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He R, Li Y, He Y, Wang Q, Zhang S, Chen S. Berberine mitigates diclofenac-induced intestinal mucosal mechanical barrier dysfunction through the restoration of autophagy by inhibiting exosome-mediated lncRNA H19. Inflammopharmacology 2024:10.1007/s10787-024-01487-y. [PMID: 38758516 DOI: 10.1007/s10787-024-01487-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/21/2024] [Indexed: 05/18/2024]
Abstract
Small intestine damage caused by diclofenac is called diclofenac enteropathy. Berberine (BBR), a class of isoquinoline alkaloids derived from Berberis vulgaris and Phellodendron amurense, is widely used in intestinal diseases. The present study evaluated the protective effect of BBR on the intestinal mucosal mechanical barrier in diclofenac enteropathy and its possible action mechanism. The in vitro animal experiment revealed that BBR downregulated the expression of long non-coding RNA H19 (lncRNA H19) in the small intestine and exosomes. In the co-culture experiment involving exosomes and intestinal epithelial cell-6 (IEC-6) cells, the results of qRT-PCR, western blotting, and immunofluorescence assays demonstrated that the elevated expression of lncRNA H19 in the small intestine, conveyed via exosomes derived from the diclofenac group, suppressed the expression levels of autophagy-associated protein 5 (Atg 5) and light chain 3 (LC 3), as well as and the tight junction (TJ) proteins zonula occludens-1 (ZO-1), claudin-1, and occluding, relative to the control group. BBR treatment attenuated exosomal lncRNA H19 levels, upregulated the expression of Atg5 and LC3 expression, enhanced TJ protein expression, and increased the light chain 3 (LC3)-II/LC3-I ratio. These findings significantly elucidated that BBR promoted the restoration of autophagy in IECs by inhibiting exosomal lncRNA H19, thereby mitigating the impairment of the intestinal mucosal mechanical barrier function in diclofenac enteropathy. The process involving exosomal lncRNA H19 regulating autophagy, thereby affecting the intestinal mucosal mechanical barrier, offers a novel perspective for the application of BBR in the treatment of diclofenac enteropathy.
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Affiliation(s)
- Ruonan He
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Ying Li
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Yi He
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Qianqian Wang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Shuo Zhang
- Department of Gastroenterology, Second Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, 310005, Zhejiang, China.
| | - Shanshan Chen
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, 310018, Zhejiang, China.
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Liao X, Wei R, Zhou J, Wu K, Li J. Emerging roles of long non-coding RNAs in osteosarcoma. Front Mol Biosci 2024; 11:1327459. [PMID: 38516191 PMCID: PMC10955361 DOI: 10.3389/fmolb.2024.1327459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
Osteosarcoma (OS) is a highly aggressive and lethal malignant bone tumor that primarily afflicts children, adolescents, and young adults. However, the molecular mechanisms underlying OS pathogenesis remain obscure. Mounting evidence implicates dysregulated long non-coding RNAs (lncRNAs) in tumorigenesis and progression. These lncRNAs play a pivotal role in modulating gene expression at diverse epigenetic, transcriptional, and post-transcriptional levels. Uncovering the roles of aberrant lncRNAs would provide new insights into OS pathogenesis and novel tools for its early diagnosis and treatment. In this review, we summarize the significance of lncRNAs in controlling signaling pathways implicated in OS development, including the Wnt/β-catenin, PI3K/AKT/mTOR, NF-κB, Notch, Hippo, and HIF-1α. Moreover, we discuss the multifaceted contributions of lncRNAs to drug resistance in OS, as well as their potential to serve as biomarkers and therapeutic targets. This review aims to encourage further research into lncRNA field and the development of more effective therapeutic strategies for patients with OS.
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Affiliation(s)
- Xun Liao
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan, China
| | - Rong Wei
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Junxiu Zhou
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan, China
| | - Ke Wu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiao Li
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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Chowdhury PR, Salvamani S, Gunasekaran B, Peng HB, Ulaganathan V. H19: An Oncogenic Long Non-coding RNA in Colorectal Cancer. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2023; 96:495-509. [PMID: 38161577 PMCID: PMC10751868 DOI: 10.59249/tdbj7410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Colorectal cancer (CRC) has been recorded amongst the most common cancers in the world, with high morbidity and mortality rates, and relatively low survival rates. With risk factors such as chronic illness, age, and lifestyle associated with the development of CRC, the incidence of CRC is increasing each year. Thus, the discovery of novel biomarkers to improve the diagnosis and prognosis of CRC has become beneficial. Long non-coding RNAs (lncRNAs) have been emerging as potential players in several tumor types, one among them is the lncRNA H19. The paternally imprinted oncofetal gene is expressed in the embryo, downregulated at birth, and reappears in tumors. H19 aids in CRC cell growth, proliferation, invasion, and metastasis via various mechanisms of action, significantly through the lncRNA-microRNA (miRNA)-messenger RNA (mRNA)-competitive endogenous RNA (ceRNA) network, where H19 behaves as a miRNA sponge. The RNA transcript of H19 obtained from the first exon of the H19 gene, miRNA-675 also promotes CRC carcinogenesis. Overexpression of H19 in malignant tissues compared to adjacent non-malignant tissues marks H19 as an independent prognostic marker in CRC. Besides its prognostic value, H19 serves as a promising target for therapy in CRC treatment.
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Affiliation(s)
- Prerana R. Chowdhury
- Division of Applied Biomedical Sciences and
Biotechnology, School of Health Sciences, International Medical University,
Kuala Lumpur, Malaysia
| | - Shamala Salvamani
- Division of Applied Biomedical Sciences and
Biotechnology, School of Health Sciences, International Medical University,
Kuala Lumpur, Malaysia
| | - Baskaran Gunasekaran
- Department of Biotechnology, Faculty of Applied
Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Hoh B. Peng
- Division of Applied Biomedical Sciences and
Biotechnology, School of Health Sciences, International Medical University,
Kuala Lumpur, Malaysia
| | - Vaidehi Ulaganathan
- Department of Biotechnology, Faculty of Applied
Sciences, UCSI University, Kuala Lumpur, Malaysia
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4
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m6A modification in inflammatory bowel disease provides new insights into clinical applications. Biomed Pharmacother 2023; 159:114298. [PMID: 36706633 DOI: 10.1016/j.biopha.2023.114298] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Inflammatory bowel disease (IBD) results from a complex interplay between genetic predisposition, environmental factors, and gut microbes. The role of N6-methyladenosine (m6A) methylation in the pathogenesis of IBD has attracted increasing attention. m6A modification not only regulates intestinal mucosal immunity and intestinal barrier function, but also affects apoptosis and autophagy in intestinal epithelial cells. Additionally, m6A modification participated in the interaction between gut microbes and the host, providing a novel direction to explore the molecular mechanisms of IBD and the theoretical basis for specific microorganism-oriented prevention and treatment measures. m6A regulators are expected to be biomarkers for predicting the prognosis of IBD patients. m6A methylation may be utilized as a novel target in the management of IBD. This review focused on the recent advances in how m6A modification causes the initiation and development of IBD, and provided new insights into optimal prevention and treatment measures for IBD.
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Wang Z, Ma J, Wu R, Kong Y, Sun C. Recent advances of long non-coding RNAs in control of hepatic gluconeogenesis. Front Endocrinol (Lausanne) 2023; 14:1167592. [PMID: 37065737 PMCID: PMC10102572 DOI: 10.3389/fendo.2023.1167592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Gluconeogenesis is the main process for endogenous glucose production during prolonged fasting, or certain pathological conditions, which occurs primarily in the liver. Hepatic gluconeogenesis is a biochemical process that is finely controlled by hormones such as insulin and glucagon, and it is of great importance for maintaining normal physiological blood glucose levels. Dysregulated gluconeogenesis induced by obesity is often associated with hyperglycemia, hyperinsulinemia, and type 2 diabetes (T2D). Long noncoding RNAs (lncRNAs) are involved in various cellular events, from gene transcription to protein translation, stability, and function. In recent years, a growing number of evidences has shown that lncRNAs play a key role in hepatic gluconeogenesis and thereby, affect the pathogenesis of T2D. Here we summarized the recent progress in lncRNAs and hepatic gluconeogenesis.
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Affiliation(s)
- Zhe Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neurogeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
| | - Jinyu Ma
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neurogeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
| | - Runze Wu
- Department of Endocrinology, Changshu No.2 People’s Hospital, Changshu, Jiangsu, China
| | - Yinghong Kong
- Department of Endocrinology, Changshu No.2 People’s Hospital, Changshu, Jiangsu, China
- *Correspondence: Yinghong Kong, ; Cheng Sun,
| | - Cheng Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neurogeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
- *Correspondence: Yinghong Kong, ; Cheng Sun,
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H19 and TUG1 lncRNAs as Novel Biomarkers for Irritable Bowel Syndrome in Diabetic Patients. Biomedicines 2022; 10:biomedicines10112978. [PMID: 36428545 PMCID: PMC9687602 DOI: 10.3390/biomedicines10112978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/10/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction: Irritable bowel syndrome (IBS) is a gastrointestinal disorder due to enteric nervous system impairment that produces different patterns of digestion. IBS is a common finding in diabetic patients. The functions of lncRNAs in IBS are still not clear and need to be further investigated. The aim of this study was to assess the diagnostic roles of lncRNA H19 and TUG1 for IBS associated with diabetes and to evaluate their association with clinical and laboratory findings. Subjects and Methods: Samples from 42 diabetic patients, 42 diabetic patients with IBS, and 42 healthy controls were obtained. The LncRNA H19 and TUG1 expressions were measured by quantitative real-time PCR. Results: The patients with IBS had significantly lower levels of lncRNA H19 and TUG1 expression than the healthy controls and diabetic-only patients (p < 0.001). LncRNA H19 and TUG1 can discriminate between diabetic-only patients and those with IBS (areas under the ROC curves of 0.95 and 0.722, respectively). The TUG1 expression levels were significantly different among types of IBS (IBS-D lower than IBS-M and IBS-C lower than IBS-M; p = 0.0165 and p = 0.043, respectively). H19 and TUG1 were downregulated in patients with poor glycemic control. lncRNA H19 and TUG1 expression in diabetic patients with IBS significantly negatively correlated with the IBS severity scoring system. Both lncRNAs’ expression significantly predicted the disease severity. LncRNA H19 expression can be an independent predictor for disease severity (adjusted odds ratio = 0.00001, 95% CI = 0−0.5, p = 0.045). Conclusions: Diabetic patients with IBS had significantly lower levels of lncRNA H19 and TUG1 expression than healthy controls and diabetic-only patients. LncRNA H19 had better diagnostic performance criteria for IBS. LncRNA H19 expression can be an independent predictor for IBS severity.
