1
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Davidson KC, Sung M, Brown KD, Contet J, Belluschi S, Hamel R, Moreno-Moral A, Dos Santos RL, Gough J, Polo JM, Daniell M, Parfitt GJ. Single nuclei transcriptomics of the in situ human limbal stem cell niche. Sci Rep 2024; 14:6749. [PMID: 38514716 PMCID: PMC10957941 DOI: 10.1038/s41598-024-57242-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
The corneal epithelium acts as a barrier to pathogens entering the eye; corneal epithelial cells are continuously renewed by uni-potent, quiescent limbal stem cells (LSCs) located at the limbus, where the cornea transitions to conjunctiva. There has yet to be a consensus on LSC markers and their transcriptome profile is not fully understood, which may be due to using cadaveric tissue without an intact stem cell niche for transcriptomics. In this study, we addressed this problem by using single nuclei RNA sequencing (snRNAseq) on healthy human limbal tissue that was immediately snap-frozen after excision from patients undergoing cataract surgery. We identified the quiescent LSCs as a sub-population of corneal epithelial cells with a low level of total transcript counts. Moreover, TP63, KRT15, CXCL14, and ITGβ4 were found to be highly expressed in LSCs and transiently amplifying cells (TACs), which constitute the corneal epithelial progenitor populations at the limbus. The surface markers SLC6A6 and ITGβ4 could be used to enrich human corneal epithelial cell progenitors, which were also found to specifically express the putative limbal progenitor cell markers MMP10 and AC093496.1.
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Affiliation(s)
- Kathryn C Davidson
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | | | - Karl D Brown
- Centre for Eye Research Australia (CERA), Melbourne, Australia
| | - Julian Contet
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | | | | | | | | | - Julian Gough
- Mogrify Limited, Cambridge, England, UK
- MRC Laboratory of Molecular Biology, Cambridge, England, UK
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.
- Mogrify Limited, Cambridge, England, UK.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.
- Adelaide Centre for Epigenetics, Faculty of Medicine Nursing and Medical Sciences, The University of Adelaide, Adelaide, Australia.
- The South Australian Immunogenomics Cancer Institute, Faculty of Medicine Nursing and Medical Sciences, The University of Adelaide, Adelaide, Australia.
| | - Mark Daniell
- Centre for Eye Research Australia (CERA), Melbourne, Australia.
| | - Geraint J Parfitt
- Mogrify Limited, Cambridge, England, UK.
- Ophthalmology Discovery Research, AbbVie, Irvine, CA, USA.
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2
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Tay HG, Andre H, Chrysostomou V, Adusumalli S, Guo J, Ren X, Tan WS, Tor JE, Moreno-Moral A, Plastino F, Bartuma H, Cai Z, Tun SBB, Barathi VA, Siew Wei GT, Grenci G, Chong LY, Holmgren A, Kvanta A, Crowston JG, Petretto E, Tryggvason K. Photoreceptor laminin drives differentiation of human pluripotent stem cells to photoreceptor progenitors that partially restore retina function. Mol Ther 2023; 31:825-846. [PMID: 36638800 PMCID: PMC10014235 DOI: 10.1016/j.ymthe.2022.12.012] [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: 01/07/2022] [Revised: 07/12/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
Blindness caused by advanced stages of inherited retinal diseases and age-related macular degeneration are characterized by photoreceptor loss. Cell therapy involving replacement with functional photoreceptor-like cells generated from human pluripotent stem cells holds great promise. Here, we generated a human recombinant retina-specific laminin isoform, LN523, and demonstrated the role in promoting the differentiation of human embryonic stem cells into photoreceptor progenitors. This chemically defined and xenogen-free method enables reproducible production of photoreceptor progenitors within 32 days. We observed that the transplantation into rd10 mice were able to protect the host photoreceptor outer nuclear layer (ONL) up to 2 weeks post transplantation as measured by full-field electroretinogram. At 4 weeks post transplantation, the engrafted cells were found to survive, mature, and associate with the host's rod bipolar cells. Visual behavioral assessment using the water maze swimming test demonstrated visual improvement in the cell-transplanted rodents. At 20 weeks post transplantation, the maturing engrafted cells were able to replace the loss of host ONL by extensive association with host bipolar cells and synapses. Post-transplanted rabbit model also provided congruent evidence for synaptic connectivity with the degenerated host retina. The results may pave the way for the development of stem cell-based therapeutics for retina degeneration.
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Affiliation(s)
- Hwee Goon Tay
- Centre for Vision Research, Duke-NUS Medical School, Singapore; Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore.
| | - Helder Andre
- Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Vicki Chrysostomou
- Centre for Vision Research, Duke-NUS Medical School, Singapore; Academic Clinical Program, Duke-NUS Medical School, Singapore
| | | | - Jing Guo
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Xiaoyuan Ren
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Wei Sheng Tan
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Jia En Tor
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Aida Moreno-Moral
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Flavia Plastino
- Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Hammurabi Bartuma
- Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Zuhua Cai
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Sai Bo Bo Tun
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Veluchamy Amutha Barathi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gavin Tan Siew Wei
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Gianluca Grenci
- Mechanobiology Institute (MBI) and Department of Biomedical Engineering, NUS, Singapore
| | - Li Yen Chong
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Arne Holmgren
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anders Kvanta
- Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan Guy Crowston
- Centre for Vision Research, Duke-NUS Medical School, Singapore; Academic Clinical Program, Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Enrico Petretto
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Karl Tryggvason
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Division of Nephrology, Department of Medicine, Duke University, Durham, NC, USA.
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3
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Muralidharan S, Torta F, Lin MK, Olona A, Bagnati M, Moreno-Moral A, Ko JH, Ji S, Burla B, Wenk MR, Rodrigues HG, Petretto E, Behmoaras J. Immunolipidomics Reveals a Globoside Network During the Resolution of Pro-Inflammatory Response in Human Macrophages. Front Immunol 2022; 13:926220. [PMID: 35844525 PMCID: PMC9280915 DOI: 10.3389/fimmu.2022.926220] [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: 04/22/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Toll-like receptor 4 (TLR4)-mediated changes in macrophages reshape intracellular lipid pools to coordinate an effective innate immune response. Although this has been previously well-studied in different model systems, it remains incompletely understood in primary human macrophages. Here we report time-dependent lipidomic and transcriptomic responses to lipopolysaccharide (LPS) in primary human macrophages from healthy donors. We grouped the variation of ~200 individual lipid species measured by LC-MS/MS into eight temporal clusters. Among all other lipids, glycosphingolipids (glycoSP) and cholesteryl esters (CE) showed a sharp increase during the resolution phase (between 8h or 16h post LPS). GlycoSP, belonging to the globoside family (Gb3 and Gb4), showed the greatest inter-individual variability among all lipids quantified. Integrative network analysis between GlycoSP/CE levels and genome-wide transcripts, identified Gb4 d18:1/16:0 and CE 20:4 association with subnetworks enriched for T cell receptor signaling (PDCD1, CD86, PTPRC, CD247, IFNG) and DC-SIGN signaling (RAF1, CD209), respectively. Our findings reveal Gb3 and Gb4 globosides as sphingolipids associated with the resolution phase of inflammatory response in human macrophages.
