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Zhang S, Wang R, Zhu X, Zhang L, Liu X, Sun L. Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy. iScience 2023; 26:108494. [PMID: 38125016 PMCID: PMC10730892 DOI: 10.1016/j.isci.2023.108494] [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: 07/02/2023] [Revised: 09/28/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Aneuploidy can globally affect the expression of the whole genome, which is detrimental to organisms. Dosage-sensitive regulators usually have multiple intermolecular interactions, and changes in their stoichiometry are responsible for the dysregulation of the regulatory network. Currently, studies on noncoding genes in aneuploidy are relatively rare. We studied the characteristics and expression profiles of long noncoding RNAs (lncRNAs) and transposable elements (TEs) in aneuploid Drosophila. It is found that lncRNAs and TEs are affected by genomic imbalance and appear to be more sensitive to an inverse dosage effect than mRNAs. Several dosage-sensitive lncRNAs and TEs were detected for their expression patterns during embryogenesis, and their biological functions in the ovary and testes were investigated using tissue-specific RNAi. This study advances our understanding of the noncoding sequences in imbalanced genomes and provides a novel perspective for the study of aneuploidy-related human diseases such as cancer.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xilin Zhu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
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2
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Bresnahan ST, Lee E, Clark L, Ma R, Rangel J, Grozinger CM, Li-Byarlay H. Examining parent-of-origin effects on transcription and RNA methylation in mediating aggressive behavior in honey bees (Apis mellifera). BMC Genomics 2023; 24:315. [PMID: 37308882 DOI: 10.1186/s12864-023-09411-4] [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: 02/23/2023] [Accepted: 05/27/2023] [Indexed: 06/14/2023] Open
Abstract
Conflict between genes inherited from the mother (matrigenes) and the father (patrigenes) is predicted to arise during social interactions among offspring if these genes are not evenly distributed among offspring genotypes. This intragenomic conflict drives parent-specific transcription patterns in offspring resulting from parent-specific epigenetic modifications. Previous tests of the kinship theory of intragenomic conflict in honey bees (Apis mellifera) provided evidence in support of theoretical predictions for variation in worker reproduction, which is associated with extreme variation in morphology and behavior. However, more subtle behaviors - such as aggression - have not been extensively studied. Additionally, the canonical epigenetic mark (DNA methylation) associated with parent-specific transcription in plant and mammalian model species does not appear to play the same role as in honey bees, and thus the molecular mechanisms underlying intragenomic conflict in this species is an open area of investigation. Here, we examined the role of intragenomic conflict in shaping aggression in honey bee workers through a reciprocal cross design and Oxford Nanopore direct RNA sequencing. We attempted to probe the underlying regulatory basis of this conflict through analyses of parent-specific RNA m6A and alternative splicing patterns. We report evidence that intragenomic conflict occurs in the context of honey bee aggression, with increased paternal and maternal allele-biased transcription in aggressive compared to non-aggressive bees, and higher paternal allele-biased transcription overall. However, we found no evidence to suggest that RNA m6A or alternative splicing mediate intragenomic conflict in this species.
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Affiliation(s)
- Sean T Bresnahan
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA.
| | - Ellen Lee
- Agricultural Research and Development Program, Central State University, Wilberforce, USA
- Department of Biological Sciences, Wright State University, Dayton, USA
| | - Lindsay Clark
- HPCBio, University of Illinois at Urbana-Champaign, Champaign, USA
- Research Scientific Computing Group, Seattle Children's Research Institute, Seattle, USA
| | - Rong Ma
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA
| | - Juliana Rangel
- Department of Entomology, Texas A&M University, College Station, USA
| | - Christina M Grozinger
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA
| | - Hongmei Li-Byarlay
- Agricultural Research and Development Program, Central State University, Wilberforce, USA.
- Department of Agricultural and Life Science, Central State University, Wilberforce, USA.
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3
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Liu T, Zhuang XX, Qin XJ, Wei LB, Gao JR. The potential role of N6-methyladenosine modification of LncRNAs in contributing to the pathogenesis of chronic glomerulonephritis. Inflamm Res 2023; 72:623-638. [PMID: 36700958 DOI: 10.1007/s00011-023-01695-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Increasing evidence indicates that N6-methyladenosine (m6A) modification of mRNAs has been shown to play a critical role in the occurrence and development of many diseases, while little is known about m6A modification in long non-coding RNAs (LncRNAs). Our study aims to investigate the potential functions of LncRNA m6A modifications in lipopolysaccharide (LPS)-induced mouse mesangial cells (MMCs), providing us with a new perspective on the molecular mechanisms of chronic glomerulonephritis (CGN) pathogenesis. METHODS Differentially methylated LncRNAs were identified by Methylated RNA immunoprecipitation sequencing (MeRIP-seq). LncRNA-mRNA and LncRNA-associated LncRNA-miRNA-mRNA (CeRNA) networks were constructed by bioinformatics analysis. Furthermore, we utilized gene ontology (GO) and pathway enrichment analyses (KEGG) to explore target genes from co-expression networks. In addition, the total level of m6A RNA methylation and expression of methyltransferase and pro-inflammatory cytokines were detected by the colorimetric quantification method and western blot, respectively. Cell viability and cell cycle stage were detected by cell counting kit-8 (CCK-8) and flow cytometry. RESULTS In total, 1141 differentially m6A-methylated LncRNAs, including 529 hypermethylated LncRNAs and 612 hypomethylated LncRNAs, were determined by MeRIP-seq. The results of GO and KEGG analysis revealed that the target mRNAs were mainly enriched in signal pathways, such as the NF-kappa B signaling pathway, MAPK signaling pathway, Toll-like receptor signaling pathway, and apoptosis signaling pathway. In addition, higher METTL3 expression was found in CGN kidney tissues using the GEO database. METTL3 knockdown in MMC cells drastically reduced the levels of m6A RNA methylation, pro-inflammatory cytokines IL6 and TNF-α, and inhibited cell proliferation and cycle progression. CONCLUSIONS Our findings provide a basis and novel insight for further investigations of m6A modifications in LncRNAs for the pathogenesis of CGN.
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Affiliation(s)
- Tao Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230011, Anhui, China
| | - Xing Xing Zhuang
- Department of Pharmacy, Chaohu Hospital of Anhui Medical University, Chaohu, 238000, Anhui, China
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230011, Anhui, China
| | - Xiu Juan Qin
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China
| | - Liang Bing Wei
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China
| | - Jia Rong Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.
- Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230031, Anhui, China.
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4
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Chen J, Lin J, Hu Y, Ye M, Yao L, Wu L, Zhang W, Wang M, Deng T, Guo F, Huang Y, Zhu B, Wang D. RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction. Nucleic Acids Res 2022; 51:D1397-D1404. [PMID: 36134718 PMCID: PMC9825423 DOI: 10.1093/nar/gkac814] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 02/06/2023] Open
Abstract
Numerous studies have shown that RNA plays an important role in the occurrence and development of diseases, and RNA-disease associations are not limited to noncoding RNAs in mammals but also exist for protein-coding RNAs. Furthermore, RNA-associated diseases are found across species including plants and nonmammals. To better analyze diseases at the RNA level and facilitate researchers in exploring the pathogenic mechanism of diseases, we decided to update and change MNDR v3.0 to RNADisease v4.0, a repository for RNA-disease association (http://www.rnadisease.org/ or http://www.rna-society.org/mndr/). Compared to the previous version, new features include: (i) expanded data sources and categories of species, RNA types, and diseases; (ii) the addition of a comprehensive analysis of RNAs from thousands of high-throughput sequencing data of cancer samples and normal samples; (iii) the addition of an RNA-disease enrichment tool and (iv) the addition of four RNA-disease prediction tools. In summary, RNADisease v4.0 provides a comprehensive and concise data resource of RNA-disease associations which contains a total of 3 428 058 RNA-disease entries covering 18 RNA types, 117 species and 4090 diseases to meet the needs of biological research and lay the foundation for future therapeutic applications of diseases.
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Affiliation(s)
| | | | | | | | | | - Le Wu
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wenhai Zhang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Meiyi Wang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tingting Deng
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Feng Guo
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yan Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bofeng Zhu
- Correspondence may also be addressed to Bofeng Zhu. Tel: +86 20 61648787; Fax: +86 20 61648787;
| | - Dong Wang
- To whom correspondence should be addressed. Tel: +86 20 61648279; Fax: +86 20 61648279;
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5
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The HBV Specially-Related Long Noncoding RNA HBV-SRL Involved in the Pathogenesis of Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:9034105. [PMID: 35847364 PMCID: PMC9286890 DOI: 10.1155/2022/9034105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022]
Abstract
Hepatitis B virus (HBV) is one of the major risk factors for HCC (hepatocellular carcinoma) occurrence with a diverse role in the pathogenesis of HCC. More works need to be performed to elucidate a more thorough understanding of the molecular mechanisms involving in HBV-induced HCC, although some mechanisms such as genome integration have been reported. In the present study, aberrantly expressed lncRNAs were identified between HCC tumor tissues with or without HBV infection. Among these molecules, HBV specially-related long noncoding RNA (HBV-SRL) was further found to correlate with poor prognosis and a shorter overall survival time in HCC patients with HBV infection. Additionally, HBV-SRL was found function as oncogene by upregulating the NF-κB2 expression. These data suggest that HBV infection altered gene expression pattern in liver cells which contributed to HBV-related HCC development, and HBV-SRL may serve as a new molecular marker or potential therapeutic target of HBV-related HCC.
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Du Y, Zhang P, Liu W, Tian J. Optical Imaging of Epigenetic Modifications in Cancer: A Systematic Review. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:88-101. [PMID: 36939779 PMCID: PMC9590553 DOI: 10.1007/s43657-021-00041-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023]
Abstract
Increasing evidence has demonstrated that abnormal epigenetic modifications are strongly related to cancer initiation. Thus, sensitive and specific detection of epigenetic modifications could markedly improve biological investigations and cancer precision medicine. A rapid development of molecular imaging approaches for the diagnosis and prognosis of cancer has been observed during the past few years. Various biomarkers unique to epigenetic modifications and targeted imaging probes have been characterized and used to discriminate cancer from healthy tissues, as well as evaluate therapeutic responses. In this study, we summarize the latest studies associated with optical molecular imaging of epigenetic modification targets, such as those involving DNA methylation, histone modification, noncoding RNA regulation, and chromosome remodeling, and further review their clinical application on cancer diagnosis and treatment. Lastly, we further propose the future directions for precision imaging of epigenetic modification in cancer. Supported by promising clinical and preclinical studies associated with optical molecular imaging technology and epigenetic drugs, the central role of epigenetics in cancer should be increasingly recognized and accepted.
