101
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Policarpo R, Sierksma A, De Strooper B, d'Ydewalle C. From Junk to Function: LncRNAs in CNS Health and Disease. Front Mol Neurosci 2021; 14:714768. [PMID: 34349622 PMCID: PMC8327212 DOI: 10.3389/fnmol.2021.714768] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/25/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.
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Affiliation(s)
- Rafaela Policarpo
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Annerieke Sierksma
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,UK Dementia Research Institute, University College London, London, United Kingdom
| | - Constantin d'Ydewalle
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
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102
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Lyu K, Chow EYC, Mou X, Chan TF, Kwok CK. RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res 2021; 49:5426-5450. [PMID: 33772593 PMCID: PMC8191793 DOI: 10.1093/nar/gkab187] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered in vivo across the tree of life, and discuss the key biological questions to be addressed in the near future.
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Affiliation(s)
- Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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103
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Liu T, Yang C, Wang W, Liu C. LncRNA SGMS1-AS1 regulates lung adenocarcinoma cell proliferation, migration, invasion, and EMT progression via miR-106a-5p/MYLI9 axis. Thorac Cancer 2021; 12:2104-2112. [PMID: 34061466 PMCID: PMC8287014 DOI: 10.1111/1759-7714.14043] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Lung cancer mainly includes non-small cell lung cancer (NSCLC). Lung adenocarcinoma (LUAD) is the main subtype of NSCLC. Long non-coding RNAs (LncRNAs) had been found to exert numerous functions on the progressions of cancers. MicroRNAs often exist as the target of LncRNAs to regulate a series of signaling pathways in human. We explored the effects and molecular mechanism of LncRNA SGMS1-AS1 on the procedures of LUAD cells. METHODS The ENCORI and GEPIA databases were used to analyze the differences in SGMS1, miR-106a-5p, and MYLIP between LUAD and normal tissue. Their expression levels were examined by RT-PCR. CCK8, colony formation, migration, and invasion assay were conducted in LUAD cells which had silenced SGMS1-AS1. To verify the relationship between SGMS1-AS1, miR-106a-5p, and MYLIP, we overexpressed miR-106a-5p inhibitor or MYLIP in LUAD cells after decreasing SGMS1-AS1 and repeated the above assays. RESULTS SGMS1-AS1 was downregulated in LUAD tissue as well as cells, which was related to good prognosis of patients with lung adenocarcinoma. Additionally, knockdown of SGMS1-AS1 promoted proliferation, migration, invasion, and epithelial mesenchymal transition (EMT) progression of LUAD cells, which meant that SGMS1-AS1 inhibited the progression of LUAD cells. Furthermore, miR-106a-5p was the direct target of SGMS1-AS1 and transfecting miR-106a-5p inhibitor could reversed the impact induced by knockdown of SGMS1-AS1. Subsequently, we found that MYLIP was the target of miR-106a-5p, which was negatively correlated with miR-106a-5p, but had high positive correlation with SGMS1-AS1. Consistently, overexpression MYLIP partly eliminated the effects on A549 cells induced by silencing of SGMS1-AS1. CONCLUSION LncRNA SGMS1-AS1 inhibits the proliferation, invasion, migration and EMT progression of LUAD cells via targeting miR-106a-5p/MYLIP axis.
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Affiliation(s)
- Ting Liu
- Department of Plumonary and Critical Care Medicine, Weifang People's Hospital, Weifang, China
| | - Chunli Yang
- Department of Plumonary and Critical Care Medicine, Weifang People's Hospital, Weifang, China
| | - Weizhen Wang
- Department of Plumonary and Critical Care Medicine, Weifang People's Hospital, Weifang, China
| | - Chunmei Liu
- Department of Plumonary and Critical Care Medicine, Weifang People's Hospital, Weifang, China
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104
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Li R, Sklutuis R, Groebner JL, Romerio F. HIV-1 Natural Antisense Transcription and Its Role in Viral Persistence. Viruses 2021; 13:v13050795. [PMID: 33946840 PMCID: PMC8145503 DOI: 10.3390/v13050795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
Natural antisense transcripts (NATs) represent a class of RNA molecules that are transcribed from the opposite strand of a protein-coding gene, and that have the ability to regulate the expression of their cognate protein-coding gene via multiple mechanisms. NATs have been described in many prokaryotic and eukaryotic systems, as well as in the viruses that infect them. The human immunodeficiency virus (HIV-1) is no exception, and produces one or more NAT from a promoter within the 3’ long terminal repeat. HIV-1 antisense transcripts have been the focus of several studies spanning over 30 years. However, a complete appreciation of the role that these transcripts play in the virus lifecycle is still lacking. In this review, we cover the current knowledge about HIV-1 NATs, discuss some of the questions that are still open and identify possible areas of future research.