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Affiliation(s)
- Sneha Muralidharan
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore,Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore,Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,*Correspondence: Jacques Behmoaras, ; Federico Torta,
| | - Michelle K. Lin
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Antoni Olona
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore
| | - Marta Bagnati
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, United Kingdom
| | - Aida Moreno-Moral
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore
| | - Jeong-Hun Ko
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, United Kingdom
| | - Shanshan Ji
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore,Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hosana G. Rodrigues
- Laboratory of Nutrients and Tissue Repair, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore,MRC London Institute of Medical Sciences (LMC), Imperial College, London, United Kingdom,Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University, Nanjing, China
| | - Jacques Behmoaras
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore,Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, United Kingdom,*Correspondence: Jacques Behmoaras, ; Federico Torta,
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4
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López Zúñiga MÁ, Moreno-Moral A, Ocaña-Granados A, Padilla-Moreno FA, Castillo-Fernández AM, Guillamón-Fernández D, Ramírez-Sánchez C, Sanchez-Palop M, Martínez-Colmenero J, Pimentel-Villar MA, Blázquez-Roselló S, Moreno-Sánchez JJ, López-Vílchez M, Prior-Sánchez I, Jódar-Moreno R, López Ruz MÁ. High-dose corticosteroid pulse therapy increases the survival rate in COVID-19 patients at risk of hyper-inflammatory response. PLoS One 2021; 16:e0243964. [PMID: 33507958 PMCID: PMC7842890 DOI: 10.1371/journal.pone.0243964] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/01/2020] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE Test whether high dose corticosteroid pulse therapy (HDCPT) with either methylprednisolone or dexamethasone is associated with increased survival in COVID-19 patients at risk of hyper-inflammatory response. Provide some initial diagnostic criteria using laboratory markers to stratify these patients. METHODS This is a prospective observational study, 318 met the inclusion criteria. 64 patients (20.1%) were treated with HDCPT by using at least 1.5mg/kg/24h of methylprednisolone or dexamethasone equivalent. A multivariate Cox regression (controlling for co-morbidities and other therapies) was carried out to determine whether HDCPT (among other interventions) was associated with decreased mortality. We also carried out a 30-day time course analysis of laboratory markers between survivors and non-survivors, to identify potential markers for patient stratification. RESULTS HDCPT showed a statistically significant decrease in mortality (HR = 0.087 [95% CI 0.021-0.36]; P < 0.001). 30-day time course analysis of laboratory marker tests showed marked differences in pro-inflammatory markers between survivors and non-survivors. As diagnostic criteria to define the patients at risk of developing a COVID-19 hyper-inflammatory response, we propose the following parameters (IL-6 > = 40 pg/ml, and/or two of the following: C-reactive protein > = 100 mg/L, D-dimer > = 1000 ng/ml, ferritin > = 500 ng/ml and lactate dehydrogenase > = 300 U/L). CONCLUSIONS HDCPT can be an effective intervention to increase COVID-19 survival rates in patients at risk of developing a COVID-19 hyper-inflammatory response, laboratory marker tests can be used to stratify these patients who should be given HDCPT. This study is not a randomized clinical trial (RCT). Future RCTs should be carried out to confirm the efficacy of HDCPT to increase the survival rates of COVID-19.
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Affiliation(s)
- Miguel Ángel López Zúñiga
- Infectious Diseases Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
- Grupo de investigación CTS 990: GEAPACECP, Universidad de Jaén, Jaén, Spain
| | | | | | | | | | | | | | | | - Justo Martínez-Colmenero
- Grupo de investigación CTS 990: GEAPACECP, Universidad de Jaén, Jaén, Spain
- Internal Medicine Service, Complejo Hospitalario de Jaén, Jaén, Spain
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5
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Yap L, Wang JW, Moreno-Moral A, Chong LY, Sun Y, Harmston N, Wang X, Chong SY, Vanezis K, Öhman MK, Wei H, Bunte R, Gosh S, Cook S, Hovatta O, de Kleijn DPV, Petretto E, Tryggvason K. In Vivo Generation of Post-infarct Human Cardiac Muscle by Laminin-Promoted Cardiovascular Progenitors. Cell Rep 2020; 31:107714. [PMID: 32460024 DOI: 10.1016/j.celrep.2020.107714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Lynn Yap
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Jiong-Wei Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Aida Moreno-Moral
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Li Yen Chong
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yi Sun
- BioLamina AB, Lö fströ ms Allé 5A, Sundbyberg 17266, Sweden
| | - Nathan Harmston
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Xiaoyuan Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Suet Yen Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Konstantinos Vanezis
- Cardiovascular Genetics and Genomics Group, MRC London Institute of Medical Sciences, Imperial Centre for Translational and Experimental Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Miina K Öhman
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Heming Wei
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore
| | - Ralph Bunte
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Sujoy Gosh
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Stuart Cook
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore; National Heart & Lung Institute, Imperial College London, Cale Street, London SW3 6LY, UK
| | - Outi Hovatta
- Division of Obstetrics and Gynecology, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
| | - Dominique P V de Kleijn
- Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore; University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Enrico Petretto
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden.
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6
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Yap L, Wang JW, Moreno-Moral A, Chong LY, Sun Y, Harmston N, Wang X, Chong SY, Vanezis K, Öhman MK, Wei H, Bunte R, Gosh S, Cook S, Hovatta O, de Kleijn DPV, Petretto E, Tryggvason K. In Vivo Generation of Post-infarct Human Cardiac Muscle by Laminin-Promoted Cardiovascular Progenitors. Cell Rep 2020; 26:3231-3245.e9. [PMID: 30893597 DOI: 10.1016/j.celrep.2019.02.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 10/02/2018] [Revised: 01/15/2019] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical-quality stem cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein and showed that LN-221 promotes differentiation of pluripotent human embryonic stem cells (hESCs) toward cardiomyocyte lineage and downregulates pluripotency and teratoma-associated genes. We developed a chemically defined, xeno-free laminin-based differentiation protocol to generate CVPs. We show high reproducibility of the differentiation protocol using time-course bulk RNA sequencing developed from different hESC lines. Single-cell RNA sequencing of CVPs derived from hESC lines supported reproducibility and identified three main progenitor subpopulations. These CVPs were transplanted into myocardial infarction mice, where heart function was measured by echocardiogram and human heart muscle bundle formation was identified histologically. This method may provide clinical-quality cells for use in regenerative cardiology.