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Function of the Long Noncoding RNAs in Hepatocellular Carcinoma: Classification, Molecular Mechanisms, and Significant Therapeutic Potentials. Bioengineering (Basel) 2022; 9:bioengineering9080406. [PMID: 36004931 PMCID: PMC9405066 DOI: 10.3390/bioengineering9080406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common and serious type of primary liver cancer. HCC patients have a high death rate and poor prognosis due to the lack of clear signs and inadequate treatment interventions. However, the molecular pathways that underpin HCC pathogenesis remain unclear. Long non-coding RNAs (lncRNAs), a new type of RNAs, have been found to play important roles in HCC. LncRNAs have the ability to influence gene expression and protein activity. Dysregulation of lncRNAs has been linked to a growing number of liver disorders, including HCC. As a result, improved understanding of lncRNAs could lead to new insights into HCC etiology, as well as new approaches for the early detection and treatment of HCC. The latest results with respect to the role of lncRNAs in controlling multiple pathways of HCC were summarized in this study. The processes by which lncRNAs influence HCC advancement by interacting with chromatin, RNAs, and proteins at the epigenetic, transcriptional, and post-transcriptional levels were examined. This critical review also highlights recent breakthroughs in lncRNA signaling pathways in HCC progression, shedding light on the potential applications of lncRNAs for HCC diagnosis and therapy.
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KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:536-540. [PMID: 34990803 PMCID: PMC9801026 DOI: 10.1016/j.gpb.2021.12.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 01/26/2023]
Abstract
KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences. As testified on empirical data, KaKs_Calculator 3.0 shows effectiveness to detect the strength and mode of selection operated on molecular sequences, accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at a whole-genome scale. The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.
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Increased Expression of Long Non-coding RNA H19 is Associated With Colon Cancer Recurrence. J Surg Res 2021; 269:59-68. [PMID: 34520983 DOI: 10.1016/j.jss.2021.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 07/22/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Colon cancer is a leading cause of cancer-related death. Long non-coding (Lnc) RNAs are critical mediators of tumor biology. H19 is a well-characterized lncRNA involved in p53 regulation and cancer progression. A specific colon cancer data set was utilized to determine if tumor H19 expression is associated with recurrence-free and overall survival. METHODS Clinical patient data from The Cancer Genome Atlas colon adenocarcinoma data set was downloaded using FirebrowseR and normalized H19 expression from the associated RNA-seq data set downloaded using cBioportal. Univariable and multivariable Cox proportional regression analyses were used to identify an association between H19 expression in colon cancer tissue and recurrence-free, and overall survival. RESULTS Three hundred eight patients were studied. Median age was 68 years (interquartile range: 58-77 years) and 156 patients (51%) were men. Increased H19 expression was associated with KRAS mutation status (P= 0.016). There was no difference in overall survival between the low and high H19 expression groups (log rank = 0.481); however, increased H19 expression was associated with reduced recurrence-free survival (Log-Rank = 0.012). On multivariable regression analysis, increased H19 expression (Hazard ratio = 1.83, 95%CI: 1.02-3.27, P= 0.042), and stage III or IV disease (Hazard ratio = 2.39, 95%CI: 1.34-4.27, P= 0.003) were risk factors for reduced recurrence-free survival. CONCLUSIONS Colon cancer H19 expression is associated with advanced stage of tumor disease and is a significant risk factor for reduced recurrence-free survival. Tumor expression of H19 may have potential for both prognostic and therapeutic uses in the future.
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Li J, Zhang Y, Zhang D, Li Y. The Role of Long Non-coding RNAs in Sepsis-Induced Cardiac Dysfunction. Front Cardiovasc Med 2021; 8:684348. [PMID: 34041287 PMCID: PMC8141560 DOI: 10.3389/fcvm.2021.684348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
Sepsis is a syndrome with life-threatening organ dysfunction induced by a dysregulated host response to infection. The heart is one of the most commonly involved organs during sepsis, and cardiac dysfunction, which is usually indicative of an extremely poor clinical outcome, is a leading cause of death in septic cases. Despite substantial improvements in the understanding of the mechanisms that contribute to the origin and responses to sepsis, the prognosis of sepsis-induced cardiac dysfunction (SICD) remains poor and its molecular pathophysiological changes are not well-characterized. The recently discovered group of mediators known as long non-coding RNAs (lncRNAs) have presented novel insights and opportunities to explore the mechanisms and development of SICD and may provide new targets for diagnosis and therapeutic strategies. LncRNAs are RNA transcripts of more than 200 nucleotides with limited or no protein-coding potential. Evidence has rapidly accumulated from numerous studies on how lncRNAs function in associated regulatory circuits during SICD. This review outlines the direct evidence of the effect of lncRNAs on SICD based on clinical trials and animal studies. Furthermore, potential functional lncRNAs in SICD that have been identified in sepsis studies are summarized with a proven biological function in research on other cardiovascular diseases.
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Affiliation(s)
- Jiawen Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yulin Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Donghui Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
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Xiao L, Rao JN, Wang JY. RNA-binding proteins and long noncoding RNAs in intestinal epithelial autophagy and barrier function. Tissue Barriers 2021; 9:1895648. [PMID: 33709880 DOI: 10.1080/21688370.2021.1895648] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The intestinal autophagy and barrier function are crucial for maintaining the epithelium homeostasis and tightly regulated through well-controlled mechanisms. RNA-binding proteins (RBPs) and long noncoding RNAs (lncRNAs) modulate gene expression at the posttranscription level and are intimately involved in different physiological processes and diverse human diseases. In this review, we first highlight the roles of several RBPs and lncRNAs in the regulation of intestinal epithelial autophagy and barrier function, particularly focusing on the emerging evidence of RBPs and lncRNAs in the control of mRNA stability and translation. We additionally discuss recent findings that the interactions between RBPs and lncRNAs alter the fate of their target transcripts and thus influence gut epithelium host defense in response to stressful environments. These exciting advances in understanding the posttranscriptional control of the epithelial autophagy and barrier function by RBPs and lncRNAs provide a strong rationale for developing new effective therapeutics based on targeting RBPs and/or lncRNAs to preserve the intestinal epithelial integrity in patients with critical illnesses.
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Affiliation(s)
- Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Jaladanki N Rao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, MD, USA.,Department of Pathology, Department of Veterans Affairs, USA
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Kay M, Soltani BM. LncRNAs in Cardiomyocyte Maturation: New Window for Cardiac Regenerative Medicine. Noncoding RNA 2021; 7:ncrna7010020. [PMID: 33802186 PMCID: PMC8005985 DOI: 10.3390/ncrna7010020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiomyocyte (CM) maturation, which is characterized by structural, functional, and metabolic specializations, is the last phase of CM development that prepares the cells for efficient and forceful contraction throughout life. Over the past decades, CM maturation has gained increased attention due to the fact that pluripotent stem cell-derived CMs are structurally, transcriptionally, and functionally immature and embryonic-like, which causes a defect in cell replacement therapy. The current challenge is to discover and understand the molecular mechanisms, which control the CM maturation process. Currently, emerging shreds of evidence emphasize the role of long noncoding RNAs (lncRNAs) in regulating different aspects of CM maturation, including myofibril maturation, electrophysiology, and Ca2+ handling maturation, metabolic maturation and proliferation to hypertrophy transition. Here, we describe the structural and functional characteristics of mature CMs. Furthermore, this review highlights the lncRNAs as crucial regulators of different aspects in CM maturation, which have the potential to be used for mature CM production. With the current advances in oligonucleotide delivery; lncRNAs may serve as putative therapeutic targets to produce highly mature CMs for research and regenerative medicine.
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Chao G, Wang Z, Yang Y, Zhang S. LncRNA H19 as a Competing Endogenous RNA to Regulate AQP Expression in the Intestinal Barrier of IBS-D Patients. Front Physiol 2021; 11:602076. [PMID: 33584332 PMCID: PMC7874183 DOI: 10.3389/fphys.2020.602076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Objective The study aimed to investigate the role of Long non-coding RNA (LncRNA) H19 in the pathogenesis of Diarrhea Irritable Bowel Syndrome (IBS-D), and further to the regulatory effect of LncRNA H19 on AQP1, 3 in the intestinal mucosa of IBS-D patients, so as to seek a new way to elucidate the mechanism of IBS in clinic. Methods The levels of LncRNA H19, AQP1, and AQP3 were detected in colonic tissues of IBS-D patients, compared with that in healthy controls. Through RNA gene interference and activation methods, small activating RNA (saRNA) and small interfering (siRNA) were transfered into Caco-2 cells in vitro experiment, and sub-group for two control group, siH19 empty vector group, siH19 interference group, overexpression H19 vector group, and overexpression H19 empty vector group. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) and Western blot were applied to evaluate the expression levels of LncRNA H19 and the amount of AQP1 and AQP3 protein expression, respectively. Results Compared with healthy volunteers, the levels of LncRNA H19, AQP1, and AQP3 in the colonic mucosa of IBS-D patients were significantly decreased (P < 0.05). The results in vitro transfection experiment revealed that the level of LncRNA H19 in the siH19 interference group was significantly declined (P < 0.05), while there was a remarkable increase in the overexpression H19 vector group (P < 0.05), compared with the corresponding control groups. The expression of AQP1 and AQP3 in Caco-2 cells was of positive correlation with the level of LncRNA H19. Conclusion That the down-regulation of LncRNA H19 resulted in the expression changes of AQP1 and AQP3 may play an important role in the occurrence and development of IBS-D.
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Affiliation(s)
- Guanqun Chao
- Department of General Practice, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Zhaojun Wang
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yi Yang
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shuo Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
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LncRNA H19 regulates smooth muscle cell functions and participates in the development of aortic dissection through sponging miR-193b-3p. Biosci Rep 2021; 41:227493. [PMID: 33403385 PMCID: PMC7823186 DOI: 10.1042/bsr20202298] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/03/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Multiple studies showed that long-chain noncoding RNA H19 (LncRNA H19) is high-expressed in human and mouse abdominal aortic aneurysms (AAAs). We speculated that it plays an important role in arterial disease, and therefore studied the role and mechanism of H19 in aortic dissection (AD). METHODS The expressions of related genes in human aortic smooth muscle cells (HASMCs) induced by platelet-derived growth factor BB (PDGF-BB) or in the aortic tissue of AD patients/mice were identified by Western blot and quantitative real-time polymerase chain reaction. The targeting relationship between H19 and miR-193b-3p was predicted and verified by bioinformatics analysis, dual luciferase assay, RNA pull-down assay, RNA immunoprecipitation (RIP), and Pearson correlation coefficient. The H19 and miR-193b-3p effects on the biological functions of tissues and cells were examined by MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide, thiazolyl blue tetrazolium bromide) assay, wound-healing assay, and Hematoxylin-Eosin (HE) staining. RESULTS LncRNA H19 was abnormally high-expressed in thoracic aorta tissues of AD patients, and it could competitively bind to and inhibit miR-193b-3p. In the PDGF-BB group, the expressions of H19, matrix metallopeptidase (MMP) 2 (MMP-2) and MMP-9 were up-regulated and the expressions of miR-193b-3p, α-SMA, and SM22α were down-regulated; moreover, the proliferation and migration rate of HASMCs were increased. However, H19 silencing reversed the regulation of PDGF-BB on HASMCs. More interestingly, miR-193b-3p inhibitor could partially reverse the effect of H19 silencing. In addition, the above results were verified by animal experiments, showing that shH19 and up-regulated miR-193b-3p could significantly reduce the thoracic aorta pathological damage in AD mice. CONCLUSION LncRNA H19 regulated smooth muscle cell function by sponging miR-193b-3p and it participated in the development of AD.
