Jamie Trott
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Yunus Alpagu
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Ee Kim Tan
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Mohammad Shboul
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 2210, Jordan
| | - Yousif Dawood
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Department of Obstetrics and Gynaecology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Michael Elsy
- Faculty of Biology, Medicine & Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Heike Wollmann
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Vincent Tano
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Carine Bonnard
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Shermaine Eng
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Gunaseelan Narayanan
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Seetanshu Junnarkar
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Stephen Wearne
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - James Strutt
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Aakash Kumar
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Lucian B Tomaz
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Pierre-Alexis Goy
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Slim Mzoughi
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Rachel Jennings
- Faculty of Biology, Medicine & Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Endocrinology Department, Manchester University NHS Foundation Trust, Grafton Street, Manchester M13 9WU, UK
| | - Jaco Hagoort
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Ascia Eskin
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Hane Lee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, CA 90095, USA
| | - Fawaz Al-Kazaleh
- Department of Obstetrics and Gynecology, University of Jordan, Amman 19241, Jordan
| | - Mohammad El-Khateeb
- National Center for Diabetes, Endocrinology and Genetics, Amman 19241, Jordan
| | - Rajaa Fathallah
- National Center for Diabetes, Endocrinology and Genetics, Amman 19241, Jordan
| | - Harsha Shah
- Department of Obstetrics and Gynaecology, Queen Charlotte's & Chelsea Hospital, Imperial College London, Du Cane Road, London W12 0HS, UK
| | - Jonathan Goeke
- Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), 60 Biopolis Street, 138672, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Ernesto Guccione
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Neil Hanley
- Faculty of Biology, Medicine & Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Endocrinology Department, Manchester University NHS Foundation Trust, Grafton Street, Manchester M13 9WU, UK
| | - Bernadette S De Bakker
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bruno Reversade
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
- Department of Paediatrics, National University of Singapore, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 12, 119228, Singapore
- Koç University School of Medicine, Medical Genetics Department, Istanbul 34450, Turkey
| | - N Ray Dunn
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
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8
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Chittezhath M, Wai CMM, Tay VSY, Chua M, Langley SR, Ali Y. TLR4 signals through islet macrophages to alter cytokine secretion during diabetes. J Endocrinol 2020; 247:87. [PMID: 32755994 DOI: 10.1530/joe-20-0131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/04/2020] [Indexed: 11/08/2022]
Abstract
Toll-like receptors (TLRs), particularly TLR4, may act as immune sensors for metabolic stress signals such as lipids and link tissue metabolic changes to innate immunity. TLR signalling is not only tissue-dependent but also cell-type dependent and recent studies suggest that TLRs are not restricted to innate immune cells alone. Pancreatic islets, a hub of metabolic hormones and cytokines, respond to TLR signalling. However, the source of TLR signalling within the islet remain poorly understood. Uncovering the specific cell source and its role in mediating TLR signalling, especially within type 2 diabetes (T2D) islet will yield new targets to tackle islet inflammation, hormone secretion dysregulation and ultimately diabetes. In the present study, we immuno-characterised TLRs linked to pancreatic islets in both healthy and obese diabetic mice. We found that while TLRs1-4 and TLR9 were expressed in mouse islets, these TLRs did not co-localise with insulin-producing β-cells. β-Cells from obese diabetic mice were also devoid of these TLRs. While TLR immunoreactivity in obese mice islets increased, this was driven mostly by increased islet endothelial cell and islet macrophage presence. Analysis of human islet single-cell RNA-seq databases revealed that macrophages were an important source of islet TLRs. However, only TLR4 and TLR8 showed variation and cell-type specificity in their expression patterns. Cell depletion experiments in isolated mouse islets showed that TLR4 signalled through macrophages to alter islet cytokine secretome. Together, these studies suggest that islet macrophages are a dominant source of TLR4-mediated signalling in both healthy and diabetic islets.
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Affiliation(s)
- Manesh Chittezhath
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Cho M M Wai
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Vanessa S Y Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Minni Chua
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Yusuf Ali
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, Singapore
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9
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Laaniste L, Srivastava PK, Stylianou J, Syed N, Cases-Cunillera S, Shkura K, Zeng Q, Rackham OJL, Langley SR, Delahaye-Duriez A, O'Neill K, Williams M, Becker A, Roncaroli F, Petretto E, Johnson MR. Integrated systems-genetic analyses reveal a network target for delaying glioma progression. Ann Clin Transl Neurol 2019; 6:1616-1638. [PMID: 31420939 PMCID: PMC6764637 DOI: 10.1002/acn3.50850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 05/01/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022] Open
Abstract
Objective To identify a convergent, multitarget proliferation characteristic for astrocytoma transformation that could be targeted for therapy discovery. Methods Using an integrated functional genomics approach, we prioritized networks associated with astrocytoma progression using the following criteria: differential co‐expression between grade II and grade III IDH1‐mutated and 1p/19q euploid astrocytomas, preferential enrichment for genetic risk to cancer, association with patient survival and sample‐level genomic features. Drugs targeting the identified multitarget network characteristic for astrocytoma transformation were computationally predicted using drug transcriptional perturbation data and validated using primary human astrocytoma cells. Results A single network, M2, consisting of 177 genes, was associated with glioma progression on the basis of the above criteria. Functionally, M2 encoded physically interacting proteins regulating cell cycle processes and analysis of genome‐wide gene‐regulatory interactions using mutual information and DNA–protein interactions revealed the known regulators of cell cycle processes FoxM1, B‐Myb, and E2F2 as key regulators of M2. These results suggest functional disruption of M2 via gene mutation or altered expression as a convergent pathway regulating astrocytoma transformation. By considering M2 as a multitarget drug target regulating astrocytoma transformation, we identified several drugs that are predicted to restore M2 expression in anaplastic astrocytoma toward its low‐grade profile and of these, we validated the known antiproliferative drug resveratrol as down‐regulating multiple nodes of M2 including at nanomolar concentrations achievable in human cerebrospinal fluid by oral dosing. Interpretation Our results identify M2 as a multitarget network characteristic for astrocytoma progression and encourage M2‐based drug screening to identify new compounds for preventing glioma transformation.
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Affiliation(s)
- Liisi Laaniste
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Julianna Stylianou
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Nelofer Syed
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Qingyu Zeng
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Sarah R Langley
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.,Duke-NUS Medical School, Singapore
| | - Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.,PROTECT, INSERM, Université Paris Diderot, Sorbonne Paris Cité, France
| | - Kevin O'Neill
- Department of Neurosurgery, Imperial College Healthcare NHS Trust, London, UK
| | - Matthew Williams
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Albert Becker
- Department of Neuropathology, University of Bonn Medical Centre, Bonn, Germany
| | - Federico Roncaroli
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Enrico Petretto
- Duke-NUS Medical School, Singapore.,MRC London Institute of Medical Sciences (LMS), Imperial College London, London, UK
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
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10
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Chothani S, Schäfer S, Adami E, Viswanathan S, Widjaja AA, Langley SR, Tan J, Wang M, Quaife NM, Jian Pua C, D'Agostino G, Guna Shekeran S, George BL, Lim S, Yiqun Cao E, van Heesch S, Witte F, Felkin LE, Christodoulou EG, Dong J, Blachut S, Patone G, Barton PJR, Hubner N, Cook SA, Rackham OJL. Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins. Circulation 2019; 140:937-951. [PMID: 31284728 PMCID: PMC6749977 DOI: 10.1161/circulationaha.119.039596] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Supplemental Digital Content is available in the text. Fibrosis is a common pathology in many cardiac disorders and is driven by the activation of resident fibroblasts. The global posttranscriptional mechanisms underlying fibroblast-to-myofibroblast conversion in the heart have not been explored.
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Affiliation(s)
- Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Sebastian Schäfer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Anissa A Widjaja
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Sarah R Langley
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Jessie Tan
- National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Mao Wang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Nicholas M Quaife
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.).,Medical Research Council-London Institute of Medical Sciences, Hammersmith Hospital Campus, United Kingdom (N.M.Q, S.A.C.).,Cardiovascular Research Centre, Royal Brompton and Harefield National Health Serfice Trust, London, United Kingdom (N.M.Q, P.J.R.B.)
| | - Chee Jian Pua
- National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Giuseppe D'Agostino
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Shamini Guna Shekeran
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Benjamin L George
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Stella Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Elaine Yiqun Cao
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.)
| | - Eleni G Christodoulou
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Jinrui Dong
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.).,Cardiovascular Research Centre, Royal Brompton and Harefield National Health Serfice Trust, London, United Kingdom (N.M.Q, P.J.R.B.)
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.).,German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H.).,Charité-Universitätsmedizin, Berlin, Germany (N.H.).,Berlin Institute of Health, Germany (N.H.)
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.).,National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.).,Medical Research Council-London Institute of Medical Sciences, Hammersmith Hospital Campus, United Kingdom (N.M.Q, S.A.C.)
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
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11
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Tan ALM, Langley SR, Tan CF, Chai JF, Khoo CM, Leow MKS, Khoo EYH, Moreno-Moral A, Pravenec M, Rotival M, Sadananthan SA, Velan SS, Venkataraman K, Chong YS, Lee YS, Sim X, Stunkel W, Liu MH, Tai ES, Petretto E. Ethnicity-Specific Skeletal Muscle Transcriptional Signatures and Their Relevance to Insulin Resistance in Singapore. J Clin Endocrinol Metab 2019; 104:465-486. [PMID: 30137523 DOI: 10.1210/jc.2018-00309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/14/2018] [Indexed: 11/19/2022]
Abstract
CONTEXT Insulin resistance (IR) and obesity differ among ethnic groups in Singapore, with the Malays more obese yet less IR than Asian-Indians. However, the molecular basis underlying these differences is not clear. OBJECTIVE As the skeletal muscle (SM) is metabolically relevant to IR, we investigated molecular pathways in SM that are associated with ethnic differences in IR, obesity, and related traits. DESIGN, SETTING, AND MAIN OUTCOME MEASURES We integrated transcriptomic, genomic, and phenotypic analyses in 156 healthy subjects representing three major ethnicities in the Singapore Adult Metabolism Study. PATIENTS This study contains Chinese (n = 63), Malay (n = 51), and Asian-Indian (n = 42) men, aged 21 to 40 years, without systemic diseases. RESULTS We found remarkable diversity in the SM transcriptome among the three ethnicities, with >8000 differentially expressed genes (40% of all genes expressed in SM). Comparison with blood transcriptome from a separate Singaporean cohort showed that >95% of SM expression differences among ethnicities were unique to SM. We identified a network of 46 genes that were specifically downregulated in Malays, suggesting dysregulation of components of cellular respiration in SM of Malay individuals. We also report 28 differentially expressed gene clusters, four of which were also enriched for genes that were found in genome-wide association studies of metabolic traits and disease and correlated with variation in IR, obesity, and related traits. CONCLUSION We identified extensive gene-expression changes in SM among the three Singaporean ethnicities and report specific genes and molecular pathways that might underpin and explain the differences in IR among these ethnic groups.