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Affiliation(s)
- Yang Du
- grid.9227.e0000000119573309CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190 China
- grid.410726.60000 0004 1797 8419The University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Pei Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190 China
- grid.412474.00000 0001 0027 0586Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Supportive Care Center and Day Oncology Unit, Peking University Cancer Hospital and Institute, Beijing, 100142 China
| | - Wei Liu
- grid.412474.00000 0001 0027 0586Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Supportive Care Center and Day Oncology Unit, Peking University Cancer Hospital and Institute, Beijing, 100142 China
| | - Jie Tian
- grid.9227.e0000000119573309CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190 China
- grid.64939.310000 0000 9999 1211Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine, Beihang University, Beijing, 100191 China
- grid.440736.20000 0001 0707 115XSchool of Life Science and Technology, Xidian University, Xi’an, 710071 Shaanxi China
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7
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Camilleri-Robles C, Amador R, Klein CC, Guigó R, Corominas M, Ruiz-Romero M. Genomic and functional conservation of lncRNAs: lessons from flies. Mamm Genome 2022; 33:328-342. [PMID: 35098341 PMCID: PMC9114055 DOI: 10.1007/s00335-021-09939-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022]
Abstract
Over the last decade, the increasing interest in long non-coding RNAs (lncRNAs) has led to the discovery of these transcripts in multiple organisms. LncRNAs tend to be specifically, and often lowly, expressed in certain tissues, cell types and biological contexts. Although lncRNAs participate in the regulation of a wide variety of biological processes, including development and disease, most of their functions and mechanisms of action remain unknown. Poor conservation of the DNA sequences encoding for these transcripts makes the identification of lncRNAs orthologues among different species very challenging, especially between evolutionarily distant species such as flies and humans or mice. However, the functions of lncRNAs are unexpectedly preserved among different species supporting the idea that conservation occurs beyond DNA sequences and reinforcing the potential of characterising lncRNAs in animal models. In this review, we describe the features and roles of lncRNAs in the fruit fly Drosophila melanogaster, focusing on genomic and functional comparisons with human and mouse lncRNAs. We also discuss the current state of advances and limitations in the study of lncRNA conservation and future perspectives.
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8
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Relationship between Expression of Plasma lncRNA-HEIH and Prognosis in Patients with Coronary Artery Disease. DISEASE MARKERS 2022; 2021:5662080. [PMID: 35003390 PMCID: PMC8741405 DOI: 10.1155/2021/5662080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 11/18/2022]
Abstract
Objective We aimed to investigate the expression of long noncoding RNA- (lncRNA-) HEIH in patients with coronary artery disease (CAD) and its impact on patients' prognosis. Patients and Methods. From July 2015 to December 2018, 250 patients who underwent coronary angiography, including 50 in the control group and 150 in the CAD group, were collected for detection of the expression of lncRNA-HEIH by real-time quantitative polymerase chain reaction (qPCR). The severity of CAD was evaluated through SYNTAX scoring system. In addition, these patients with CAD were followed up for 3 years, and the major cardiac adverse events such as myocardial infarction and revascularization were recorded. Results The expression of lncRNA-HEIH in plasma of patients with CAD was remarkably higher than that in the control subjects and was verified to be relevant to the severity of CAD. Meanwhile, it was found that CAD patients with high expression of lncRNA-HEIH had higher rates of dyslipidemia as well as CAD family history and higher overall incidence of major cardiac adverse events than those with low expression of lncRNA-HEIH. Conclusions lncRNA-HEIH expression is upregulated in the plasma of CAD patients, which is capable of affecting the prognosis of patients.
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Rogoyski O, Gerber AP. RNA-binding proteins modulate drug sensitivity of cancer cells. Emerg Top Life Sci 2021; 5:681-685. [PMID: 34328175 PMCID: PMC8726047 DOI: 10.1042/etls20210193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/16/2022]
Abstract
As our understanding of the complex network of regulatory pathways for gene expression continues to grow, avenues of investigation for how these new findings can be utilised in therapeutics are emerging. The recent growth of interest in the RNA binding protein (RBP) interactome has revealed it to be rich in targets linked to, and causative of diseases. While this is, in and of itself, very interesting, evidence is also beginning to arise for how the RBP interactome can act to modulate the response of diseases to existing therapeutic treatments, especially in cancers. Here we highlight this topic, providing examples of work that exemplifies such modulation of chemotherapeutic sensitivity.
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Affiliation(s)
- Oliver Rogoyski
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, U.K
| | - André P. Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, U.K
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10
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Tamgue O, Mezajou CF, Ngongang NN, Kameni C, Ngum JA, Simo USF, Tatang FJ, Akami M, Ngono AN. Non-Coding RNAs in the Etiology and Control of Major and Neglected Human Tropical Diseases. Front Immunol 2021; 12:703936. [PMID: 34737736 PMCID: PMC8560798 DOI: 10.3389/fimmu.2021.703936] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs) including microRNAs (miRs) and long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in immune cells development and function. Their expression is altered in different physiological and disease conditions, hence making them attractive targets for the understanding of disease etiology and the development of adjunctive control strategies, especially within the current context of mitigated success of control measures deployed to eradicate these diseases. In this review, we summarize our current understanding of the role of ncRNAs in the etiology and control of major human tropical diseases including tuberculosis, HIV/AIDS and malaria, as well as neglected tropical diseases including leishmaniasis, African trypanosomiasis and leprosy. We highlight that several ncRNAs are involved at different stages of development of these diseases, for example miR-26-5p, miR-132-3p, miR-155-5p, miR-29-3p, miR-21-5p, miR-27b-3p, miR-99b-5p, miR-125-5p, miR-146a-5p, miR-223-3p, miR-20b-5p, miR-142-3p, miR-27a-5p, miR-144-5p, miR-889-5p and miR-582-5p in tuberculosis; miR-873, MALAT1, HEAL, LINC01426, LINC00173, NEAT1, NRON, GAS5 and lincRNA-p21 in HIV/AIDS; miR-451a, miR-let-7b and miR-106b in malaria; miR-210, miR-30A-5P, miR-294, miR-721 and lncRNA 7SL RNA in leishmaniasis; and miR-21, miR-181a, miR-146a in leprosy. We further report that several ncRNAs were investigated as diseases biomarkers and a number of them showed good potential for disease diagnosis, including miR-769-5p, miR-320a, miR-22-3p, miR-423-5p, miR-17-5p, miR-20b-5p and lncRNA LOC152742 in tuberculosis; miR-146b-5p, miR-223, miR-150, miR-16, miR-191 and lncRNA NEAT1 in HIV/AIDS; miR-451 and miR-16 in malaria; miR-361-3p, miR-193b, miR-671, lncRNA 7SL in leishmaniasis; miR-101, miR-196b, miR-27b and miR-29c in leprosy. Furthermore, some ncRNAs have emerged as potential therapeutic targets, some of which include lncRNAs NEAT1, NEAT2 and lnr6RNA, 152742 in tuberculosis; MALAT1, HEAL, SAF, lincRNA-p21, NEAT1, GAS5, NRON, LINC00173 in HIV/AIDS; miRNA-146a in malaria. Finally, miR-135 and miR-126 were proposed as potential targets for the development of therapeutic vaccine against leishmaniasis. We also identify and discuss knowledge gaps that warrant for increased research work. These include investigation of the role of ncRNAs in the etiology of African trypanosomiasis and the assessment of the diagnostic potential of ncRNAs for malaria, and African trypanosomiasis. The potential targeting of ncRNAs for adjunctive therapy against tuberculosis, leishmaniasis, African trypanosomiasis and leprosy, as well as their targeting in vaccine development against tuberculosis, HIV/AIDS, malaria, African trypanosomiasis and leprosy are also new avenues to explore.
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Affiliation(s)
- Ousman Tamgue
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | | | | | - Charleine Kameni
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Jubilate Afuoti Ngum
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | | | - Fabrice Junior Tatang
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Mazarin Akami
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Annie Ngane Ngono
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
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11
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Zhou H, Ni J, Wu S, Ma F, Jin P, Li S. lncRNA-CR46018 positively regulates the Drosophila Toll immune response by interacting with Dif/Dorsal. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 124:104183. [PMID: 34174242 DOI: 10.1016/j.dci.2021.104183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
The Toll signaling pathway is highly conserved from insects to mammals. Drosophila is a model species that is commonly used to study innate immunity. Although many studies have assessed protein-coding genes that regulate the Toll pathway, it is unclear whether long noncoding RNAs (lncRNAs) play regulatory roles in the Toll pathway. Here, we evaluated the expression of the lncRNA CR46018 in Drosophila. Our results showed that this lncRNA was significantly overexpressed after infection of Drosophila with Micrococcus luteus. A CR46018-overexpressing Drosophila strain was then constructed; we expected that CR46018 overexpression would enhance the expression of various antimicrobial peptides downstream of the Toll pathway, regardless of infection with M. luteus. RNA-seq analysis of CR46018-overexpressing Drosophila after infection with M. luteus showed that upregulated genes were mainly enriched in Toll and Imd signaling pathways. Moreover, bioinformatics predictions and RNA-immunoprecipitation experiments showed that CR46018 interacted with the transcription factors Dif and Dorsal to enhance the Toll pathway. During gram-positive bacterial infection, flies overexpressing CR46018 showed favorable survival compared with flies in the control group. Overall, our current work not only reveals a new immune regulatory factor, lncRNA-CR46018, and explores its potential regulatory model, but also provides a new perspective for the effect of immune disorders on the survival of Drosophila melanogaster.
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Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, PR China.
| | - Jiajia Ni
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, PR China.
| | - Shanshan Wu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, PR China.
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, PR China.
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, PR China.
| | - Shengjie Li
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Byproduct Resource Utilization, School of Food Science, Nanjing Xiaozhuang University, Nanjing, 211171, PR China.