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15
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Wang B, Suen CW, Ma H, Wang Y, Kong L, Qin D, Lee YWW, Li G. The Roles of H19 in Regulating Inflammation and Aging. Front Immunol 2020; 11:579687. [PMID: 33193379 PMCID: PMC7653221 DOI: 10.3389/fimmu.2020.579687] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
Accumulating evidence suggests that long non-coding RNA H19 correlates with several aging processes. However, the role of H19 in aging remains unclear. Many studies have elucidated a close connection between H19 and inflammatory genes. Chronic systemic inflammation is an established factor associated with various diseases during aging. Thus, H19 might participate in the development of age-related diseases by interplay with inflammation and therefore provide a protective function against age-related diseases. We investigated the inflammatory gene network of H19 to understand its regulatory mechanisms. H19 usually controls gene expression by acting as a microRNA sponge, or through mir-675, or by leading various protein complexes to genes at the chromosome level. The regulatory gene network has been intensively studied, whereas the biogenesis of H19 remains largely unknown. This literature review found that the epithelial-mesenchymal transition (EMT) and an imprinting gene network (IGN) might link H19 with inflammation. Evidence indicates that EMT and IGN are also tightly controlled by environmental stress. We propose that H19 is a stress-induced long non-coding RNA. Because environmental stress is a recognized age-related factor, inflammation and H19 might serve as a therapeutic axis to fight against age-related diseases.
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Affiliation(s)
- Bin Wang
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chun Wai Suen
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Haibin Ma
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yan Wang
- Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ling Kong
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Dajiang Qin
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuk Wai Wayne Lee
- Department of Orthopaedics & Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Gang Li
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Department of Orthopaedics & Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China.,Ministry of Education Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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16
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Peng L, Jiang J, Tang B, Nice EC, Zhang YY, Xie N. Managing therapeutic resistance in breast cancer: from the lncRNAs perspective. Theranostics 2020; 10:10360-10377. [PMID: 32929354 PMCID: PMC7482807 DOI: 10.7150/thno.49922] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/04/2020] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC) is the most common female malignancy and the second leading cause of cancer-related death worldwide. In spite of significant advances in clinical management, the mortality of BC continues to increase due to the frequent occurrence of treatment resistance. Intensive studies have been conducted to elucidate the molecular mechanisms underlying BC therapeutic resistance, including increased drug efflux, altered drug targets, activated bypass signaling pathways, maintenance of cancer stemness, and deregulated immune response. Emerging evidence suggests that long noncoding RNAs (lncRNAs) are intimately involved in BC therapy resistance through multiple modes of action. Therefore, an in-depth understanding of the implication of lncRNAs in resistance to clinical therapies may improve the clinical outcome of BC patients. Here, we highlight the role and underlying mechanisms of lncRNAs in regulating BC treatment resistance with an emphasis on lncRNAs-mediated resistance in different clinical scenarios, and discuss the potential of lncRNAs as novel biomarkers or therapeutic targets to improve BC therapy response.
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Affiliation(s)
- Liyuan Peng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Bo Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Yuan-Yuan Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, P.R. China
| | - Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
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17
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Abstract
The advent of deep sequencing technologies led to the identification of a considerable amount of noncoding RNA transcripts, which are increasingly recognized for their functions in controlling cardiovascular diseases. MicroRNAs have already been studied for a decade, leading to the identification of several vasculoprotective and detrimental species, which might be considered for therapeutic targeting. Other noncoding RNAs such as circular RNAs, YRNAs, or long noncoding RNAs are currently gaining increasing attention, and first studies provide insights into their functions as mediators or antagonists of vascular diseases in vivo. The present review article will provide an overview of the different types of noncoding RNAs controlling the vasculature and focus on the developing field of long noncoding RNAs.
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Affiliation(s)
- Nicolas Jaé
- From the Institute for Cardiovascular Regeneration (N.J., S.D.), Goethe University Frankfurt, Germany
| | - Stefanie Dimmeler
- From the Institute for Cardiovascular Regeneration (N.J., S.D.), Goethe University Frankfurt, Germany.,Cardiopulmonary Institute (S.D.), Goethe University Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK) and Cardiopulmonary Institute (CPI), Partner Site Rhine-Main, Frankfurt (S.D.)
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18
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Abstract
Hepatocellular carcinoma (HCC) is the most frequent subtype of primary liver cancer and one of the leading causes of cancer-related death worldwide. However, the molecular mechanisms underlying HCC pathogenesis have not been fully understood. Emerging evidences have recently suggested the crucial role of long noncoding RNAs (lncRNAs) in the tumorigenesis and progression of HCC. Various HCC-related lncRNAs have been shown to possess aberrant expression and participate in cancerous phenotypes (e.g. persistent proliferation, evading apoptosis, accelerated vessel formation and gain of invasive capability) through their binding with DNA, RNA or proteins, or encoding small peptides. Thus, a deeper understanding of lncRNA dysregulation would provide new insights into HCC pathogenesis and novel tools for the early diagnosis and treatment of HCC. In this review, we summarize the dysregulation of lncRNAs expression in HCC and their tumor suppressive or oncogenic roles during HCC tumorigenesis. Moreover, we discuss the diagnostic and therapeutic potentials of lncRNAs in HCC.
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19
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Yu TX, Chung HK, Xiao L, Piao JJ, Lan S, Jaladanki SK, Turner DJ, Raufman JP, Gorospe M, Wang JY. Long Noncoding RNA H19 Impairs the Intestinal Barrier by Suppressing Autophagy and Lowering Paneth and Goblet Cell Function. Cell Mol Gastroenterol Hepatol 2019; 9:611-625. [PMID: 31862317 PMCID: PMC7078540 DOI: 10.1016/j.jcmgh.2019.12.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The protective intestinal mucosal barrier consists of multiple elements including mucus and epithelial layers and immune defense; nonetheless, barrier dysfunction is common in various disorders. The imprinted and developmentally regulated long noncoding RNA H19 is involved in many cell processes and diseases. Here, we investigated the role of H19 in regulating Paneth and goblet cells and autophagy, and its impact on intestinal barrier dysfunction induced by septic stress. METHODS Studies were conducted in H19-deficient (H19-/-) mice, mucosal tissues from patients with sepsis, primary enterocytes, and Caco-2 cells. Septic stress was induced by cecal ligation and puncture (CLP), and gut permeability was detected by tracer fluorescein isothiocyanate-dextran assays. The function of Paneth and goblet cells was examined by immunostaining for lysozyme and mucin 2, respectively, and autophagy was examined by microtubule-associated proteins 1A/1B light chain 3 II immunostaining and Western blot analysis. Intestinal organoids were isolated from H19-/- and control littermate mice and treated with lipopolysaccharide (LPS). RESULTS Intestinal mucosal tissues in mice 24 hours after exposure to CLP and in patients with sepsis showed high H19 levels, associated with intestinal barrier dysfunction. Targeted deletion of the H19 gene in mice enhanced the function of Paneth and goblet cells and promoted autophagy in the small intestinal mucosa. Knockout of H19 protected Paneth and goblet cells against septic stress, preserved autophagy activation, and promoted gut barrier function after exposure to CLP. Compared with organoids from control littermate mice, intestinal organoids isolated from H19-/- mice had increased numbers of lysozyme- and mucin 2-positive cells and showed increased tolerance to LPS. Conversely, ectopic overexpression of H19 in cultured intestinal epithelial cells prevented rapamycin-induced autophagy and abolished the rapamycin-induced protection of the epithelial barrier against LPS. CONCLUSIONS In investigations of mice, human tissues, primary organoids, and intestinal epithelial cells, we found that increased H19 inhibited the function of Paneth and goblet cells and suppressed autophagy, thus potentially contributing to barrier dysfunction in intestinal pathologies.
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Affiliation(s)
- Ting-Xi Yu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Hee K Chung
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland; Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Jun-Jie Piao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Shaoyang Lan
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Suraj K Jaladanki
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Douglas J Turner
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland; Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Jean-Pierre Raufman
- Baltimore Veterans Affairs Medical Center, Baltimore, Maryland; Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland; Baltimore Veterans Affairs Medical Center, Baltimore, Maryland; Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland.
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20
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Smith KN, Miller SC, Varani G, Calabrese JM, Magnuson T. Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification. Genetics 2019; 213:1093-1110. [PMID: 31796550 PMCID: PMC6893379 DOI: 10.1534/genetics.119.302661] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Lineage specification in early development is the basis for the exquisitely precise body plan of multicellular organisms. It is therefore critical to understand cell fate decisions in early development. Moreover, for regenerative medicine, the accurate specification of cell types to replace damaged/diseased tissue is strongly dependent on identifying determinants of cell identity. Long noncoding RNAs (lncRNAs) have been shown to regulate cellular plasticity, including pluripotency establishment and maintenance, differentiation and development, yet broad phenotypic analysis and the mechanistic basis of their function remains lacking. As components of molecular condensates, lncRNAs interact with almost all classes of cellular biomolecules, including proteins, DNA, mRNAs, and microRNAs. With functions ranging from controlling alternative splicing of mRNAs, to providing scaffolding upon which chromatin modifiers are assembled, it is clear that at least a subset of lncRNAs are far from the transcriptional noise they were once deemed. This review highlights the diversity of lncRNA interactions in the context of cell fate specification, and provides examples of each type of interaction in relevant developmental contexts. Also highlighted are experimental and computational approaches to study lncRNAs.