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Affiliation(s)
- Rui Li
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Rachel Sklutuis
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Jennifer L. Groebner
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
- Correspondence:
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105
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Cui S, Li C. RHPN1‑AS1 promotes ovarian carcinogenesis by sponging miR‑485‑5p and releasing TPX2 mRNA. Oncol Rep 2021; 45:111. [PMID: 33907841 PMCID: PMC8082340 DOI: 10.3892/or.2021.8062] [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: 08/13/2020] [Accepted: 02/05/2021] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play a crucial role in cancer development. However, researchers have yet to identify the underlying association between lncRNAs and ovarian cancer (OC). The aim of the present study was to examine the effect of lncRNA RHPN1-AS1 (RHPN1-AS1) on OC cells and tissues. Reverse transcriptase-quantitative PCR (RT-qPCR) was utilized to quantify RHPN1-AS1, miR-485-5p, and TPX2 mRNA expression in samples with OC. Luciferase-reporter assay, RNA immunoprecipitation (RIP) assay, and RNA pull-down assay were then employed to validate the target relationship among RHPN1-AS1, miR-485-5p and TPX2. Cell Counting Kit-8, BrdU, wound-healing, cell-adhesion, and flow cytometry assays were also employed to assess cell viability, proliferation, migration, adhesion and apoptosis, respectively, in SKOV3 and OVCAR3 cell lines. Findings revealed that RHPN1-AS1 demonstrated a higher expression level in OC cell lines and tissues. In addition, RHPN1-AS1 enhanced the adhesion, proliferation and migration of OC cell lines but decreased apoptosis of OC cells. It was also observed that the relationship between RHPN1-AS1 and miR-485-5p was negative and that RHPN1-AS1 could sponge miR-485-5p to regulate the proliferation, apoptosis, adhesion, and migration abilities of OC cells. Moreover, TPX2 was targeted by miR-485-5p and was significantly overexpressed in OC cell lines and tissues. Experimental investigations also revealed that TPX2 promoted the proliferation, adhesion, and migration of OC cells but suppressed the apoptosis of SKOV3 and OVCAR3 cells. In summary, RHPN1-AS1 played a tumor promotive role by sponging miR-485-5p to increase TPX2 expression in OC tumorigenesis.
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Affiliation(s)
- Shoubin Cui
- Department of Gynaecology and Obstetrics, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong 264100, P.R. China
| | - Cui Li
- Department of Gynaecology and Obstetrics, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong 264100, P.R. China
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106
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Madeira C, Costa PM. Proteomics in systems toxicology. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:55-91. [PMID: 34340774 DOI: 10.1016/bs.apcsb.2021.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins are the ultimate product of gene expression. As they hinge between gene transcription and phenotype, they offer a more realistic perspective of toxicopathic effects, responses and even susceptibility to insult than targeting genes and mRNAs while dodging some inter-individual variability that hinders measuring downstream endpoints like metabolites or enzyme activity. Toxicologists have long focused on proteins as biomarkers but the advent of proteomics shifted risk assessment from narrow single-endpoint analyses to whole-proteome screening, enabling deriving protein-centric adverse outcome pathways (AOPs), which are pivotal for the derivation of Systems Biology informally named Systems Toxicology. Especially if coupled pathology, the identification of molecular initiating events (MIEs) and AOPs allow predictive modeling of toxicological pathways, which now stands as the frontier for the next generation of toxicologists. Advances in mass spectrometry, bioinformatics, protein databases and top-down proteomics create new opportunities for mechanistic and effects-oriented research in all fields, from ecotoxicology to pharmacotoxicology.
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Affiliation(s)
- Carolina Madeira
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal
| | - Pedro M Costa
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal.
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107
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Ma Y, Ma L, Cao Y, Zhai J. Construction of a ceRNA-based lncRNA-mRNA network to identify functional lncRNAs in polycystic ovarian syndrome. Aging (Albany NY) 2021; 13:8481-8496. [PMID: 33714202 PMCID: PMC8034915 DOI: 10.18632/aging.202659] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022]
Abstract
Polycystic ovary syndrome (PCOS) is a prevalent endocrine and metabolic disorder in women of childbearing age. Recent studies suggest important roles for lncRNAs in PCOS development. Based on the hypothesis that lncRNAs are able to regulate mRNA functions by competitive binding to shared miRNAs, the present work sought to construct a PCOS-related lncRNA-mRNA network (PCLMN) to identify key lncRNAs with dysregulated expression and potential prognostic and therapeutic relevance. A global background network was constructed after retrieving lncRNA-miRNA and miRNA-mRNA pairs from the lncRNASNP2, miRTarBase and StarBase databases. Based on gene expression profiles from ovarian granulosa cells from PCOS patients and controls in the GEO’s GSE95728 dataset, the PCLMN was then constructed by applying hypergeometric testing. Using topological analysis, we identified 3 lncRNAs (LINC00667, AC073172.1 and H19) ranking within the top-ten gene lists for all three centrality measures. We then explored their subcellular localization, performed functional module analyses, and identified 4 sex hormone-related transcription factors as potential regulators of their expression. Significant associations with inflammation, oxidative stress, and apoptosis-related processes and pathways were revealed for the key lncRNAs in our PCMLN. Further studies verifying the mRNA/lncRNA relationships identified herein are needed to clarify their clinical significance.