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Affiliation(s)
- Amelia Li Min Tan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | - Sarah R Langley
- Duke-National University of Singapore Medical School, Singapore
- National Heart Centre Singapore, Singapore
| | - Chee Fan Tan
- Nanyang Institute of Technology in Health and Medicine, Nanyang Technological University, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Chin Meng Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
- Division of Endocrinology, Department of Medicine, National University Health System, Singapore
| | - Melvin Khee-Shing Leow
- Duke-National University of Singapore Medical School, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Endocrinology, Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Eric Yin Hao Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Endocrinology, Department of Medicine, National University Health System, Singapore
| | | | - Michal Pravenec
- Institute Of Physiology, Czech Academy Of Sciences, Prague, Czech Republic
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Suresh Anand Sadananthan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
| | - S Sendhil Velan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kavita Venkataraman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yung Seng Lee
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Paediatrics Endocrinology, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Walter Stunkel
- Experimental Biotherapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Mei Hui Liu
- Department of Chemistry, Food Science & Technology Programme, National University of Singapore, Singapore
| | - E Shyong Tai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
- Division of Endocrinology, Department of Medicine, National University Health System, Singapore
| | - Enrico Petretto
- Duke-National University of Singapore Medical School, Singapore
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12
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Ooi J, Langley SR, Xu X, Utami KH, Sim B, Huang Y, Harmston NP, Tay YL, Ziaei A, Zeng R, Low D, Aminkeng F, Sobota RM, Ginhoux F, Petretto E, Pouladi MA. Unbiased Profiling of Isogenic Huntington Disease hPSC-Derived CNS and Peripheral Cells Reveals Strong Cell-Type Specificity of CAG Length Effects. Cell Rep 2019; 26:2494-2508.e7. [DOI: 10.1016/j.celrep.2019.02.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/17/2018] [Accepted: 02/01/2019] [Indexed: 02/02/2023] Open
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13
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Barwari T, Eminaga S, Mayr U, Lu R, Armstrong PC, Chan MV, Sahraei M, Fernández-Fuertes M, Moreau T, Barallobre-Barreiro J, Lynch M, Yin X, Schulte C, Baig F, Pechlaner R, Langley SR, Zampetaki A, Santer P, Weger M, Plasenzotti R, Schosserer M, Grillari J, Kiechl S, Willeit J, Shah AM, Ghevaert C, Warner TD, Fernández-Hernando C, Suárez Y, Mayr M. Inhibition of profibrotic microRNA-21 affects platelets and their releasate. JCI Insight 2018; 3:123335. [PMID: 30385722 PMCID: PMC6238735 DOI: 10.1172/jci.insight.123335] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 07/06/2018] [Accepted: 09/26/2018] [Indexed: 12/22/2022] Open
Abstract
Fibrosis is a major contributor to organ disease for which no specific therapy is available. MicroRNA-21 (miR-21) has been implicated in the fibrogenetic response, and inhibitors of miR-21 are currently undergoing clinical trials. Here, we explore how miR-21 inhibition may attenuate fibrosis using a proteomics approach. Transfection of miR-21 mimic or inhibitor in murine cardiac fibroblasts revealed limited effects on extracellular matrix (ECM) protein secretion. Similarly, miR-21–null mouse hearts showed an unaltered ECM composition. Thus, we searched for additional explanations as to how miR-21 might regulate fibrosis. In plasma samples from the community-based Bruneck Study, we found a marked correlation of miR-21 levels with several platelet-derived profibrotic factors, including TGF-β1. Pharmacological miR-21 inhibition with an antagomiR reduced the platelet release of TGF-β1 in mice. Mechanistically, Wiskott-Aldrich syndrome protein, a negative regulator of platelet TGF-β1 secretion, was identified as a direct target of miR-21. miR-21–null mice had lower platelet and leukocyte counts compared with littermate controls but higher megakaryocyte numbers in the bone marrow. Thus, to our knowledge this study reports a previously unrecognized effect of miR-21 inhibition on platelets. The effect of antagomiR-21 treatment on platelet TGF-β1 release, in particular, may contribute to the antifibrotic effects of miR-21 inhibitors. MicroRNA-21 inhibition may convey its therapeutic benefits in fibrosis through its action in bone marrow cells rather than targeting fibroblasts directly.
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Affiliation(s)
- Temo Barwari
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Seda Eminaga
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Ursula Mayr
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Ruifang Lu
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Paul C Armstrong
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Melissa V Chan
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Mahnaz Sahraei
- Department of Comparative Medicine and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Marta Fernández-Fuertes
- Department of Comparative Medicine and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Thomas Moreau
- Department of Haematology, University of Cambridge, National Health Blood Service Centre, Cambridge, United Kingdom
| | | | - Marc Lynch
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Xiaoke Yin
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Christian Schulte
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Ferheen Baig
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Raimund Pechlaner
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Sarah R Langley
- Duke-NUS Medical School, Singapore.,National Heart Centre Singapore, Singapore
| | - Anna Zampetaki
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | | | - Martin Weger
- Department of Internal Medicine, Bruneck Hospital, Bruneck, Italy
| | - Roberto Plasenzotti
- Medical University of Vienna, Institute of Biomedical Research, Vienna, Austria
| | - Markus Schosserer
- Christian Doppler Laboratory on Biotechnology of Skin Aging, Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johannes Grillari
- Christian Doppler Laboratory on Biotechnology of Skin Aging, Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stefan Kiechl
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Johann Willeit
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Ajay M Shah
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Cedric Ghevaert
- Department of Haematology, University of Cambridge, National Health Blood Service Centre, Cambridge, United Kingdom
| | - Timothy D Warner
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Carlos Fernández-Hernando
- Department of Comparative Medicine and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yajaira Suárez
- Department of Comparative Medicine and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
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14
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Srivastava PK, Bagnati M, Delahaye-Duriez A, Ko JH, Rotival M, Langley SR, Shkura K, Mazzuferi M, Danis B, van Eyll J, Foerch P, Behmoaras J, Kaminski RM, Petretto E, Johnson MR. Genome-wide analysis of differential RNA editing in epilepsy. Genome Res 2018; 27:440-450. [PMID: 28250018 PMCID: PMC5340971 DOI: 10.1101/gr.210740.116] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [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: 05/31/2016] [Accepted: 01/10/2017] [Indexed: 02/03/2023]
Abstract
The recoding of genetic information through RNA editing contributes to proteomic diversity, but the extent and significance of RNA editing in disease is poorly understood. In particular, few studies have investigated the relationship between RNA editing and disease at a genome-wide level. Here, we developed a framework for the genome-wide detection of RNA sites that are differentially edited in disease. Using RNA-sequencing data from 100 hippocampi from mice with epilepsy (pilocarpine–temporal lobe epilepsy model) and 100 healthy control hippocampi, we identified 256 RNA sites (overlapping with 87 genes) that were significantly differentially edited between epileptic cases and controls. The degree of differential RNA editing in epileptic mice correlated with frequency of seizures, and the set of genes differentially RNA-edited between case and control mice were enriched for functional terms highly relevant to epilepsy, including “neuron projection” and “seizures.” Genes with differential RNA editing were preferentially enriched for genes with a genetic association to epilepsy. Indeed, we found that they are significantly enriched for genes that harbor nonsynonymous de novo mutations in patients with epileptic encephalopathy and for common susceptibility variants associated with generalized epilepsy. These analyses reveal a functional convergence between genes that are differentially RNA-edited in acquired symptomatic epilepsy and those that contribute risk for genetic epilepsy. Taken together, our results suggest a potential role for RNA editing in the epileptic hippocampus in the occurrence and severity of epileptic seizures.
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Affiliation(s)
| | - Marta Bagnati
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, United Kingdom
| | - Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom
| | - Jeong-Hun Ko
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, United Kingdom
| | - Maxime Rotival
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France
| | - Sarah R Langley
- Duke-NUS Medical School, Singapore 169857, Republic of Singapore
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom
| | | | | | | | - Patrik Foerch
- Neuroscience TA, UCB Pharma, 1420 Braine-l'Alleud, Belgium
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, United Kingdom
| | | | - Enrico Petretto
- Duke-NUS Medical School, Singapore 169857, Republic of Singapore
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom
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15
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Auce P, Francis B, Langley SR, Jorgensen A, Marson AG, Sills GJ. PO039 Gwas for early remission in newly diagnosed focal epilepsy. J Neurol Psychiatry 2017. [DOI: 10.1136/jnnp-2017-abn.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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16
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Langley SR, Willeit K, Didangelos A, Matic LP, Skroblin P, Barallobre-Barreiro J, Lengquist M, Rungger G, Kapustin A, Kedenko L, Lu R, Barwari T, Suna G, Yin X, Iglseder B, Paulweber B, Willeit P, Shalhoub J, Pasterkamp G, Monaco C, Hedin U, M. Shanahan C, Willeit J, Kielch SK, Mayr M. 203 Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques. Heart 2017. [DOI: 10.1136/heartjnl-2017-311726.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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17
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Langley SR, Willeit K, Didangelos A, Matic LP, Skroblin P, Barallobre-Barreiro J, Lengquist M, Rungger G, Kapustin A, Kedenko L, Molenaar C, Lu R, Barwari T, Suna G, Yin X, Iglseder B, Paulweber B, Willeit P, Shalhoub J, Pasterkamp G, Davies AH, Monaco C, Hedin U, Shanahan CM, Willeit J, Kiechl S, Mayr M. Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques. J Clin Invest 2017; 127:1546-1560. [PMID: 28319050 PMCID: PMC5373893 DOI: 10.1172/jci86924] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [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: 02/23/2016] [Accepted: 01/19/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND. The identification of patients with high-risk atherosclerotic plaques prior to the manifestation of clinical events remains challenging. Recent findings question histology- and imaging-based definitions of the “vulnerable plaque,” necessitating an improved approach for predicting onset of symptoms. METHODS. We performed a proteomics comparison of the vascular extracellular matrix and associated molecules in human carotid endarterectomy specimens from 6 symptomatic versus 6 asymptomatic patients to identify a protein signature for high-risk atherosclerotic plaques. Proteomics data were integrated with gene expression profiling of 121 carotid endarterectomies and an analysis of protein secretion by lipid-loaded human vascular smooth muscle cells. Finally, epidemiological validation of candidate biomarkers was performed in two community-based studies. RESULTS. Proteomics and at least one of the other two approaches identified a molecular signature of plaques from symptomatic patients that comprised matrix metalloproteinase 9, chitinase 3-like-1, S100 calcium binding protein A8 (S100A8), S100A9, cathepsin B, fibronectin, and galectin-3-binding protein. Biomarker candidates measured in 685 subjects in the Bruneck study were associated with progression to advanced atherosclerosis and incidence of cardiovascular disease over a 10-year follow-up period. A 4-biomarker signature (matrix metalloproteinase 9, S100A8/S100A9, cathepsin D, and galectin-3-binding protein) improved risk prediction and was successfully replicated in an independent cohort, the SAPHIR study. CONCLUSION. The identified 4-biomarker signature may improve risk prediction and diagnostics for the management of cardiovascular disease. Further, our study highlights the strength of tissue-based proteomics for biomarker discovery. FUNDING. UK: British Heart Foundation (BHF); King’s BHF Center; and the National Institute for Health Research Biomedical Research Center based at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London in partnership with King’s College Hospital. Austria: Federal Ministry for Transport, Innovation and Technology (BMVIT); Federal Ministry of Science, Research and Economy (BMWFW); Wirtschaftsagentur Wien; and Standortagentur Tirol.
