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Ruffo P, De Amicis F, Giardina E, Conforti FL. Long-noncoding RNAs as epigenetic regulators in neurodegenerative diseases. Neural Regen Res 2022; 18:1243-1248. [PMID: 36453400 PMCID: PMC9838156 DOI: 10.4103/1673-5374.358615] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The growing and rapid development of high-throughput sequencing technologies have allowed a greater understanding of the mechanisms underlying gene expression regulation. Editing the epigenome and epitranscriptome directs the fate of the transcript influencing the functional outcome of each mRNA. In this context, non-coding RNAs play a decisive role in addressing the expression regulation at the gene and chromosomal levels. Long-noncoding RNAs, consisting of more than 200 nucleotides, have been shown to act as epigenetic regulators in several key molecular processes involving neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington's disease. Long-noncoding RNAs are abundantly expressed in the central nervous system, suggesting that their deregulation could trigger neuronal degeneration through RNA modifications. The evaluation of their diagnostic significance and therapeutic potential could lead to new treatments for these diseases for which there is no cure.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Francesca De Amicis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Rome, Italy,Department of Biomedicine & Prevention, Tor Vergata University of Rome, Rome, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy,Correspondence to: Francesca Luisa Conforti, .
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2
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Ni YQ, Xu H, Liu YS. Roles of Long Non-coding RNAs in the Development of Aging-Related Neurodegenerative Diseases. Front Mol Neurosci 2022; 15:844193. [PMID: 35359573 PMCID: PMC8964039 DOI: 10.3389/fnmol.2022.844193] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/09/2022] [Indexed: 12/12/2022] Open
Abstract
Aging-related neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), and amyotrophic lateral sclerosis (ALS), are gradually becoming the primary burden of society and cause significant health-care concerns. Aging is a critical independent risk factor for neurodegenerative diseases. The pathological alterations of neurodegenerative diseases are tightly associated with mitochondrial dysfunction, inflammation, and oxidative stress, which in turn stimulates the further progression of neurodegenerative diseases. Given the potential research value, lncRNAs have attracted considerable attention. LncRNAs play complex and dynamic roles in multiple signal transduction axis of neurodegeneration. Emerging evidence indicates that lncRNAs exert crucial regulatory effects in the initiation and development of aging-related neurodegenerative diseases. This review compiles the underlying pathological mechanisms of aging and related neurodegenerative diseases. Besides, we discuss the roles of lncRNAs in aging. In addition, the crosstalk and network of lncRNAs in neurodegenerative diseases are also explored.
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Affiliation(s)
- Yu-Qing Ni
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - Hui Xu
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - You-Shuo Liu
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
- *Correspondence: You-Shuo Liu,
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3
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Regulation of cardiomyocyte fate plasticity: a key strategy for cardiac regeneration. Signal Transduct Target Ther 2021; 6:31. [PMID: 33500391 PMCID: PMC7838318 DOI: 10.1038/s41392-020-00413-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/11/2020] [Accepted: 10/26/2020] [Indexed: 01/14/2023] Open
Abstract
With the high morbidity and mortality rates, cardiovascular diseases have become one of the most concerning diseases worldwide. The heart of adult mammals can hardly regenerate naturally after injury because adult cardiomyocytes have already exited the cell cycle, which subseqently triggers cardiac remodeling and heart failure. Although a series of pharmacological treatments and surgical methods have been utilized to improve heart functions, they cannot replenish the massive loss of beating cardiomyocytes after injury. Here, we summarize the latest research progress in cardiac regeneration and heart repair through altering cardiomyocyte fate plasticity, which is emerging as an effective strategy to compensate for the loss of functional cardiomyocytes and improve the impaired heart functions. First, residual cardiomyocytes in damaged hearts re-enter the cell cycle to acquire the proliferative capacity by the modifications of cell cycle-related genes or regulation of growth-related signals. Additionally, non-cardiomyocytes such as cardiac fibroblasts, were shown to be reprogrammed into cardiomyocytes and thus favor the repair of damaged hearts. Moreover, pluripotent stem cells have been shown to transform into cardiomyocytes to promote heart healing after myocardial infarction (MI). Furthermore, in vitro and in vivo studies demonstrated that environmental oxygen, energy metabolism, extracellular factors, nerves, non-coding RNAs, etc. play the key regulatory functions in cardiac regeneration. These findings provide the theoretical basis of targeting cellular fate plasticity to induce cardiomyocyte proliferation or formation, and also provide the clues for stimulating heart repair after injury.