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Affiliation(s)
- Yue Ma
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Linna Ma
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yurong Cao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Zhai
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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108
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Tian Y, Guan Y, Su Y, Yang T, Yu H. TRPM2-AS Promotes Bladder Cancer by Targeting miR-22-3p and Regulating GINS2 mRNA Expression. Onco Targets Ther 2021; 14:1219-1237. [PMID: 33658791 PMCID: PMC7914110 DOI: 10.2147/ott.s282151] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/19/2021] [Indexed: 12/24/2022] Open
Abstract
Background Bladder cancer (BLCA) refers to the malignancy growth that spreads from the bladder linings to the bladder muscles. However, the impact of miR-22-3p and lncRNA TRPM2-AS on this tumor has generated divergent views in the literature. This research aimed to study the effects of lncRNA TRPM2-AS on BLCA and its interaction with miR-22-3p and GINS2 mRNA. Methods qRT-PCR was employed to measure the expression of TRPM2-AS, miR-22-3p and GINS2 mRNA in bladder tissues and cells. The subcellular localization of TRPM2-AS in T24 and 5637 cell lines was identified using a cell fractionation system. Luciferase assay, RIP assay and RNA pull-down assay were later performed to validate the direct binding relationship between TRPM2-AS, miR-22-3p and GINS2 mRNA. Several experiments were conducted to determine the viability, proliferation, colony formation and apoptosis of the cell lines. Results Findings indicated that TRPM2-AS was significantly upregulated in BLCA tissues and cell lines. Apart from that, it was observed that TRPM2-AS knockdown significantly inhibited the viability, proliferation and colony formation of BCLA cells, but it promoted the apoptosis of the BCLA cells. A significant downstream target of TRPM2-AS, miR-22-3p was found to show a lower expression level in BLCA tissues and cell lines. However, the inhibition of miR-22-3p considerably enhanced BLCA cell phenotypes. As well as discovering that GINS2 mRNA was a downstream target of miR-22-3p and was significantly upregulated in BLCA, experimental results also indicated that the knockdown of GINS2 suppressed BLCA cell phenotypes. Conclusion This research confirmed that TRPM2-AS could promote BCLA by binding to miR-22-3p to increase GINS2 expression. This novel interactome in BLCA cell lines might provide more insights into BLCA therapy.
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Affiliation(s)
- Yudong Tian
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, People's Republic of China
| | - Yanbin Guan
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, 450046, People's Republic of China
| | - Yang Su
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, People's Republic of China
| | - Tao Yang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, People's Republic of China
| | - Haizhou Yu
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, People's Republic of China
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109
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Liau WS, Samaddar S, Banerjee S, Bredy TW. On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain. RNA Biol 2021; 18:1025-1036. [PMID: 33397182 DOI: 10.1080/15476286.2020.1868165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The majority of transcriptionally active RNA derived from the mammalian genome does not code for protein. Long noncoding RNA (lncRNA) is the most abundant form of noncoding RNA found in the brain and is involved in many aspects of cellular metabolism. Beyond their fundamental role in the nucleus as decoys for RNA-binding proteins associated with alternative splicing or as guides for the epigenetic regulation of protein-coding gene expression, recent findings indicate that activity-induced lncRNAs also regulate neural plasticity. In this review, we discuss how lncRNAs may exert molecular control over brain function beyond their known roles in the nucleus. We propose that subcellular localization is a critical feature of experience-dependent lncRNA activity in the brain, and that lncRNA-mediated control over RNA metabolism at the synapse serves to regulate local mRNA stability and translation, thereby influencing neuronal function, learning and memory.
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Affiliation(s)
- Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | | | | | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
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110
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Mungamuri SK, Nagasuryaprasad K. Epigenetic mechanisms of hepatocellular carcinoma progression: Potential therapeutic opportunities. EPIGENETICS AND METABOLOMICS 2021:279-296. [DOI: 10.1016/b978-0-323-85652-2.00008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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111
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Norioun H, Motovali-Bashi M, Javadirad SM. Hsa-miR-27a-3p overexpression in men with nonobstructive azoospermia: A case-control study. Int J Reprod Biomed 2020; 18:961-968. [PMID: 33349804 PMCID: PMC7749971 DOI: 10.18502/ijrm.v13i11.7963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/04/2019] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
Background The role of KDM3A and its downstream genes in male fertility has been approved in animal models. Additionally, the expression shrinkage of KDM3A is significantly correlated with human azoospermia phenotype. Aberrant expression of micro-RNAs could mislead spermatogenesis and mostly lead to diverse phenotypes of male infertility. Objective The aim of this study was to evaluate the expression level of hsa-miR-27a-3p in azoospermic men to reveal its possible association with infertility. Materials and Methods This case-control study was conducted on 30 azoospermic men, of whom, 19 had non obstructive azoospermia (NOA) and 11 obstructive azoospermia (OA) according to the pathological examinations. Comprehensive bioinformatics investigations were performed securely and hsa-miR-27a-3p was selected afterward. Reverse Transcriptase-quantitative polymerase chain reaction (RT-qPCR) method was used and statistical analysis was performed to compare the expression level of hsa-miR-27a-3p in both OA and NOA individuals. Results In silico analysis suggested hsa-miR-27a-3p, with its potential binding ability to target KDM3A transcripts. The expression analysis of candidate hsa-miR-27a-3p indicated its significant overexpression in NOA men. Conclusion The hsa-miR-27a-3p was overexpressed in NOA men compared to OA-control individuals. As a consequence, the overexpressed micro-RNA could downregulate directly KDM3A and indirectly TNP1 and PRM1. Therefore, spermatogenesis could be misled and male infertility could be developed.