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Affiliation(s)
- Keriayn N Smith
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sarah C Miller
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
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21
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Li DY, Busch A, Jin H, Chernogubova E, Pelisek J, Karlsson J, Sennblad B, Liu S, Lao S, Hofmann P, Bäcklund A, Eken SM, Roy J, Eriksson P, Dacken B, Ramanujam D, Dueck A, Engelhardt S, Boon RA, Eckstein HH, Spin JM, Tsao PS, Maegdefessel L. H19 Induces Abdominal Aortic Aneurysm Development and Progression. Circulation 2019; 138:1551-1568. [PMID: 29669788 DOI: 10.1161/circulationaha.117.032184] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Long noncoding RNAs have emerged as critical molecular regulators in various biological processes and diseases. Here we sought to identify and functionally characterize long noncoding RNAs as potential mediators in abdominal aortic aneurysm development. METHODS We profiled RNA transcript expression in 2 murine abdominal aortic aneurysm models, Angiotensin II (ANGII) infusion in apolipoprotein E-deficient ( ApoE-/-) mice (n=8) and porcine pancreatic elastase instillation in C57BL/6 wild-type mice (n=12). The long noncoding RNA H19 was identified as 1 of the most highly upregulated transcripts in both mouse aneurysm models compared with sham-operated controls. This was confirmed by quantitative reverse transcription-polymerase chain reaction and in situ hybridization. RESULTS Experimental knock-down of H19, utilizing site-specific antisense oligonucleotides (LNA-GapmeRs) in vivo, significantly limited aneurysm growth in both models. Upregulated H19 correlated with smooth muscle cell (SMC) content and SMC apoptosis in progressing aneurysms. Importantly, a similar pattern could be observed in human abdominal aortic aneurysm tissue samples, and in a novel preclinical LDLR-/- (low-density lipoprotein receptor) Yucatan mini-pig aneurysm model. In vitro knock-down of H19 markedly decreased apoptotic rates of cultured human aortic SMCs, whereas overexpression of H19 had the opposite effect. Notably, H19-dependent apoptosis mechanisms in SMCs appeared to be independent of miR-675, which is embedded in the first exon of the H19 gene. A customized transcription factor array identified hypoxia-inducible factor 1α as the main downstream effector. Increased SMC apoptosis was associated with cytoplasmic interaction between H19 and hypoxia-inducible factor 1α and sequential p53 stabilization. Additionally, H19 induced transcription of hypoxia-inducible factor 1α via recruiting the transcription factor specificity protein 1 to the promoter region. CONCLUSIONS The long noncoding RNA H19 is a novel regulator of SMC survival in abdominal aortic aneurysm development and progression. Inhibition of H19 expression might serve as a novel molecular therapeutic target for aortic aneurysm disease.
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Affiliation(s)
- Daniel Y Li
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar (D.Y.L., A. Busch, J.P., S.L., H.-H.E., L.M.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Albert Busch
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar (D.Y.L., A. Busch, J.P., S.L., H.-H.E., L.M.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Hong Jin
- Department of Medicine (H.J., E.C., A. Bäcklund; S.M.E., P.E., L.M.), Karolinska Institutet, Stockholm, Sweden
| | - Ekaterina Chernogubova
- Department of Medicine (H.J., E.C., A. Bäcklund; S.M.E., P.E., L.M.), Karolinska Institutet, Stockholm, Sweden
| | - Jaroslav Pelisek
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar (D.Y.L., A. Busch, J.P., S.L., H.-H.E., L.M.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Joakim Karlsson
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden (J.K.)
| | - Bengt Sennblad
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden (B.S.)
| | - Shengliang Liu
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar (D.Y.L., A. Busch, J.P., S.L., H.-H.E., L.M.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Shen Lao
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar (D.Y.L., A. Busch, J.P., S.L., H.-H.E., L.M.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Patrick Hofmann
- Institute of Cardiovascular Regeneration, University Hospital Frankfurt, and German Center for Cardiovascular Research (DZHK), partner site Rhein-Main, Frankfurt, Germany (P.H., R.A.B.)
| | - Alexandra Bäcklund
- Department of Medicine (H.J., E.C., A. Bäcklund; S.M.E., P.E., L.M.), Karolinska Institutet, Stockholm, Sweden
| | - Suzanne M Eken
- Department of Medicine (H.J., E.C., A. Bäcklund; S.M.E., P.E., L.M.), Karolinska Institutet, Stockholm, Sweden
| | - Joy Roy
- Department of Molecular Medicine and Surgery (J.R.), Karolinska Institutet, Stockholm, Sweden
| | - Per Eriksson
- Department of Medicine (H.J., E.C., A. Bäcklund; S.M.E., P.E., L.M.), Karolinska Institutet, Stockholm, Sweden
| | | | - Deepak Ramanujam
- Institute of Pharmacology and Toxicology (D.R., A.D., S.E.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Anne Dueck
- Institute of Pharmacology and Toxicology (D.R., A.D., S.E.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology (D.R., A.D., S.E.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Reinier A Boon
- Institute of Cardiovascular Regeneration, University Hospital Frankfurt, and German Center for Cardiovascular Research (DZHK), partner site Rhein-Main, Frankfurt, Germany (P.H., R.A.B.)
| | - Hans-Henning Eckstein
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar (D.Y.L., A. Busch, J.P., S.L., H.-H.E., L.M.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Joshua M Spin
- Division of Cardiovascular Medicine, Stanford University, CA (J.M.S., P.S.T.)
| | - Philip S Tsao
- Division of Cardiovascular Medicine, Stanford University, CA (J.M.S., P.S.T.)
| | - Lars Maegdefessel
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar (D.Y.L., A. Busch, J.P., S.L., H.-H.E., L.M.), Technical University Munich, and German Center for Cardiovascular Research (DZHK), partner site Munich, Germany.,Department of Medicine (H.J., E.C., A. Bäcklund; S.M.E., P.E., L.M.), Karolinska Institutet, Stockholm, Sweden
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22
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Fabbri M, Girnita L, Varani G, Calin GA. Decrypting noncoding RNA interactions, structures, and functional networks. Genome Res 2019; 29:1377-1388. [PMID: 31434680 PMCID: PMC6724670 DOI: 10.1101/gr.247239.118] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that ncRNAs, like many large proteins, have a multidomain architecture that organizes them spatially and functionally. As ncRNAs are beginning to be imprecisely classified into functional families, we review here how their structural properties might inform their functions with focus on structural architecture–function relationships. We will describe the properties of “interactor elements” (IEs) involved in direct physical interaction with nucleic acids, proteins, or lipids and of “structural elements” (SEs) directing their wiring within the “ncRNA interactor networks” through the emergence of secondary and/or tertiary structures. We suggest that spectrums of “letters” (ncRNA elements) are assembled into “words” (ncRNA domains) that are further organized into “phrases” (complete ncRNA structures) with functional meaning (signaling output) through complex “sentences” (the ncRNA interactor networks). This semiotic analogy can guide the exploitation of ncRNAs as new therapeutic targets through the development of IE-blockers and/or SE-lockers that will change the interactor partners’ spectrum of proteins, RNAs, DNAs, or lipids and consequently influence disease phenotypes.
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Affiliation(s)
- Muller Fabbri
- University of Hawaii Cancer Center, Cancer Biology Program, Honolulu, Hawaii 96813, USA
| | - Leonard Girnita
- Department of Oncology-Pathology, Cellular and Molecular Tumor Pathology, Karolinska Institute, and Karolinska University Hospital, Stockholm, 17164 Sweden
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - George A Calin
- Department of Experimental Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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23
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Xiao L, Gorospe M, Wang JY. Long noncoding RNAs in intestinal epithelium homeostasis. Am J Physiol Cell Physiol 2019; 317:C93-C100. [PMID: 31042423 DOI: 10.1152/ajpcell.00092.2019] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The epithelium of the mammalian intestinal mucosa is a rapidly self-renewing tissue in the body, and its homeostasis is preserved through well-controlled mechanisms. Long noncoding RNAs (lncRNAs) regulate a variety of biological functions and are intimately involved in the pathogenesis of diverse human diseases. Here we highlight the roles of several lncRNAs expressed in the intestinal epithelium, including uc.173, SPRY4-IT1, H19, and Gata6, in maintaining the integrity of the intestinal epithelium, focusing on the emerging evidence of lncRNAs in the regulation of intestinal mucosal regeneration and epithelial barrier function. We also discuss recent results that the interactions between lncRNAs with microRNAs and the RNA-binding protein HuR influence epithelial homeostasis. With rapidly advancing knowledge of lncRNAs, there is also growing recognition that lncRNAs in the intestinal epithelium might be promising therapeutic targets in our efforts to protect the integrity of the intestinal epithelium in response to stressful environments.
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Affiliation(s)
- Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine , Baltimore, Maryland.,Baltimore Veterans Affairs Medical Center , Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health , Baltimore, Maryland
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine , Baltimore, Maryland.,Baltimore Veterans Affairs Medical Center , Baltimore, Maryland.,Department of Pathology, University of Maryland School of Medicine , Baltimore, Maryland
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24
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Wang J, Zhang X, Chen W, Hu X, Li J, Liu C. Regulatory roles of long noncoding RNAs implicated in cancer hallmarks. Int J Cancer 2019; 146:906-916. [PMID: 30873588 DOI: 10.1002/ijc.32277] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/18/2019] [Accepted: 03/11/2019] [Indexed: 12/16/2022]
Abstract
Cancer cells acquire numerous biological properties (designated "cancer hallmarks"), such as cell survival and energy metabolism, that facilitate tumor growth and metastatic dissemination during development. To date, eight hallmarks of cancer have been identified that provide a logical framework for understanding the remarkable diversity of neoplastic diseases, as proposed by Douglas Hanahan and Robert A. Weinberg. Long noncoding RNAs (lncRNAs), a category of transcripts widely demonstrated to exert significant regulatory effects on biological processes, have attracted considerable research attention due to their association with the occurrence and development of cancer. The mechanisms by which lncRNAs exert their functions require elucidation to optimize their potential utility as alternative biomarkers and therapeutic targets during tumor occurrence and progression. In this review, we have discussed recent research progress on lncRNAs involved in various cancer hallmarks and their related mechanisms of action, with a view to providing an updated picture of their immense therapeutic potential in the fight against cancer.
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Affiliation(s)
- Jun Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China.,Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China.,State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xiang Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China.,State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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25
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Su H, Xu X, Yan C, Shi Y, Hu Y, Dong L, Ying S, Ying K, Zhang R. LncRNA H19 promotes the proliferation of pulmonary artery smooth muscle cells through AT 1R via sponging let-7b in monocrotaline-induced pulmonary arterial hypertension. Respir Res 2018; 19:254. [PMID: 30547791 PMCID: PMC6295077 DOI: 10.1186/s12931-018-0956-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/29/2018] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is related to inflammation, and the lncRNA H19 is associated with inflammation. However, whether PDGF-BB-H19-let-7b-AT1R axis contributes to the pathogenesis of PAH has not been thoroughly elucidated to date. This study investigated the role of H19 in PAH and its related mechanism. METHODS In the present study, SD rats, C57/BL6 mice and H19-/- mice were injected with monocrotaline (MCT) to establish a PAH model. H19 was detected in the cytokine-stimulated pulmonary arterial smooth muscle cells (PASMCs), serum and lungs of rats/mice. H19 overexpression and knockdown experiments were also conducted. A dual luciferase reporter assay was used to explore whether let-7b is a sponge miRNA of H19, and AT1R is a novel target of let-7b. A CCK-8 assay and flow cytometry were used to analyse cell proliferation. RESULTS The results showed that H19 was highly expressed in the serum and lungs of MCT-induced rats/mice, and H19 was upregulated by PDGF-BB in vitro. H19 upregulated AT1R expression via sponging miRNA let-7b following PDGF-BB stimulation. AT1R is a novel target of let-7b. Moreover, the overexpression of H19 and AT1R could facilitate PASMCs proliferation in vitro. H19 knockout protected mice from pulmonary artery remodeling and PAH following MCT treatment. CONCLUSION Our study showed that H19 is highly expressed in MCT-induced rodent lungs and upregulated by PDGF-BB. The H19-let-7b-AT1R axis contributed to the pathogenesis of PAH by stimulating PASMCs proliferation. The H19 knockout had a protective role in the development of PAH. H19 may be a potential tar-get for the treatment of PAH.