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Pant T, Dhanasekaran A, Fang J, Bai X, Bosnjak ZJ, Liang M, Ge ZD. Current status and strategies of long noncoding RNA research for diabetic cardiomyopathy. BMC Cardiovasc Disord 2018; 18:197. [PMID: 30342478 PMCID: PMC6196023 DOI: 10.1186/s12872-018-0939-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/12/2018] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are endogenous RNA transcripts longer than 200 nucleotides which regulate epigenetically the expression of genes but do not have protein-coding potential. They are emerging as potential key regulators of diabetes mellitus and a variety of cardiovascular diseases. Diabetic cardiomyopathy (DCM) refers to diabetes mellitus-elicited structural and functional abnormalities of the myocardium, beyond that caused by ischemia or hypertension. The purpose of this review was to summarize current status of lncRNA research for DCM and discuss the challenges and possible strategies of lncRNA research for DCM. A systemic search was performed using PubMed and Google Scholar databases. Major conference proceedings of diabetes mellitus and cardiovascular disease occurring between January, 2014 to August, 2018 were also searched to identify unpublished studies that may be potentially eligible. The pathogenesis of DCM involves elevated oxidative stress, myocardial inflammation, apoptosis, and autophagy due to metabolic disturbances. Thousands of lncRNAs are aberrantly regulated in DCM. Manipulating the expression of specific lncRNAs, such as H19, metastasis-associated lung adenocarcinoma transcript 1, and myocardial infarction-associated transcript, with genetic approaches regulates potently oxidative stress, myocardial inflammation, apoptosis, and autophagy and ameliorates DCM in experimental animals. The detail data regarding the regulation and function of individual lncRNAs in DCM are limited. However, lncRNAs have been considered as potential diagnostic and therapeutic targets for DCM. Overexpression of protective lncRNAs and knockdown of detrimental lncRNAs in the heart are crucial for defining the role and function of lncRNAs of interest in DCM, however, they are technically challenging due to the length, short life, and location of lncRNAs. Gene delivery vectors can provide exogenous sources of cardioprotective lncRNAs to ameliorate DCM, and CRISPR–Cas9 genome editing technology may be used to knockdown specific lncRNAs in DCM. In summary, current data indicate that LncRNAs are a vital regulator of DCM and act as the promising diagnostic and therapeutic targets for DCM.
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Affiliation(s)
- Tarun Pant
- Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Centre for Biotechnology, Anna University, Chennai, Tamil Nadu, India
| | | | - Juan Fang
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Xiaowen Bai
- Department of Cell Biology, Neurology & Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Zeljko J Bosnjak
- Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Mingyu Liang
- Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Zhi-Dong Ge
- Department of Ophthalmology, Stanford School of Medicine, 1651 Page Mill Road, Stanford, CA, 94304, USA.