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Affiliation(s)
- Lynn Yap
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Jiong-Wei Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Aida Moreno-Moral
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Li Yen Chong
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yi Sun
- BioLamina AB, Löfströms Allé 5A, Sundbyberg 17266, Sweden
| | - Nathan Harmston
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Xiaoyuan Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Suet Yen Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Konstantinos Vanezis
- Cardiovascular Genetics and Genomics Group MRC London Institute of Medical Sciences, Imperial Centre for Translational and Experimental Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Miina K Öhman
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Heming Wei
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore
| | - Ralph Bunte
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Sujoy Gosh
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Stuart Cook
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore; National Heart & Lung Institute, Imperial College London, Cale Street, London SW3 6LY, UK
| | - Outi Hovatta
- Division of Obstetrics and Gynecology, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
| | - Dominique P V de Kleijn
- Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore; University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Enrico Petretto
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden.
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7
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Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E. Author Correction: WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling. Nat Commun 2019; 10:4085. [PMID: 31501434 PMCID: PMC6733793 DOI: 10.1038/s41467-019-12060-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Aida Moreno-Moral
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Francesco Pesce
- Department of Emergency and Organ Transplantation (DETO), University of Bari, 70124, Bari, Italy
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Massimiliano Mancini
- SOC di Anatomia Patologica, Ospedale San Giovanni di Dio, 50123, Florence, Italy
| | - Ee Ling Heng
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institute Pasteur, 75015, Paris, France
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Nathan Harmston
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Owen J L Rackham
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Wei-Ping Yu
- Animal Gene Editing Laboratory, BRC, A*STAR20 Biopolis Way, Singapore, 138668, Republic of Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
| | | | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares - CNIC, 28029, Madrid, Spain
| | - Gianni Angelini
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol, BS2 89HW, UK
| | - Cristina Beltrami
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 142 00, Praha 4, Czech Republic
| | - Sebastian Schafer
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Stuart A Cook
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore.
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK.
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8
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Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E. WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling. Nat Commun 2019; 10:3616. [PMID: 31399586 PMCID: PMC6689010 DOI: 10.1038/s41467-019-11551-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 10/10/2018] [Accepted: 07/19/2019] [Indexed: 01/03/2023] Open
Abstract
Cardiac fibrosis is a final common pathology in inherited and acquired heart diseases that causes cardiac electrical and pump failure. Here, we use systems genetics to identify a pro-fibrotic gene network in the diseased heart and show that this network is regulated by the E3 ubiquitin ligase WWP2, specifically by the WWP2-N terminal isoform. Importantly, the WWP2-regulated pro-fibrotic gene network is conserved across different cardiac diseases characterized by fibrosis: human and murine dilated cardiomyopathy and repaired tetralogy of Fallot. Transgenic mice lacking the N-terminal region of the WWP2 protein show improved cardiac function and reduced myocardial fibrosis in response to pressure overload or myocardial infarction. In primary cardiac fibroblasts, WWP2 positively regulates the expression of pro-fibrotic markers and extracellular matrix genes. TGFβ1 stimulation promotes nuclear translocation of the WWP2 isoforms containing the N-terminal region and their interaction with SMAD2. WWP2 mediates the TGFβ1-induced nucleocytoplasmic shuttling and transcriptional activity of SMAD2.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Aida Moreno-Moral
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Francesco Pesce
- Department of Emergency and Organ Transplantation (DETO), University of Bari, 70124, Bari, Italy
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Massimiliano Mancini
- SOC di Anatomia Patologica, Ospedale San Giovanni di Dio, 50123, Florence, Italy
| | - Ee Ling Heng
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institute Pasteur, 75015, Paris, France
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Nathan Harmston
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Owen J L Rackham
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Wei-Ping Yu
- Animal Gene Editing Laboratory, BRC, A*STAR20 Biopolis Way, Singapore, 138668, Republic of Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
| | | | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares - CNIC, 28029, Madrid, Spain
| | - Gianni Angelini
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol, BS2 89HW, UK
| | - Cristina Beltrami
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 142 00, Praha 4, Czech Republic
| | - Sebastian Schafer
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Stuart A Cook
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore.
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK.
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9
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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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10
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Bagnati M, Moreno-Moral A, Ko JH, Nicod J, Harmston N, Imprialou M, Game L, Gil J, Petretto E, Behmoaras J. Systems genetics identifies a macrophage cholesterol network associated with physiological wound healing. JCI Insight 2019; 4:e125736. [PMID: 30674726 PMCID: PMC6413785 DOI: 10.1172/jci.insight.125736] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/18/2018] [Indexed: 01/18/2023] Open
Abstract
Among other cells, macrophages regulate the inflammatory and reparative phases during wound healing but genetic determinants and detailed molecular pathways that modulate these processes are not fully elucidated. Here, we took advantage of normal variation in wound healing in 1,378 genetically outbred mice, and carried out macrophage RNA-sequencing profiling of mice with extreme wound healing phenotypes (i.e., slow and fast healers, n = 146 in total). The resulting macrophage coexpression networks were genetically mapped and led to the identification of a unique module under strong trans-acting genetic control by the Runx2 locus. This macrophage-mediated healing network was specifically enriched for cholesterol and fatty acid biosynthetic processes. Pharmacological blockage of fatty acid synthesis with cerulenin resulted in delayed wound healing in vivo, and increased macrophage infiltration in the wounded skin, suggesting the persistence of an unresolved inflammation. We show how naturally occurring sequence variation controls transcriptional networks in macrophages, which in turn regulate specific metabolic pathways that could be targeted in wound healing.
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Affiliation(s)
- Marta Bagnati
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom (UK)
| | | | - Jeong-Hun Ko
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom (UK)
| | - Jérôme Nicod
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Martha Imprialou
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom (UK)
| | - Laurence Game
- Genomics Laboratory, Medical Research Council (MRC) London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital, London, UK
| | - Jesus Gil
- Cell Proliferation Group, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Enrico Petretto
- Duke-NUS Medical School, Singapore, Singapore
- MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom (UK)
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11
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Tjin MS, Chua AWC, Moreno-Moral A, Chong LY, Tang PY, Harmston NP, Cai Z, Petretto E, Tan BK, Tryggvason K. Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture. Nat Commun 2018; 9:4432. [PMID: 30377295 PMCID: PMC6207750 DOI: 10.1038/s41467-018-06934-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 04/27/2018] [Accepted: 09/27/2018] [Indexed: 12/18/2022] Open
Abstract
The current expansion of autologous human keratinocytes to resurface severe wound defects still relies on murine feeder layer and calf serum in the cell culture system. Through our characterization efforts of the human skin basement membrane and murine feeder layer 3T3-J2, we identified two biologically relevant recombinant laminins-LN-511 and LN-421- as potential candidates to replace the murine feeder. Herein, we report a completely xeno-free and defined culture system utilizing these laminins which enables robust expansion of adult human skin keratinocytes. We demonstrate that our laminin system is comparable to the 3T3-J2 co-culture system in terms of basal markers' profile, colony-forming efficiency and the ability to form normal stratified epidermal structure in both in vitro and in vivo models. These results show that the proposed system may not only provide safer keratinocyte use in the clinics, but also facilitate the broader use of other cultured human epithelial cells in regenerative medicine.