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Affiliation(s)
- Sarah R. Langley
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
- Duke-NUS Medical School, Singapore
| | - Karin Willeit
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Athanasios Didangelos
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
| | - Ljubica Perisic Matic
- Department of Molecular Medicine and Surgery, Vascular Surgery, Karolinska Institute, Stockholm, Sweden
| | - Philipp Skroblin
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
| | | | - Mariette Lengquist
- Department of Molecular Medicine and Surgery, Vascular Surgery, Karolinska Institute, Stockholm, Sweden
| | - Gregor Rungger
- Department of Neurology, Bruneck Hospital, Bruneck, Italy
| | - Alexander Kapustin
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
| | - Ludmilla Kedenko
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Chris Molenaar
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
- Nikon Imaging Centre, King’s College London, London, United Kingdom
| | - Ruifang Lu
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
| | - Temo Barwari
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
| | - Gonca Suna
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
| | - Xiaoke Yin
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
| | - Bernhard Iglseder
- Department of Geriatric Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Peter Willeit
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Joseph Shalhoub
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Gerard Pasterkamp
- Laboratory of Clinical Chemistry and Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alun H. Davies
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Claudia Monaco
- Kennedy Institute, University of Oxford, Oxford, United Kingdom
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Vascular Surgery, Karolinska Institute, Stockholm, Sweden
| | - Catherine M. Shanahan
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
| | - Johann Willeit
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Stefan Kiechl
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Manuel Mayr
- King’s British Heart Foundation Centre, King’s College London, London, United Kingdom
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18
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Delahaye-Duriez A, Srivastava P, Shkura K, Langley SR, Laaniste L, Moreno-Moral A, Danis B, Mazzuferi M, Foerch P, Gazina EV, Richards K, Petrou S, Kaminski RM, Petretto E, Johnson MR. Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery. Genome Biol 2016; 17:245. [PMID: 27955713 PMCID: PMC5154105 DOI: 10.1186/s13059-016-1097-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/02/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated systems-level analysis of brain gene expression data to identify molecular networks disrupted in epilepsy. RESULTS We identified a co-expression network of 320 genes (M30), which is significantly enriched for non-synonymous de novo mutations ascertained from patients with monogenic epilepsy and for common variants associated with polygenic epilepsy. The genes in the M30 network are expressed widely in the human brain under tight developmental control and encode physically interacting proteins involved in synaptic processes. The most highly connected proteins within the M30 network were preferentially disrupted by deleterious de novo mutations for monogenic epilepsy, in line with the centrality-lethality hypothesis. Analysis of M30 expression revealed consistent downregulation in the epileptic brain in heterogeneous forms of epilepsy including human temporal lobe epilepsy, a mouse model of acquired temporal lobe epilepsy, and a mouse model of monogenic Dravet (SCN1A) disease. These results suggest functional disruption of M30 via gene mutation or altered expression as a convergent mechanism regulating susceptibility to epilepsy broadly. Using the large collection of drug-induced gene expression data from Connectivity Map, several drugs were predicted to preferentially restore the downregulation of M30 in epilepsy toward health, most notably valproic acid, whose effect on M30 expression was replicated in neurons. CONCLUSIONS Taken together, our results suggest targeting the expression of M30 as a potential new therapeutic strategy in epilepsy.
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Affiliation(s)
- Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.
- MRC Clinical Sciences Centre, Imperial College London, London, UK.
- Université Paris 13, Sorbonne Paris Cité, UFR de Santé, Médecine et Biologie Humaine, Paris, France.
- PROTECT, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
| | - Prashant Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Sarah R Langley
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
- Duke-NUS Medical School, 8 College Road, 169857, Singapore, Republic of Singapore
| | - Liisi Laaniste
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Aida Moreno-Moral
- MRC Clinical Sciences Centre, Imperial College London, London, UK
- Duke-NUS Medical School, 8 College Road, 169857, Singapore, Republic of Singapore
| | - Bénédicte Danis
- Neuroscience TA, UCB Pharma, S.A, Allée de la Recherche, 60, 1070, Brussels, Belgium
| | - Manuela Mazzuferi
- Neuroscience TA, UCB Pharma, S.A, Allée de la Recherche, 60, 1070, Brussels, Belgium
| | - Patrik Foerch
- Neuroscience TA, UCB Pharma, S.A, Allée de la Recherche, 60, 1070, Brussels, Belgium
| | - Elena V Gazina
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Kay Richards
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Steven Petrou
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
- The Centre for Neural Engineering, The Department of Electrical Engineering, The University of Melbourne, Parkville, Victoria, 3052, Australia
- The Australian Research Council Centre of Excellence for Integrative Brain Function, Parkville, Victoria, 3052, Australia
| | - Rafal M Kaminski
- Neuroscience TA, UCB Pharma, S.A, Allée de la Recherche, 60, 1070, Brussels, Belgium
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, London, UK.
- Duke-NUS Medical School, 8 College Road, 169857, Singapore, Republic of Singapore.
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.
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19
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Gomes RSM, Skroblin P, Munster AB, Tomlins H, Langley SR, Zampetaki A, Yin X, Wardle FC, Mayr M. "Young at heart": Regenerative potential linked to immature cardiac phenotypes. J Mol Cell Cardiol 2016; 92:105-8. [PMID: 26827899 PMCID: PMC4796039 DOI: 10.1016/j.yjmcc.2016.01.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 01/15/2023]
Abstract
The adult human myocardium is incapable of regeneration; yet, the zebrafish (Danio rerio) can regenerate damaged myocardium. Similar to the zebrafish heart, hearts of neonatal, but not adult mice are capable of myocardial regeneration. We performed a proteomics analysis of adult zebrafish hearts and compared their protein expression profile to hearts from neonatal and adult mice. Using difference in-gel electrophoresis (DIGE), there was little overlap between the proteome from adult mouse (> 8 weeks old) and adult zebrafish (18 months old) hearts. Similarly, there was a significant degree of mismatch between the protein expression in neonatal and adult mouse hearts. Enrichment analysis of the selected proteins revealed over-expression of DNA synthesis-related proteins in the cardiac proteome of the adult zebrafish heart similar to neonatal and 4 days old mice, whereas in hearts of adult mice there was a mitochondria-related predominance in protein expression. Importantly, we noted pronounced differences in the myofilament composition: the adult zebrafish heart lacks many of the myofilament proteins of differentiated adult cardiomyocytes such as the ventricular isoforms of myosin light chains and nebulette. Instead, troponin I and myozenin 1 were expressed as skeletal isoforms rather than cardiac isoforms. The relative immaturity of the adult zebrafish heart was further supported by cardiac microRNA data. Our assessment of zebrafish and mammalian hearts challenges the assertions on the translational potential of cardiac regeneration in the zebrafish model. The immature myofilament composition of the fish heart may explain why adult mouse and human cardiomyocytes lack this endogenous repair mechanism. Proteomics reveals minimal overlap between adult mouse and adult zebrafish hearts. Gene expression analysis confirms profound differences in myofilament composition. The adult zebrafish heart is more similar to a newborn mouse heart. The relative immaturity is further supported by cardiac microRNA data.
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Affiliation(s)
- Renata S M Gomes
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Philipp Skroblin
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Alex B Munster
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Hannah Tomlins
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Sarah R Langley
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Anna Zampetaki
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Xiaoke Yin
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Fiona C Wardle
- Cardiovascular Development, Randall Division, King's College London, UK
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, UK.
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20
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Zampetaki A, Willeit P, Burr S, Yin X, Langley SR, Kiechl S, Klein R, Rossing P, Chaturvedi N, Mayr M. Angiogenic microRNAs Linked to Incidence and Progression of Diabetic Retinopathy in Type 1 Diabetes. Diabetes 2016; 65:216-27. [PMID: 26395742 DOI: 10.2337/db15-0389] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 09/16/2015] [Indexed: 12/13/2022]
Abstract
Circulating microRNAs (miRNAs) have emerged as novel biomarkers of diabetes. The current study focuses on the role of circulating miRNAs in patients with type 1 diabetes and their association with diabetic retinopathy. A total of 29 miRNAs were quantified in serum samples (n = 300) using a nested case-control study design in two prospective cohorts of the DIabetic REtinopathy Candesartan Trial (DIRECT): PROTECT-1 and PREVENT-1. The PREVENT-1 trial included patients without retinopathy at baseline; the PROTECT-1 trial included patients with nonproliferative retinopathy at baseline. Two miRNAs previously implicated in angiogenesis, miR-27b and miR-320a, were associated with incidence and with progression of retinopathy: the odds ratio per SD higher miR-27b was 0.57 (95% CI 0.40, 0.82; P = 0.002) in PREVENT-1, 0.78 (0.57, 1.07; P = 0.124) in PROTECT-1, and 0.67 (0.50, 0.92; P = 0.012) combined. The respective odds ratios for higher miR-320a were 1.57 (1.07, 2.31; P = 0.020), 1.43 (1.05, 1.94; P = 0.021), and 1.48 (1.17, 1.88; P = 0.001). Proteomics analyses in endothelial cells returned the antiangiogenic protein thrombospondin-1 as a common target of both miRNAs. Our study identifies two angiogenic miRNAs, miR-320a and miR-27b, as potential biomarkers for diabetic retinopathy.
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Affiliation(s)
- Anna Zampetaki
- King's British Heart Foundation Centre of Research Excellence, King's College London, London, U.K
| | - Peter Willeit
- King's British Heart Foundation Centre of Research Excellence, King's College London, London, U.K. Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K. Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Simon Burr
- King's British Heart Foundation Centre of Research Excellence, King's College London, London, U.K
| | - Xiaoke Yin
- King's British Heart Foundation Centre of Research Excellence, King's College London, London, U.K
| | - Sarah R Langley
- King's British Heart Foundation Centre of Research Excellence, King's College London, London, U.K
| | - Stefan Kiechl
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI
| | - Peter Rossing
- Steno Diabetes Centre, University of Copenhagen, Copenhagen, Denmark
| | - Nishi Chaturvedi
- Institute of Cardiovascular Science, University College London, London, U.K.
| | - Manuel Mayr
- King's British Heart Foundation Centre of Research Excellence, King's College London, London, U.K.