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Affiliation(s)
- Hamid Norioun
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Majid Motovali-Bashi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Seyed Morteza Javadirad
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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112
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Elcheva IA, Spiegelman VS. The Role of cis- and trans-Acting RNA Regulatory Elements in Leukemia. Cancers (Basel) 2020; 12:E3854. [PMID: 33419342 PMCID: PMC7766907 DOI: 10.3390/cancers12123854] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
RNA molecules are a source of phenotypic diversity and an operating system that connects multiple genetic and metabolic processes in the cell. A dysregulated RNA network is a common feature of cancer. Aberrant expression of long non-coding RNA (lncRNA), micro RNA (miRNA), and circular RNA (circRNA) in tumors compared to their normal counterparts, as well as the recurrent mutations in functional regulatory cis-acting RNA motifs have emerged as biomarkers of disease development and progression, opening avenues for the design of novel therapeutic approaches. This review looks at the progress, challenges and future prospects of targeting cis-acting and trans-acting RNA elements for leukemia diagnosis and treatment.
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Affiliation(s)
- Irina A. Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
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113
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Zhou X, Cui J, Meng J, Luan Y. Interactions and links among the noncoding RNAs in plants under stresses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3235-3248. [PMID: 33025081 DOI: 10.1007/s00122-020-03690-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/16/2020] [Indexed: 05/11/2023]
Abstract
The complex interplay among sRNAs, lncRNAs and circRNAs has been implicated in plants under biotic and abiotic stresses. Here, we review current advances in our understanding of ncRNA interactions and links, which have considerable potential for improving the agronomic traits and the environmental adaptability of plants. Plants can respond to biotic or abiotic stresses. To cope with various conditions, numerous intricate molecular regulatory mechanisms have evolved in plants. Noncoding RNAs (ncRNAs) can be divided into small noncoding RNAs (sRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). Emerging evidence has demonstrated that interplay among the ncRNAs acts as a novel layer in the regulatory mechanisms, which has attracted substantial interest. Links between sRNAs can affect plant immune responses and development in synergistic or antagonistic manners. Additionally, multiple interactions between lncRNAs and sRNAs are involved in crop breeding, disease resistance and high tolerance to environmental stresses. Here, we summarize current knowledge of the interactions and links among the ncRNAs in plant responses to stresses and the methods for identifying ncRNA interactions. Furthermore, challenges and prospects for further progress in elucidating ncRNA interactions and links are highlighted.
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Affiliation(s)
- Xiaoxu Zhou
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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114
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Kashyap MP, Sinha R, Mukhtar MS, Athar M. Epigenetic regulation in the pathogenesis of non-melanoma skin cancer. Semin Cancer Biol 2020; 83:36-56. [PMID: 33242578 DOI: 10.1016/j.semcancer.2020.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Understanding of cancer with the help of ever-expanding cutting edge technological tools and bioinformatics is revolutionizing modern cancer research by broadening the space of discovery window of various genomic and epigenomic processes. Genomics data integrated with multi-omics layering have advanced cancer research. Uncovering such layers of genetic mutations/modifications, epigenetic regulation and their role in the complex pathophysiology of cancer progression could lead to novel therapeutic interventions. Although a plethora of literature is available in public domain defining the role of various tumor driver gene mutations, understanding of epigenetic regulation of cancer is still emerging. This review focuses on epigenetic regulation association with the pathogenesis of non-melanoma skin cancer (NMSC). NMSC has higher prevalence in Caucasian populations compared to other races. Due to lack of proper reporting to cancer registries, the incidence rates for NMSC worldwide cannot be accurately estimated. However, this is the most common neoplasm in humans, and millions of new cases per year are reported in the United States alone. In organ transplant recipients, the incidence of NMSC particularly of squamous cell carcinoma (SCC) is very high and these SCCs frequently become metastatic and lethal. Understanding of solar ultraviolet (UV) light-induced damage and impaired DNA repair process leading to DNA mutations and nuclear instability provide an insight into the pathogenesis of metastatic neoplasm. This review discusses the recent advances in the field of epigenetics of NMSCs. Particularly, the role of DNA methylation, histone hyperacetylation and non-coding RNA such as long-chain noncoding (lnc) RNAs, circular RNAs and miRNA in the disease progression are summarized.