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Affiliation(s)
- Hua Su
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Xiaoling Xu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Chao Yan
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Yangfeng Shi
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Yanjie Hu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Liangliang Dong
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Songmin Ying
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Zhejiang, Hangzhou China
| | - Kejing Ying
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Ruifeng Zhang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
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Dhanoa JK, Sethi RS, Verma R, Arora JS, Mukhopadhyay CS. Long non-coding RNA: its evolutionary relics and biological implications in mammals: a review. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2018; 60:25. [PMID: 30386629 PMCID: PMC6201556 DOI: 10.1186/s40781-018-0183-7] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/05/2018] [Indexed: 02/08/2023]
Abstract
The central dogma of gene expression propounds that DNA is transcribed to mRNA and finally gets translated into protein. Only 2–3% of the genomic DNA is transcribed to protein-coding mRNA. Interestingly, only a further minuscule part of genomic DNA encodes for long non-coding RNAs (lncRNAs) which are characteristically more than 200 nucleotides long and can be transcribed from both protein-coding (e.g. H19 and TUG1) as well as non-coding DNA by RNA polymerase II. The lncRNAs do not have open reading frames (with some exceptions), 3`-untranslated regions (3’-UTRs) and necessarily these RNAs lack any translation-termination regions, however, these can be spliced, capped and polyadenylated as mRNA molecules. The flexibility of lncRNAs confers them specific 3D-conformations that eventually enable the lncRNAs to interact with proteins, DNA or other RNA molecules via base pairing or by forming networks. The lncRNAs play a major role in gene regulation, cell differentiation, cancer cell invasion and metastasis and chromatin remodeling. Deregulation of lncRNA is also responsible for numerous diseases in mammals. Various studies have revealed their significance as biomarkers for prognosis and diagnosis of cancer. The aim of this review is to overview the salient features, evolution, biogenesis and biological importance of these molecules in the mammalian system.
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Affiliation(s)
- Jasdeep Kaur Dhanoa
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Ram Saran Sethi
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Ramneek Verma
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Jaspreet Singh Arora
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Chandra Sekhar Mukhopadhyay
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
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Lu Q, Gong W, Wang J, Ji K, Sun X, Xu C, Du L, Wang Y, Liu Q. Analysis of changes to lncRNAs and their target mRNAs in murine jejunum after radiation treatment. J Cell Mol Med 2018; 22:6357-6367. [PMID: 30324649 PMCID: PMC6237565 DOI: 10.1111/jcmm.13940] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/08/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022] Open
Abstract
LncRNAs have been reported to play an important role in various diseases. However, their role in the radiation‐induced intestinal injury is unknown. The goal of the present study was to analyse the potential mechanistic role of lncRNAs in the radiation‐induced intestinal injury. Mice were divided into two groups: Control (non‐irradiated) and irradiated. Irradiated mice were administered 14 Gy of abdominal irradiation (ABI) and were assessed 3.5 days after irradiation. Changes to the jejuna of ABI mice were analysed using RNA‐Seq for alterations to both lncRNA and mRNA. These results were validated using qRT‐PCR. LncRNAs targets were predicted based on analysis of lncRNAs‐miRNAs‐mRNAs interaction. 29 007 lncRNAs and 17 142 mRNAs were detected in the two groups. At 3.5 days post‐irradiation, 91 lncRNAs and 57 lncRNAs were significantly up‐ and downregulated respectively. Similarly, 752 mRNAs and 400 mRNAs were significantly up‐ and downregulated respectively. qRT‐PCR was used to verify the altered expression of four lncRNAs (ENSMUST00000173070, AK157361, AK083183, AK038898) and four mRNAs (Mboat1, Nek10, Ccl24, Cyp2c55). Gene ontology and KEGG pathway analyses indicated the predicted genes were mainly involved in the VEGF signalling pathway. This study reveals that the expression of lncRNAs was altered in the jejuna of mice post‐irradiation. Moreover, it provides a resource for the study of lncRNAs in the radiation‐induced intestinal injury.
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Affiliation(s)
- Qianying Lu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Wei Gong
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Jinhan Wang
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Kaihua Ji
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Xiaohui Sun
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Chang Xu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Liqing Du
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Yan Wang
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Qiang Liu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
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Zhang X, Li DY, Reilly MP. Long intergenic noncoding RNAs in cardiovascular diseases: Challenges and strategies for physiological studies and translation. Atherosclerosis 2018; 281:180-188. [PMID: 30316538 DOI: 10.1016/j.atherosclerosis.2018.09.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/05/2018] [Accepted: 09/27/2018] [Indexed: 12/25/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as important mediators of many biological processes relevant to human pathophysiologies, including cardiovascular diseases. In vitro studies have provided important knowledge of cellular functions and mechanisms for an increasing number of lincRNAs. Dysregulated lncRNAs have been associated with cell fate programming and development, vascular diseases, atherosclerosis, dyslipidemia and metabolic syndrome, and cardiac pathological hypertrophy. However, functional interrogation of individual lincRNAs in physiological and disease states is largely limited. The complex nature of lincRNA actions and poor species conservation of human lincRNAs pose substantial challenges to physiological studies in animal model systems and in clinical translation. This review summarizes recent findings of specific lincRNA physiological studies, including MALAT1, MeXis, Lnc-DC and others, in the context of cardiovascular diseases, examines complex mechanisms of lincRNA actions, reviews in vivo research strategies to delineate lincRNA functions and highlights challenges and approaches for physiological studies of primate-specific lincRNAs.
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Affiliation(s)
- Xuan Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Daniel Y Li
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA; Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA.
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Geng H, Bu HF, Liu F, Wu L, Pfeifer K, Chou PM, Wang X, Sun J, Lu L, Pandey A, Bartolomei MS, De Plaen IG, Wang P, Yu J, Qian J, Tan XD. In Inflamed Intestinal Tissues and Epithelial Cells, Interleukin 22 Signaling Increases Expression of H19 Long Noncoding RNA, Which Promotes Mucosal Regeneration. Gastroenterology 2018; 155:144-155. [PMID: 29621481 PMCID: PMC6475625 DOI: 10.1053/j.gastro.2018.03.058] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/02/2018] [Accepted: 03/22/2018] [Indexed: 02/01/2023]
Abstract
BACKGROUND & AIMS Inflammation affects regeneration of the intestinal epithelia; long noncoding RNAs (lncRNAs) regulate cell functions, such as proliferation, differentiation, and migration. We investigated the mechanisms by which the lncRNA H19, imprinted maternally expressed transcript (H19) regulates regeneration of intestinal epithelium using cell cultures and mouse models of inflammation. METHODS We performed RNA-sequencing transcriptome analyses of intestinal tissues from mice with lipopolysaccharide (LPS)-induced sepsis to identify lncRNAs associated with inflammation; findings were confirmed by quantitative real-time polymerase chain reaction and in situ hybridization analyses of intestinal tissues from mice with sepsis or dextran sulfate sodium (DSS)-induced mucosal wound healing and patients with ulcerative colitis compared to healthy individuals (controls). We screened cytokines for their ability to induce expression of H19 in HT-29 cells and intestinal epithelial cells (IECs), and confirmed findings in crypt epithelial organoids derived from mouse small intestine. IECs were incubated with different signal transduction inhibitors and effects on H19 lncRNA levels were measured. We assessed intestinal epithelial proliferation or regeneration in H19ΔEx1/+ mice given LPS or DSS vs wild-type littermates (control mice). H19 was overexpressed in IECs using lentiviral vectors and cell proliferation was measured. We performed RNA antisense purification, RNA immunoprecipitation, and luciferase reporter assays to study functions of H19 in IECs. RESULTS In RNA-sequencing transcriptome analysis of lncRNA expression in intestinal tissues from mice, we found that levels of H19 lncRNA changed significantly with LPS exposure. Levels of H19 lncRNA increased in intestinal tissues of patients with ulcerative colitis, mice with LPS-induced and polymicrobial sepsis, or mice with DSS-induced colitis, compared with controls. Increased H19 lncRNA localized to epithelial cells in the intestine, regardless of Lgr5 messenger RNA expression. Exposure of IECs to interleukin 22 (IL22) increased levels of H19 lncRNA with time and dose, which required STAT3 and protein kinase A activity. IL22 induced expression of H19 in mouse intestinal epithelial organoids within 6 hours. Exposure to IL22 increased growth of intestinal epithelial organoids derived from control mice, but not H19ΔEx1/+ mice. Overexpression of H19 in HT-29 cells increased their proliferation. Intestinal mucosa healed more slowly after withdrawal of DSS from H19ΔEx1/+ mice vs control mice. Crypt epithelial cells from H19ΔEx1/+ mice proliferated more slowly than those from control mice after exposure to LPS. H19 lncRNA bound to p53 and microRNAs that inhibit cell proliferation, including microRNA 34a and let-7; H19 lncRNA binding blocked their function, leading to increased expression of genes that promote regeneration of the epithelium. CONCLUSIONS The level of lncRNA H19 is increased in inflamed intestinal tissues from mice and patients. The inflammatory cytokine IL22 induces expression of H19 in IECs, which is required for intestinal epithelial proliferation and mucosal healing. H19 lncRNA appears to inhibit p53 protein and microRNA 34a and let-7 to promote proliferation of IECs and epithelial regeneration.