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21
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Kaudewitz D, Skroblin P, Bender LH, Barwari T, Willeit P, Pechlaner R, Sunderland NP, Willeit K, Morton AC, Armstrong PC, Chan MV, Lu R, Yin X, Gracio F, Dudek K, Langley SR, Zampetaki A, de Rinaldis E, Ye S, Warner TD, Saxena A, Kiechl S, Storey RF, Mayr M. Association of MicroRNAs and YRNAs With Platelet Function. Circ Res 2015; 118:420-432. [PMID: 26646931 DOI: 10.1161/circresaha.114.305663] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 12/08/2015] [Indexed: 12/21/2022]
Abstract
RATIONALE Platelets shed microRNAs (miRNAs). Plasma miRNAs change on platelet inhibition. It is unclear whether plasma miRNA levels correlate with platelet function. OBJECTIVE To link small RNAs to platelet reactivity. METHODS AND RESULTS Next-generation sequencing of small RNAs in plasma revealed 2 peaks at 22 to 23 and 32 to 33 nucleotides corresponding to miRNAs and YRNAs, respectively. Among YRNAs, predominantly, fragments of RNY4 and RNY5 were detected. Plasma miRNAs and YRNAs were measured in 125 patients with a history of acute coronary syndrome who had undergone detailed assessment of platelet function 30 days after the acute event. Using quantitative real-time polymerase chain reactions, 92 miRNAs were assessed in patients with acute coronary syndrome on different antiplatelet therapies. Key platelet-related miRNAs and YRNAs were correlated with platelet function tests. MiR-223 (rp=0.28; n=121; P=0.002), miR-126 (rp=0.22; n=121; P=0.016), and other abundant platelet miRNAs and YRNAs showed significant positive correlations with the vasodilator-stimulated phosphoprotein phosphorylation assay. YRNAs, miR-126, and miR-223 were also among the small RNAs showing the greatest dependency on platelets and strongly correlated with plasma levels of P-selectin, platelet factor 4, and platelet basic protein in the population-based Bruneck study (n=669). A single-nucleotide polymorphism that facilitates processing of pri-miR-126 to mature miR-126 accounted for a rise in circulating platelet activation markers. Inhibition of miR-126 in mice reduced platelet aggregation. MiR-126 directly and indirectly affects ADAM9 and P2Y12 receptor expression. CONCLUSIONS Levels of platelet-related plasma miRNAs and YRNAs correlate with platelet function tests in patients with acute coronary syndrome and platelet activation markers in the general population. Alterations in miR-126 affect platelet reactivity.
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Affiliation(s)
| | - Philipp Skroblin
- King's British Heart Foundation Centre, King's College London, UK
| | - Lukas H Bender
- King's British Heart Foundation Centre, King's College London, UK
| | - Temo Barwari
- King's British Heart Foundation Centre, King's College London, UK
| | - Peter Willeit
- Department of Public Health and Primary Care, University of Cambridge, UK.,Department of Neurology, Medical University Innsbruck, Austria
| | | | | | - Karin Willeit
- Department of Neurology, Medical University Innsbruck, Austria
| | - Allison C Morton
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Paul C Armstrong
- William Harvey Research Institute, Queen Mary University of London, UK
| | - Melissa V Chan
- William Harvey Research Institute, Queen Mary University of London, UK
| | - Ruifang Lu
- King's British Heart Foundation Centre, King's College London, UK
| | - Xiaoke Yin
- King's British Heart Foundation Centre, King's College London, UK
| | - Filipe Gracio
- Biomedical Research Centre, King's College London, UK
| | - Katarzyna Dudek
- King's British Heart Foundation Centre, King's College London, UK
| | - Sarah R Langley
- King's British Heart Foundation Centre, King's College London, UK
| | - Anna Zampetaki
- King's British Heart Foundation Centre, King's College London, UK
| | | | - Shu Ye
- Department of Cardiovascular Sciences, University of Leicester, UK
| | - Timothy D Warner
- William Harvey Research Institute, Queen Mary University of London, UK
| | - Alka Saxena
- Biomedical Research Centre, King's College London, UK
| | - Stefan Kiechl
- Department of Neurology, Medical University Innsbruck, Austria
| | - Robert F Storey
- Department of Cardiovascular Science, University of Sheffield, UK
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, UK
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22
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Langley SR, Mayr M. Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics. J Proteomics 2015; 129:83-92. [PMID: 26193490 DOI: 10.1016/j.jprot.2015.07.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [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: 03/09/2015] [Revised: 07/10/2015] [Accepted: 07/13/2015] [Indexed: 01/03/2023]
Abstract
UNLABELLED Label-free LC-MS/MS proteomics has proven itself to be a powerful method for evaluating protein identification and quantification from complex samples. For comparative proteomics, several methods have been used to detect the differential expression of proteins from such data. We have assessed seven methods used across the literature for detecting differential expression from spectral count quantification: Student's t-test, significance analysis of microarrays (SAM), normalised spectral abundance factor (NSAF), normalised spectral abundance factor-power law global error model (NSAF-PLGEM), spectral index (SpI), DESeq and QSpec. We used 2000 simulated datasets as well as publicly available data from a proteomic standards study to assess the ability of these methods to detect differential expression in varying effect sizes and proportions of differentially expressed proteins. At two false discovery rate (FDR) levels, we find that several of the methods detect differential expression within the data with reasonable precision, others detect differential expression at the expense of low precision, and finally, others which fail to identify any differentially expressed proteins. The inability of these seven methods to fully capture the differential landscape, even at the largest effect size, illustrates some of the limitations of the existing technologies and the statistical methodologies. SIGNIFICANCE In label-free mass spectrometry experiments, protein identification and quantification have always been important, but there is now a growing focus on comparative proteomics. Detecting differential expression in protein levels can inform on important biological mechanisms and provide direction for further study. Given the high cost and labour intensive nature of validation experiments, statistical methods are important for prioritising proteins of interest. Here, we have performed a comparative analysis to investigate the statistical methodologies for detecting differential expression and provide a reference for future experimental designs. This article is part of a Special Issue entitled: Computational Proteomics.
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Affiliation(s)
- Sarah R Langley
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK; King's British Heart Foundation Centre, King's College London, London, UK.
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, UK
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23
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Roncon P, Soukupovà M, Binaschi A, Falcicchia C, Zucchini S, Ferracin M, Langley SR, Petretto E, Johnson MR, Marucci G, Michelucci R, Rubboli G, Simonato M. MicroRNA profiles in hippocampal granule cells and plasma of rats with pilocarpine-induced epilepsy--comparison with human epileptic samples. Sci Rep 2015; 5:14143. [PMID: 26382856 PMCID: PMC4585664 DOI: 10.1038/srep14143] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [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] [Received: 04/21/2015] [Accepted: 08/12/2015] [Indexed: 12/12/2022] Open
Abstract
The identification of biomarkers of the transformation of normal to epileptic tissue would help to stratify patients at risk of epilepsy following brain injury, and inform new treatment strategies. MicroRNAs (miRNAs) are an attractive option in this direction. In this study, miRNA microarrays were performed on laser-microdissected hippocampal granule cell layer (GCL) and on plasma, at different time points in the development of pilocarpine-induced epilepsy in the rat: latency, first spontaneous seizure and chronic epileptic phase. Sixty-three miRNAs were differentially expressed in the GCL when considering all time points. Three main clusters were identified that separated the control and chronic phase groups from the latency group and from the first spontaneous seizure group. MiRNAs from rats in the chronic phase were compared to those obtained from the laser-microdissected GCL of epileptic patients, identifying several miRNAs (miR-21-5p, miR-23a-5p, miR-146a-5p and miR-181c-5p) that were up-regulated in both human and rat epileptic tissue. Analysis of plasma samples revealed different levels between control and pilocarpine-treated animals for 27 miRNAs. Two main clusters were identified that segregated controls from all other groups. Those miRNAs that are altered in plasma before the first spontaneous seizure, like miR-9a-3p, may be proposed as putative biomarkers of epileptogenesis.
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Affiliation(s)
- Paolo Roncon
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, Italy
| | - Marie Soukupovà
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, Italy
| | - Anna Binaschi
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, Italy
| | - Chiara Falcicchia
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, Italy
| | - Silvia Zucchini
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, Italy.,National Institute of Neuroscience, Italy.,Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Italy
| | - Manuela Ferracin
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Italy.,Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Italy
| | - Sarah R Langley
- Division of Brain Sciences, Imperial College London, Charing Cross Hospital,UK
| | - Enrico Petretto
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, UK
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College London, Charing Cross Hospital,UK
| | - Gianluca Marucci
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), Section of Pathology, Bellaria Hospital, Bologna, Italy
| | - Roberto Michelucci
- IRCCS Institute of Neurological Sciences, Section of Neurology, Bellaria Hospital, Bologna, Italy
| | - Guido Rubboli
- IRCCS Institute of Neurological Sciences, Section of Neurology, Bellaria Hospital, Bologna, Italy.,Danish Epilepsy Center, Filadelfia/University of Copenhagen, Dianalund, Denmark
| | - Michele Simonato
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, Italy.,National Institute of Neuroscience, Italy.,Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Italy
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24
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Goedeke L, Salerno A, Ramírez CM, Guo L, Allen RM, Yin X, Langley SR, Esau C, Wanschel A, Fisher EA, Suárez Y, Baldán A, Mayr M, Fernández-Hernando C. Long-term therapeutic silencing of miR-33 increases circulating triglyceride levels and hepatic lipid accumulation in mice. EMBO Mol Med 2015; 6:1133-41. [PMID: 25038053 PMCID: PMC4197861 DOI: 10.15252/emmm.201404046] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Plasma high-density lipoprotein (HDL) levels show a strong inverse correlation with atherosclerotic vascular disease. Previous studies have demonstrated that antagonism of miR-33 in vivo increases circulating HDL and reverse cholesterol transport (RCT), thereby reducing the progression and enhancing the regression of atherosclerosis. While the efficacy of short-term anti-miR-33 treatment has been previously studied, the long-term effect of miR-33 antagonism in vivo remains to be elucidated. Here, we show that long-term therapeutic silencing of miR-33 increases circulating triglyceride (TG) levels and lipid accumulation in the liver. These adverse effects were only found when mice were fed a high-fat diet (HFD). Mechanistically, we demonstrate that chronic inhibition of miR-33 increases the expression of genes involved in fatty acid synthesis such as acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS) in the livers of mice treated with miR-33 antisense oligonucleotides. We also report that anti-miR-33 therapy enhances the expression of nuclear transcription Y subunit gamma (NFYC), a transcriptional regulator required for DNA binding and full transcriptional activation of SREBP-responsive genes, including ACC and FAS. Taken together, these results suggest that persistent inhibition of miR-33 when mice are fed a high-fat diet (HFD) might cause deleterious effects such as moderate hepatic steatosis and hypertriglyceridemia. These unexpected findings highlight the importance of assessing the effect of chronic inhibition of miR-33 in non-human primates before we can translate this therapy to humans.