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Affiliation(s)
- Mahendra Pratap Kashyap
- UAB Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rajesh Sinha
- UAB Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mohammad Athar
- UAB Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Cao M, Zhang M, Yang N, Fu Q, Su B, Zhang X, Li Q, Yan X, Thongda W, Li C. Full length transcriptome profiling reveals novel immune-related genes in black rockfish (Sebastes schlegelii). FISH & SHELLFISH IMMUNOLOGY 2020; 106:1078-1086. [PMID: 32947030 DOI: 10.1016/j.fsi.2020.09.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Lacking full-length transcriptome for black rockfish (Sebastes schlegelii) limits novel gene discoveries and gene structures analysis. Therefore, we constructed the full-length transcriptome of black rockfish using Single-Molecule Real-Time Sequencing technology. Totally, we produced 21.73 Gb raw reads containing 298,904 circular consensus sequence (CCS) reads. Full-length (FL) and Non-full-length (NFL) isoforms were obtained based on the presence of 5' and 3' primers as well as poly (A) tails. The results showed 70.71% reads were identified as FL isoforms. Moreover, the average length of these PacBio isoforms is 2,632 bp, which is much longer than the length of the unigenes with the average length of 589 bp which generated from Illumina platform. Meanwhile, we identified 43,068 non-redundant transcripts, 12,485 alternative splicing (AS), 6,320 polyadenylation (APA) and 499 gene fusions as well as numerous long non-coding RNAs based on mapped FL isoforms. In addition, we identified 147 and 528 immune-related genes from novel genes and unmapped transcripts. The provided dataset can be utilized to discover novel genes and construct a comprehensive transcript dataset for black rockfish.
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Affiliation(s)
- Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qi Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xu Yan
- College of Marine Science and Biological Engineering, Qingdao University of Science & Technology, Qingdao, 266011, China
| | - Wilawan Thongda
- Center of Excellence for Shrimp Molecular Biology and Biology (CENTEX Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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116
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Bossanyi MA, Carpentier V, Glouzon JPS, Ouangraoua A, Anselmetti Y. aliFreeFoldMulti: alignment-free method to predict secondary structures of multiple RNA homologs. NAR Genom Bioinform 2020; 2:lqaa086. [PMID: 33575631 PMCID: PMC7671329 DOI: 10.1093/nargab/lqaa086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/19/2020] [Indexed: 11/18/2022] Open
Abstract
Predicting RNA structure is crucial for understanding RNA’s mechanism of action. Comparative approaches for the prediction of RNA structures can be classified into four main strategies. The three first—align-and-fold, align-then-fold and fold-then-align—exploit multiple sequence alignments to improve the accuracy of conserved RNA-structure prediction. Align-and-fold methods perform generally better, but are also typically slower than the other alignment-based methods. The fourth strategy—alignment-free—consists in predicting the conserved RNA structure without relying on sequence alignment. This strategy has the advantage of being the faster, while predicting accurate structures through the use of latent representations of the candidate structures for each sequence. This paper presents aliFreeFoldMulti, an extension of the aliFreeFold algorithm. This algorithm predicts a representative secondary structure of multiple RNA homologs by using a vector representation of their suboptimal structures. aliFreeFoldMulti improves on aliFreeFold by additionally computing the conserved structure for each sequence. aliFreeFoldMulti is assessed by comparing its prediction performance and time efficiency with a set of leading RNA-structure prediction methods. aliFreeFoldMulti has the lowest computing times and the highest maximum accuracy scores. It achieves comparable average structure prediction accuracy as other methods, except TurboFoldII which is the best in terms of average accuracy but with the highest computing times. We present aliFreeFoldMulti as an illustration of the potential of alignment-free approaches to provide fast and accurate RNA-structure prediction methods.
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Affiliation(s)
- Marc-André Bossanyi
- CoBIUS lab, Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
| | - Valentin Carpentier
- CoBIUS lab, Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
| | - Jean-Pierre S Glouzon
- CoBIUS lab, Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
| | - Aïda Ouangraoua
- CoBIUS lab, Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
| | - Yoann Anselmetti
- CoBIUS lab, Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
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Epigenetic and non-coding regulation of alcohol abuse and addiction. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:63-86. [PMID: 33461665 DOI: 10.1016/bs.irn.2020.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alcohol use disorder is a chronic debilitated condition adversely affecting the lives of millions of individuals throughout the modern world. Individuals suffering from an alcohol use disorder diagnosis frequently have serious cooccurring conditions, which often further exacerbates problematic drinking behavior. Comprehending the biochemical processes underlying the progression and perpetuation of disease is essential for mitigating maladaptive behavior in order to restore both physiological and psychological health. The range of cellular and biological systems contributing to, and affected by, alcohol use disorder and other comorbid disorders necessitates a fundamental grasp of intricate functional relationships that govern molecular biology. Epigenetic factors are recognized as essential mediators of cellular behavior, orchestrating a symphony of gene expression changes within multicellular environments that are ultimately responsible for directing human behavior. Understanding the epigenetic and transcriptional regulatory mechanisms involved in the pathogenesis of disease is important for improving available pharmacotherapies and reducing the incidence of alcohol abuse and cooccurring conditions.
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118
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Shin TJ, Lee KH, Cho JY. Epigenetic Mechanisms of LncRNAs Binding to Protein in Carcinogenesis. Cancers (Basel) 2020; 12:E2925. [PMID: 33050646 PMCID: PMC7599656 DOI: 10.3390/cancers12102925] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Epigenetic dysregulation is an important feature for cancer initiation and progression. Long non-coding RNAs (lncRNAs) are transcripts that stably present as RNA forms with no translated protein and have lengths larger than 200 nucleotides. LncRNA can epigenetically regulate either oncogenes or tumor suppressor genes. Nowadays, the combined research of lncRNA plus protein analysis is gaining more attention. LncRNA controls gene expression directly by binding to transcription factors of target genes and indirectly by complexing with other proteins to bind to target proteins and cause protein degradation, reduced protein stability, or interference with the binding of other proteins. Various studies have indicated that lncRNA contributes to cancer development by modulating genes epigenetically and studies have been done to determine which proteins are combined with lncRNA and contribute to cancer development. In this review, we look in depth at the epigenetic regulatory function of lncRNAs that are capable of complexing with other proteins in cancer development.