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12
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Jiang H, Lou P, Chen X, Wu C, Shao S. Deregulation of lncRNA HIST1H2AG-6 and AIM1-3 in peripheral blood mononuclear cells is associated with newly diagnosed type 2 diabetes. BMC Med Genomics 2021; 14:149. [PMID: 34092238 PMCID: PMC8182924 DOI: 10.1186/s12920-021-00994-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) is mainly affected by genetic and environmental factors; however, the correlation of long noncoding RNAs (lncRNAs) with T2DM remains largely unknown. Methods Microarray analysis was performed to identify the differentially expressed lncRNAs and messenger RNAs (mRNAs) in patients with T2DM and healthy controls, and the expression of two candidate lncRNAs (lnc-HIST1H2AG-6 and lnc-AIM1-3) were further validated using quantitative real-time polymerase chain reaction (qRT-PCR). Spearman’s rank correlation coefficient was used to measure the degree of association between the two candidate lncRNAs and differentially expressed mRNAs. Furthermore, the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and GO (Gene Ontology) enrichment analysis were used to reveal the biological functions of the two candidate lncRNAs. Additionally, multivariate logistic regression analysis and receiver operating characteristic (ROC) curve analysis were performed. Results The microarray analysis revealed that there were 55 lncRNAs and 36 mRNAs differentially expressed in patients with T2DM compared with healthy controls. Notably, lnc-HIST1H2AG-6 was significantly upregulated and lnc-AIM1-3 was significantly downregulated in patients with T2DM, which was validated in a large-scale qRT-PCR examination (90 controls and 100 patients with T2DM). Spearman’s rank correlation coefficient revealed that both lncRNAs were correlated with 36 differentially expressed mRNAs. Furthermore, functional enrichment (KEGG and GO) analysis demonstrated that the two lncRNA-related mRNAs might be involved in multiple biological functions, including cell programmed death, negative regulation of insulin receptor signal, and starch and sucrose metabolism. Multivariate logistic regression analysis revealed that lnc-HIST1H2AG-6 and lnc-AIM1-3 were significantly correlated with T2DM (OR = 5.791 and 0.071, respectively, both P = 0.000). Furthermore, the ROC curve showed that the expression of lnc-HIST1H2AG-6 and lnc-AIM1-3 might be used to differentiate patients with T2DM from healthy controls (area under the ROC curve = 0.664 and 0.769, respectively). Conclusion The profiles of lncRNA and mRNA were significantly changed in patients with T2DM. The expression levels of lnc-HIST1H2AG-6 and lnc-AIM1-3 genes were significantly correlated with some features of T2DM, which may be used to distinguish patients with T2DM from healthy controls and may serve as potential novel biomarkers for diagnosis in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00994-z.
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Affiliation(s)
- Hui Jiang
- Department of Endocrinology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, China
| | - Peian Lou
- Xuzhou Center for Disease Control Prevention, Xuzhou, 221000, China
| | - Xiaoluo Chen
- Department of Endocrinology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, China
| | - Chenguang Wu
- Department of Endocrinology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, China
| | - Shihe Shao
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China.
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13
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Vitorino R, Guedes S, Amado F, Santos M, Akimitsu N. The role of micropeptides in biology. Cell Mol Life Sci 2021; 78:3285-3298. [PMID: 33507325 PMCID: PMC11073438 DOI: 10.1007/s00018-020-03740-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022]
Abstract
Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance has been demonstrated. This review discusses different types of micropeptides as well as methods to identify them, such as computational approaches, ribosome profiling, and mass spectrometry.
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Affiliation(s)
- Rui Vitorino
- Departamento de Cirurgia E Fisiologia, Faculdade de Medicina da Universidade Do Porto, UnIC, Porto, Portugal.
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal.
| | - Sofia Guedes
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manuel Santos
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal
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14
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Barshir R, Fishilevich S, Iny-Stein T, Zelig O, Mazor Y, Guan-Golan Y, Safran M, Lancet D. GeneCaRNA: A Comprehensive Gene-centric Database of Human Non-coding RNAs in the GeneCards Suite. J Mol Biol 2021; 433:166913. [PMID: 33676929 DOI: 10.1016/j.jmb.2021.166913] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/14/2021] [Accepted: 02/25/2021] [Indexed: 12/20/2022]
Abstract
Non-coding RNA (ncRNA) genes assume increasing biological importance, with growing associations with diseases. Many ncRNA sources are transcript-centric, but for non-coding variant analysis and disease decipherment it is essential to transform this information into a comprehensive set of genome-mapped ncRNA genes. We present GeneCaRNA, a new all-inclusive gene-centric ncRNA database within the GeneCards Suite. GeneCaRNA information is integrated from four community-backed data structures: the major transcript database RNAcentral with its 20 encompassed databases, and the ncRNA entries of three major gene resources HGNC, Ensembl and NCBI Gene. GeneCaRNA presents 219,587 ncRNA gene pages, a 7-fold increase from those available in our three gene mining sources. Each ncRNA gene has wide-ranging annotation, mined from >100 worldwide sources, providing a powerful GeneCards-leveraged search. The latter empowers VarElect, our disease-gene interpretation tool, allowing one to systematically decipher ncRNA variants. The combined power of GeneCaRNA with GeneHancer, our regulatory elements database, facilitates wide-ranging scrutiny of the non-coding terra incognita of gene networks and whole genome analyses.
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Affiliation(s)
- Ruth Barshir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Tsippi Iny-Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Ofer Zelig
- LifeMap Sciences Inc., Alameda, CA 94501, USA.
| | - Yaron Mazor
- LifeMap Sciences Inc., Alameda, CA 94501, USA.
| | | | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
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15
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Zhou X, He J, Chen J, Cui Y, Ou Z, Zu X, Liu N. Silencing of MEG3 attenuated the role of lipopolysaccharides by modulating the miR-93-5p/PTEN pathway in Leydig cells. Reprod Biol Endocrinol 2021; 19:33. [PMID: 33639974 PMCID: PMC7913434 DOI: 10.1186/s12958-021-00712-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/11/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Leydig cells reflect the activation of inflammation, decrease of androgen production, inhibition of cell growth and promotion of cell apoptosis under orchitis. Maternally expressed gene 3 (MEG3) exerts a crucial role in various human diseases, but under orchitis, the role and underlying molecular mechanism of MEG3 in Leydig cells remain unclear. METHODS Lipofectamine 2000 was used for the cell transfections. qPCR and western blots assay were applied to assess the gene expression. ELISA assay was used to measure the TNFα, IL6 and testosterone secretion. CCK8 and EdU assay was employ to test the cell viability and proliferation respectively. Luciferase reporter and RIP assay were introduced to detect the binding of miR-93-5p with MEG3 and PTEN. RESULTS Lipopolysaccharides (LPS) induced TNFα and IL6 secretion, lowered testosterone production, inhibited cell viability and proliferation, and induced cell apoptosis in Leydig cells. MEG3 was upregulated in Leydig cells treated with LPS and that knockdown of MEG3 inhibited the role of LPS in Leydig cells. MEG3 absorbed miR-93-5p and that suppression of miR-93-5p restored the role of silenced MEG3 in Leydig cells under LPS treatment. miR-93-5p inhibited PTEN expression and that over-expressed PTEN alleviated the effect of miR-93-5p in Leydig cells treated with LPS. LPS activated the MEG3/miR-93-5p/PTEN signalling pathway in Leydig cells. CONCLUSIONS This study revealed that MEG3 serves as a molecular sponge to absorb miR-93-5p, thus leading to elevation of PTEN expression in Leydig cells under LPS treatment, offering a theoretical basis on which to establish potential new treatment strategies for orchitis.
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Affiliation(s)
- Xu Zhou
- Reproductive Medicine Center, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Jingliang He
- Reproductive Medicine Center, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Yu Cui
- Department of Urology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Zhenyu Ou
- Department of Urology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
| | - Nenghui Liu
- Reproductive Medicine Center, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
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16
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Ding XB, Jin J, Tao YT, Guo WP, Ruan L, Yang QL, Chen PC, Yao H, Zhang HB, Chen X. Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5756140. [PMID: 32103267 DOI: 10.1093/database/baaa005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/03/2019] [Accepted: 01/13/2020] [Indexed: 12/14/2022]
Abstract
Drosophila melanogaster is a well-established model organism that is widely used in genetic studies. This species enjoys the availability of a wide range of research tools, well-annotated reference databases and highly similar gene circuitry to other insects. To facilitate molecular mechanism studies in Drosophila, we present the Predicted Drosophila Interactome Resource (PDIR), a database of high-quality predicted functional gene interactions. These interactions were inferred from evidence in 10 public databases providing information for functional gene interactions from diverse perspectives. The current version of PDIR includes 102 835 putative functional associations with balanced sensitivity and specificity, which are expected to cover 22.56% of all Drosophila protein interactions. This set of functional interactions is a good reference for hypothesis formulation in molecular mechanism studies. At the same time, these interactions also serve as a high-quality reference interactome for gene set linkage analysis (GSLA), which is a web tool for the interpretation of the potential functional impacts of a set of changed genes observed in transcriptomics analyses. In a case study, we show that the PDIR/GSLA system was able to produce a more comprehensive and concise interpretation of the collective functional impact of multiple simultaneously changed genes compared with the widely used gene set annotation tools, including PANTHER and David. PDIR and its associated GSLA service can be accessed at http://drosophila.biomedtzc.cn.
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Affiliation(s)
- Xiao-Bao Ding
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China
| | - Jie Jin
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China
| | - Yu-Tian Tao
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China
| | - Wen-Ping Guo
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China
| | - Li Ruan
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China
| | - Qiao-Lei Yang
- Institute of Pharmaceutical Biotechnology and the First Affiliated Hospital Department of Radiation Oncology, Zhejiang University School of Medicine, 866 Yuhantang Rd, Hangzhou 310058, China
| | - Peng-Cheng Chen
- Institute of Pharmaceutical Biotechnology and the First Affiliated Hospital Department of Radiation Oncology, Zhejiang University School of Medicine, 866 Yuhantang Rd, Hangzhou 310058, China
| | - Heng Yao
- Institute of Pharmaceutical Biotechnology and the First Affiliated Hospital Department of Radiation Oncology, Zhejiang University School of Medicine, 866 Yuhantang Rd, Hangzhou 310058, China
| | - Hai-Bo Zhang
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China
| | - Xin Chen
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China.,Institute of Pharmaceutical Biotechnology and the First Affiliated Hospital Department of Radiation Oncology, Zhejiang University School of Medicine, 866 Yuhantang Rd, Hangzhou 310058, China.,Joint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, 866 Yuhantang Rd, Hangzhou 310058, China
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17
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Ning L, Cui T, Zheng B, Wang N, Luo J, Yang B, Du M, Cheng J, Dou Y, Wang D. MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation. Nucleic Acids Res 2021; 49:D160-D164. [PMID: 32833025 PMCID: PMC7779040 DOI: 10.1093/nar/gkaa707] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Many studies have indicated that non-coding RNA (ncRNA) dysfunction is closely related to numerous diseases. Recently, accumulated ncRNA-disease associations have made related databases insufficient to meet the demands of biomedical research. The constant updating of ncRNA-disease resources has become essential. Here, we have updated the mammal ncRNA-disease repository (MNDR, http://www.rna-society.org/mndr/) to version 3.0, containing more than one million entries, four-fold increment in data compared to the previous version. Experimental and predicted circRNA-disease associations have been integrated, increasing the number of categories of ncRNAs to five, and the number of mammalian species to 11. Moreover, ncRNA-disease related drug annotations and associations, as well as ncRNA subcellular localizations and interactions, were added. In addition, three ncRNA-disease (miRNA/lncRNA/circRNA) prediction tools were provided, and the website was also optimized, making it more practical and user-friendly. In summary, MNDR v3.0 will be a valuable resource for the investigation of disease mechanisms and clinical treatment strategies.