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Affiliation(s)
- Leigh Goedeke
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine Yale University School of Medicine, New Haven, CT, USA Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, USA Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, NY, USA
| | - Alessandro Salerno
- Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, USA Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, NY, USA
| | - Cristina M Ramírez
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine Yale University School of Medicine, New Haven, CT, USA Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, USA Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, NY, USA
| | - Liang Guo
- Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, USA Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, NY, USA
| | - Ryan M Allen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Center for Cardiovascular Research, Saint Louis University School of Medicine, Saint Louis, MO, USA
| | - Xiaoke Yin
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Sarah R Langley
- King's British Heart Foundation Centre, King's College London, London, UK
| | | | - Amarylis Wanschel
- Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, USA Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, NY, USA
| | - Edward A Fisher
- Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, USA Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, NY, USA
| | - Yajaira Suárez
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine Yale University School of Medicine, New Haven, CT, USA Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, USA Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, NY, USA
| | - Angel Baldán
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Center for Cardiovascular Research, Saint Louis University School of Medicine, Saint Louis, MO, USA
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine Yale University School of Medicine, New Haven, CT, USA Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, USA Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, NY, USA
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25
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Johnson MR, Behmoaras J, Bottolo L, Krishnan ML, Pernhorst K, Santoscoy PLM, Rossetti T, Speed D, Srivastava PK, Chadeau-Hyam M, Hajji N, Dabrowska A, Rotival M, Razzaghi B, Kovac S, Wanisch K, Grillo FW, Slaviero A, Langley SR, Shkura K, Roncon P, De T, Mattheisen M, Niehusmann P, O'Brien TJ, Petrovski S, von Lehe M, Hoffmann P, Eriksson J, Coffey AJ, Cichon S, Walker M, Simonato M, Danis B, Mazzuferi M, Foerch P, Schoch S, De Paola V, Kaminski RM, Cunliffe VT, Becker AJ, Petretto E. Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus. Nat Commun 2015; 6:6031. [PMID: 25615886 DOI: 10.1038/ncomms7031] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/04/2014] [Indexed: 01/20/2023] Open
Abstract
Gene-regulatory network analysis is a powerful approach to elucidate the molecular processes and pathways underlying complex disease. Here we employ systems genetics approaches to characterize the genetic regulation of pathophysiological pathways in human temporal lobe epilepsy (TLE). Using surgically acquired hippocampi from 129 TLE patients, we identify a gene-regulatory network genetically associated with epilepsy that contains a specialized, highly expressed transcriptional module encoding proconvulsive cytokines and Toll-like receptor signalling genes. RNA sequencing analysis in a mouse model of TLE using 100 epileptic and 100 control hippocampi shows the proconvulsive module is preserved across-species, specific to the epileptic hippocampus and upregulated in chronic epilepsy. In the TLE patients, we map the trans-acting genetic control of this proconvulsive module to Sestrin 3 (SESN3), and demonstrate that SESN3 positively regulates the module in macrophages, microglia and neurons. Morpholino-mediated Sesn3 knockdown in zebrafish confirms the regulation of the transcriptional module, and attenuates chemically induced behavioural seizures in vivo.
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Affiliation(s)
- Michael R Johnson
- Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, London W12 0NN, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Leonardo Bottolo
- Department of Mathematics, Imperial College London, 180 Queen's Gate, London SW7 2AZ, UK
| | - Michelle L Krishnan
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, St Thomas' Hospital, King's College London, London SE1 7EH, UK
| | - Katharina Pernhorst
- Section of Translational Epileptology, Department of Neuropathology, University of Bonn, Sigmund Freud Street 25, Bonn D-53127, Germany
| | - Paola L Meza Santoscoy
- Department of Biomedical Science, Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Tiziana Rossetti
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Doug Speed
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, London W12 0NN, UK.,Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, MRC/PHE Centre for Environment and Health, Imperial College London, St Mary's Hospital, Norfolk Place, W21PG London, UK
| | - Nabil Hajji
- Department of Medicine, Centre for Pharmacology and Therapeutics, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Aleksandra Dabrowska
- Department of Medicine, Centre for Pharmacology and Therapeutics, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Maxime Rotival
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Banafsheh Razzaghi
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Stjepana Kovac
- Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Klaus Wanisch
- Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Federico W Grillo
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Anna Slaviero
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Sarah R Langley
- Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, London W12 0NN, UK.,Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, London W12 0NN, UK.,Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Paolo Roncon
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, 44121 Ferrara, Italy.,National Institute of Neuroscience, 44121 Ferrara, Italy
| | - Tisham De
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Manuel Mattheisen
- Department of Genomics, Life and Brain Center, University of Bonn, D-53127 Bonn, Germany.,Institute of Human Genetics, University of Bonn, D-53127 Bonn, Germany.,Institute for Genomic Mathematics, University of Bonn, D-53127 Bonn, Germany
| | - Pitt Niehusmann
- Section of Translational Epileptology, Department of Neuropathology, University of Bonn, Sigmund Freud Street 25, Bonn D-53127, Germany
| | - Terence J O'Brien
- Department of Medicine, RMH, University of Melbourne, Royal Melbourne Hospital, Royal Parade, Parkville, Victoria 3050, Australia
| | - Slave Petrovski
- Department of Neurology, Royal Melbourne Hospital, Melbourne, Parkville, Victoria 3050, Australia
| | - Marec von Lehe
- Department of Neurosurgery, University of Bonn Medical Center, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Department of Biomedicine, University of Basel, Hebelstrasse 20, 4056 Basel, Switzerland
| | - Johan Eriksson
- Folkhälsan Research Centre, Topeliusgatan 20, 00250 Helsinki, Finland.,Helsinki University Central Hospital, Unit of General Practice, Haartmaninkatu 4, Helsinki 00290, Finland.,Department of General Practice and Primary Health Care, University of Helsinki, 407, PO Box 20, Tukholmankatu 8 B, Helsinki 00014, Finland
| | - Alison J Coffey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Department of Biomedicine, University of Basel, Hebelstrasse 20, 4056 Basel, Switzerland
| | - Matthew Walker
- Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Michele Simonato
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, 44121 Ferrara, Italy.,National Institute of Neuroscience, 44121 Ferrara, Italy.,Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Bénédicte Danis
- Neuroscience TA, UCB Biopharma SPRL, Avenue de l'industrie, R9, B-1420 Braine l'Alleud, Belgium
| | - Manuela Mazzuferi
- Neuroscience TA, UCB Biopharma SPRL, Avenue de l'industrie, R9, B-1420 Braine l'Alleud, Belgium
| | - Patrik Foerch
- Neuroscience TA, UCB Biopharma SPRL, Avenue de l'industrie, R9, B-1420 Braine l'Alleud, Belgium
| | - Susanne Schoch
- Section of Translational Epileptology, Department of Neuropathology, University of Bonn, Sigmund Freud Street 25, Bonn D-53127, Germany.,Department of Epileptology, University of Bonn Medical Center, Sigmund-Freud-Strasse 25, Bonn D-53127, Germany
| | - Vincenzo De Paola
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Rafal M Kaminski
- Neuroscience TA, UCB Biopharma SPRL, Avenue de l'industrie, R9, B-1420 Braine l'Alleud, Belgium
| | - Vincent T Cunliffe
- Department of Biomedical Science, Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Albert J Becker
- Section of Translational Epileptology, Department of Neuropathology, University of Bonn, Sigmund Freud Street 25, Bonn D-53127, Germany
| | - Enrico Petretto
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK.,Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
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26
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Johnson MD, Mueller M, Adamowicz-Brice M, Collins MJ, Gellert P, Maratou K, Srivastava PK, Rotival M, Butt S, Game L, Atanur SS, Silver N, Norsworthy PJ, Langley SR, Petretto E, Pravenec M, Aitman TJ. Genetic analysis of the cardiac methylome at single nucleotide resolution in a model of human cardiovascular disease. PLoS Genet 2014; 10:e1004813. [PMID: 25474312 PMCID: PMC4256262 DOI: 10.1371/journal.pgen.1004813] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 12/05/2013] [Accepted: 10/09/2014] [Indexed: 12/03/2022] Open
Abstract
Epigenetic marks such as cytosine methylation are important determinants of cellular and whole-body phenotypes. However, the extent of, and reasons for inter-individual differences in cytosine methylation, and their association with phenotypic variation are poorly characterised. Here we present the first genome-wide study of cytosine methylation at single-nucleotide resolution in an animal model of human disease. We used whole-genome bisulfite sequencing in the spontaneously hypertensive rat (SHR), a model of cardiovascular disease, and the Brown Norway (BN) control strain, to define the genetic architecture of cytosine methylation in the mammalian heart and to test for association between methylation and pathophysiological phenotypes. Analysis of 10.6 million CpG dinucleotides identified 77,088 CpGs that were differentially methylated between the strains. In F1 hybrids we found 38,152 CpGs showing allele-specific methylation and 145 regions with parent-of-origin effects on methylation. Cis-linkage explained almost 60% of inter-strain variation in methylation at a subset of loci tested for linkage in a panel of recombinant inbred (RI) strains. Methylation analysis in isolated cardiomyocytes showed that in the majority of cases methylation differences in cardiomyocytes and non-cardiomyocytes were strain-dependent, confirming a strong genetic component for cytosine methylation. We observed preferential nucleotide usage associated with increased and decreased methylation that is remarkably conserved across species, suggesting a common mechanism for germline control of inter-individual variation in CpG methylation. In the RI strain panel, we found significant correlation of CpG methylation and levels of serum chromogranin B (CgB), a proposed biomarker of heart failure, which is evidence for a link between germline DNA sequence variation, CpG methylation differences and pathophysiological phenotypes in the SHR strain. Together, these results will stimulate further investigation of the molecular basis of locally regulated variation in CpG methylation and provide a starting point for understanding the relationship between the genetic control of CpG methylation and disease phenotypes. Epigenetic marks provide information that is not encoded in the primary DNA sequence itself but in modifications of genomic DNA and of the associated proteins. Methylation of genomic DNA at cytosine residues is an important epigenetic modification that is associated with developmental processes, carcinogenesis and other diseases. Genome-wide extent of, and reasons for inter-individual differences in cytosine methylation, and their association with phenotypic variation are poorly characterised. To address these questions we have determined and compared the genome-wide methylation patterns in heart tissue of two inbred rat strains, the spontaneously hypertensive rat, an animal model of human disease and a control rat strain. Comparison of methylation differences between genetically identical animals from the same strain and differences between animals from different strains allowed us to quantify association of epigenetic and genetic differences. We show that differences in an individual's germline DNA sequence are important determinants of the variability in methylation between individuals. Comparison with previous reports implicates common mechanisms for regulation of cytosine methylation that are highly conserved across species. Finally, we find correlation between a proposed blood biomarker for heart failure and variation in DNA methylation, suggesting a link between germline DNA sequence variation, methylation and a disease-related phenotype.