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Affiliation(s)
- Monica Suryana Tjin
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Alvin Wen Choong Chua
- Department of Plastic Reconstructive & Aesthetic Surgery, Singapore General Hospital, 20 College Road, Singapore, 169856, Singapore.
- Skin Bank Unit, Singapore General Hospital, Singapore, 169608, Singapore.
| | - Aida Moreno-Moral
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Li Yen Chong
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Po Yin Tang
- Department of Anatomical Pathology, Singapore General Hospital, 20 College Road, Singapore, 169856, Singapore
| | - Nathan Peter Harmston
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Zuhua Cai
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Bien Keem Tan
- Department of Plastic Reconstructive & Aesthetic Surgery, Singapore General Hospital, 20 College Road, Singapore, 169856, Singapore
- Skin Bank Unit, Singapore General Hospital, Singapore, 169608, Singapore
| | - Karl Tryggvason
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17771, Stockholm, Sweden.
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12
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Sigmundsson K, Ojala JR, Öhman MK, Österholm AM, Moreno-Moral A, Domogatskaya A, Chong LY, Sun Y, Chai X, Steele JA, George B, Patarroyo M, Nilsson AS, Rodin S, Ghosh S, Stevens MM, Petretto E, Tryggvason K. Culturing functional pancreatic islets on α5-laminins and curative transplantation to diabetic mice. Matrix Biol 2018; 70:5-19. [DOI: 10.1016/j.matbio.2018.03.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 12/15/2022]
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Olona A, Terra X, Ko JH, Grau-Bové C, Pinent M, Ardevol A, Diaz AG, Moreno-Moral A, Edin M, Bishop-Bailey D, Zeldin DC, Aitman TJ, Petretto E, Blay M, Behmoaras J. Epoxygenase inactivation exacerbates diet and aging-associated metabolic dysfunction resulting from impaired adipogenesis. Mol Metab 2018; 11:18-32. [PMID: 29656108 PMCID: PMC6001407 DOI: 10.1016/j.molmet.2018.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/23/2018] [Accepted: 03/05/2018] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE When molecular drivers of healthy adipogenesis are perturbed, this can cause hepatic steatosis. The role of arachidonic acid (AA) and its downstream enzymatic cascades, such as cyclooxygenase, in adipogenesis is well established. The exact contribution of the P450 epoxygenase pathway, however, remains to be established. Enzymes belonging to this pathway are mainly encoded by the CYP2J locus which shows extensive allelic expansion in mice. Here we aimed to establish the role of endogenous epoxygenase during adipogenesis under homeostatic and metabolic stress conditions. METHODS We took advantage of the simpler genetic architecture of the Cyp2j locus in the rat and used a Cyp2j4 (orthologue of human CYP2J2) knockout rat in two models of metabolic dysfunction: physiological aging and cafeteria diet (CAF). The phenotyping of Cyp2j4-/- rats under CAF was integrated with proteomics (LC-MS/MS) and lipidomics (LC-MS) analyses in the liver and the adipose tissue. RESULTS We report that Cyp2j4 deletion causes adipocyte dysfunction under metabolic challenges. This is characterized by (i) down-regulation of white adipose tissue (WAT) PPARγ and C/EBPα, (ii) adipocyte hypertrophy, (iii) extracellular matrix remodeling, and (iv) alternative usage of AA pathway. Specifically, in Cyp2j4-/- rats treated with a cafeteria diet, the dysfunctional adipogenesis is accompanied by exacerbated weight gain, hepatic lipid accumulation, and dysregulated gluconeogenesis. CONCLUSION These results suggest that AA epoxygenases are essential regulators of healthy adipogenesis. Our results uncover their synergistic role in fine-tuning AA pathway in obesity-mediated hepatic steatosis.
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Affiliation(s)
- Antoni Olona
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK
| | - Ximena Terra
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK; Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Jeong-Hun Ko
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK
| | - Carme Grau-Bové
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK; Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Montserrat Pinent
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Anna Ardevol
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Ana Garcia Diaz
- Renal and Vascular Inflammation Section, Department of Medicine, Imperial College London, London, W12 0NN, UK
| | - Aida Moreno-Moral
- Duke-NUS Medical School, National University of Singapore, 169857, Singapore
| | - Matthew Edin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - David Bishop-Bailey
- Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, UK
| | - Darryl C Zeldin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Timothy J Aitman
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Enrico Petretto
- Duke-NUS Medical School, National University of Singapore, 169857, Singapore
| | - Mayte Blay
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK.
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14
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Solimena M, Schulte AM, Marselli L, Ehehalt F, Richter D, Kleeberg M, Mziaut H, Knoch KP, Parnis J, Bugliani M, Siddiq A, Jörns A, Burdet F, Liechti R, Suleiman M, Margerie D, Syed F, Distler M, Grützmann R, Petretto E, Moreno-Moral A, Wegbrod C, Sönmez A, Pfriem K, Friedrich A, Meinel J, Wollheim CB, Baretton GB, Scharfmann R, Nogoceke E, Bonifacio E, Sturm D, Meyer-Puttlitz B, Boggi U, Saeger HD, Filipponi F, Lesche M, Meda P, Dahl A, Wigger L, Xenarios I, Falchi M, Thorens B, Weitz J, Bokvist K, Lenzen S, Rutter GA, Froguel P, von Bülow M, Ibberson M, Marchetti P. Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes. Diabetologia 2018; 61:641-657. [PMID: 29185012 PMCID: PMC5803296 DOI: 10.1007/s00125-017-4500-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/29/2017] [Indexed: 01/25/2023]
Abstract
AIMS/HYPOTHESIS Pancreatic islet beta cell failure causes type 2 diabetes in humans. To identify transcriptomic changes in type 2 diabetic islets, the Innovative Medicines Initiative for Diabetes: Improving beta-cell function and identification of diagnostic biomarkers for treatment monitoring in Diabetes (IMIDIA) consortium ( www.imidia.org ) established a comprehensive, unique multicentre biobank of human islets and pancreas tissues from organ donors and metabolically phenotyped pancreatectomised patients (PPP). METHODS Affymetrix microarrays were used to assess the islet transcriptome of islets isolated either by enzymatic digestion from 103 organ donors (OD), including 84 non-diabetic and 19 type 2 diabetic individuals, or by laser capture microdissection (LCM) from surgical specimens of 103 PPP, including 32 non-diabetic, 36 with type 2 diabetes, 15 with impaired glucose tolerance (IGT) and 20 with recent-onset diabetes (<1 year), conceivably secondary to the pancreatic disorder leading to surgery (type 3c diabetes). Bioinformatics tools were used to (1) compare the islet transcriptome of type 2 diabetic vs non-diabetic OD and PPP as well as vs IGT and type 3c diabetes within the PPP group; and (2) identify transcription factors driving gene co-expression modules correlated with insulin secretion ex vivo and glucose tolerance in vivo. Selected genes of interest were validated for their expression and function in beta cells. RESULTS Comparative transcriptomic analysis identified 19 genes differentially expressed (false discovery rate ≤0.05, fold change ≥1.5) in type 2 diabetic vs non-diabetic islets from OD and PPP. Nine out of these 19 dysregulated genes were not previously reported to be dysregulated in type 2 diabetic islets. Signature genes included TMEM37, which inhibited Ca2+-influx and insulin secretion in beta cells, and ARG2 and PPP1R1A, which promoted insulin secretion. Systems biology approaches identified HNF1A, PDX1 and REST as drivers of gene co-expression modules correlated with impaired insulin secretion or glucose tolerance, and 14 out of 19 differentially expressed type 2 diabetic islet signature genes were enriched in these modules. None of these signature genes was significantly dysregulated in islets of PPP with impaired glucose tolerance or type 3c diabetes. CONCLUSIONS/INTERPRETATION These studies enabled the stringent definition of a novel transcriptomic signature of type 2 diabetic islets, regardless of islet source and isolation procedure. Lack of this signature in islets from PPP with IGT or type 3c diabetes indicates differences possibly due to peculiarities of these hyperglycaemic conditions and/or a role for duration and severity of hyperglycaemia. Alternatively, these transcriptomic changes capture, but may not precede, beta cell failure.