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5
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Poller W, Dimmeler S, Heymans S, Zeller T, Haas J, Karakas M, Leistner DM, Jakob P, Nakagawa S, Blankenberg S, Engelhardt S, Thum T, Weber C, Meder B, Hajjar R, Landmesser U. Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives. Eur Heart J 2018; 39:2704-2716. [PMID: 28430919 PMCID: PMC6454570 DOI: 10.1093/eurheartj/ehx165] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/14/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023] Open
Abstract
Recent research has demonstrated that the non-coding genome plays a key role in genetic programming and gene regulation during development as well as in health and cardiovascular disease. About 99% of the human genome do not encode proteins, but are transcriptionally active representing a broad spectrum of non-coding RNAs (ncRNAs) with important regulatory and structural functions. Non-coding RNAs have been identified as critical novel regulators of cardiovascular risk factors and cell functions and are thus important candidates to improve diagnostics and prognosis assessment. Beyond this, ncRNAs are rapidly emgerging as fundamentally novel therapeutics. On a first level, ncRNAs provide novel therapeutic targets some of which are entering assessment in clinical trials. On a second level, new therapeutic tools were developed from endogenous ncRNAs serving as blueprints. Particularly advanced is the development of RNA interference (RNAi) drugs which use recently discovered pathways of endogenous short interfering RNAs and are becoming versatile tools for efficient silencing of protein expression. Pioneering clinical studies include RNAi drugs targeting liver synthesis of PCSK9 resulting in highly significant lowering of LDL cholesterol or targeting liver transthyretin (TTR) synthesis for treatment of cardiac TTR amyloidosis. Further novel drugs mimicking actions of endogenous ncRNAs may arise from exploitation of molecular interactions not accessible to conventional pharmacology. We provide an update on recent developments and perspectives for diagnostic and therapeutic use of ncRNAs in cardiovascular diseases, including atherosclerosis/coronary disease, post-myocardial infarction remodelling, and heart failure.
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Affiliation(s)
- Wolfgang Poller
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Johann Wolfgang Goethe Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany
- DZHK, Site Rhein-Main, Frankfurt, Germany
| | - Stephane Heymans
- Center for Heart Failure Research, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Mahir Karakas
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - David-Manuel Leistner
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Philipp Jakob
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Stefan Engelhardt
- Institute for Pharmacology and Toxikology, Technische Universität München, Biedersteiner Strasse 29, München, Germany
- DZHK, Site Munich, Munich, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Christian Weber
- DZHK, Site Munich, Munich, Germany
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität, Pettenkoferstrasse 8a/9, Munich, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Roger Hajjar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ulf Landmesser
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
- Berlin Institute of Health, Kapelle-Ufer 2, Berlin, Germany
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6
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Xing W, Gao W, Mao G, Zhang J, Lv X, Wang G, Yan J. Long non-coding RNAs in aging organs and tissues. Clin Exp Pharmacol Physiol 2017; 44 Suppl 1:30-37. [PMID: 28602041 DOI: 10.1111/1440-1681.12795] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/27/2017] [Accepted: 05/07/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Wenmin Xing
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Wenyan Gao
- Institute of Materia Medica; Zhejiang Academy of Medical Sciences; Hangzhou China
| | - Genxiang Mao
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Jing Zhang
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Xiaoling Lv
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Guofu Wang
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Jing Yan
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
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7
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Wang F, Su X, Liu C, Wu M, Li B. Prognostic Value of Plasma Long Noncoding RNA ANRIL for In-Stent Restenosis. Med Sci Monit 2017; 23:4733-4739. [PMID: 28970468 PMCID: PMC5635947 DOI: 10.12659/msm.904352] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background In-stent restenosis (ISR) remains a major cause of failure of contemporary percutaneous revascularization therapies. Invasive biomarkers to improve the prognosis of ISR should be considered. This study aimed to investigate the association between plasma ANRIL expression and ISR. Material/Methods A total of 444 patients were included in this research. Serial coronary angiography was performed at baseline (before and after intervention) and within 36 months’ follow-up. ISR was defined as >50% diameter stenosis at follow-up. ANRIL expression was quantified using reverse transcription-PCR. An area under the ROC curve (auROC) was generated to assess the diagnostic values of ANRIL. Logistic regression models were used to assess the independent risk factors for ISR. Results Plasma ANRIL expression was significantly increased in patients with ISR, as compared with that in patients without ISR (1.6 [1.1–2.5] vs. 0.9 [0.6–1.3], P<0.001). The auROC (95% confidence interval [CI]) of plasma ANRIL in diagnosing ISR was 0.745 (0.687–0.811). Multiple logistic regression models indicated that drinking (odds ratio [OR]=2.09, 95% CI: 1.08–4.04, P=0.028), hypertension (OR=2.01, 95% CI: 1.14–3.57, P=0.017), diabetes (OR=3.15, 95% CI: 1.63–3.57, P<0.001), low-density lipoprotein (OR=3.14, 95% CI: 1.57–6.31, P=0.001), and ANRIL (OR=2.21, 95% CI: 1.68–2.92, P<0.001) were the independent risk factors for ISR. Conclusions We found that higher ANRIL expression is associated with ISR, indicating that ANRIL may be an optimal prognostic factor for ISR.