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Affiliation(s)
- Michelle D. Johnson
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Michael Mueller
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Martyna Adamowicz-Brice
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Melissa J. Collins
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Pascal Gellert
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- Institute of Clinical Sciences, Imperial College, London, United Kingdom
| | - Klio Maratou
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- Institute of Clinical Sciences, Imperial College, London, United Kingdom
| | - Prashant K. Srivastava
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Maxime Rotival
- Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Shahena Butt
- Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Laurence Game
- Genomics Core Laboratory, MRC Clinical Sciences Centre, London, United Kingdom
| | - Santosh S. Atanur
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Nicholas Silver
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Penny J. Norsworthy
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Sarah R. Langley
- Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Enrico Petretto
- Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Michal Pravenec
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
| | - Timothy J. Aitman
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- Institute of Clinical Sciences, Imperial College, London, United Kingdom
- * E-mail:
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27
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Zampetaki A, Attia R, Mayr U, Gomes RSM, Phinikaridou A, Yin X, Langley SR, Willeit P, Lu R, Fanshawe B, Fava M, Barallobre-Barreiro J, Molenaar C, So PW, Abbas A, Jahangiri M, Waltham M, Botnar R, Smith A, Mayr M. Role of miR-195 in aortic aneurysmal disease. Circ Res 2014; 115:857-66. [PMID: 25201911 DOI: 10.1161/circresaha.115.304361] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RATIONALE Abdominal aortic aneurysms constitute a degenerative process in the aortic wall. Both the miR-29 and miR-15 families have been implicated in regulating the vascular extracellular matrix. OBJECTIVE Our aim was to assess the effect of the miR-15 family on aortic aneurysm development. METHODS AND RESULTS Among the miR-15 family members, miR-195 was differentially expressed in aortas of apolipoprotein E-deficient mice on angiotensin II infusion. Proteomics analysis of the secretome of murine aortic smooth muscle cells, after miR-195 manipulation, revealed that miR-195 targets a cadre of extracellular matrix proteins, including collagens, proteoglycans, elastin, and proteins associated with elastic microfibrils, albeit miR-29b showed a stronger effect, particularly in regulating collagens. Systemic and local administration of cholesterol-conjugated antagomiRs revealed better inhibition of miR-195 compared with miR-29b in the uninjured aorta. However, in apolipoprotein E-deficient mice receiving angiotensin II, silencing of miR-29b, but not miR-195, led to an attenuation of aortic dilation. Higher aortic elastin expression was accompanied by an increase of matrix metalloproteinases 2 and 9 in mice treated with antagomiR-195. In human plasma, an inverse correlation of miR-195 was observed with the presence of abdominal aortic aneurysms and aortic diameter. CONCLUSIONS We provide the first evidence that miR-195 may contribute to the pathogenesis of aortic aneurysmal disease. Although inhibition of miR-29b proved more effective in preventing aneurysm formation in a preclinical model, miR-195 represents a potent regulator of the aortic extracellular matrix. Notably, plasma levels of miR-195 were reduced in patients with abdominal aortic aneurysms suggesting that microRNAs might serve as a noninvasive biomarker of abdominal aortic aneurysms.
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Affiliation(s)
- Anna Zampetaki
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.).
| | - Rizwan Attia
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Ursula Mayr
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Renata S M Gomes
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Alkystis Phinikaridou
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Xiaoke Yin
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Sarah R Langley
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Peter Willeit
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Ruifang Lu
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Bruce Fanshawe
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Marika Fava
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Javier Barallobre-Barreiro
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Chris Molenaar
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Po-Wah So
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Abeera Abbas
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Marjan Jahangiri
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Matthew Waltham
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Rene Botnar
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Alberto Smith
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.)
| | - Manuel Mayr
- From the King's British Heart Foundation Centre (A.Z., R.A., U.M., R.S.M.G., A.P., X.Y., S.R.L., R.L., B.F., M.F., J.B.-B., C.M., A.A., M.W., R.B., A.S., M.M.) and Institute of Psychiatry (P.-W.S.), King's College London, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (P.W.); and Department of Cardiac Surgery, St George's Healthcare NHS Trust, London, United Kingdom (M.F., M.J.).
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28
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Cuello F, Shankar-Hari M, Mayr U, Yin X, Marshall M, Willeit P, Langley SR, Terblanche M, Shah AM, Mayr M. P258Redox-state of pentraxin 3 as a novel biomarker for resolution of inflammation and survival in sepsis. Cardiovasc Res 2014. [DOI: 10.1093/cvr/cvu082.189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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Cuello F, Shankar-Hari M, Mayr U, Yin X, Marshall M, Suna G, Willeit P, Langley SR, Jayawardhana T, Zeller T, Terblanche M, Shah AM, Mayr M. Redox state of pentraxin 3 as a novel biomarker for resolution of inflammation and survival in sepsis. Mol Cell Proteomics 2014; 13:2545-57. [PMID: 24958171 PMCID: PMC4188985 DOI: 10.1074/mcp.m114.039446] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In an endotoxaemic mouse model of sepsis, a tissue-based proteomics approach for biomarker discovery identified long pentraxin 3 (PTX3) as the lead candidate for inflamed myocardium. When the redox-sensitive oligomerization state of PTX3 was further investigated, PTX3 accumulated as an octamer as a result of disulfide-bond formation in heart, kidney, and lung—common organ dysfunctions seen in patients with sepsis. Oligomeric moieties of PTX3 were also detectable in circulation. The oligomerization state of PTX3 was quantified over the first 11 days in critically ill adult patients with sepsis. On admission day, there was no difference in the oligomerization state of PTX3 between survivors and non-survivors. From day 2 onward, the conversion of octameric to monomeric PTX3 was consistently associated with a greater survival after 28 days of follow-up. For example, by day 2 post-admission, octameric PTX3 was barely detectable in survivors, but it still constituted more than half of the total PTX3 in non-survivors (p < 0.001). Monomeric PTX3 was inversely associated with cardiac damage markers NT-proBNP and high-sensitivity troponin I and T. Relative to the conventional measurements of total PTX3 or NT-proBNP, the oligomerization of PTX3 was a superior predictor of disease outcome.
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Affiliation(s)
- Friederike Cuello
- From the ‡King's British Heart Foundation Centre, King's College London, SE5 9NU London, UK; §Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Centre, University Medical Center Hamburg-Eppendorf, Hamburg, 20246 Germany; ¶DZHK (German Center for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany
| | - Manu Shankar-Hari
- ‖Critical Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, SE1 7EH UK; **Division of Asthma Allergy and Lung Biology, King's College, London SE1 9RT, UK
| | - Ursula Mayr
- From the ‡King's British Heart Foundation Centre, King's College London, SE5 9NU London, UK
| | - Xiaoke Yin
- From the ‡King's British Heart Foundation Centre, King's College London, SE5 9NU London, UK
| | - Melanie Marshall
- From the ‡King's British Heart Foundation Centre, King's College London, SE5 9NU London, UK
| | - Gonca Suna
- From the ‡King's British Heart Foundation Centre, King's College London, SE5 9NU London, UK
| | - Peter Willeit
- ‡‡Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; §§Department of Neurology, Innsbruck Medical University, Innsbruck, 6020 Austria
| | - Sarah R Langley
- From the ‡King's British Heart Foundation Centre, King's College London, SE5 9NU London, UK
| | - Tamani Jayawardhana
- From the ‡King's British Heart Foundation Centre, King's College London, SE5 9NU London, UK
| | - Tanja Zeller
- ¶¶Clinic for General and Interventional Cardiology, University Heart Centre Hamburg, Hamburg 20246, Germany
| | - Marius Terblanche
- ‖Critical Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, SE1 7EH UK
| | - Ajay M Shah
- From the ‡King's British Heart Foundation Centre, King's College London, SE5 9NU London, UK
| | - Manuel Mayr
- From the ‡King's British Heart Foundation Centre, King's College London, SE5 9NU London, UK;
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30
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Stegemann C, Pechlaner R, Willeit P, Langley SR, Mangino M, Mayr U, Menni C, Moayyeri A, Santer P, Rungger G, Spector TD, Willeit J, Kiechl S, Mayr M. Lipidomics Profiling and Risk of Cardiovascular Disease in the Prospective Population-Based Bruneck Study. Circulation 2014; 129:1821-31. [DOI: 10.1161/circulationaha.113.002500] [Citation(s) in RCA: 349] [Impact Index Per Article: 34.9] [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: 12/23/2022]
Abstract
Background—
The bulk of cardiovascular disease risk is not explained by traditional risk factors. Recent advances in mass spectrometry allow the identification and quantification of hundreds of lipid species. Molecular lipid profiling by mass spectrometry may improve cardiovascular risk prediction.
Methods and Results—
Lipids were extracted from 685 plasma samples of the prospective population-based Bruneck Study (baseline evaluation in 2000). One hundred thirty-five lipid species from 8 different lipid classes were profiled by shotgun lipidomics with the use of a triple-quadrupole mass spectrometer. Levels of individual species of cholesterol esters (CEs), lysophosphatidylcholines, phosphatidylcholines, phosphatidylethanolamines (PEs), sphingomyelins, and triacylglycerols (TAGs) were associated with cardiovascular disease over a 10-year observation period (2000–2010, 90 incident events). Among the lipid species with the strongest predictive value were TAGs and CEs with a low carbon number and double-bond content, including TAG(54:2) and CE(16:1), as well as PE(36:5) (
P
=5.1×10
−7
, 2.2×10
−4
, and 2.5×10
−3
, respectively). Consideration of these 3 lipid species on top of traditional risk factors resulted in improved risk discrimination and classification for cardiovascular disease (cross-validated ΔC index, 0.0210 [95% confidence interval, 0.0010-0.0422]; integrated discrimination improvement, 0.0212 [95% confidence interval, 0.0031-0.0406]; and continuous net reclassification index, 0.398 [95% confidence interval, 0.175-0.619]). A similar shift in the plasma fatty acid composition was associated with cardiovascular disease in the UK Twin Registry (n=1453, 45 cases).
Conclusions—
This study applied mass spectrometry-based lipidomics profiling to population-based cohorts and identified molecular lipid signatures for cardiovascular disease. Molecular lipid species constitute promising new biomarkers that outperform the conventional biochemical measurements of lipid classes currently used in clinics.