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Affiliation(s)
- Michele Solimena
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany.
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), 01307, Dresden, Germany.
| | - Anke M Schulte
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Industriepark Höchst, Building H821, 65926, Frankfurt am Main, Germany.
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, Cisanello University Hospital, University of Pisa, Via Paradisa 2, 56126, Pisa, Italy
| | - Florian Ehehalt
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Daniela Richter
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
| | - Manuela Kleeberg
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Hassan Mziaut
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
| | - Klaus-Peter Knoch
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
| | - Julia Parnis
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Marco Bugliani
- Department of Clinical and Experimental Medicine, Cisanello University Hospital, University of Pisa, Via Paradisa 2, 56126, Pisa, Italy
| | - Afshan Siddiq
- Queen Mary University of London, Dawson Hall, London, UK
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, London, UK
| | - Anne Jörns
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Frédéric Burdet
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, bâtiment Génopode, 1015, Lausanne, Switzerland
| | - Robin Liechti
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, bâtiment Génopode, 1015, Lausanne, Switzerland
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, Cisanello University Hospital, University of Pisa, Via Paradisa 2, 56126, Pisa, Italy
| | - Daniel Margerie
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Industriepark Höchst, Building H821, 65926, Frankfurt am Main, Germany
| | - Farooq Syed
- Department of Clinical and Experimental Medicine, Cisanello University Hospital, University of Pisa, Via Paradisa 2, 56126, Pisa, Italy
| | - Marius Distler
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Robert Grützmann
- Department of Surgery, University Hospital of Erlangen, Erlangen, Germany
| | - Enrico Petretto
- Medical Research Council (MRC), Institute of Medical Sciences, Imperial College London, London, UK
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Aida Moreno-Moral
- Medical Research Council (MRC), Institute of Medical Sciences, Imperial College London, London, UK
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Carolin Wegbrod
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
| | - Anke Sönmez
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
| | - Katja Pfriem
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
| | - Anne Friedrich
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
| | - Jörn Meinel
- Department of Pathology, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Claes B Wollheim
- Department of Cell Physiology and Metabolism, Geneva University Medical Center, Geneva, Switzerland
| | - Gustavo B Baretton
- Department of Pathology, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Raphael Scharfmann
- INSERM, U1016, Institut Cochin, Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Everson Nogoceke
- F. Hoffmann-La Roche Ltd, Roche Innovation Center Basel, Basel, Switzerland
| | - Ezio Bonifacio
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
- Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany
| | - Dorothée Sturm
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Birgit Meyer-Puttlitz
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Industriepark Höchst, Building H821, 65926, Frankfurt am Main, Germany
| | - Ugo Boggi
- Department of Clinical and Experimental Medicine, Cisanello University Hospital, University of Pisa, Via Paradisa 2, 56126, Pisa, Italy
| | - Hans-Detlev Saeger
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Franco Filipponi
- Department of Clinical and Experimental Medicine, Cisanello University Hospital, University of Pisa, Via Paradisa 2, 56126, Pisa, Italy
| | | | - Paolo Meda
- Department of Cell Physiology and Metabolism, Geneva University Medical Center, Geneva, Switzerland
| | - Andreas Dahl
- Biotechnology Center, TU Dresden, Dresden, Germany
| | - Leonore Wigger
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, bâtiment Génopode, 1015, Lausanne, Switzerland
| | - Ioannis Xenarios
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, bâtiment Génopode, 1015, Lausanne, Switzerland
| | - Mario Falchi
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, London, UK
| | - Bernard Thorens
- Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Jürgen Weitz
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- German Center for Diabetes Research (DZD), Munich Neuherberg, Germany
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Krister Bokvist
- Lilly Research Laboratories, Eli Lilly, Indianapolis, IN, USA
| | - Sigurd Lenzen
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Philippe Froguel
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, London, UK
- CNRS-UMR8199, Lille Pasteur Institute, Lille, France
- Lille University Hospital, Lille, France
- European Genomic Institute for Diabetes (EGID), Lille, France
| | - Manon von Bülow
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Industriepark Höchst, Building H821, 65926, Frankfurt am Main, Germany
| | - Mark Ibberson
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, bâtiment Génopode, 1015, Lausanne, Switzerland.
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Cisanello University Hospital, University of Pisa, Via Paradisa 2, 56126, Pisa, Italy.