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Affiliation(s)
- Fang Wang
- Department of Cardiology, Wuhan Asia Heart Hospital, Wuhan, Hubei, China (mainland)
| | - Xi Su
- Department of Cardiology, Wuhan Asia Heart Hospital, Wuhan, Hubei, China (mainland)
| | - Chengwei Liu
- Department of Cardiology, Wuhan Asia Heart Hospital, Wuhan, Hubei, China (mainland)
| | - Mingxiang Wu
- Department of Cardiology, Wuhan Asia Heart Hospital, Wuhan, Hubei, China (mainland)
| | - Bei Li
- Department of Cardiology, Wuhan Asia Heart Hospital, Wuhan, Hubei, China (mainland)
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8
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Helsley RN, Zhou C. Epigenetic impact of endocrine disrupting chemicals on lipid homeostasis and atherosclerosis: a pregnane X receptor-centric view. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx017. [PMID: 29119010 PMCID: PMC5672952 DOI: 10.1093/eep/dvx017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/08/2017] [Accepted: 09/02/2017] [Indexed: 05/25/2023]
Abstract
Despite the major advances in developing diagnostic techniques and effective treatments, atherosclerotic cardiovascular disease (CVD) is still the leading cause of mortality and morbidity worldwide. While considerable progress has been achieved to identify gene variations and environmental factors that contribute to CVD, much less is known about the role of "gene-environment interactions" in predisposing individuals to CVD. Our chemical environment has significantly changed in the last few decades, and there are more than 100,000 synthetic chemicals in the market. Recent large-scale human population studies have associated exposure to certain chemicals including many endocrine disrupting chemicals (EDCs) with increased CVD risk, and animal studies have also confirmed that some EDCs can cause aberrant lipid homeostasis and increase atherosclerosis. However, the underlying mechanisms of how exposure to those EDCs influences CVD risk remain elusive. Numerous EDCs can activate the nuclear receptor pregnane X receptor (PXR) that functions as a xenobiotic sensor to regulate host xenobiotic metabolism. Recent studies have demonstrated the novel functions of PXR in lipid homeostasis and atherosclerosis. In addition to directly regulating transcription, PXR has been implicated in the epigenetic regulation of gene transcription. Exposure to many EDCs can also induce epigenetic modifications, but little is known about how the changes relate to the onset or progression of CVD. In this review, we will discuss recent research on PXR and EDCs in the context of CVD and propose that PXR may play a previously unrealized role in EDC-mediated epigenetic modifications that affect lipid homeostasis and atherosclerosis.
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Affiliation(s)
- Robert N Helsley
- Department of Pharmacology and Nutritional Sciences, Center for Metabolic Disease Research, University of Kentucky, Lexington, KY 40536, USA
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Changcheng Zhou
- Department of Pharmacology and Nutritional Sciences, Center for Metabolic Disease Research, University of Kentucky, Lexington, KY 40536, USA
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9
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Derrett-Smith EC, Martyanov V, Chighizola CB, Moinzadeh P, Campochiaro C, Khan K, Wood TA, Meroni PL, Abraham DJ, Ong VH, Lafyatis R, Whitfield ML, Denton CP. Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature. Arthritis Res Ther 2017; 19:156. [PMID: 28676069 PMCID: PMC5496265 DOI: 10.1186/s13075-017-1360-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 06/06/2017] [Indexed: 01/23/2023] Open
Abstract
Background Systemic sclerosis (SSc; scleroderma) is an uncommon autoimmune rheumatic disease characterised by autoimmunity, vasculopathy and fibrosis. Gene expression profiling distinguishes scleroderma from normal skin, and can detect different subsets of disease, with potential to identify prognostic biomarkers of organ involvement or response to therapy. We have performed gene expression profiling in skin samples from patients with limited cutaneous SSc (lcSSc). Methods Total RNA was extracted from clinically uninvolved skin biopsies of 15 patients with lcSSc and 8 healthy controls (HC). Gene expression profiling was performed on a DNA oligonucleotide microarray chip. Differentially expressed genes (DEG) were identified using significance analysis of microarrays (SAM). Functional enrichment analysis of gene signatures was done via g:Profiler. Results There were 218 DEG between lcSSc and