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Affiliation(s)
- Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Boyang Zheng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Nuo Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Beilei Yang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Mengze Du
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, B24 Yinquan South Road, Qingyuan 511518, Guangdong Province, People's Republic of China
| | - Jun Cheng
- Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital)
| | - Yiying Dou
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
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18
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Qin C, Jin L, Li J, Zha W, Ding H, Liu X, Zhu X. Long Noncoding RNA LINC02163 Accelerates Malignant Tumor Behaviors in Breast Cancer by Regulating the MicroRNA-511-3p/HMGA2 Axis. Oncol Res 2020; 28:483-495. [PMID: 32571448 PMCID: PMC7751230 DOI: 10.3727/096504020x15928179818438] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Long intergenic nonprotein-coding RNA 02163 (LINC02163) has been reported to be upregulated and work as an oncogene in gastric cancer. The aims of the present study were to determine the expression profile and clinical value of LINC02163 in breast cancer. Additionally, the detailed functions of LINC02163 in breast cancer were explored, and relevant molecular events were elucidated. In this study, LINC02163 was upregulated in breast cancer, and its expression level was closely associated with tumor size, lymph node metastasis, and TNM stage. Patients with breast cancer presenting high LINC02163 expression exhibited shorter overall survival than those presenting low LINC02163 expression. Knockdown of LINC02163 resulted in a decrease in breast cancer cell proliferation, migration, and invasion and an increase in cell apoptosis in vitro. In addition, silencing of LINC02163 impeded breast cancer tumor growth in vivo. Mechanistic investigation revealed that LINC02163 served as a competing endogenous RNA for microRNA-511-3p (miR-511-3p) and consequently upregulated the expression of the high-mobility group A2 (HMGA2), a downstream target of miR-511-3p. Intriguingly, miR-511-3p inhibition and HMGA2 restoration counteracted the effects of LINC02163 deficiency on the malignant properties of breast cancer cells. LINC02163 exerts cancer-promoting effects during the initiation and progression of breast cancer via regulation of the miR-511-3p/HMGA2 axis. Our findings add to our understanding of the roles of the LINC02163/miR-511-3p/HMGA2 pathway as a regulator of breast cancer pathogenesis and may be useful in the development of lncRNA-directed cancer diagnosis, prognosis, and therapy.
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Affiliation(s)
- Chenglin Qin
- *Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
- †Department of General Surgery, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng City No. 1 People’s Hospital, Yancheng, Jiangsu, P.R. China
| | - Linfang Jin
- *Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
- ‡Department of Pathology, Affiliated Hospital of Jiangnan University (Wuxi Fourth People’s Hospital), Wuxi, Jiangsu, P.R. China
| | - Jia Li
- *Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
- §Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, P.R. China
| | - Wenzhang Zha
- †Department of General Surgery, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng City No. 1 People’s Hospital, Yancheng, Jiangsu, P.R. China
| | - Huiming Ding
- †Department of General Surgery, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng City No. 1 People’s Hospital, Yancheng, Jiangsu, P.R. China
| | - Xiaorong Liu
- *Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
- ¶Department of General Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, P.R. China
| | - Xun Zhu
- *Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
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Ravi P, Singh SP, Kang JW, Tran S, Dasari RR, So PTC, Liepmann D, Katti K, Katti D, Renugopalakrishnan V, Paulmurugan R. Spectrochemical Probing of MicroRNA Duplex Using Spontaneous Raman Spectroscopy for Biosensing Applications. Anal Chem 2020; 92:14423-14431. [PMID: 32985868 DOI: 10.1021/acs.analchem.0c02401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MicroRNAs are emerging as both diagnostic and therapeutic targets in different human pathologies. An accurate understanding of the structural dependency of microRNAs for their biological functions is essential for designing synthetic oligos with various base and linkage modifications that can transform into highly sensitive diagnostic devices and therapeutic molecules. In this proof-of-principle study, we have utilized label-free spontaneous Raman spectroscopy to understand the structural differences in sense and antisense microRNA-21 by hybridizing them with complementary RNA and DNA oligos. Overall, the results suggest that the changes in the Raman band at 785 cm-1 originating from the phosphodiester bond of the nucleic acid backbone, linking 5' phosphate of the nucleic acid with 3' OH of the other nucleotide, can serve as a marker to identify these structural variations. Our results support the application of Raman spectroscopy in discerning intramolecular (ssRNA and ssDNA) and intermolecular (RNA-RNA, RNA-DNA, and DNA-DNA hybrids) interactions of nucleic acids. This is potentially useful for developing biosensors to quantify microRNAs in clinical samples and to design therapeutic microRNAs with robust functionality.
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Affiliation(s)
- Preetham Ravi
- Center for Engineered Cancer Testbeds, and Department of Civil and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58108, United States.,Department of Chemistry, Northeastern University, Boston, Massachusetts 02115, United States.,Boston Children's Hospital, Boston, Massachusetts 02115, United States.,Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Surya Pratap Singh
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka 580011, India
| | - Jeon Woong Kang
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sarah Tran
- Cellular Pathway Imaging Laboratory (CPIL), Department of Radiology, Stanford University School of Medicine, 3155 Porter Drive, Suite 2236, Palo Alto, California 94304, United States
| | - Ramachandra R Dasari
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Peter T C So
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Dorian Liepmann
- Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Kalpana Katti
- Center for Engineered Cancer Testbeds, and Department of Civil and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Dinesh Katti
- Center for Engineered Cancer Testbeds, and Department of Civil and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Venkatesan Renugopalakrishnan
- Department of Chemistry, Northeastern University, Boston, Massachusetts 02115, United States.,Boston Children's Hospital, Boston, Massachusetts 02115, United States.,Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ramasamy Paulmurugan
- Cellular Pathway Imaging Laboratory (CPIL), Department of Radiology, Stanford University School of Medicine, 3155 Porter Drive, Suite 2236, Palo Alto, California 94304, United States
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Wang X, Bai X, Yan Z, Guo X, Zhang Y. The lncRNA TUG1 promotes cell growth and migration in colorectal cancer via the TUG1-miR-145-5p-TRPC6 pathway. Biochem Cell Biol 2020; 99:249-260. [PMID: 32985219 DOI: 10.1139/bcb-2020-0017] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Colorectal cancer (CRC) is the third-most prevalent malignant tumor. Taurine upregulated gene 1 (TUG1), a long non-coding RNA (lncRNA), is reportedly involved in the physiological and pathological processes of CRC. However, the role of TUG1 in the progression of CRC and its underlying mechanisms are largely unknown. Here, we measured the expression of TUG1 in clinical samples from CRC patients and found that the expression level of TUG1 was higher in CRC tissues compared with the normal adjacent tissues. We then performed knockdown of TUG1 with siRNAs in two CRC cell lines and found that TUG1 knockdown inhibited the viability, proliferation, and migration of CRC cells, and reduced the ability of CRC cells to form subcutaneous tumors. Furthermore, we discovered that TUG1 affects the cellular processes in CRC cells by sponging miR-145-5p. We further found that miR-145-5p inhibits the expression of the protein-encoding gene Transient Receptor Potential Cation Channel Subfamily C Member 6 (TRPC6), and that overexpression of TRPC6 restored the inhibitory role of miR-145-5p in CRC cells. In conclusion, we have demonstrated that TUG1 exerts its role by modulating the TUG1-miR-145-5p-TRPC6 regulatory axis, thus revealing a novel molecular mechanism for the effects of TUG1 in the progression of CRC. Our data indicate that the TUG1-miR-145-5p-TRPC6 signaling pathway could serve as a target for the diagnosis and treatment of CRC.
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Affiliation(s)
- Xiaoqiang Wang
- Lanzhou University Second Hospital; Lanzhou University Second Clinical Medical College, China
| | - Xiaomin Bai
- Lanzhou University Second Hospital; Lanzhou University Second Clinical Medical College, China
| | - Zhonghui Yan
- Lanzhou University Second Hospital; Lanzhou University Second Clinical Medical College, China
| | - Xinyu Guo
- Lanzhou University Second Hospital; Lanzhou University Second Clinical Medical College, China
| | - Youcheng Zhang
- Department of General Surgery, Lanzhou University Second Hospital; Lanzhou University Second Clinical Medical College, Lanzhou, Gansu, China
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21
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Chen C, Zong M, Lu Y, Guo Y, Lv H, Xie L, Fu Z, Cheng Y, Si Y, Ye B, Fan L. Differentially expressed lnc-NOS2P3-miR-939-5p axis in chronic heart failure inhibits myocardial and endothelial cells apoptosis via iNOS/TNFα pathway. J Cell Mol Med 2020; 24:11381-11396. [PMID: 32844595 PMCID: PMC7576245 DOI: 10.1111/jcmm.15740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 07/06/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022] Open
Abstract
Inflammatory cytokine‐induced cell apoptosis is important for initiation and progression of chronic heart failure (CHF). Non‐coding RNAs, including long non‐coding RNAs and microRNAs, have emerged as critical regulators of this pathological process. The role in regulating inflammation and induction to cell apoptosis in CHF is not well understood. This study found CHF patients had elevated serum miR‐939‐5p, with greater increase in New York Heart Association (NYHA) I‐II patients than in NYHA III‐IV. Moreover, miR‐939‐5p was positively correlated with B‐type natriuretic peptide (BNP) in NYHA III‐IV patients, while not in NYHA I‐II. Further study showed miR‐939‐5p mimics promoted cell proliferation and inhibited inflammatory cytokine‐induced apoptosis of HUVECs and H9C2, while inhibition of endogenous miR‐939‐5p produced the opposite effects. Induced nitric oxide synthase (iNOS) and tumour necrosis factor α (TNFα) were identified as target genes of miR‐939‐5p. Additionally, lncRNA‐NOS2P3 acted as an endogenous sponge RNA to inhibit miR‐939‐5p expression, regulate the expression of iNOS/TNFα and control inflammation‐induced cells apoptosis. These suggest that CHF patients exhibited elevated serum miR‐939‐5p level especially in NYHA I‐II grades. And lnc‐NOS2P3‐miR‐939‐5p‐iNOS/TNFα pathway regulated inflammatory cytokine‐induced endothelial and myocardial cells apoptosis and provided a promising strategy for diagnosis and treatment of CHF.