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Affiliation(s)
| | | | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (T.-J.S.); (K.-H.L.)
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119
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Chen M, Huang B, Zhu L, Chen K, Liu M, Zhong C. Structural and Functional Overview of TEAD4 in Cancer Biology. Onco Targets Ther 2020; 13:9865-9874. [PMID: 33116572 PMCID: PMC7547805 DOI: 10.2147/ott.s266649] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/13/2020] [Indexed: 12/11/2022] Open
Abstract
TEA domain transcription factor 4 (TEAD4) is an important member of the TEAD family. As a downstream effector of the Hippo pathway, TEAD4 has essential roles in cell proliferation, cell survival, tissue regeneration, and stem cell maintenance. TEAD4 contains a TEA DNA binding domain that binds the promoters of target genes and a Yes-associated protein/transcriptional co-activator with PDZ-binding motif (YAP/TAZ) binding domain that associates with transcriptional cofactors. TEAD4 coordinates with YAP, TAZ, VGLL, and other transcription factors to regulate different cellular processes in cancer via its transcriptional output. Moreover, TEAD4 undergoes post-translational modifications and subcellular translocations, and both processes have been shown to shed new insights on how TEAD transcriptional activity can be modified. In summary, TEAD4 has important roles in cancer, including epithelial-mesenchymal transition (EMT), metastasis, cancer stem cell dynamics, and chemotherapeutic drug resistance, suggesting that TEAD4 may be a promising prognostic biomarker in cancer.
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Affiliation(s)
- Mu Chen
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai200120, People’s Republic of China
| | - Bingsong Huang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai200120, People’s Republic of China
| | - Lei Zhu
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai200120, People’s Republic of China
| | - Kui Chen
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai200120, People’s Republic of China
| | - Min Liu
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai200120, People’s Republic of China
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai200120, People’s Republic of China
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120
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Zhou H, Li F, Ye W, Wang M, Zhou X, Feng J, Liu L, Wang X. Correlation Between Plasma CircRNA-089763 and Postoperative Cognitive Dysfunction in Elderly Patients Undergoing Non-cardiac Surgery. Front Behav Neurosci 2020; 14:587715. [PMID: 33132863 PMCID: PMC7573279 DOI: 10.3389/fnbeh.2020.587715] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/07/2020] [Indexed: 11/13/2022] Open
Abstract
In our previous experiment, we found that there were abnormal levels of circRNA-089763 in the plasma exosomes of patients with postoperative cognitive dysfunction (POCD) after cardiac surgery. Therefore, the aim of this study was to further investigate the relationship between plasma circRNA-089763 level and POCD in elderly patients after non-cardiac surgery. A prospective cohort study was conducted to select elderly patients undergoing elective non-cardiac surgery. A total of 72 patients were enrolled in this study, and cognitive functions were assessed 1 day before and 3 days after surgery by a series of neuropsychological measurements. Next, patients were divided into POCD and non-POCD (NPOCD) groups according to the Z score method. Blood was collected the day before and 3 days after surgery, and the plasma circRNA-089763 level was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Then, the difference and correlation in plasma circRNA-089763 levels between the POCD and NPOCD groups were analyzed. On the third day after surgery, the incidence of POCD was 30.56%. The relative level of circRNA-089763 in the POCD group was 2.41 times higher than that in the NPOCD group (t = 4.711, p < 0.001), patients in POCD group had higher age (t = 5.971, p < 0.001), higher American Society of Anesthesiologists classification (χ2 = 14.726, p < 0.001), less years of education (t = 2.449, p = 0.017), more intraoperative blood loss (t = 3.196, p = 0.002), and higher visual analog scale (VAS) scores (t = 10.45, p < 0.001). The binary logistic regression analysis showed that the circRNA-089763 level, age, and intraoperative blood loss were independently associated with POCD (OR: 2.75, 95% CI: 1.261–5.999, p = 0.011; OR: 1.32, 95% CI: 1.114–1.565, p = 0.001; OR: 1.017, 95% CI: 1.004–1.03, p = 0.011). These results demonstrated that the circRNA-089763 plasma level was related to POCD after non-cardiac surgery in elderly patients.