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Affiliation(s)
- Hua Geng
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Heng-Fu Bu
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Fangyi Liu
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College, Beijing, People's Republic of China
| | - Longtao Wu
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Department of Surgery, University of Chicago, Chicago, Illinois
| | - Karl Pfeifer
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland
| | - Pauline M Chou
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Xiao Wang
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jiaren Sun
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Ashutosh Pandey
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Isabelle G De Plaen
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Peng Wang
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jindan Yu
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jiaming Qian
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College, Beijing, People's Republic of China
| | - Xiao-Di Tan
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
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Ren J, Ding L, Zhang D, Shi G, Xu Q, Shen S, Wang Y, Wang T, Hou Y. Carcinoma-associated fibroblasts promote the stemness and chemoresistance of colorectal cancer by transferring exosomal lncRNA H19. Theranostics 2018; 8:3932-3948. [PMID: 30083271 PMCID: PMC6071523 DOI: 10.7150/thno.25541] [Citation(s) in RCA: 486] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in the pathology of various tumors, including colorectal cancer (CRC). The crosstalk between carcinoma- associated fibroblasts (CAFs) and cancer cells in the tumor microenvironment promotes tumor development and confers chemoresistance. In this study, we further investigated the underlying tumor-promoting roles of CAFs and the molecular mediators involved in these processes. Methods: The AOM/DSS-induced colitis-associated cancer (CAC) mouse model was established, and RNA sequencing was performed. Small interfering RNA (siRNA) sequences were used to knock down H19. Cell apoptosis was measured by flow cytometry. SW480 cells with H19 stably knocked down were used to establish a xenograft model. The indicated protein levels in xenograft tumor tissues were confirmed by immunohistochemistry assay, and cell apoptosis was analyzed by TUNEL apoptosis assay. RNA-FISH and immunofluorescence assays were performed to assess the expression of H19 in tumor stroma and cancer nests. The AldeRed ALDH detection assay was performed to detect intracellular aldehyde dehydrogenase (ALDH) enzyme activity. Isolated exosomes were identified by transmission electron microscopy, nanoparticle tracking and Western blotting. Results: H19 was highly expressed in the tumor tissues of CAC mice compared with the expression in normal colon tissues. The up-regulation of H19 was also confirmed in CRC patient samples at different tumor node metastasis (TNM) stages. Moreover, H19 was associated with the stemness of colorectal cancer stem cells (CSCs) in CRC specimens. H19 promoted the stemness of CSCs and increased the frequency of tumor-initiating cells. RNA-FISH showed higher expression of H19 in tumor stroma than in cancer nests. Of note, H19 was enriched in CAF-derived conditioned medium and exosomes, which in turn promoted the stemness of CSCs and the chemoresistance of CRC cells in vitro and in vivo. Furthermore, H19 activated the β-catenin pathway via acting as a competing endogenous RNA sponge for miR-141 in CRC, while miR-141 significantly inhibited the stemness of CRC cells. Conclusion: CAFs promote the stemness and chemoresistance of CRC by transferring exosomal H19. H19 activated the β-catenin pathway via acting as a competing endogenous RNA sponge for miR-141, while miR-141 inhibited the stemness of CRC cells. Our findings indicate that H19 expressed by CAFs of the colorectal tumor stroma contributes to tumor development and chemoresistance.
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Mainieri A, Haig D. Lost in translation: The 3'-UTR of IGF1R as an ancient long noncoding RNA. EVOLUTION MEDICINE AND PUBLIC HEALTH 2018; 2018:82-91. [PMID: 29644076 PMCID: PMC5887972 DOI: 10.1093/emph/eoy008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/21/2018] [Indexed: 12/20/2022]
Abstract
Background and objectives The insulin-like growth factor (IGF) signaling system is a major arena of intragenomic conflict over embryonic growth between imprinted genes of maternal and paternal origin and the IGF type 1 receptor (IGF1R) promotes proliferation of many human cancers. The 3'-untranslated region (3'-UTR) of the mouse Igf1r mRNA is targeted by miR-675-3p derived from the imprinted H19 long noncoding RNA. We undertook a comparative sequence analysis of vertebrate IGF1R 3'-UTRs to determine the evolutionary history of miR-675 target sequences and to identify conserved features that are likely to be involved in post-transcriptional regulation of IGF1R translation. Methodology Sequences of IGF1R 3'-UTRs were obtained from public databases and analyzed using publicly available algorithms. Results A very long 3'-UTR is a conserved feature of vertebrate IGF1R mRNAs. We found that some ancient microRNAs, such as let-7 and mir-182, have predicted binding sites that are conserved between cartilaginous fish and mammals. One very conserved region is targeted by multiple, maternally expressed imprinted microRNAs that appear to have evolved more recently than the targeted sequences. Conclusions and implications The conserved structures we identify in the IGF1R 3'-UTR are strong candidates for regulating cell proliferation during development and carcinogenesis. These conserved structures are now targeted by multiple imprinted microRNAs. These observations emphasize the central importance of IGF signaling pathways in the mediation of intragenomic conflicts over embryonic growth and identify possible targets for therapeutic interventions in cancer.
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Affiliation(s)
- Avantika Mainieri
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Mechanistic Insight into Long Noncoding RNAs and the Placenta. Int J Mol Sci 2017; 18:ijms18071371. [PMID: 28653993 PMCID: PMC5535864 DOI: 10.3390/ijms18071371] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are classified as RNAs greater than 200 nucleotides in length that do not produce a protein product. lncRNAs are expressed with cellular and temporal specificity and have been shown to play a role in many cellular events, including the regulation of gene expression, post-transcriptional modifications and epigenetic modifications. Since lncRNAs were first discovered, there has been increasing evidence that they play important roles in the development and function of most organs, including the placenta. The placenta is an essential transient organ that facilitates communication and nutrient exchange between the mother and foetus. The placenta is of foetal origin and begins to form shortly after the embryo implants into the uterine wall. The placenta relies heavily on the successful differentiation and function of trophoblast cells, including invasion as well as the formation of the maternal/foetal interface. Here, we review the current literature surrounding the involvement of lncRNAs in the development and function of trophoblasts and the human placenta.
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A G-quadruplex structure at the 5' end of the H19 coding region regulates H19 transcription. Sci Rep 2017; 8:45815. [PMID: 28367967 PMCID: PMC5377947 DOI: 10.1038/srep45815] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/06/2017] [Indexed: 12/15/2022] Open
Abstract
The H19 gene, one of the best known imprinted genes, encodes a long non-coding RNA that regulates cell proliferation and differentiation. H19 RNA is widely expressed in embryonic tissues, but its expression is restricted in only a few tissues after birth. However, regulation of H19 gene expression remains poorly understood outside the context of genomic imprinting. Here we identified evolutionarily conserved guanine (G)-rich repeated motifs at the 5′ end of the H19 coding region that are consistent with theoretically deduced G-quadruplex sequences. Circular dichroism spectroscopy and electrophoretic mobility shift assays with G-quadruplex-specific ligands revealed that the G-rich motif, located immediately downstream of the transcription start site (TSS), forms a G-quadruplex structure in vitro. By using a series of mutant forms of H19 harboring deletion or G-to-A substitutions, we found that the H19-G-quadruplex regulates H19 gene expression. We further showed that transcription factors Sp1 and E2F1 were associated with the H19-G-quadruplex to either suppress or promote the H19 transcription, respectively. Moreover, H19 expression during differentiation of mouse embryonic stem cells appears to be regulated by a genomic H19 G-quadruplex. These results demonstrate that the G-quadruplex structure immediately downstream of the TSS functions as a novel regulatory element for H19 gene expression.
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Insights from Global Analyses of Long Noncoding RNAs in Breast Cancer. CURRENT PATHOBIOLOGY REPORTS 2017; 5:23-34. [PMID: 28616363 DOI: 10.1007/s40139-017-0122-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW The goal of this review was to compare and contrast the results and implications from several recent transcriptomic studies that analyzed the expression of lncRNAs in breast cancer. How many lncRNAs are dysregulated in breast cancer? Do dysregulated lncRNAs contribute to breast cancer etiology? Are lncRNAs viable biomarkers in breast cancer? RECENT FINDINGS Transcriptomic profiling of breast cancer tissues, mostly from The Cancer Genome Atlas, identified thousands of long noncoding RNAs that are expressed and dysregulated in breast cancer. The expression of lncRNAs alone can divide patients into molecular subtypes. Subsequent functional studies demonstrated that several of these lncRNAs have important roles in breast cancer cell biology. SUMMARY Thousands of lncRNAs are dysregulated in breast cancer that can be developed as biomarkers for prognostic or therapeutic purposes. The reviewed reports provide a roadmap to guide functional studies to discover lncRNAs with critical biological functions relating to breast cancer development and progression.
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Ohtsuka M, Ling H, Ivan C, Pichler M, Matsushita D, Goblirsch M, Stiegelbauer V, Shigeyasu K, Zhang X, Chen M, Vidhu F, Bartholomeusz GA, Toiyama Y, Kusunoki M, Doki Y, Mori M, Song S, Gunther JR, Krishnan S, Slaby O, Goel A, Ajani JA, Radovich M, Calin GA. H19 Noncoding RNA, an Independent Prognostic Factor, Regulates Essential Rb-E2F and CDK8-β-Catenin Signaling in Colorectal Cancer. EBioMedicine 2016; 13:113-124. [PMID: 27789274 PMCID: PMC5264449 DOI: 10.1016/j.ebiom.2016.10.026] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 02/06/2023] Open
Abstract
High H19 expression in primary tumors is an independent predictor of short overall survival in CRC patients. RB1-E2F and CDK8-β-catenin signaling are essential in mediating the oncogenic activity of H19 in CRC. Combined analysis of H19 and its targets further improved the prediction power on overall survival of CRC patients.
Long noncoding RNAs (lncRNAs) are transcripts at least 200 nucleotides long that do not code for proteins. The clinical relevance of lncRNAs in colorectal cancer (CRC) is largely unknown. Here we identified that H19 expression in primary tumors is an independent prognostic predictor of poor prognosis of CRC patients and further proved its oncogenic role. To characterize the mechanisms, we profiled gene expression changes following H19 modulation in CRC cell lines and analyzed gene expression association in clinical datasets. Our data revealed important cancer-signaling pathways, including the RB1-E2F and the CDK8-β-catenin signaling, underlying H19 function. The clinical significance of long noncoding RNAs (lncRNAs) in colorectal cancer (CRC) remains largely unexplored. Here, we analyzed a large panel of lncRNA candidates with The Cancer Genome Atlas (TCGA) CRC dataset, and identified H19 as the most significant lncRNA associated with CRC patient survival. We further validated such association in two independent CRC cohorts. H19 silencing blocked G1-S transition, reduced cell proliferation, and inhibited cell migration. We profiled gene expression changes to gain mechanism insight of H19 function. Transcriptome data analysis revealed not only previously identified mechanisms such as Let-7 regulation by H19, but also RB1-E2F1 function and β-catenin activity as essential upstream regulators mediating H19 function. Our experimental data showed that H19 affects phosphorylation of RB1 protein by regulating gene expression of CDK4 and CCND1. We further demonstrated that reduced CDK8 expression underlies changes of β-catenin activity, and identified that H19 interacts with macroH2A, an essential regulator of CDK8 gene transcription. However, the relevance of H19-macroH2A interaction in CDK8 regulation remains to be experimentally determined. We further explored the clinical relevance of above mechanisms in clinical samples, and showed that combined analysis of H19 with its targets improved prognostic value of H19 in CRC.