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Affiliation(s)
- Cuncun Chen
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ming Zong
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ying Lu
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yide Guo
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Honggen Lv
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lihong Xie
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhiyan Fu
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yu Cheng
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuying Si
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bei Ye
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lieying Fan
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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22
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Tsurumi A, Li WX. Aging mechanisms-A perspective mostly from Drosophila. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10026. [PMID: 36619249 PMCID: PMC9744567 DOI: 10.1002/ggn2.10026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 01/11/2023]
Abstract
A mechanistic understanding of the natural aging process, which is distinct from aging-related disease mechanisms, is essential for developing interventions to extend lifespan or healthspan. Here, we discuss current trends in aging research and address conceptual and experimental challenges in the field. We examine various molecular markers implicated in aging with an emphasis on the role of heterochromatin and epigenetic changes. Studies in model organisms have been advantageous in elucidating conserved genetic and epigenetic mechanisms and assessing interventions that affect aging. We highlight the use of Drosophila, which allows controlled studies for evaluating genetic and environmental contributors to aging conveniently. Finally, we propose the use of novel methodologies and future strategies using Drosophila in aging research.
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Affiliation(s)
- Amy Tsurumi
- Department of SurgeryMassachusetts General Hospital, and Harvard Medical SchoolBostonMassachusettsUSA,Department of Microbiology and ImmunologyHarvard Medical SchoolBostonMassachusettsUSA,Shriners Hospitals for Children‐Boston®BostonMassachusettsUSA
| | - Willis X. Li
- Department of MedicineUniversity of California at San DiegoLa JollaCaliforniaUSA
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23
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Everett LJ, Huang W, Zhou S, Carbone MA, Lyman RF, Arya GH, Geisz MS, Ma J, Morgante F, St Armour G, Turlapati L, Anholt RRH, Mackay TFC. Gene expression networks in the Drosophila Genetic Reference Panel. Genome Res 2020; 30:485-496. [PMID: 32144088 PMCID: PMC7111517 DOI: 10.1101/gr.257592.119] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/28/2020] [Indexed: 01/02/2023]
Abstract
A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. This question is best addressed in a genetic mapping population in which all molecular polymorphisms are known and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable elements, and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, as well as genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses.
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Affiliation(s)
- Logan J Everett
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Wen Huang
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Shanshan Zhou
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Mary Anna Carbone
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Richard F Lyman
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Gunjan H Arya
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Matthew S Geisz
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA.,University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27516, USA
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, JiangXi Agricultural University, JiangXi, China
| | - Fabio Morgante
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Genevieve St Armour
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Lavanya Turlapati
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Robert R H Anholt
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Trudy F C Mackay
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
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Li X, Cao Q, Wang Y, Wang Y. Retracted Article: LncRNA OIP5-AS1 contributes to ox-LDL-induced inflammation and oxidative stress through regulating the miR-128-3p/CDKN2A axis in macrophages. RSC Adv 2019; 9:41709-41719. [PMID: 35541591 PMCID: PMC9076472 DOI: 10.1039/c9ra08322g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/02/2019] [Indexed: 12/22/2022] Open
Abstract
Long non-coding RNA OIP5-AS1 (lncRNA OIP5-AS1) and microRNA-128-3p (miRNA-128-3p) have been reported to play significant roles in human diseases. However, their role in atherosclerosis (AS) has been less studied. The aim of this research was to reveal the roles and functional mechanisms of OIP5-AS1 and miRNA-128-3p in AS development. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot assays were performed to detect gene expression. Cell proliferation and apoptosis were assessed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and flow cytometry analysis, respectively. In addition, ELISA was employed to determine the levels of interleukin (IL)-6, IL-1β, and tumor necrosis factor (TNF)-α. Oxidative stress was examined using a relevant kit. Furthermore, the interaction between miR-128-3p and OIP5-AS1 or cyclin-dependent kinase inhibitor 2A (CDKN2A) was predicted using StarBase, and then confirmed using the dual-luciferase reporter assay or the RNA immunoprecipitation (RIP) assay. We found that OIP5-AS1 and CDKN2A levels were upregulated and the miR-128-3p level was downregulated in oxidized low-density lipoprotein (ox-LDL)-induced THP1 cells. OIP5-AS1 knockdown weakened the regulatory effect of ox-LDL on cell progression. Interestingly, OIP5-AS1 directly interacted with miR-128-3p and miR-128-3p-targeted CDKN2A. Furthermore, OIP5-AS1 regulated ox-LDL-induced cell progression through modulating miR-128-3p expression, and miR-128-3p exerted its influence by modulating the CDKN2A level. Finally, we confirmed that OIP5-AS1 suppressed miR-128-3p expression to increase the level of CDKN2A. In conclusion, our findings demonstrate that OIP5-AS1 knockdown repressed the effect of ox-LDL on cell progression through regulating the miR-128-3p/CDKN2A axis, providing a potential target for the treatment of AS.
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Affiliation(s)
- Xiaojuan Li
- Department of Central Sterile Supply, The First Affiliated Hospital of Henan University of Science and Technology No. 24, Jinghua Road Luoyang 471003 China +86-0379-64830544
| | - Quansheng Cao
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Henan University of Science and Technology Luoyang China
| | - Yanyu Wang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Henan University of Science and Technology Luoyang China
| | - Yongsheng Wang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Henan University of Science and Technology Luoyang China
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25
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Insights into the Functions of LncRNAs in Drosophila. Int J Mol Sci 2019; 20:ijms20184646. [PMID: 31546813 PMCID: PMC6770079 DOI: 10.3390/ijms20184646] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs longer than 200 nucleotides (nt). LncRNAs have high spatiotemporal specificity, and secondary structures have been preserved throughout evolution. They have been implicated in a range of biological processes and diseases and are emerging as key regulators of gene expression at the epigenetic, transcriptional, and post-transcriptional levels. Comparative analyses of lncRNA functions among multiple organisms have suggested that some of their mechanisms seem to be conserved. Transcriptome studies have found that some Drosophila lncRNAs have highly specific expression patterns in embryos, nerves, and gonads. In vivo studies of lncRNAs have revealed that dysregulated expression of lncRNAs in Drosophila may result in impaired embryo development, impaired neurological and gonadal functions, and poor stress resistance. In this review, we summarize the epigenetic, transcriptional, and post-transcriptional mechanisms of lncRNAs and mainly focus on recent insights into the transcriptome studies and biological functions of lncRNAs in Drosophila.
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26
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Murillo-Maldonado JM, Riesgo-Escovar JR. The various and shared roles of lncRNAs during development. Dev Dyn 2019; 248:1059-1069. [PMID: 31454122 DOI: 10.1002/dvdy.108] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 01/03/2023] Open
Abstract
lncRNAs, genes transcribed but not translated, longer than 200 nucleotides, are classified as a separate class of nonprotein coding genes. Since their discovery, largely from RNAseq data, a number of pioneer studies have begun to unravel its myriad functions, centered on gene expression regulation, suggesting developmental and evolutionary conservation. Since they do not code for proteins and have no open reading frames, their functional constraints likely differ from that of protein coding genes, or of genes where the majority of the nucleotide sequence is required for function, like tRNAs. This has complicated assessment of both developmental and evolutionary conservation, and the identification of homologs in different species. Here we argue that other characteristics: general synteny and particular chromosomal placement regardless of sequence, sequence micro-motifs, and secondary structure allow for "homologs" to be identified and compared, confirming developmental and evolutionary conservation of lncRNAs. We conclude exemplifying a case in point: that of the evolutionarily conserved lncRNA acal, characterized and required for embryogenesis in Drosophila.
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Affiliation(s)
- Juan M Murillo-Maldonado
- Developmental Neurobiology and Neurophysiology, Instituto de Neurobología, Campus UNAM Juriquilla, Universidad Nacional Autónoma de Mexico, Santiago de Querétaro, Querétaro, Mexico
| | - Juan R Riesgo-Escovar
- Developmental Neurobiology and Neurophysiology, Instituto de Neurobología, Campus UNAM Juriquilla, Universidad Nacional Autónoma de Mexico, Santiago de Querétaro, Querétaro, Mexico
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27
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Lü S, Liu Y, Cui J, Yang B, Li G, Guo Y, Kuang H, Wang Q. Mechanism of Caulophyllum robustum Maxim against rheumatoid arthritis using LncRNA-mRNA chip analysis. Gene 2019; 722:144105. [PMID: 31521702 DOI: 10.1016/j.gene.2019.144105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Caulophyllum robustum Maxim (CRM) is a medicinal compound of the Northeast and is commonly used in China for the treatment of rheumatic pain and rheumatoid arthritis (RA). A preliminary study found that CRM has good anti-inflammatory, analgesic and immunosuppressive effects. However, the specific links and targets for its function remain unclear. Our study aimed to provide a mechanism for the action of Caulophyllum robustum Maxim extraction (CRME) against RA and to establish a method for studying disease treatment using Chinese medicine. METHODS The 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT) method was used to detect the toxicity of CRME in L929 cells, and the concentration ranges of the blank, model, and CRME drug groups were determined. Differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) were identified between the three groups. Gene Ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways of the differentially expressed genes. Expression of Hist1h2bj, Hist1h2ba, Zfp36, Ccl3, Cxcl2 and Egr1 in the blank, model and drug groups was detected by quantitative real-time PCR (qRT-PCR), and the role of CRME on the above factors was determined to ensure consistency with the chip data. RESULTS A total of 329 significantly upregulated genes and 141 downregulated genes were identified between the blank and model groups. A total of 218 significantly upregulated genes and 191 downregulated genes were identified between the CRME drug group and model group. CRME has a significant role in multiple pathways involved in the occurrence and development of RA. Additionally, Hist1h2bj, Hist1h2ba, Zfp36, Ccl3, Cxcl2, and Egr1 were observed in modules of the lncRNA-mRNA weighted co-expression network, consistent with the chip data. CONCLUSIONS CRME has regulatory effects on inflammatory factors, the histone family, chemokines and their ligands that are related to RA-related cytokines, the RA pathway, the TNF signaling pathway, the Toll receptor-like signaling pathway, the chemokine signaling pathways and other pathways are related to the course of RA.