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Affiliation(s)
- Hongli Zhou
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Fuyu Li
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Wanlin Ye
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Maozhou Wang
- Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xian Zhou
- Department of Internal Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jianguo Feng
- Laboratory of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Li Liu
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiaobin Wang
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Safarzadeh E, Asadzadeh Z, Safaei S, Hatefi A, Derakhshani A, Giovannelli F, Brunetti O, Silvestris N, Baradaran B. MicroRNAs and lncRNAs-A New Layer of Myeloid-Derived Suppressor Cells Regulation. Front Immunol 2020; 11:572323. [PMID: 33133086 PMCID: PMC7562789 DOI: 10.3389/fimmu.2020.572323] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/28/2020] [Indexed: 12/23/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) constitute an important component in regulating immune responses in several abnormal physiological conditions such as cancer. Recently, novel regulatory tumor MDSC biology modulating mechanisms, including differentiation, expansion and function, were defined. There is growing evidence that miRNAs and long non-coding RNAs (lncRNA) are involved in modulating transcriptional factors to become complex regulatory networks that regulate the MDSCs in the tumor microenvironment. It is possible that aberrant expression of miRNAs and lncRNA contributes to MDSC biological characteristics under pathophysiological conditions. This review provides an overview on miRNAs and lncRNAs epiregulation of MDSCs development and immunosuppressive functions in cancer.
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Affiliation(s)
- Elham Safarzadeh
- Department of Microbiology & Immunology, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Asadzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sahar Safaei
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Arash Hatefi
- Department of Pharmaceutics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Afshin Derakhshani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Medical Oncology Unit-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Francesco Giovannelli
- Medical Oncology Unit-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Oronzo Brunetti
- Medical Oncology Unit-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Nicola Silvestris
- Medical Oncology Unit-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy.,Department of Biomedical Sciences and Human Oncology, Department of Internal Medicine and Oncology (DIMO)-University of Bari, Bari, Italy
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Role of Non-coding RNAs in Fungal Pathogenesis and Antifungal Drug Responses. CURRENT CLINICAL MICROBIOLOGY REPORTS 2020. [DOI: 10.1007/s40588-020-00151-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abstract
Purpose of Review
Non-coding RNAs (ncRNAs), including regulatory small RNAs (sRNAs) and long non-coding RNAs (lncRNAs), constitute a significant part of eukaryotic genomes; however, their roles in fungi are just starting to emerge. ncRNAs have been shown to regulate gene expression in response to varying environmental conditions (like stress) and response to chemicals, including antifungal drugs. In this review, I highlighted recent studies focusing on the functional roles of ncRNAs in pathogenic fungi.
Recent Findings
Emerging evidence suggests sRNAs (small RNAs) and lncRNAs (long non-coding RNAs) play an important role in fungal pathogenesis and antifungal drug response. Their roles include posttranscriptional gene silencing, histone modification, and chromatin remodeling. Fungal pathogens utilize RNA interference (RNAi) mechanisms to regulate pathogenesis-related genes and can also transfer sRNAs inside the host to suppress host immunity genes to increase virulence. Hosts can also transfer sRNAs to induce RNAi in fungal pathogens to reduce virulence. Additionally, sRNAs and lncRNAs also regulate gene expression in response to antifungal drugs increasing resistance (and possibly tolerance) to drugs.
Summary
Herein, I discuss what is known about ncRNAs in fungal pathogenesis and antifungal drug responses. Advancements in genomic technologies will help identify the ncRNA repertoire in fungal pathogens, and functional studies will elucidate their mechanisms. This will advance our understanding of host-fungal interactions and potentially help develop better treatment strategies.
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123
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Chantsalnyam T, Lim DY, Tayara H, Chong KT. ncRDeep: Non-coding RNA classification with convolutional neural network. Comput Biol Chem 2020; 88:107364. [DOI: 10.1016/j.compbiolchem.2020.107364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/04/2020] [Accepted: 08/18/2020] [Indexed: 12/21/2022]
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Cai Y, Li Y, Sun B, Wang H, Zhang W, Zhao Y, Zhao H, Zhang J, Xu J, Wang Y. LncRNA PTCSC3 and lncRNA HULC Negatively Affect Each Other to Regulate Cancer Cell Invasion and Migration in Gastric Cancer. Cancer Manag Res 2020; 12:8535-8543. [PMID: 32982446 PMCID: PMC7502400 DOI: 10.2147/cmar.s254944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/13/2020] [Indexed: 11/23/2022] Open
Abstract
Background LncRNA PTCSC3 (PTCSC3) inhibits thyroid cancer cervical carcinoma and glioma, while its roles in gastric cancer are unknown. Studies have reported that HULC could serve as a potential biomarker for the diagnosis and prognosis of gastric cancer (GC). Our study aimed to investigate the potential interaction between PTCSC3 and HULC in gastric cancer. Methods This study enrolled 77 gastric cancer patients at the First Affiliated Hospital of Anhui Medical University from January 2016 to January 2018. RT-qPCR was performed to analyze gene expression levels. Cell transfections were carried out to evaluate gene interactions. Transwell assays and wound healing assays were used to analyze the effects of transfection on cell invasion and migration. Western blotting was also used to illustrate the possibility that lncRNA PTCSC3 and lncRNA HULC negatively affected each other through WNT signal path. Results We showed that PTCSC3 was downregulated in tumor tissues of gastric cancer patients in comparison to that in adjacent healthy tissues, and an inverse correlation between the expression levels of PTCSC3 and AJCC stage was observed. LncRNA HULC (HULC) was upregulated in tumor and inversely correlated with PTCSC3 in tumor tissues. Overexpression of PTCSC3 mediated the inhibition of HULC, while overexpression of HULC also mediated the inhibition of PTCSC3. PTCSC3 inhibited, while HULC promoted invasion and migration of gastric cancer cells. In addition, overexpression of HULC attenuated the effects of overexpression of PTCSC3. However, overexpression of PTCSC3 showed no significant effects on cell proliferation. We also found that PTCSC3/HULC affected each other to regulate cell invasion and migration through the Wnt/β-catenin signaling. Conclusion Therefore, overexpression of PTCSC3 inhibited the invasion and migration of gastric cancer cells, and the function of PTCSC3 is associated with HULC.