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15
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Moreno-Moral A, Bagnati M, Koturan S, Ko JH, Fonseca C, Harmston N, Game L, Martin J, Ong V, Abraham DJ, Denton CP, Behmoaras J, Petretto E. Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk. Ann Rheum Dis 2018; 77:596-601. [PMID: 29348297 PMCID: PMC5890626 DOI: 10.1136/annrheumdis-2017-212454] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [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: 09/27/2017] [Revised: 12/05/2017] [Accepted: 12/27/2017] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Several common and rare risk variants have been reported for systemic sclerosis (SSc), but the effector cell(s) mediating the function of these genetic variants remains to be elucidated. While innate immune cells have been proposed as the critical targets to interfere with the disease process underlying SSc, no studies have comprehensively established their effector role. Here we investigated the contribution of monocyte-derived macrophages (MDMs) in mediating genetic susceptibility to SSc. METHODS We carried out RNA sequencing and genome-wide genotyping in MDMs from 57 patients with SSc and 15 controls. Our differential expression and expression quantitative trait locus (eQTL) analysis in SSc was further integrated with epigenetic, expression and eQTL data from skin, monocytes, neutrophils and lymphocytes. RESULTS We identified 602 genes upregulated and downregulated in SSc macrophages that were significantly enriched for genes previously implicated in SSc susceptibility (P=5×10-4), and 270 cis-regulated genes in MDMs. Among these, GSDMA was reported to carry an SSc risk variant (rs3894194) regulating expression of neighbouring genes in blood. We show that GSDMA is upregulated in SSc MDMs (P=8.4×10-4) but not in the skin, and is a significant eQTL in SSc macrophages and lipopolysaccharide/interferon gamma (IFNγ)-stimulated monocytes. Furthermore, we identify an SSc macrophage transcriptome signature characterised by upregulation of glycolysis, hypoxia and mTOR signalling and a downregulation of IFNγ response pathways. CONCLUSIONS Our data further establish the link between macrophages and SSc, and suggest that the contribution of the rs3894194 risk variant to SSc susceptibility can be mediated by GSDMA expression in macrophages.
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Affiliation(s)
- Aida Moreno-Moral
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Marta Bagnati
- Centre for Complement and Inflammation Research, Hammersmith Hospital, Imperial College London, London, UK
| | - Surya Koturan
- Centre for Complement and Inflammation Research, Hammersmith Hospital, Imperial College London, London, UK
| | - Jeong-Hun Ko
- Centre for Complement and Inflammation Research, Hammersmith Hospital, Imperial College London, London, UK
| | - Carmen Fonseca
- Division of Medicine, Department of Inflammation, Centre for Rheumatology and Connective Tissue Diseases, Royal Free and University College Medical School, University College London, London, UK
| | - Nathan Harmston
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Laurence Game
- Genomics Laboratory, MRC London Institute of Medical Sciences, Hammersmith Hospital, Imperial College London, London, UK
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Cientıficas, Granada, Spain
| | - Voon Ong
- Division of Medicine, Department of Inflammation, Centre for Rheumatology and Connective Tissue Diseases, Royal Free and University College Medical School, University College London, London, UK
| | - David J Abraham
- Division of Medicine, Department of Inflammation, Centre for Rheumatology and Connective Tissue Diseases, Royal Free and University College Medical School, University College London, London, UK
| | - Christopher P Denton
- Division of Medicine, Department of Inflammation, Centre for Rheumatology and Connective Tissue Diseases, Royal Free and University College Medical School, University College London, London, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Hammersmith Hospital, Imperial College London, London, UK
| | - Enrico Petretto
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore.,Faculty of Medicine, Medical Research Council (MRC) London Institute of Medical Sciences, Imperial College London, London, UK
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16
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Schafer S, Viswanathan S, Widjaja AA, Lim WW, Moreno-Moral A, DeLaughter DM, Ng B, Patone G, Chow K, Khin E, Tan J, Chothani SP, Ye L, Rackham OJL, Ko NSJ, Sahib NE, Pua CJ, Zhen NTG, Xie C, Wang M, Maatz H, Lim S, Saar K, Blachut S, Petretto E, Schmidt S, Putoczki T, Guimarães-Camboa N, Wakimoto H, van Heesch S, Sigmundsson K, Lim SL, Soon JL, Chao VTT, Chua YL, Tan TE, Evans SM, Loh YJ, Jamal MH, Ong KK, Chua KC, Ong BH, Chakaramakkil MJ, Seidman JG, Seidman CE, Hubner N, Sin KYK, Cook SA. IL-11 is a crucial determinant of cardiovascular fibrosis. Nature 2017; 552:110-115. [PMID: 29160304 PMCID: PMC5807082 DOI: 10.1038/nature24676] [Citation(s) in RCA: 380] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 11/02/2017] [Indexed: 02/06/2023]
Abstract
Fibrosis is a common pathology in cardiovascular disease. In the heart, fibrosis causes mechanical and electrical dysfunction and in the kidney, it predicts the onset of renal failure. Transforming growth factor β1 (TGFβ1) is the principal pro-fibrotic factor, but its inhibition is associated with side effects due to its pleiotropic roles. We hypothesized that downstream effectors of TGFβ1 in fibroblasts could be attractive therapeutic targets and lack upstream toxicity. Here we show, using integrated imaging-genomics analyses of primary human fibroblasts, that upregulation of interleukin-11 (IL-11) is the dominant transcriptional response to TGFβ1 exposure and required for its pro-fibrotic effect. IL-11 and its receptor (IL11RA) are expressed specifically in fibroblasts, in which they drive non-canonical, ERK-dependent autocrine signalling that is required for fibrogenic protein synthesis. In mice, fibroblast-specific Il11 transgene expression or Il-11 injection causes heart and kidney fibrosis and organ failure, whereas genetic deletion of Il11ra1 protects against disease. Therefore, inhibition of IL-11 prevents fibroblast activation across organs and species in response to a range of important pro-fibrotic stimuli. These results reveal a central role of IL-11 in fibrosis and we propose that inhibition of IL-11 is a potential therapeutic strategy to treat fibrotic diseases.