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Affiliation(s)
- Shaowa Lü
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Yutian Liu
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Jie Cui
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Bingyou Yang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Guoyu Li
- Pharmaceutical College, Harbin University of Commerce, Harbin 150086, China
| | - Yuyan Guo
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Haixue Kuang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China.
| | - Qiuhong Wang
- Pharmaceutical College, Guangdong Pharmaceutical University, Guangzhou 510224, China.
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28
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Xue R, Li Y, Li X, Ma J, An C, Ma Z. miR-185 affected the EMT, cell viability, and proliferation via DNMT1/MEG3 pathway in TGF-β1-induced renal fibrosis. Cell Biol Int 2019; 43:1152-1162. [PMID: 30095214 DOI: 10.1002/cbin.11046] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Kidney fibrosis is usually the final manifestation of a wide variety of renal diseases. Recent years, research reported that long non-coding RNAs (lncRNAs) played important roles in a variety of human diseases. However, the role and underlying mechanisms of lncRNAs in kidney fibrosis were complicated and largely unclear. In our study, we constructed the cell model of renal fibrosis in HK2 cells using transforming growth factor β1 (TGF-β1) and found that lncRNA maternally expressed gene 3 (MEG3) was downregulated in TGF-β1-induced renal fibrosis. We then found that overexpressed MEG3 inhibited the TGF-β1-induced promotion of epithelial-mesenchymal transition, cell viability, and proliferation. Furthermore, we demonstrated that DNA methyltransferases 1 (DNMT1) regulated the MEG3 expression by altering the CpGs methylation level of MEG3 promoter in TGF-β1-induced renal fibrosis. In addition, we further revealed that miR-185 could regulate the DNMT1 expression and thus, modulate the MEG3 in TGF-β1-induced renal fibrosis. Ultimately, our study illustrated that the modulation of the miR-185/ DNMT1/ MEG3 pathway exerted important roles in TGF-β1-induced renal fibrosis. In summary, our finding displayed a novel regulatory mechanism for TGF-β1-induced renal fibrosis, which provided a new potential therapeutic target for renal fibrosis.
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Affiliation(s)
- Rong Xue
- Department of Nephrology, Gansu Provincial Hospital, 730000, China
| | - Yingping Li
- Department of Nephrology, Gansu Provincial Hospital, 730000, China
| | - Xiaoli Li
- Department of Nephrology, Gansu Provincial Hospital, 730000, China
| | - Jingang Ma
- Institute for Drug and Instrument Control of LanZhou Military Command, 730000, China
| | - Caiping An
- Department of Nephrology, Gansu Provincial Hospital, 730000, China
| | - Zhigang Ma
- Department of Nephrology, Gansu Provincial Hospital, 730000, China
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29
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Wang Z, Han Y, Xing X, Jiang C, Guo H, Guan Y. MiRNA-98 inhibits ovarian carcinoma cell proliferation, migration and invasion via targeting SALL4. Minerva Med 2019; 112:154-155. [PMID: 31282134 DOI: 10.23736/s0026-4806.19.06179-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhenjie Wang
- Medical Records Room, Weifang People's Hospital, Weifang, China
| | - Yan Han
- Department of Obstetrics, The People's Hospital of Zhangqiu Area, Jinan, China
| | - Xia Xing
- Department of Obstetrics, The People's Hospital of Zhangqiu Area, Jinan, China
| | - Caixia Jiang
- Department of Endocrinology, The People's Hospital of Zhangqiu Area, Jinan, China
| | - Hong Guo
- Health Management Center, The People's Hospital of Zhangqiu Area, Jinan, China
| | - Yun Guan
- Department of Respiratory Medicine, Weifang People's Hospital, Weifang, China -
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30
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The Association of HOTAIR with the Diagnosis and Prognosis of Gastric Cancer and Its Effect on the Proliferation of Gastric Cancer Cells. Can J Gastroenterol Hepatol 2019; 2019:3076345. [PMID: 31281803 PMCID: PMC6590613 DOI: 10.1155/2019/3076345] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/02/2019] [Accepted: 05/20/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are a group of noncoding RNA with the length of more than 200nt. They have been identified as important diagnostic and prognostic molecules for many cancers and play an important role in the development of cancers. However, their clinical value and roles in gastric cancer (GC) remain unclear. METHODS The expression levels of HOTAIR in 54 GC tissues and their matched adjacent nontumor tissues from GC patients and 24 normal mucosa or those with minimal gastritis as healthy controls were determined by qRT-PCR. The expression levels of HOTAIR in human GC cell lines and a normal gastric epithelium cell line were also assessed by qRT-PCR. The potential relationships between its level in GC tissues and the clinicopathological features were analyzed. Furthermore, a receiver operating characteristic (ROC) curve was constructed. Additionally, the correlation between this lncRNA and overall survival (OS) was analyzed. SiRNA transfection was used to silence the expression of HOTAIR in GC cells. And cell proliferation and cell cycle assays were employed to determine the effect of HOTAIR on GC cell growth. Western blot was performed for the detection of the P53, P21, and Bcl2 proteins. RESULTS The expression levels of HOTAIR were significantly upregulated in GC tissues and cell lines. Increased HOTAIR was associated with tumor differentiation, lymph node and distant metastasis, and clinical stage. Furthermore, the area under the ROC curve (AUC) was up to 0.8416 (95 % CI=0.7661 to 0.9170, P<0.0001). The sensitivity and specificity were 66.67 and 87.04%, respectively. The correlation between HOTAIR expression and overall survival (OS) was statistically significant. The hazard ratio was 2.681, and 95% CI of ratio was 1.370 to 5.248. In addition, knockdown of HOTAIR can inhibit GC cell growth and affect cell cycle distribution. And knockdown of HOTAIR could enhance the protein levels of P21 and P53. CONCLUSION The present study demonstrated that HOTAIR was highly expressed in GC tissues and may serve as a potential diagnostic and prognostic biomarker for GC. And HOTAIR promoted GC cell proliferation.
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Yu MJ, Zhao N, Shen H, Wang H. Long Noncoding RNA MRPL39 Inhibits Gastric Cancer Proliferation and Progression by Directly Targeting miR-130. Genet Test Mol Biomarkers 2019; 22:656-663. [PMID: 30452299 DOI: 10.1089/gtmb.2018.0151] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Gastric cancer (GC) is one of the most prevalent malignant tumors displaying both high incidence and mortality throughout much of the world. Recently, long noncoding RNAs (lncRNAs) have been implicated in the development and progression of GC. MATERIALS AND METHODS In the present study, we investigated the biological function and molecular mechanisms of lncRNA MRPL39 in GC. RESULTS We found that MRPL39 was significantly downregulated in GC tissues and cell lines and that its expression level was negatively associated with carcinoma size, tumor, lymph node, metastasis (TNM) stage, and lymphatic metastasis. Patients with low MRPL39 expression levels revealed a short overall and disease-free survival period. Over-expression of MRPL39 in the GC cell lines BGC823 and SGC-7901 inhibited cell growth, proliferation, migration, and invasion. MiR-130, a putative target gene of MRPL39, displayed an inverse association with the expression of MRPL39 in GC tissues and cell lines. Moreover, a luciferase assay demonstrated a direct binding between the miR-130 and MRPL39, and the reintroduction of miR-130 abrogated the anti-tumor effect of MRPL39 on GC cells. CONCLUSION Taken together, these findings indicate that MRPL39 serves as a tumor suppressor by directly targeting miR-130 in GC, which suggests that it might be a novel biomarker in the diagnosis and prognosis of GC.
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Affiliation(s)
- Ming Jun Yu
- Department of Surgery, Hangzhou Third Hospital , Hangzhou, China
| | - Na Zhao
- Department of Surgery, Hangzhou Third Hospital , Hangzhou, China
| | - Haibin Shen
- Department of Surgery, Hangzhou Third Hospital , Hangzhou, China
| | - Haiming Wang
- Department of Surgery, Hangzhou Third Hospital , Hangzhou, China
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32
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Yan L, Liu Z, Yin H, Guo Z, Luo Q. Silencing of MEG3 inhibited ox‐LDL‐induced inflammation and apoptosis in macrophages via modulation of the MEG3/miR‐204/CDKN2A regulatory axis. Cell Biol Int 2019; 43:409-420. [PMID: 30672051 DOI: 10.1002/cbin.11105] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 01/19/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Long Yan
- Neurovascular SurgeryThe First Bethune Hospital of Jilin University71 Xinmin Street, Chaoyang DistrictChangchun City130012Jilin ProvincePeople's Republic of China
| | - Zhanchuan Liu
- The Second Hospital of Jilin UniversityChangchun City130012China
| | - Haoyuan Yin
- Neurovascular SurgeryThe First Bethune Hospital of Jilin University71 Xinmin Street, Chaoyang DistrictChangchun City130012Jilin ProvincePeople's Republic of China
| | - Zhenjie Guo
- Neurovascular SurgeryThe First Bethune Hospital of Jilin University71 Xinmin Street, Chaoyang DistrictChangchun City130012Jilin ProvincePeople's Republic of China
| | - Qi Luo
- Neurovascular SurgeryThe First Bethune Hospital of Jilin University71 Xinmin Street, Chaoyang DistrictChangchun City130012Jilin ProvincePeople's Republic of China
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Gómez J, Lorca R, Reguero JR, Martín M, Morís C, Alonso B, Iglesias S, Díaz-Molina B, Avanzas P, Coto E. Genetic variation at the long noncoding RNA H19 gene is associated with the risk of hypertrophic cardiomyopathy. Epigenomics 2018; 10:865-873. [DOI: 10.2217/epi-2017-0175] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Aim: The long noncoding RNA H19 and its host micro RNA miR-675 have been found deregulated in cardiac hypertrophy and heart failure tissues. Our aim was to investigate whether the H19 gene variants were associated with the risk of hypertrophic cardiomyopathy (HCM). Patients & methods: We genotyped two H19 tag single nucleotide polymorphisms in 405 HCM patients and 550 controls, and sequenced this gene in 100 patients. Results: The rs2107425 C was significantly increased in sarcomere no-mutation patients (n = 225; p = 0.01): CC versus CT + TT, p = 0.017; odd ratios: 1.51. Sequencing of the H19 coding transcript identified two patients heterozygous carriers for a rare variant, rs945977096 G/A, that was absent among the controls. Conclusion: Our study suggested a significant association between H19 variants and the risk of developing HCM.