HC samples (false discovery rate <10%): 181/218 DEG were upregulated in lcSSc samples. Hierarchical clustering of DEG suggested the presence of two separate groups of lcSSc samples: “limited 1” and “limited 2”. The limited-1 group (13 samples, 10 unique patients) showed upregulation of genes involved in cell adhesion, cardiovascular system (CVS) development, extracellular matrix and immune and inflammatory response. The CVS development signature was of particular interest as its genes showed very strong enrichment in response to wounding, response to transforming growth factor (TGF)-β and kinase cascade. Neither limited-2 samples (six samples, five unique patients) nor HC samples showed functional enrichment. There were no significant differences in demographic or clinical parameters between these two groups. These results were confirmed using a second independent cohort. Conclusions Our study suggests the presence of molecular subsets in lcSSc based on gene expression profiling of biopsies from uninvolved skin. This may reflect important differences in pathogenesis within these patient groups. We identify differential expression of a subset of genes that relate to CVS and are enriched in fibrotic signalling. This may shed light on mechanisms of vascular disease in SSc. The enrichment in profibrotic profile suggests that dysregulated gene expression may contribute to vasculopathy and fibrosis in different disease subsets. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1360-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emma C Derrett-Smith
- Centre for Rheumatology and Connective Tissue Diseases, University College London, London, UK.,University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Viktor Martyanov
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Cecilia B Chighizola
- Experimental Laboratory of Immunological and Rheumatologic Researches, IRCCS Istituto Auxologico Italiano, University of Milan, Milan, Italy
| | - Pia Moinzadeh
- Department of Dermatology and Venerology, University of Cologne, Cologne, Germany
| | - Corrado Campochiaro
- Centre for Rheumatology and Connective Tissue Diseases, University College London, London, UK
| | - Korsa Khan
- Centre for Rheumatology and Connective Tissue Diseases, University College London, London, UK
| | - Tammara A Wood
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Pier Luigi Meroni
- Experimental Laboratory of Immunological and Rheumatologic Researches, IRCCS Istituto Auxologico Italiano, University of Milan, Milan, Italy
| | - David J Abraham
- Centre for Rheumatology and Connective Tissue Diseases, University College London, London, UK
| | - Voon H Ong
- Centre for Rheumatology and Connective Tissue Diseases, University College London, London, UK
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Christopher P Denton
- Centre for Rheumatology and Connective Tissue Diseases, University College London, London, UK.
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10
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Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish. Sci Rep 2017; 7:1250. [PMID: 28455512 PMCID: PMC5430783 DOI: 10.1038/s41598-017-00823-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/14/2017] [Indexed: 01/01/2023] Open
Abstract
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as potential key regulators of heart development and related diseases, but their identities and functions remain elusive. In this study, we sought to identify and characterize the cardiac lincRNA transcriptome in the experimentally accessible zebrafish model by integrating bioinformatics analysis with experimental validation. By conducting genome-wide RNA sequencing profiling of zebrafish embryonic hearts, adult hearts, and adult muscle, we generated a high-confidence set of 813 cardiac lincRNA transcripts, 423 of which are novel. Among these lincRNAs, 564 are expressed in the embryonic heart, and 730 are expressed in the adult heart, including 2 novel lincRNAs, TCONS_00000891 and TCONS_00028686, which exhibit cardiac-enriched expression patterns in adult heart. Using a method similar to a fetal gene program, we identified 51 lincRNAs with differential expression patterns between embryonic and adult hearts, among which TCONS_00009015 responded to doxorubicin-induced cardiac stress. In summary, our genome-wide systematic identification and characterization of cardiac lincRNAs lays the foundation for future studies in this vertebrate model to elucidate crucial roles for cardiac lincRNAs during heart development and cardiac diseases.
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