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Affiliation(s)
- Sebastian Schafer
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | | | | | | | | | - Daniel M DeLaughter
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | | | - Ester Khin
- Duke-National University of Singapore Medical School, Singapore
| | - Jessie Tan
- National Heart Centre Singapore, Singapore
| | | | - Lei Ye
- National Heart Centre Singapore, Singapore
| | | | - Nicole S J Ko
- Duke-National University of Singapore Medical School, Singapore
| | - Norliza E Sahib
- Duke-National University of Singapore Medical School, Singapore
| | | | | | - Chen Xie
- National Heart Centre Singapore, Singapore
| | - Mao Wang
- Duke-National University of Singapore Medical School, Singapore
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | - Shiqi Lim
- National Heart Centre Singapore, Singapore
| | - Kathrin Saar
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | - Enrico Petretto
- Duke-National University of Singapore Medical School, Singapore
| | - Sabine Schmidt
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | - Tracy Putoczki
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3050, Australia
| | - Nuno Guimarães-Camboa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | | | - See L Lim
- National Heart Centre Singapore, Singapore
| | - Jia L Soon
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | - Victor T T Chao
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | | | | | - Sylvia M Evans
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, USA
| | - Yee J Loh
- National Heart Centre Singapore, Singapore
- Kandang Kerbau Women's and Children's Hospital, Singapore
| | | | - Kim K Ong
- National Heart Centre Singapore, Singapore
- Kandang Kerbau Women's and Children's Hospital, Singapore
| | - Kim C Chua
- National Heart Centre Singapore, Singapore
| | | | | | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, Massachusettes 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Kenny Y K Sin
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | - Stuart A Cook
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
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17
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Heinig M, Adriaens ME, Schafer S, van Deutekom HWM, Lodder EM, Ware JS, Schneider V, Felkin LE, Creemers EE, Meder B, Katus HA, Rühle F, Stoll M, Cambien F, Villard E, Charron P, Varro A, Bishopric NH, George AL, Dos Remedios C, Moreno-Moral A, Pesce F, Bauerfeind A, Rüschendorf F, Rintisch C, Petretto E, Barton PJ, Cook SA, Pinto YM, Bezzina CR, Hubner N. Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy. Genome Biol 2017; 18:170. [PMID: 28903782 PMCID: PMC5598015 DOI: 10.1186/s13059-017-1286-z] [Citation(s) in RCA: 58] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 07/19/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genetic variation is an important determinant of RNA transcription and splicing, which in turn contributes to variation in human traits, including cardiovascular diseases. RESULTS Here we report the first in-depth survey of heart transcriptome variation using RNA-sequencing in 97 patients with dilated cardiomyopathy and 108 non-diseased controls. We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls, affecting known as well as novel dilated cardiomyopathy genes. Moreover, we show a widespread effect of genetic variation on the regulation of transcription, isoform usage, and allele-specific expression. Systematic annotation of genome-wide association SNPs identifies 60 functional candidate genes for heart phenotypes, representing 20% of all published heart genome-wide association loci. Focusing on the dilated cardiomyopathy phenotype we found that eQTL variants are also enriched for dilated cardiomyopathy genome-wide association signals in two independent cohorts. CONCLUSIONS RNA transcription, splicing, and allele-specific expression are each important determinants of the dilated cardiomyopathy phenotype and are controlled by genetic factors. Our results represent a powerful resource for the field of cardiovascular genetics.
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Affiliation(s)
- Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, München, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Michiel E Adriaens
- Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands.,Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
| | - Sebastian Schafer
- National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.,Division of Cardiovascular & Metabolic Disorders, Duke-National University of Singapore, 169857, Singapore, Singapore
| | - Hanneke W M van Deutekom
- Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Elisabeth M Lodder
- Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield Hospitals and Imperial College London, London, UK.,Medical Research Council (MRC) London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Valentin Schneider
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield Hospitals and Imperial College London, London, UK
| | - Esther E Creemers
- Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg & Department of Cardiology, Angiology and Pneumology, University Heidelberg, Heidelberg, Germany.,Deutsches Zentrum für Herz-Kreislauf-Forschung, Heidelberg/Mannheim, Germany
| | - Hugo A Katus
- Institute for Cardiomyopathies Heidelberg & Department of Cardiology, Angiology and Pneumology, University Heidelberg, Heidelberg, Germany.,Deutsches Zentrum für Herz-Kreislauf-Forschung, Heidelberg/Mannheim, Germany
| | - Frank Rühle
- Institute of Human Genetics, Genetic Epidemiology, University of Münster, Münster, Germany
| | - Monika Stoll
- Institute of Human Genetics, Genetic Epidemiology, University of Münster, Münster, Germany.,Department of Biochemistry, Genetic Epidemiology and Statistical Genetics, CARIM School for Cardiovascular Diseases, Maastricht Center for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - François Cambien
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, F-75013, Paris, France.,ICAN Institute for Cardiometabolism and Nutrition, F-75013, Paris, France
| | - Eric Villard
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, F-75013, Paris, France.,ICAN Institute for Cardiometabolism and Nutrition, F-75013, Paris, France
| | - Philippe Charron
- ICAN Institute for Cardiometabolism and Nutrition, F-75013, Paris, France.,Université Versailles Saint Quentin, AP-HP, CESP, INSERM U1018, Hôpital Ambroise Paré, Boulogne-Billancourt, France
| | - Andras Varro
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Nanette H Bishopric
- Department of Medicine, University of Miami School of Medicine, Miami, FL, USA.,Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, USA
| | - Alfred L George
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA.,Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Cristobal Dos Remedios
- Sydney Heart Bank, Department of Anatomy, Bosch Institute, The University of Sydney, Sydney, Australia
| | - Aida Moreno-Moral
- Program in Cardiovascular and Metabolic Disorders, Center for Computational Biology, DUKE-NUS Medical School, Singapore, 169857, Singapore
| | - Francesco Pesce
- National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield Hospitals and Imperial College London, London, UK
| | - Anja Bauerfeind
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Franz Rüschendorf
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Carola Rintisch
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Center for Computational Biology, DUKE-NUS Medical School, Singapore, 169857, Singapore
| | - Paul J Barton
- National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield Hospitals and Imperial College London, London, UK
| | - Stuart A Cook
- National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.,Division of Cardiovascular & Metabolic Disorders, Duke-National University of Singapore, 169857, Singapore, Singapore.,National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield Hospitals and Imperial College London, London, UK.,Medical Research Council (MRC) London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Yigal M Pinto
- Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Connie R Bezzina
- Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands.
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13125, Berlin, Germany. .,Deutsches Zentrum für Herz-Kreislauf-Forschung, Heidelberg/Mannheim, Germany. .,Charité-Universitätsmedizin, Berlin, Germany. .,Deutsches Zentrum für Herz-Kreislauf-Forschung, Berlin, Germany.
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18
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Schaefer S, Viswanathan S, Widjaja A, Hubner N, Moreno-Moral A, Soon JL, Chao VT, Chakaramakkil MJ, Sin KY, Cook SA. 2885Integrated target discovery screens identify a novel therapeutic target for cardiovascular fibrosis. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx494.2885] [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: 11/14/2022] Open
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Abstract
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.
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Affiliation(s)
- Aida Moreno-Moral
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Francesco Pesce
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, Hammersmith Campus, Imperial Centre for Translational and Experimental Medicine, London, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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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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Abstract
Complementary to traditional gene mapping approaches used to identify the hereditary components of complex diseases, integrative genomics and systems genetics have emerged as powerful strategies to decipher the key genetic drivers of molecular pathways that underlie disease. Broadly speaking, integrative genomics aims to link cellular-level traits (such as mRNA expression) to the genome to identify their genetic determinants. With the characterization of several cellular-level traits within the same system, the integrative genomics approach evolved into a more comprehensive study design, called systems genetics, which aims to unravel the complex biological networks and pathways involved in disease, and in turn map their genetic control points. The first fully integrated systems genetics study was carried out in rats, and the results, which revealed conserved trans-acting genetic regulation of a pro-inflammatory network relevant to type 1 diabetes, were translated to humans. Many studies using different organisms subsequently stemmed from this example. The aim of this Review is to describe the most recent advances in the fields of integrative genomics and systems genetics applied in the rat, with a focus on studies of complex diseases ranging from inflammatory to cardiometabolic disorders. We aim to provide the genetics community with a comprehensive insight into how the systems genetics approach came to life, starting from the first integrative genomics strategies [such as expression quantitative trait loci (eQTLs) mapping] and concluding with the most sophisticated gene network-based analyses in multiple systems and disease states. Although not limited to studies that have been directly translated to humans, we will focus particularly on the successful investigations in the rat that have led to primary discoveries of genes and pathways relevant to human disease.