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Affiliation(s)
- Juan Gómez
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
| | - Rebeca Lorca
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
| | - Julián R Reguero
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
| | - María Martín
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - César Morís
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Departamento de Medicina, Universidad de Oviedo, Oviedo, Spain
| | - Belén Alonso
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
| | - Sara Iglesias
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
| | - Beatriz Díaz-Molina
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
| | - Pablo Avanzas
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
| | - Eliecer Coto
- Unidad de Referencia de Cardiopatías Familiares-HUCA, Genética Molecular y Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Departamento de Medicina, Universidad de Oviedo, Oviedo, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
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Khaled ML, Bykhovskaya Y, Yablonski SER, Li H, Drewry MD, Aboobakar IF, Estes A, Gao XR, Stamer WD, Xu H, Allingham RR, Hauser MA, Rabinowitz YS, Liu Y. Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas. Invest Ophthalmol Vis Sci 2018; 59:2717-2728. [PMID: 29860458 PMCID: PMC5984031 DOI: 10.1167/iovs.18-24267] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/23/2018] [Indexed: 12/22/2022] Open
Abstract
Purpose Keratoconus (KC) is the most common corneal ectasia. We aimed to determine the differential expression of coding and long noncoding RNAs (lncRNAs) in human corneas affected with KC. Methods From the corneas of 10 KC patients and 8 non-KC healthy controls, 200 ng total RNA was used to prepare sequencing libraries with the SMARTer Stranded RNA-Seq kit after ribosomal RNA depletion, followed by paired-end 50-bp sequencing with Illumina Sequencer. Differential analysis was done using TopHat/Cufflinks with a gene file from Ensembl and a lncRNA file from NONCODE. Pathway analysis was performed using WebGestalt. Using the expression level of differentially expressed coding and noncoding RNAs in each sample, we correlated their expression levels in KC and controls separately and identified significantly different correlations in KC against controls followed by visualization using Cytoscape. Results Using |fold change| ≥ 2 and a false discovery rate ≤ 0.05, we identified 436 coding RNAs and 584 lncRNAs with differential expression in the KC-affected corneas. Pathway analysis indicated the enrichment of genes involved in extracellular matrix, protein binding, glycosaminoglycan binding, and cell migration. Our correlation analysis identified 296 pairs of significant KC-specific correlations containing 117 coding genes enriched in functions related to cell migration/motility, extracellular space, cytokine response, and cell adhesion. Our study highlighted the potential roles of several genes (CTGF, SFRP1, AQP5, lnc-WNT4-2:1, and lnc-ALDH3A2-2:1) and pathways (TGF-β, WNT signaling, and PI3K/AKT pathways) in KC pathogenesis. Conclusions Our RNA-Seq-based differential expression and correlation analyses have identified many potential KC contributing coding and noncoding RNAs.
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Affiliation(s)
- Mariam Lofty Khaled
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Yelena Bykhovskaya
- Regenerative Medicine Institute and Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Sarah E. R. Yablonski
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
- STAR Program, Augusta University, Augusta, Georgia, United States
| | - Hanzhou Li
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Michelle D. Drewry
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Inas F. Aboobakar
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Amy Estes
- Department of Ophthalmology, Augusta University, Augusta, Georgia, United States
| | - X. Raymond Gao
- Department of Ophthalmology and Visual Science, University of Illinois at Chicago, Chicago, Illinois, United States
| | - W. Daniel Stamer
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Hongyan Xu
- Department of Population Health Sciences, Augusta University, Augusta, Georgia, United States
| | - R. Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Michael A. Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Yaron S. Rabinowitz
- Regenerative Medicine Institute and Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
- James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
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Gao J, Tang Q, Zhu X, Wang S, Zhang Y, Liu W, Gao Z, Yang H. Long noncoding RNAs show differential expression profiles and display ceRNA potential in cholesteatoma pathogenesis. Oncol Rep 2018; 39:2091-2100. [PMID: 29565455 PMCID: PMC5928766 DOI: 10.3892/or.2018.6320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/16/2018] [Indexed: 11/05/2022] Open
Abstract
Cholesteatoma is a pathologically benign but clinically destructive middle ear disease, which is caused by excessive epidermal migration and uncontrolled hyperproliferation of keratinocytes of squamous epithelium, leading to various clinical manifestations and serious complications, such as hearing loss, dizziness, facial paralysis, meningitis, and hydrocephalus. However, the pathogenesis of cholesteatoma is still not fully understood. Herein, we performed microarray analysis to identify the differentially expressed patterns of lncRNAs in cholesteatoma for the first time. Our data indicated that compared with matched normal skin tissue, lncRNA expression profiles were significantly altered in cholesteatoma. A total of 787 lncRNAs were identified (fold change ≥2.0, P<0.05), consisting of 181 upregulated and 606 downregulated lncRNAs. Furthermore, by constructing an lncRNA/miRNA/mRNA competing endogenous RNA (ceRNA) network, we found that lncRNAs, such as lncRNA‑uc001kfc.1, had ceRNA potential in cholesteatoma formation. In conclusion, lncRNAs were aberrantly expressed in cholesteatoma compared with normal skin tissues and may play important roles in cholesteatoma formation. Our findings shed novel light on the molecular mechanism of cholesteatoma pathogenesis and suggest that lncRNAs may be potential therapeutic targets for cholesteatoma.
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Affiliation(s)
- Juanjuan Gao
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Qi Tang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Xiaohui Zhu
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Shihua Wang
- Center of Excellence in Tissue Engineering, Key Laboratory of Beijing, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Yongli Zhang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Wenbin Liu
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Zhiqiang Gao
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Hua Yang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
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Zhou YX, Wang C, Mao LW, Wang YL, Xia LQ, Zhao W, Shen J, Chen J. Long noncoding RNA HOTAIR mediates the estrogen-induced metastasis of endometrial cancer cells via the miR-646/NPM1 axis. Am J Physiol Cell Physiol 2018; 314:C690-C701. [PMID: 29466670 DOI: 10.1152/ajpcell.00222.2017] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
LncRNA homeobox (HOX) transcript antisense intergenic RNA (HOTAIR) has been confirmed to be involved in the tumorigenic progression of endometrial carcinoma (EC). However, the molecular mechanisms of HOTAIR in EC are not fully elucidated. The expression of HOTAIR and miR-646 in human EC tissues was determined by qRT-PCR. The effect of miR-646 on EC cells was assessed by the cell viability, migration, and invasion using CCK-8 assays and transwell assays. RNA-binding protein immunoprecipitation assays and RNA pull-down assays were performed to explore the interaction between HOTAIR and miR-646. The regulation of miR-646 on nucleophosmin 1 (NPM1) was tested using luciferase reporter assays. MiR-646 expression was significantly decreased both in human EC tissues ( n = 23) and cell lines (Ishikawa and HEC-1-A) compared with the control. Moreover, miR-646 expression was negatively related to HOTAIR in human EC tissues ( n = 23). Our results also showed that miR-646 overexpression considerably attenuated the E2-promoted viability, migration, and invasion of Ishikawa and HEC-1-A cells in vitro. In addition, HOTAIR was confirmed to regulate the viability, migration, and invasion of EC cells through negative regulating miR-646. More importantly, we also demonstrated that NPM1 was the target of miR-646, and HOTAIR promoted NPM1 expression through interacting with miR-646 in EC cells. Taken together, our findings presented that HOTAIR could regulate NPM1 via interacting with miR-646, thereby governing the viability, migration, and invasion of EC cells.
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Affiliation(s)
- Yun-Xiao Zhou
- Department of Gynaecology, The First Affiliated Hospital of Zhejiang University Medical College , Zhejiang , China
| | - Chuan Wang
- Department of Gynaecology, JinYun County People's Hospital , Zhejiang , China
| | - Li-Wei Mao
- Department of Obstetrics and Gynaecology, Jingning County People's Hospital , Zhejiang , China
| | - Yan-Li Wang
- Department of Pathology, The First Affiliated Hospital of Zhejiang University Medical College , Zhejiang , China
| | - Li-Qun Xia
- Department of Gynaecology, The First Affiliated Hospital of Zhejiang University Medical College , Zhejiang , China
| | - Wei Zhao
- Department of Gynaecology, The First Affiliated Hospital of Zhejiang University Medical College , Zhejiang , China
| | - Jie Shen
- Department of Gynaecology, The First Affiliated Hospital of Zhejiang University Medical College , Zhejiang , China
| | - Jun Chen
- Department of Urology, The First Affiliated Hospital of Zhejiang University Medical College , Zhejiang , China
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Liang H, Pan Z, Zhao X, Liu L, Sun J, Su X, Xu C, Zhou Y, Zhao D, Xu B, Li X, Yang B, Lu Y, Shan H. LncRNA PFL contributes to cardiac fibrosis by acting as a competing endogenous RNA of let-7d. Theranostics 2018; 8:1180-1194. [PMID: 29464008 PMCID: PMC5817119 DOI: 10.7150/thno.20846] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 11/06/2017] [Indexed: 12/12/2022] Open
Abstract
Rationale: Cardiac fibrosis is associated with various cardiovascular diseases and can eventually lead to heart failure. Dysregulation of long non-coding RNAs (lncRNAs) has recently been recognized as one of the key mechanisms involved in cardiac diseases. However, the potential roles and underlying mechanisms of lncRNAs in cardiac fibrosis have not been explicitly delineated. Methods and Results: Using a combination of in vitro and in vivo studies, we identified a lncRNA NONMMUT022555, which is designated as a pro-fibrotic lncRNA (PFL), and revealed that PFL is up-regulated in the hearts of mice in response to myocardial infarction (MI) as well as in the fibrotic cardiac fibroblasts (CFs). We found that knockdown of PFL by adenoviruses carrying shRNA attenuated cardiac interstitial fibrosis and improved ejection fraction (EF) and fractional shortening (FS) in MI mice. Further study showed that forced expression of PFL promoted proliferation, fibroblast-myofibroblast transition and fibrogenesis in mice CFs by regulating let-7d, whereas silencing PFL mitigated TGF-β1-induced myofibroblast generation and fibrogenesis. More importantly, PFL acted as a competitive endogenous RNA (ceRNA) of let-7d, as forced expression of PFL reduced the expression and activity of let-7d. Moreover, let-7d levels were decreased in the MI mice and in fibrotic CFs. Inhibition of let-7d resulted in fibrogenesis in CFs, whereas forced expression of let-7d abated fibrogenesis through targeting platelet-activating factor receptor (Ptafr). Furthermore, overexpression of let-7d by adenoviruses carrying let-7d precursor impeded cardiac fibrosis and improved cardiac function in MI mice. Conclusion: Taken together, our study elucidated the role and mechanism of PFL in cardiac fibrosis, indicating the potential role of PFL inhibition as a novel therapy for cardiac fibrosis.