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Affiliation(s)
- Christin Stegemann
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Raimund Pechlaner
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Peter Willeit
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Sarah R. Langley
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Massimo Mangino
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Ursula Mayr
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Cristina Menni
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Alireza Moayyeri
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Peter Santer
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Gregor Rungger
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Tim D. Spector
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Johann Willeit
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Stefan Kiechl
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
| | - Manuel Mayr
- From the King’s British Heart Foundation Centre (C.S., S.R.L., U.M., M. Mayr) and Department of Twin Research & Genetic Epidemiology (M. Mangino, C.M., A.M., T.D.R.), King’s College London, London, UK; Department of Neurology, Medical University Innsbruck, Innsbruck, Austria (R.P., P.W., J.W., S.K.); Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK (P.W.); and Departments of Laboratory Medicine and Neurology, Bruneck Hospital, Bruneck, Italy (P.S., G.R.)
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Beyer C, Zampetaki A, Lin NY, Kleyer A, Perricone C, Iagnocco A, Distler A, Langley SR, Gelse K, Sesselmann S, Lorenzini R, Niemeier A, Swoboda B, Distler JHW, Santer P, Egger G, Willeit J, Mayr M, Schett G, Kiechl S. Signature of circulating microRNAs in osteoarthritis. Ann Rheum Dis 2014; 74:e18. [DOI: 10.1136/annrheumdis-2013-204698] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Abonnenc M, Nabeebaccus AA, Mayr U, Barallobre-Barreiro J, Dong X, Cuello F, Sur S, Drozdov I, Langley SR, Lu R, Stathopoulou K, Didangelos A, Yin X, Zimmermann WH, Shah AM, Zampetaki A, Mayr M. Extracellular matrix secretion by cardiac fibroblasts: role of microRNA-29b and microRNA-30c. Circ Res 2013; 113:1138-47. [PMID: 24006456 DOI: 10.1161/circresaha.113.302400] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RATIONALE MicroRNAs (miRNAs), in particular miR-29b and miR-30c, have been implicated as important regulators of cardiac fibrosis. OBJECTIVE To perform a proteomics comparison of miRNA effects on extracellular matrix secretion by cardiac fibroblasts. METHODS AND RESULTS Mouse cardiac fibroblasts were transfected with pre-/anti-miR of miR-29b and miR-30c, and their conditioned medium was analyzed by mass spectrometry. miR-29b targeted a cadre of proteins involved in fibrosis, including multiple collagens, matrix metalloproteinases, and leukemia inhibitory factor, insulin-like growth factor 1, and pentraxin 3, 3 predicted targets of miR-29b. miR-29b also attenuated the cardiac fibroblast response to transforming growth factor-β. In contrast, miR-30c had little effect on extracellular matrix production but opposite effects regarding leukemia inhibitory factor and insulin-like growth factor 1. Both miRNAs indirectly affected cardiac myocytes. On transfection with pre-miR-29b, the conditioned medium of cardiac fibroblasts lost its ability to support adhesion of rat ventricular myocytes and led to a significant reduction of cardiac myocyte proteins (α-actinin, cardiac myosin-binding protein C, and cardiac troponin I). Similarly, cardiomyocytes derived from mouse embryonic stem cells atrophied under pre-miR-29 conditioned medium, whereas pre-miR-30c conditioned medium had a prohypertrophic effect. Levels of miR-29a, miR-29c, and miR-30c, but not miR-29b, were significantly reduced in a mouse model of pathological but not physiological hypertrophy. Treatment with antagomiRs to miR-29b induced excess fibrosis after aortic constriction without overt deterioration in cardiac function. CONCLUSIONS Our proteomic analysis revealed novel molecular targets of miRNAs that are linked to a fibrogenic cardiac phenotype. Such comprehensive screening methods are essential to define the concerted actions of miRNAs in cardiovascular disease.
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Affiliation(s)
- Mélanie Abonnenc
- From the King's British Heart Foundation Centre, King's College London, London, United Kingdom
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Stegemann C, Didangelos A, Barallobre-Barreiro J, Langley SR, Mandal K, Jahangiri M, Mayr M. Proteomic Identification of Matrix Metalloproteinase Substrates in the Human Vasculature. ACTA ACUST UNITED AC 2013; 6:106-17. [DOI: 10.1161/circgenetics.112.964452] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Matrix metalloproteinases (MMPs) play a key role in cardiovascular disease, in particular aneurysm formation and plaque rupture. Surprisingly, little is known about MMP substrates in the vasculature.
Methods and Results—
We used a proteomics approach to identify vascular substrates for 3 MMPs, 1 of each of the 3 major classes of MMPs: Human arteries were incubated with MMP-3 (a member of stromelysins), MMP-9 (considered a gelatinase), and MMP-14 (considered a member of the collagenases and of the membrane-bound MMPs). Candidate substrates were identified by mass spectrometry based on increased release from the arterial tissue on digestion, spectral evidence for proteolytic degradation after gel separation, and identification of nontryptic cleavage sites. Using this approach, novel candidates were identified, including extracellular matrix proteins associated with the basement membrane, elastic fibers (emilin-1), and other extracellular proteins (periostin, tenascin-X). Seventy-four nontryptic cleavage sites were detected, many of which were shared among different MMPs. The proteomics findings were validated by immunoblotting and by digesting recombinant/purified proteins with exogenous MMPs. As proof-of-principle, results were related to in vivo pathology by searching for corresponding degradation products in human aortic tissue with different levels of endogenous MMP-9.
Conclusions—
The application of proteomics to identify MMP targets is a new frontier in cardiovascular research. Our current classification of MMPs based on few substrates is an oversimplification of a complex area of biology. This study provides a more comprehensive assessment of potential MMP substrates in the vasculature and represents a valuable resource for future investigations.
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Affiliation(s)
- Christin Stegemann
- From the King’s British Heart Foundation Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); The James Black Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); Division of Cardiac Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD (K.M.); and Department of Cardiac Surgery, St. George’s Healthcare NHS Trust, London, United Kingdom (M.J.)
| | - Athanasios Didangelos
- From the King’s British Heart Foundation Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); The James Black Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); Division of Cardiac Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD (K.M.); and Department of Cardiac Surgery, St. George’s Healthcare NHS Trust, London, United Kingdom (M.J.)
| | - Javier Barallobre-Barreiro
- From the King’s British Heart Foundation Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); The James Black Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); Division of Cardiac Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD (K.M.); and Department of Cardiac Surgery, St. George’s Healthcare NHS Trust, London, United Kingdom (M.J.)
| | - Sarah R. Langley
- From the King’s British Heart Foundation Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); The James Black Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); Division of Cardiac Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD (K.M.); and Department of Cardiac Surgery, St. George’s Healthcare NHS Trust, London, United Kingdom (M.J.)
| | - Kaushik Mandal
- From the King’s British Heart Foundation Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); The James Black Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); Division of Cardiac Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD (K.M.); and Department of Cardiac Surgery, St. George’s Healthcare NHS Trust, London, United Kingdom (M.J.)
| | - Marjan Jahangiri
- From the King’s British Heart Foundation Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); The James Black Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); Division of Cardiac Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD (K.M.); and Department of Cardiac Surgery, St. George’s Healthcare NHS Trust, London, United Kingdom (M.J.)
| | - Manuel Mayr
- From the King’s British Heart Foundation Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); The James Black Centre, King’s College London, London, United Kingdom (C.S., A.D., J.B.-B., S.L., M.M.); Division of Cardiac Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD (K.M.); and Department of Cardiac Surgery, St. George’s Healthcare NHS Trust, London, United Kingdom (M.J.)
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Willeit P, Zampetaki A, Dudek K, Kaudewitz D, King A, Kirkby NS, Crosby-Nwaobi R, Prokopi M, Drozdov I, Langley SR, Sivaprasad S, Markus HS, Mitchell JA, Warner TD, Kiechl S, Mayr M. Circulating microRNAs as novel biomarkers for platelet activation. Circ Res 2013; 112:595-600. [PMID: 23283721 DOI: 10.1161/circresaha.111.300539] [Citation(s) in RCA: 318] [Impact Index Per Article: 28.9] [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: 01/30/2023]
Abstract
RATIONALE MicroRNA (miRNA) biomarkers are attracting considerable interest. Effects of medication, however, have not been investigated thus far. OBJECTIVE To analyze changes in plasma miRNAs in response to antiplatelet therapy. METHODS AND RESULTS Profiling for 377 miRNAs was performed in platelets, platelet microparticles, platelet-rich plasma, platelet-poor plasma, and serum. Platelet-rich plasma showed markedly higher levels of miRNAs than serum and platelet-poor plasma. Few abundant platelet miRNAs, such as miR-24, miR-197, miR-191, and miR-223, were also increased in serum compared with platelet-poor plasma. In contrast, antiplatelet therapy significantly reduced miRNA levels. Using custom-made quantitative real-time polymerase chain reaction plates, 92 miRNAs were assessed in a dose-escalation study in healthy volunteers at 4 different time points: at baseline without therapy, at 1 week with 10 mg prasugrel, at 2 weeks with 10 mg prasugrel plus 75 mg aspirin, and at 3 weeks with 10 mg prasugrel plus 300 mg aspirin. Findings in healthy volunteers were confirmed by individual TaqMan quantitative real-time polymerase chain reaction assays (n=9). Validation was performed in an independent cohort of patients with symptomatic atherosclerosis (n=33), who received low-dose aspirin at baseline. Plasma levels of platelet miRNAs, such as miR-223, miR-191, and others, that is, miR-126 and miR-150, decreased on further platelet inhibition. CONCLUSIONS Our study demonstrated a substantial platelet contribution to the circulating miRNA pool and identified miRNAs responsive to antiplatelet therapy. It also highlights that antiplatelet therapy and preparation of blood samples could be confounding factors in case-control studies relating plasma miRNAs to cardiovascular disease.
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Affiliation(s)
- Peter Willeit
- Department of Neurology, Medical University Innsbruck, Austria
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Yin X, Dwyer J, Langley SR, Mayr U, Xing Q, Drozdov I, Nabeebaccus A, Shah AM, Madhu B, Griffiths J, Edwards LM, Mayr M. Effects of perhexiline-induced fuel switch on the cardiac proteome and metabolome. J Mol Cell Cardiol 2012; 55:27-30. [PMID: 23277191 PMCID: PMC3573230 DOI: 10.1016/j.yjmcc.2012.12.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 12/01/2012] [Accepted: 12/14/2012] [Indexed: 11/24/2022]
Abstract
Perhexiline is a potent anti-anginal drug used for treatment of refractory angina and other forms of heart disease. It provides an oxygen sparing effect in the myocardium by creating a switch from fatty acid to glucose metabolism through partial inhibition of carnitine palmitoyltransferase 1 and 2. However, the precise molecular mechanisms underlying the cardioprotective effects elicited by perhexiline are not fully understood. The present study employed a combined proteomics, metabolomics and computational approach to characterise changes in murine hearts upon treatment with perhexiline. According to results based on difference in-gel electrophoresis, the most profound change in the cardiac proteome related to the activation of the pyruvate dehydrogenase complex. Metabolomic analysis by high-resolution nuclear magnetic resonance spectroscopy showed lower levels of total creatine and taurine in hearts of perhexiline-treated mice. Creatine and taurine levels were also significantly correlated in a cross-correlation analysis of all metabolites. Computational modelling suggested that far from inducing a simple shift from fatty acid to glucose oxidation, perhexiline may cause complex rebalancing of carbon and nucleotide phosphate fluxes, fuelled by increased lactate and amino acid uptake, to increase metabolic flexibility and to maintain cardiac output. This article is part of a Special Issue entitled "Focus on Cardiac Metabolism".