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Affiliation(s)
- Aida Moreno-Moral
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
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Lewin A, Saadi H, Peters JE, Moreno-Moral A, Lee JC, Smith KGC, Petretto E, Bottolo L, Richardson S. MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues. Bioinformatics 2015; 32:523-32. [PMID: 26504141 PMCID: PMC4743623 DOI: 10.1093/bioinformatics/btv568] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 12/05/2014] [Accepted: 09/03/2015] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION Analysing the joint association between a large set of responses and predictors is a fundamental statistical task in integrative genomics, exemplified by numerous expression Quantitative Trait Loci (eQTL) studies. Of particular interest are the so-called ': hotspots ': , important genetic variants that regulate the expression of many genes. Recently, attention has focussed on whether eQTLs are common to several tissues, cell-types or, more generally, conditions or whether they are specific to a particular condition. RESULTS We have implemented MT-HESS, a Bayesian hierarchical model that analyses the association between a large set of predictors, e.g. SNPs, and many responses, e.g. gene expression, in multiple tissues, cells or conditions. Our Bayesian sparse regression algorithm goes beyond ': one-at-a-time ': association tests between SNPs and responses and uses a fully multivariate model search across all linear combinations of SNPs, coupled with a model of the correlation between condition/tissue-specific responses. In addition, we use a hierarchical structure to leverage shared information across different genes, thus improving the detection of hotspots. We show the increase of power resulting from our new approach in an extensive simulation study. Our analysis of two case studies highlights new hotspots that would remain undetected by standard approaches and shows how greater prediction power can be achieved when several tissues are jointly considered. AVAILABILITY AND IMPLEMENTATION C[Formula: see text] source code and documentation including compilation instructions are available under GNU licence at http://www.mrc-bsu.cam.ac.uk/software/.
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Affiliation(s)
- Alex Lewin
- Department of Mathematics, Brunel University London
| | - Habib Saadi
- Department of Epidemiology and Biostatistics, Imperial College London, London
| | - James E Peters
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge
| | | | - James C Lee
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge
| | - Kenneth G C Smith
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, London, UK, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Leonardo Bottolo
- Department of Mathematics, Imperial College London, London, UK and Department of Medical Genetics, University of Cambridge
| | - Sylvia Richardson
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge
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Xiao X, Moreno-Moral A, Rotival M, Bottolo L, Petretto E. Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules. PLoS Genet 2014; 10:e1004006. [PMID: 24391511 PMCID: PMC3879165 DOI: 10.1371/journal.pgen.1004006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [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: 05/09/2013] [Accepted: 10/22/2013] [Indexed: 12/27/2022] Open
Abstract
Recent high-throughput efforts such as ENCODE have generated a large body of genome-scale transcriptional data in multiple conditions (e.g., cell-types and disease states). Leveraging these data is especially important for network-based approaches to human disease, for instance to identify coherent transcriptional modules (subnetworks) that can inform functional disease mechanisms and pathological pathways. Yet, genome-scale network analysis across conditions is significantly hampered by the paucity of robust and computationally-efficient methods. Building on the Higher-Order Generalized Singular Value Decomposition, we introduce a new algorithmic approach for efficient, parameter-free and reproducible identification of network-modules simultaneously across multiple conditions. Our method can accommodate weighted (and unweighted) networks of any size and can similarly use co-expression or raw gene expression input data, without hinging upon the definition and stability of the correlation used to assess gene co-expression. In simulation studies, we demonstrated distinctive advantages of our method over existing methods, which was able to recover accurately both common and condition-specific network-modules without entailing ad-hoc input parameters as required by other approaches. We applied our method to genome-scale and multi-tissue transcriptomic datasets from rats (microarray-based) and humans (mRNA-sequencing-based) and identified several common and tissue-specific subnetworks with functional significance, which were not detected by other methods. In humans we recapitulated the crosstalk between cell-cycle progression and cell-extracellular matrix interactions processes in ventricular zones during neocortex expansion and further, we uncovered pathways related to development of later cognitive functions in the cortical plate of the developing brain which were previously unappreciated. Analyses of seven rat tissues identified a multi-tissue subnetwork of co-expressed heat shock protein (Hsp) and cardiomyopathy genes (Bag3, Cryab, Kras, Emd, Plec), which was significantly replicated using separate failing heart and liver gene expression datasets in humans, thus revealing a conserved functional role for Hsp genes in cardiovascular disease.
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Affiliation(s)
- Xiaolin Xiao
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Aida Moreno-Moral
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Maxime Rotival
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Leonardo Bottolo
- Department of Mathematics, Imperial College, London, United Kingdom
| | - Enrico Petretto
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
- * E-mail:
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Moreno-Moral A, Mancini M, D'Amati G, Camici P, Petretto E. Transcriptional network analysis for the regulation of left ventricular hypertrophy and microvascular remodeling. J Cardiovasc Transl Res 2013; 6:931-44. [PMID: 23929067 DOI: 10.1007/s12265-013-9504-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 06/11/2013] [Accepted: 07/21/2013] [Indexed: 12/31/2022]
Abstract
Hypertension and cardiomyopathies share maladaptive changes of cardiac morphology, eventually leading to heart failure. These include left ventricular hypertrophy (LVH), myocardial fibrosis, and structural remodeling of coronary microcirculation, which is the morphologic hallmark of coronary microvascular dysfunction. To pinpoint the complex molecular mechanisms and pathways underlying LVH-associated cardiac remodeling independent of blood pressure effects, we employed gene network approaches to the rat heart. We used the Spontaneously Hypertensive Rat model showing many features of human hypertensive cardiomyopathy, for which we collected histological and histomorphometric data of the heart and coronary vasculature, and genome-wide cardiac gene expression. Here, we provide a large catalogue of gene co-expression networks in the heart that are significantly associated with quantitative variation in LVH, microvascular remodeling, and fibrosis-related traits. Many of these networks were significantly conserved to human idiopathic and/or ischemic cardiomyopathy patients, suggesting a potential role for these co-expressed genes in human heart disease.
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Affiliation(s)
- Aida Moreno-Moral
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Imperial Centre for Translational and Experimental Medicine (ICTEM) Building, Du Cane Road, London, W12 0NN, UK
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