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Affiliation(s)
- Masahisa Ohtsuka
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Research Unit for non-coding RNA and genome editing, Division of Oncology, Medical University of Graz, Austria
| | - Daisuke Matsushita
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew Goblirsch
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Verena Stiegelbauer
- Research Unit for non-coding RNA and genome editing, Division of Oncology, Medical University of Graz, Austria
| | - Kunitoshi Shigeyasu
- Center for Gastrointestinal Research, Baylor Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Xinna Zhang
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Meng Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fnu Vidhu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Geoffrey A Bartholomeusz
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuji Toiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Masato Kusunoki
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jillian R Gunther
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sunil Krishnan
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ondrej Slaby
- Central European Institute of Technology, Molecular Oncology II, Masaryk University, Brno, Czech Republic
| | - Ajay Goel
- Center for Gastrointestinal Research, Baylor Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Milan Radovich
- Department of Surgery, Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Long Non-coding RNAs in the Cytoplasm. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:73-80. [PMID: 27163185 PMCID: PMC4880952 DOI: 10.1016/j.gpb.2016.03.005] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/03/2016] [Accepted: 03/02/2016] [Indexed: 12/11/2022]
Abstract
An enormous amount of long non-coding RNAs (lncRNAs) transcribed from eukaryotic genome are important regulators in different aspects of cellular events. Cytoplasm is the residence and the site of action for many lncRNAs. The cytoplasmic lncRNAs play indispensable roles with multiple molecular mechanisms in animal and human cells. In this review, we mainly talk about functions and the underlying mechanisms of lncRNAs in the cytoplasm. We highlight relatively well-studied examples of cytoplasmic lncRNAs for their roles in modulating mRNA stability, regulating mRNA translation, serving as competing endogenous RNAs, functioning as precursors of microRNAs, and mediating protein modifications. We also elaborate the perspectives of cytoplasmic lncRNA studies.
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Raveh E, Matouk IJ, Gilon M, Hochberg A. The H19 Long non-coding RNA in cancer initiation, progression and metastasis - a proposed unifying theory. Mol Cancer 2015; 14:184. [PMID: 26536864 PMCID: PMC4632688 DOI: 10.1186/s12943-015-0458-2] [Citation(s) in RCA: 398] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/20/2015] [Indexed: 02/07/2023] Open
Abstract
The imprinted oncofetal long non-coding RNA (lncRNA) H19 is expressed in the embryo, down-regulated at birth and then reappears in tumors. Its role in tumor initiation and progression has long been a subject of controversy, although accumulating data suggest that H19 is one of the major genes in cancer. It is actively involved in all stages of tumorigenesis and is expressed in almost every human cancer. In this review we delineate the various functions of H19 during the different stages in the complex process of tumor progression. H19 up-regulation allows cells to enter a "selfish" survival mode in response to stress conditions, such as destabilization of the genome and hypoxia, by accelerating their proliferation rate and increasing overall cellular resistance to stress. This response is tightly correlated with nullification, dysfunction or significant down-regulation of the master tumor suppressor gene P53. The growing evidence of H19's involvement in both proliferation and differentiation processes, together with its involvement in epithelial to mesenchymal transition (EMT) and also mesenchymal to epithelial transition (MET), has led us to conclude that some of the recent disputes and discrepancies arising from current research findings can be resolved from a viewpoint supporting the oncogenic properties of H19. According to a holistic approach, the versatile, seemingly contradictory functions of H19 are essential to, and differentially harnessed by, the tumor cell depending on its context within the process of tumor progression.
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Affiliation(s)
- Eli Raveh
- The Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Imad J Matouk
- The Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Michal Gilon
- The Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Abraham Hochberg
- The Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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Wu AM, Ni WF, Huang ZY, Li QL, Wu JB, Xu HZ, Yin LH. Analysis of differentially expressed lncRNAs in differentiation of bone marrow stem cells into neural cells. J Neurol Sci 2015; 351:160-167. [PMID: 25820029 DOI: 10.1016/j.jns.2015.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/11/2015] [Accepted: 03/05/2015] [Indexed: 12/24/2022]
Abstract
Many studies have reported micro RNAs involved in the differentiation of bone marrow mesenchymal stem cells (BMSCs) into neural cells; however, the roles of long non-coding RNAs (lncRNAs) in the differentiation of BMSCs into neural cells remain poorly understood. We used microarray assays to compare the lncRNA and messenger RNA (mRNA) expression profiles in BMSCs and neural-induced BMSCs. We found a total of 24 lncRNAs and 738 mRNAs that were upregulated and 32 lncRNAs and 682 mRNAs that were downregulated in samples induced for 3h; 27 lncRNAs and 864 mRNAs that were upregulated and 37 lncRNAs and 968 mRNAs that were downregulated in 6h samples; and 23 lncRNAs and 1159 mRNAs that were upregulated or downregulated in both the 3h and 6h samples. For 23 differentially lncRNAs and 83 differentially mRNAs, 256 matched lncRNA-mRNA pairs were found. GO (Gene ontology) analysis showed that these lncRNAs were associated with biological processes, cellular components, and molecular functions. Twenty-five pathways were identified by pathway analysis. Then, RT-qPCR validation of the differentially expressed H19, Esco2, Pcdhb18, and RGD1560277 genes confirmed the microarray data. Our study revealed the expression patterns of lncRNAs in the differentiation of BMSCs into neural cells, and many lncRNAs were differentially expressed in induced BMSCs, suggesting that they may play key roles in processes of differentiation. Our findings may promote the use of BMSCs to treat neurodegenerative diseases and trauma.
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Affiliation(s)
- Ai-Min Wu
- Laboratory of Internal Medicine, The First Affiliated Hospital of Wenzhou Medical University, 2# Fuxue Road, Wenzhou 325027, People's Republic of China; The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Wen-Fei Ni
- The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Zhe-Yu Huang
- The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Qing-Long Li
- The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Jian-Bo Wu
- Laboratory of Internal Medicine, The First Affiliated Hospital of Wenzhou Medical University, 2# Fuxue Road, Wenzhou 325027, People's Republic of China
| | - Hua-Zi Xu
- The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Li-Hui Yin
- Laboratory of Internal Medicine, The First Affiliated Hospital of Wenzhou Medical University, 2# Fuxue Road, Wenzhou 325027, People's Republic of China.
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Zhu M, Chen Q, Liu X, Sun Q, Zhao X, Deng R, Wang Y, Huang J, Xu M, Yan J, Yu J. lncRNA H19/miR-675 axis represses prostate cancer metastasis by targeting TGFBI. FEBS J 2014; 281:3766-75. [PMID: 24988946 DOI: 10.1111/febs.12902] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/24/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Abstract
Prostate cancer is a leading cause of cancer-related mortality in men worldwide and there is a lack of effective treatment options for advanced (metastatic) prostate cancer. Currently, limited knowledge is available concerning the role of long non-coding RNAs in prostate cancer metastasis. In this study, we found that long non-coding RNA H19 (H19) and H19-derived microRNA-675 (miR-675) were significantly downregulated in the metastatic prostate cancer cell line M12 compared with the non-metastatic prostate epithelial cell line P69. Upregulation of H19 in P69 and PC3 cells significantly increased the level of miR-675 and repressed cell migration; however, ectopic expression of H19 in M12 cells could not increase the level of miR-675 and therefore had no effect on cell migration. Furthermore, we found that the expression level of either H19 or miR-675 in P69 cells was negatively associated with the expression of transforming growth factor β induced protein (TGFBI), an extracellular matrix protein involved in cancer metastasis. Dual luciferase reporter assays showed that miR-675 directly bound with 3'UTR of TGFBI mRNA to repress its translation. Taken together, we show for the first time that the H19-miR-675 axis acts as a suppressor of prostate cancer metastasis, which may have possible diagnostic and therapeutic potential for advanced prostate cancer.
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Affiliation(s)
- Miaojun Zhu
- Department of Oncology, No. 3 People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, China; Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, China
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Frey WD, Kim J. APeg3: regulation of Peg3 through an evolutionarily conserved ncRNA. Gene 2014; 540:251-7. [PMID: 24582979 DOI: 10.1016/j.gene.2014.02.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/23/2014] [Accepted: 02/26/2014] [Indexed: 12/14/2022]
Abstract
Mammalian APeg3 is an antisense gene that is localized within the 3'-untranslated region of the imprinted gene, Peg3. APeg3 is expressed only in the vasopressinergic neurons of the hypothalamus, thus is predicted to play significant roles in this specific area of the brain. In the current study, we investigate the functions of APeg3 with comparative genomics and cell line-based functional approaches. The transcribed region of APeg3 displays high levels of sequence conservation among placental mammals, but without any obvious open reading frame, suggesting that APeg3 may have been selected as a ncRNA gene during eutherian evolution. This has been further supported by the detection of a conserved local RNA secondary structure within APeg3. RNA secondary structure analyses indicate a single conserved hairpin-loop structure towards the 5' end of the transcript. The results from cell line-based transfection experiments demonstrate that APeg3 has the potential to down-regulate the transcription and protein levels of Peg3. The observed down-regulation by APeg3 is also somewhat orientation-independent. Overall, these results suggest that APeg3 has evolved as a ncRNA gene and controls the function of its sense gene Peg3 within specific neuronal cells.
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Affiliation(s)
- Wesley D Frey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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Dey BK, Pfeifer K, Dutta A. The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration. Genes Dev 2014; 28:491-501. [PMID: 24532688 PMCID: PMC3950346 DOI: 10.1101/gad.234419.113] [Citation(s) in RCA: 388] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The H19 long noncoding RNA is repressed after birth, except in skeletal muscle. Dey et al. discover that H19 exon1 encodes miR-675-3p and miR-675-5p. The inhibition of myogenesis by H19 depletion is rescued by expression of miR-675-3p and miR-675-5p. The abnormal skeletal muscle regeneration in H19-deficient mice is rectified by reintroducing miR-675-3p and miR-675-5p. These miRs target the anti-differentiation Smad transcription factors and the DNA replication initiation factor Cdc6. In summary, H19 gives rise to microRNAs to promote skeletal muscle differentiation and regeneration. Regulated expression of the H19 long noncoding RNA gene has been well characterized as a paradigm for genomic imprinting, but the H19 RNA's biological function remains largely unclear. H19 is abundantly expressed maternally in embryonic tissues but is strongly repressed after birth, and significant transcription persists only in skeletal muscle. Thus, we examined the role of the H19 RNA in skeletal muscle differentiation and regeneration. Knockdown of H19 RNA in myoblast cells and H19 knockout mouse satellite cells decreases differentiation. H19 exon1 encodes two conserved microRNAs, miR-675-3p and miR-675-5p, both of which are induced during skeletal muscle differentiation. The inhibition of myogenesis by H19 depletion during myoblast differentiation is rescued by exogenous expression of miR-675-3p and miR-675-5p. H19-deficient mice display abnormal skeletal muscle regeneration after injury, which is rectified by reintroduction of miR-675-3p and miR-675-5p. miR-675-3p and miR-675-5p function by directly targeting and down-regulating the anti-differentiation Smad transcription factors critical for the bone morphogenetic protein (BMP) pathway and the DNA replication initiation factor Cdc6. Therefore, the H19 long noncoding RNA has a critical trans-regulatory function in skeletal muscle differentiation and regeneration that is mediated by the microRNAs encoded within H19.