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Affiliation(s)
- Xiaoke Yin
- King's BHF Centre, King's College London, UK
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36
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Abstract
The conventional reductionist approach to cardiovascular research investigates individual candidate factors or linear signalling pathways but ignores more complex interactions in biological systems. The advent of molecular profiling technologies that focus on a global characterization of whole complements allows an exploration of the interconnectivity of pathways during pathophysiologically relevant processes, but has brought about the issue of statistical analysis and data integration. Proteins identified by differential expression as well as those in protein–protein interaction networks identified through experiments and through computational modelling techniques can be used as an initial starting point for functional analyses. In combination with other ‘-omics’ technologies, such as transcriptomics and metabolomics, proteomics explores different aspects of disease, and the different pillars of observations facilitate the data integration in disease-specific networks. Ultimately, a systems biology approach may advance our understanding of cardiovascular disease processes at a ‘biological pathway’ instead of a ‘single molecule’ level and accelerate progress towards disease-modifying interventions.
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Affiliation(s)
- Sarah R Langley
- King's British Heart Foundation Centre, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
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37
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Langley SR, Bottolo L, Kunes J, Zicha J, Zidek V, Hubner N, Cook SA, Pravenec M, Aitman TJ, Petretto E. Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans. Cardiovasc Res 2012; 97:653-65. [PMID: 23118132 DOI: 10.1093/cvr/cvs329] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [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: 01/11/2023] Open
Abstract
AIMS Human genome-wide association studies (GWAS) of hypertension identified only few susceptibility loci with large effect that were replicated across populations. The vast majority of genes detected by GWAS has small effect and the regulatory mechanisms through which these genetic variants cause disease remain mostly unclear. Here, we used comparative genomics between human and an established rat model of hypertension to explore the transcriptional mechanisms mediating the effect of genes identified in 15 hypertension GWAS. METHODS AND RESULTS Time series analysis of radiotelemetric blood pressure (BP) was performed to assess 11 parameters of BP variation in recombinant inbred strains derived from the spontaneously hypertensive rat. BP data were integrated with ∼27 000 expression quantative trait loci (eQTLs) mapped across seven tissues, detecting >8000 significant associations between eQTL genes and BP variation in the rat. We then compiled a large catalogue of human genes from GWAS of hypertension and identified a subset of 2292 rat-human orthologous genes. Expression levels for 795 (34%) of these genes correlated with BP variation across rat tissues: 51 genes were cis-regulated, whereas 459 were trans-regulated and enriched for 'calcium signalling pathway' (P = 9.6 × 10(-6)) and 'ion channel' genes (P = 3.5 × 10(-7)), which are important determinants of hypertension. We identified 158 clusters of trans-eQTLs, annotated the underlying 'master regulator' genes and found significant over-representation in the human hypertension gene set (enrichment P = 5 × 10(-4)). CONCLUSION We showed extensive conservation of trans-regulated genes and their master regulators between rat and human hypertension. These findings reveal that small-effect genes associated with hypertension by human GWAS are likely to exert their action through coordinate regulation of pathogenic pathways.
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Affiliation(s)
- Sarah R Langley
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
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38
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Lin B, Huntley D, Abuali G, Langley SR, Sindelar G, Petretto E, Butcher S, Grimm S. Determining signalling nodes for apoptosis by a genetic high-throughput screen. PLoS One 2011; 6:e25023. [PMID: 21966401 PMCID: PMC3178610 DOI: 10.1371/journal.pone.0025023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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: 01/27/2011] [Accepted: 08/25/2011] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND With the ever-increasing information emerging from the various sequencing and gene annotation projects, there is an urgent need to elucidate the cellular functions of the newly discovered genes. The genetically regulated cell suicide of apoptosis is especially suitable for such endeavours as it is governed by a vast number of factors. METHODOLOGY/PRINCIPAL FINDINGS We have set up a high-throughput screen in 96-well microtiter plates for genes that induce apoptosis upon their individual transfection into human cells. Upon screening approximately 100,000 cDNA clones we determined 74 genes that initiate this cellular suicide programme. A thorough bioinformatics analysis of these genes revealed that 91% are novel apoptosis regulators. Careful sequence analysis and functional annotation showed that the apoptosis factors exhibit a distinct functional distribution that distinguishes the cell death process from other signalling pathways. While only a minority of classic signal transducers were determined, a substantial number of the genes fall into the transporter- and enzyme-category. The apoptosis factors are distributed throughout all cellular organelles and many signalling circuits, but one distinct signalling pathway connects at least some of the isolated genes. Comparisons with microarray data suggest that several genes are dysregulated in specific types of cancers and degenerative diseases. CONCLUSIONS/SIGNIFICANCE Many unknown genes for cell death were revealed through our screen, supporting the enormous complexity of cell death regulation. Our results will serve as a repository for other researchers working with genomics data related to apoptosis or for those seeking to reveal novel signalling pathways for cell suicide.
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Affiliation(s)
- Bevan Lin
- Division of Experimental Medicine, Imperial College London, London, United Kingdom
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Bottolo L, Chadeau-Hyam M, Hastie DI, Langley SR, Petretto E, Tiret L, Tregouet D, Richardson S. ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration. ACTA ACUST UNITED AC 2011; 27:587-8. [PMID: 21233165 PMCID: PMC3035799 DOI: 10.1093/bioinformatics/btq684] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [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: 11/13/2022]
Abstract
SUMMARY ESS++ is a C++ implementation of a fully Bayesian variable selection approach for single and multiple response linear regression. ESS++ works well both when the number of observations is larger than the number of predictors and in the 'large p, small n' case. In the current version, ESS++ can handle several hundred observations, thousands of predictors and a few responses simultaneously. The core engine of ESS++ for the selection of relevant predictors is based on Evolutionary Monte Carlo. Our implementation is open source, allowing community-based alterations and improvements. AVAILABILITY C++ source code and documentation including compilation instructions are available under GNU licence at http://bgx.org.uk/software/ESS.html.
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Affiliation(s)
- Leonardo Bottolo
- Department of Epidemiology and Biostatistics, Imperial College London, UK.
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Petretto E, Bottolo L, Langley SR, Heinig M, McDermott-Roe C, Sarwar R, Pravenec M, Hübner N, Aitman TJ, Cook SA, Richardson S. New insights into the genetic control of gene expression using a Bayesian multi-tissue approach. PLoS Comput Biol 2010; 6:e1000737. [PMID: 20386736 PMCID: PMC2851562 DOI: 10.1371/journal.pcbi.1000737] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [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: 08/24/2009] [Accepted: 03/03/2010] [Indexed: 01/29/2023] Open
Abstract
The majority of expression quantitative trait locus (eQTL) studies have been carried out in single tissues or cell types, using methods that ignore information shared across tissues. Although global analysis of RNA expression in multiple tissues is now feasible, few integrated statistical frameworks for joint analysis of gene expression across tissues combined with simultaneous analysis of multiple genetic variants have been developed to date. Here, we propose Sparse Bayesian Regression models for mapping eQTLs within individual tissues and simultaneously across tissues. Testing these on a set of 2,000 genes in four tissues, we demonstrate that our methods are more powerful than traditional approaches in revealing the true complexity of the eQTL landscape at the systems-level. Highlighting the power of our method, we identified a two-eQTL model (cis/trans) for the Hopx gene that was experimentally validated and was not detected by conventional approaches. We showed common genetic regulation of gene expression across four tissues for ∼27% of transcripts, providing >5 fold increase in eQTLs detection when compared with single tissue analyses at 5% FDR level. These findings provide a new opportunity to uncover complex genetic regulatory mechanisms controlling global gene expression while the generality of our modelling approach makes it adaptable to other model systems and humans, with broad application to analysis of multiple intermediate and whole-body phenotypes. Integrated analysis of genome-wide genetic polymorphisms and gene expression profiles from different tissues or cell types has been highly successful in identifying genes modulating complex phenotypes in animal models and humans. However, an important limitation of the current approaches consists in their sole application to individual tissues, thus ignoring information shared across different tissues. To uncover complex genetic regulatory mechanisms controlling gene expression at the whole organism's level, it is essential to develop appropriate analytical methods for the analysis of genome-wide genetic polymorphisms and gene expression profiles simultaneously in multiple tissues. This paper presents a novel, fully integrated Bayesian approach for mapping the genetic components of gene expression within and across multiple tissues. In addition to increased power and enhanced mapping resolution when compared with traditional approaches, our model directly provides information on potential systemic effects on transcriptional profiles and co-existing local (cis) and distant (trans) genetic control of gene expression. We also discuss the possibility to extend our approach for the analysis of different phenotypes, and other study designs, thus providing an integrated computational tool to explore the genetic control underlying transcriptional regulation at the systems-level, beyond the single tissue resolution.
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Affiliation(s)
- Enrico Petretto
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Leonardo Bottolo
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Sarah R. Langley
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | - Chris McDermott-Roe
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Rizwan Sarwar
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences and Centre for Applied Genomics, Prague, Czech Republic
- Charles University in Prague, Institute of Biology and Medical Genetics of the First Faculty of Medicine and General Teaching Hospital, Prague, Czech Republic
| | - Norbert Hübner
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Timothy J. Aitman
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
- Section of Molecular Genetics and Rheumatology, Division and Faculty of Medicine, Imperial College, London, United Kingdom
| | - Stuart A. Cook
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Sylvia Richardson
- Department of Epidemiology and Biostatistics, Faculty of Medicine, Imperial College, London, United Kingdom
- * E-mail:
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41
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Abstract
Recent advances in mouse genomics have revealed considerable variation in the form of single-nucleotide polymorphisms (SNPs) among common inbred strains. This has made it possible to characterize closely related strains and to identify genes that differ; such genes may be causal for quantitative phenotypes. The mouse strains DBA/1J and DBA/2J differ by just 5.6% at the SNP level. These strains exhibit differences in a number of metabolic and lipid phenotypes, such as plasma levels of triglycerides (TGs) and HDL. A cross between these strains revealed multiple quantitative trait loci (QTLs) in 294 progeny. We identified significant TG QTLs on chromosomes (Chrs) 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 16, and 19, and significant HDL QTLs on Chrs 3, 9, and 16. Some QTLs mapped to chromosomes with limited variability between the two strains, thus facilitating the identification of candidate genes. We suggest that Tshr is the QTL gene for Chr 12 TG and HDL levels and that Ihh may account for the TG QTL on Chr 1. This cross highlights the advantage of crossing closely related strains for subsequent identification of QTL genes.
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