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Affiliation(s)
- Haihai Liang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Zhenwei Pan
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Xiaoguang Zhao
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Li Liu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Jian Sun
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Xiaomin Su
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Chaoqian Xu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Yuhong Zhou
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Dandan Zhao
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Bozhi Xu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Xuelian Li
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Baofeng Yang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Yanjie Lu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
| | - Hongli Shan
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, Heilongjiang 150081, P. R. China
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Lo Piccolo L. Drosophila as a Model to Gain Insight into the Role of lncRNAs in Neurological Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1076:119-146. [PMID: 29951818 DOI: 10.1007/978-981-13-0529-0_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is now clear that the majority of transcription in humans results in the production of long non-protein-coding RNAs (lncRNAs) with a variable length spanning from 200 bp up to several kilobases. To date, we have a limited understanding of the lncRNA function, but a huge number of evidences have suggested that lncRNAs represent an outstanding asset for cells. In particular, temporal and spatial expression of lncRNAs appears to be important for proper neurological functioning. Stunningly, abnormal lncRNA function has been found as being critical for the onset of neurological disorders. This chapter focus on the lncRNAs with a role in diseases affecting the central nervous system with particular regard for the lncRNAs causing those neurodegenerative diseases that exhibit dementia and/or motor dysfunctions. A specific section will be dedicated to the human neuronal lncRNAs that have been modelled in Drosophila. Finally, even if only few examples have been reported so far, an overview of the Drosophila lncRNAs with neurological functions will be also included in this chapter.
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Affiliation(s)
- Luca Lo Piccolo
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine 2-2 Yamadaoka, Suita Osaka, 565-0871, Japan.
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SNHG1 promotes cell proliferation by acting as a sponge of miR-145 in colorectal cancer. Oncotarget 2017; 9:2128-2139. [PMID: 29416759 PMCID: PMC5788627 DOI: 10.18632/oncotarget.23255] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/05/2017] [Indexed: 02/07/2023] Open
Abstract
ncRNAs are important regulatory molecules and involve in many physiological cellular processes. Small nucleolar RNA host gene 1 (SNHG1) is a host to 8 snoRNAs and is located in 11q12.3 region of the chromosome. It has been reported to be involved in several cancers. However, the role of SNHG1 in the tumorigenesis of colorectal cancer is still unknown. In this study, SNHG1 was upregulated in colorectal cancers, and SNHG1 expression was correlated with advanced colorectal cancer stage and tumor recurrence. We found that SNHG1 promoted cell proliferation by acting as a sponge of miR-145, a well known tumor suppressor of colorectal cancer. Furthermore, the survival analysis indicated that colorectal cancer patients with higher expression of SNHG1 had a worse prognosis. These findings suggested that SNHG1 may act as a potential therapeutic target for the treatment of colorectal cancer.
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Gao JR, Qin XJ, Jiang H, Gao YC, Guo MF, Jiang NN. Potential role of lncRNAs in contributing to pathogenesis of chronic glomerulonephritis based on microarray data. Gene 2017; 643:46-54. [PMID: 29199037 DOI: 10.1016/j.gene.2017.11.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/04/2017] [Accepted: 11/29/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Chronic glomerulonephritis (CGN) is the most common form of primary glomerular disease with unclear molecular mechanisms, which related to immune-mediated inflammatory diseases. Our study intended to identify potential long non-coding RNAs (lncRNAs) and genes, and to determine the potential molecular mechanisms of CGN pathogenesis. METHODS The microarray of GSE64265 and GSE46295 were downloaded from the Gene Expression Omnibus database, GSE64265 including 3 rats control kidney tissues and 5 rats model kidney tissues, GSE46295 including 3 rats control kidney tissues and 3 rats model kidney tissues, which was on the basis of GPL1355 platform. Identification of differentially expressed lncRNAs and mRNAs were performed between the 2 groups. Gene ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways for the differentially expressed mRNAs. LncRNA-mRNA weighted co-expression network was constructed using the WGCNA package to analyses for the genes in the modules. The protein-protein interaction (PPI) network was visualized. RESULTS A total of 40 significantly up-regulated and 24 down-regulated lncRNAs, 653 up-regulated and 128 down-regulated mRNAs were identified. Additionally, Cdk1, with the highest connectivity degree in PPI network, was noteworthy enriched in cell cycle. Seven lncRNAs: NONRATT026650, LOC102547664, NONRATT77021989, NONRATT012453, LOC102551856, LOC102553536 and NONRATT7047175 were observed in the modules of lncRNA-mRNA weighted co-expression network. CONCLUSIONS LncRNAs NONRATT026650, LOC102547664, NONRATT77021989, NONRATT012453, LOC102551856, LOC102553536 and NONRATT7047175 were differentially expressed and might play important roles in the development of CGN. Key genes, such as Cd44, Rftn1, Runx1, may be crucial biomarkers for CGN.
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Affiliation(s)
- Jia-Rong Gao
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China.
| | - Xiu-Juan Qin
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
| | - Hui Jiang
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
| | - Ya-Chen Gao
- Department of Nephrology, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
| | - Ming-Fei Guo
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
| | - Nan-Nan Jiang
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
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Zhu B, Gong Y, Yan G, Wang D, Qiao Y, Wang Q, Liu B, Hou J, Li R, Tang C. Down-regulation of lncRNA MEG3 promotes hypoxia-induced human pulmonary artery smooth muscle cell proliferation and migration via repressing PTEN by sponging miR-21. Biochem Biophys Res Commun 2017; 495:2125-2132. [PMID: 29198701 DOI: 10.1016/j.bbrc.2017.11.185] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022]
Abstract
Hypoxia-induced pulmonary hypertension is a life-threatening disease arising from a progressive increase in pulmonary vascular resistance, irreversible pulmonary vascular remodeling and resulting in right ventricular failure. Recent studies suggested that pulmonary artery smooth muscle cell proliferation and migration played an important role in the pathogenesis of hypoxia-induced pulmonary hypertension. However, the mechanisms of hypoxia-induced pulmonary hypertension are complicated and largely unclear. In this study, we discovered that lncRNA MEG3 was down-regulated in human pulmonary artery smooth muscle cell in hypoxia, and inhibition of MEG3 promoted the cell proliferation and cell migration in both normal and hypoxia condition. Further study demonstrated that MEG3 exerted its function via regulation of miR-21 expression in both normal and hypoxia condition. In addition, we displayed the modulation of PTEN by miR-21 and their role in hypoxia. Ultimately, our study illustrated that MEG3 exerts its role via miR-21/PTEN axis in human pulmonary artery smooth muscle cell under both normal and hypoxia conditions.
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Affiliation(s)
- Boqian Zhu
- Department of Cardiology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Yaoyao Gong
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Gaoliang Yan
- Department of Cardiology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Dong Wang
- Department of Cardiology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Yong Qiao
- Department of Cardiology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Qingjie Wang
- Department of Cardiology, Changzhou Second Hospital of Nanjing Medical University, Changzhou, China
| | - Bo Liu
- Department of Cardiology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Jiantong Hou
- Department of Cardiology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Ruifeng Li
- Department of Cardiology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Chengchun Tang
- Department of Cardiology, Zhongda Hospital, Southeast University, Nanjing, China.
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Zhang H, Lu W. LncRNA SNHG12 regulates gastric cancer progression by acting as a molecular sponge of miR‑320. Mol Med Rep 2017; 17:2743-2749. [PMID: 29207106 DOI: 10.3892/mmr.2017.8143] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/04/2017] [Indexed: 11/05/2022] Open
Abstract
Gastric cancer (GC) is one of the most common malignancies worldwide. Previous studies have focused on long non‑coding RNAs (lncRNAs), which have important roles in the development and progression of GC. The present study aimed to clarify the expression and function of lncRNA small nucleolar RNA host gene 12 (SNHG12) in GC. The expression and the clinical characteristics of GC were analyzed in the samples from patients with GC and matched adjacent normal tissues. The present study determined that SNHG12 was significantly overexpressed in GC and its expression level was highly associated with tumor size, tumor‑node‑metastasis stage, distant metastasis, lymphatic metastasis. Patients with high SNHG12 expression had a short survival period. Additionally, inhibition of SNHG12 in GC cell lines SGC‑7901 and AGS suppressed cell growth, colony formation, proliferation and invasion. MicroRNA (miR)‑320, a putative target gene of SNHG12, was inversely correlated with SNHG12 expression in GC tissues and cell lines. In addition, the present study determined that miR‑320 was directly regulated by SNHG12 and suppression of miR‑320 expression reversed the inhibitory effects of SNHG12 siRNA on GC cell proliferation and invasion. These findings revealed that SNHG12 acts as a tumor promoter by directly targeting miR‑320 in GC, suggesting a potential novel biomarker for the diagnosis and prognosis of GC.
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Affiliation(s)
- Hanyun Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University, Medical College, Hangzhou, Zhejiang 310009, P.R. China
| | - Wenjie Lu
- Department of General Surgery, The Second Affiliated Hospital of Zhejiang University, Medical College, Hangzhou, Zhejiang 310009, P.R. China
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