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Affiliation(s)
- Bijan K Dey
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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Long non-coding RNA H19 promotes glioma cell invasion by deriving miR-675. PLoS One 2014; 9:e86295. [PMID: 24466011 PMCID: PMC3900504 DOI: 10.1371/journal.pone.0086295] [Citation(s) in RCA: 242] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/13/2013] [Indexed: 12/21/2022] Open
Abstract
H19 RNA has been characterized as an oncogenic long non-coding RNA (lncRNA) in breast and colon cancer. However, the role and function of lncRNA H19 in glioma development remain unclear. In this study, we identified that H19/miR-675 signaling was critical for glioma progression. By analyzing glioma gene expression data sets, we found increased H19 in high grade gliomas. H19 depletion via siRNA inhibited invasion in glioma cells. Further, we found H19 positively correlated with its derivate miR-675 expression and reduction of H19 inhibited miR-675 expression. Bioinformatics and luciferase reporter assays showed that miR-675 modulated Cadherin 13 expression by directly targeting the binding site within the 3′ UTR. Finally, introduction of miR-675 abrogated H19 knockdown-induced cell invasion inhibition in glioma cells. To our knowledge, it is first time to demonstrate that H19 regulates glioma development by deriving miR-675 and provide important clues for understanding the key roles of lncRNA-miRNA functional network in glioma.
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Fuke T, Mizuno S, Nagai T, Hasegawa T, Horikawa R, Miyoshi Y, Muroya K, Kondoh T, Numakura C, Sato S, Nakabayashi K, Tayama C, Hata K, Sano S, Matsubara K, Kagami M, Yamazawa K, Ogata T. Molecular and clinical studies in 138 Japanese patients with Silver-Russell syndrome. PLoS One 2013; 8:e60105. [PMID: 23533668 PMCID: PMC3606247 DOI: 10.1371/journal.pone.0060105] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 02/21/2013] [Indexed: 12/22/2022] Open
Abstract
Background Recent studies have revealed relative frequency and characteristic phenotype of two major causative factors for Silver-Russell syndrome (SRS), i.e. epimutation of the H19-differentially methylated region (DMR) and uniparental maternal disomy 7 (upd(7)mat), as well as multilocus methylation abnormalities and positive correlation between methylation index and body and placental sizes in H19-DMR epimutation. Furthermore, rare genomic alterations have been found in a few of patients with idiopathic SRS. Here, we performed molecular and clinical findings in 138 Japanese SRS patients, and examined these matters. Methodology/Principal Findings We identified H19-DMR epimutation in cases 1–43 (group 1), upd(7)mat in cases 44–52 (group 2), and neither H19-DMR epimutation nor upd(7)mat in cases 53–138 (group 3). Multilocus analysis revealed hyper- or hypomethylated DMRs in 2.4% of examined DMRs in group 1; in particular, an extremely hypomethylated ARHI-DMR was identified in case 13. Oligonucleotide array comparative genomic hybridization identified a ∼3.86 Mb deletion at chromosome 17q24 in case 73. Epigenotype-phenotype analysis revealed that group 1 had more reduced birth length and weight, more preserved birth occipitofrontal circumference (OFC), more frequent body asymmetry and brachydactyly, and less frequent speech delay than group 2. The degree of placental hypoplasia was similar between the two groups. In group 1, the methylation index for the H19-DMR was positively correlated with birth length and weight, present height and weight, and placental weight, but with neither birth nor present OFC. Conclusions/Significance The results are grossly consistent with the previously reported data, although the frequency of epimutations is lower in the Japanese SRS patients than in the Western European SRS patients. Furthermore, the results provide useful information regarding placental hypoplasia in SRS, clinical phenotypes of the hypomethylated ARHI-DMR, and underlying causative factors for idiopathic SRS.
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Affiliation(s)
- Tomoko Fuke
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Aichi, Japan
| | - Toshiro Nagai
- Department of Pediatrics, Dokkyo Medical University Koshigaya Hospital, Saitama, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism, National Center for Child Health and Development, Tokyo, Japan
| | - Yoko Miyoshi
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Koji Muroya
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Tatsuro Kondoh
- Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Isahaya, Japan
| | - Chikahiko Numakura
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Seiji Sato
- Department of Pediatrics, Saitama Municipal Hospital, Saitama, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shinichiro Sano
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuki Yamazawa
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
- * E-mail:
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Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, Lehmann J, Missal K, Mosig A, Müller B, Prohaska SJ, Stadler BMR, Stadler PF, Tanzer A, Washietl S, Witwer C. Evolutionary patterns of non-coding RNAs. Theory Biosci 2012; 123:301-69. [PMID: 18202870 DOI: 10.1016/j.thbio.2005.01.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Accepted: 01/24/2005] [Indexed: 01/04/2023]
Abstract
A plethora of new functions of non-coding RNAs (ncRNAs) have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this "Modern RNA World" and its components. In this contribution, we attempt to provide at least a cursory overview of the diversity of ncRNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates and study the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA (miRNA) family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution of miRNAs in metazoans, which suggests an explosive increase in the miRNA repertoire in vertebrates. The analysis of the transcription of ncRNAs suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from introns of a mRNA) can change on evolutionary time scales. The let-7 family demonstrates, that even the mode of transcription (as intron or as exon) can change among paralogous ncRNA.
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Mitra SA, Mitra AP, Triche TJ. A central role for long non-coding RNA in cancer. Front Genet 2012; 3:17. [PMID: 22363342 PMCID: PMC3279698 DOI: 10.3389/fgene.2012.00017] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 01/28/2012] [Indexed: 01/29/2023] Open
Abstract
Long non-coding RNAs (ncRNAs) have been shown to regulate important biological processes that support normal cellular functions. Aberrant regulation of these essential functions can promote tumor development. In this review, we underscore the importance of the regulatory role played by this distinct class of ncRNAs in cancer-associated pathways that govern mechanisms such as cell growth, invasion, and metastasis. We also highlight the possibility of using these unique RNAs as diagnostic and prognostic biomarkers in malignancies.
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Affiliation(s)
- Sheetal A Mitra
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles Los Angeles, CA, USA
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A nucleolar protein, H19 opposite tumor suppressor (HOTS), is a tumor growth inhibitor encoded by a human imprinted H19 antisense transcript. Proc Natl Acad Sci U S A 2011; 108:16759-64. [PMID: 21940503 DOI: 10.1073/pnas.1110904108] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The H19 gene, which localizes within a chromosomal region on human chromosome 11p15 that is commonly lost in Wilms tumor (WT), encodes an imprinted untranslated RNA. However, the biological significance of the H19 noncoding transcript remains unresolved because replacement of the RNA transcript with a neocassette has no obvious phenotypic effect. Here we show that the human H19 locus also encodes a maternally expressed, translated gene, antisense to the known H19 transcript, which is conserved in primates. This gene, termed HOTS for H19 opposite tumor suppressor, encodes a protein that localizes to the nucleus and nucleolus and that interacts with the human enhancer of rudimentary homolog (ERH) protein. WTs that show loss of heterozygosity of 11p15 or loss of imprinting of IGF2 also silence HOTS (7/7 and 10/10, respectively). Overexpression of HOTS inhibits Wilms, rhabdoid, rhabdomyosarcoma, and choriocarcinoma tumor cell growth, and silencing HOTS by RNAi increases in vitro colony formation and in vivo tumor growth. These results demonstrate that the human H19 locus harbors an imprinted gene encoding a tumor suppressor protein within the long-sought WT2 locus.
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Gabory A, Ripoche MA, Le Digarcher A, Watrin F, Ziyyat A, Forné T, Jammes H, Ainscough JFX, Surani MA, Journot L, Dandolo L. H19 acts as a trans regulator of the imprinted gene network controlling growth in mice. Development 2009; 136:3413-21. [PMID: 19762426 DOI: 10.1242/dev.036061] [Citation(s) in RCA: 266] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The imprinted H19 gene produces a non-coding RNA of unknown function. Mice lacking H19 show an overgrowth phenotype, due to a cis effect of the H19 locus on the adjacent Igf2 gene. To explore the function of the RNA itself, we produced transgenic mice overexpressing H19. We observed postnatal growth reduction in two independent transgenic lines and detected a decrease of Igf2 expression in embryos. An extensive analysis of several other genes from the newly described imprinted gene network (IGN) was performed in both loss- and gain-of-function animals. We found that H19 deletion leads to the upregulation of several genes of the IGN. This overexpression is restored to the wild-type level by transgenic expression of H19. We therefore propose that the H19 gene participates as a trans regulator in the fine-tuning of this IGN in the mouse embryo. This is the first in vivo evidence of a functional role for the H19 RNA. Our results also bring further experimental evidence for the existence of the IGN and open new perspectives in the comprehension of the role of genomic imprinting in embryonic growth and in human imprinting pathologies.
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Affiliation(s)
- Anne Gabory
- Genetics and Development Department, Inserm U567, CNRS UMR 8104, University of Paris Descartes, Institut Cochin, Paris, France
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Abstract
Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.
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Yamazawa K, Kagami M, Fukami M, Matsubara K, Ogata T. Monozygotic female twins discordant for Silver-Russell syndrome and hypomethylation of the H19-DMR. J Hum Genet 2008; 53:950-955. [PMID: 18709478 DOI: 10.1007/s10038-008-0329-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 07/14/2008] [Indexed: 01/09/2023]
Abstract
Silver-Russell syndrome (SRS) is characterized by growth failure and dysmorphic features, and is frequently caused by hypomethylation of the paternally derived H19-DMR (epimutation). We observed 5 8/12-year-old female twins discordant for SRS. One twin exhibited SRS-compatible features, such as pre- and postnatal growth failure, relative macrocephaly, triangular face, left hemihypotrophy, and bilateral fifth finger clinodactyly, whereas the other twin showed apparently normal phenotype. Microsatellite analysis for 26 loci on multiple chromosomes showed monozygosity. Methylation analysis for the H19-DMR indicated epimutation in roughly half of cells in the affected twin and normal patterns in the unaffected twin and the parents. X-inactivation analysis revealed random X-inactivation with a nearly identical pattern between the twins. The discordant methylation pattern of the H19-DMR may primarily be due to a failure to maintain the DNA methyltransferase-1-dependent methylation imprint around the pre-implantation S phase, because such failure would result in the production of two different cell clones, one with normally methylated DMR and the other with demethylated DMR, leading to the separation of cells with different characters and resultant twinning.
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Affiliation(s)
- Kazuki Yamazawa
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.
- Department of Pediatrics, Keio University School of Medicine, Tokyo, 160-8582, Japan.
| | - Masayo Kagami
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Keiko Matsubara
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
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50
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Molecular and clinical findings and their correlations in Silver-Russell syndrome: implications for a positive role of IGF2 in growth determination and differential imprinting regulation of the IGF2–H19 domain in bodies and placentas. J Mol Med (Berl) 2008; 86:1171-81. [DOI: 10.1007/s00109-008-0377-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 05/08/2008] [Accepted: 05/30/2008] [Indexed: 01/15/2023]
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