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Affiliation(s)
- Yi Cai
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Yang Li
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Bin Sun
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Hugen Wang
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Weiping Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Yuanyuan Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Haodong Zhao
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Jianlin Zhang
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Jianming Xu
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Yalei Wang
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
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Abstract
Circular RNAs (circRNAs) are covalently circularized RNA moieties that despite being relatively abundant were only recently identified and have only begun to be investigated within the last couple of years. Even though there are many thousands of genes that appear capable of producing circRNAs, and the fact that many circRNAs appear to be highly evolutionarily conserved, the function of all but a few remain to be fully explored. What has been determined, however, is that circRNAs play key regulatory roles in many aspects of biology with focus being given to their function in cancer. Most of the studies to date have found that circRNAs act as master regulator of gene expression most often than not acting to regulate levels though sequestration or "sponging" of other gene expression regulators, particularly miRNAs. They can also function directly modulating transcription, or by interfering with splicing mechanisms. Some circRNAs can also be translated into functional proteins or peptides. A combination of tissue and developmental stage specific expression along with an innate resistance to RNAse activity means that circRNAs show perhaps their greatest potential as novel biomarkers of cancer. In this chapter we consider the current state of knowledge regarding these molecules, their synthesis, function, and association with cancer. We also consider some of the challenges that remain to be overcome to allow this emerging class of RNAs to fulfill their potential in clinical practice.
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Affiliation(s)
- Carla Solé
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain
| | - Charles Henderson Lawrie
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
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Hu TJ, Huang HB, Shen HB, Chen W, Yang ZH. Role of long non-coding RNA MALAT1 in chronic obstructive pulmonary disease. Exp Ther Med 2020; 20:2691-2697. [PMID: 32765763 PMCID: PMC7401856 DOI: 10.3892/etm.2020.8996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a pathological inflammatory condition of the lungs that is associated with high rates of mortality. Although long non-coding RNAs (lncRNAs) serve a role in lung diseases, their functions in COPD pathogenesis are relatively unknown. The present study aimed to assess the role of differentially expressed lncRNAs in COPD. Expression profile analysis of six lncRNAs in age-matched COPD and non-COPD tissues were conducted. Among the six tested lncRNAs, metastasis-associated in lung adenocarcinoma transcript 1 (MALAT1) was the most consistently overexpressed in COPD lung tissue specimens. To model COPD in vitro, human lung fibroblasts were treated with transforming growth factor-β (TGF-β) and MALAT1 was knocked down by small interfering RNA. This promoted cell viability and concurrently inhibited the expression of mesenchymal proteins, fibronectin and α-smooth muscle actin. In COPD, cell senescence is linked to the activation of mammalian target of rapamycin complex 1 (mTORC1). Upon gene silencing of MALAT1 in non-TGF-β-treated cells, cells demonstrated constitutive activation of mTORC1, which was assessed by the protein expression levels of mTORC1 substrate S6 kinase (S6K1). By contrast, upon MALAT1 silencing in the TGF-β-treated cells, mTORC1 activation was not suppressed, despite the mesenchymal cell markers protein expression levels being downregulated. Thus, lncRNA MALAT1 may represent a potent biomarker in COPD patients and may act as a target for both diagnostic and therapeutic purposes.
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Affiliation(s)
- Tian-Jun Hu
- Department of Thoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315012, P.R. China
| | - Hong-Bo Huang
- Department of Thoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315012, P.R. China
| | - Hai-Bo Shen
- Department of Thoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315012, P.R. China
| | - Wei Chen
- Zhongyuan Union Clinical Laboratory Co. Ltd., Tianjin 300384, P.R. China
- Zhongyuan-Vcan Genetic Technology Co. Ltd., Beijing 100176, P.R. China
| | - Zhen-Hua Yang
- Department of Thoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315012, P.R. China
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127
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Alves MBR, Celeghini ECC, Belleannée C. From Sperm Motility to Sperm-Borne microRNA Signatures: New Approaches to Predict Male Fertility Potential. Front Cell Dev Biol 2020; 8:791. [PMID: 32974342 PMCID: PMC7471662 DOI: 10.3389/fcell.2020.00791] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
In addition to the paternal genome, spermatozoa carry several intrinsic factors, including organelles (e.g., centrioles and mitochondria) and molecules (e.g., proteins and RNAs), which are involved in important steps of reproductive biology such as spermatogenesis, sperm maturation, oocyte fertilization and embryo development. These factors constitute potential biomarkers of "viable sperm" and male fertility status and may become major assets for diagnosing instances of idiopathic male infertility in both humans and livestock animals. A better understanding of the mechanism of action of these sperm intrinsic factors in the regulation of reproductive and developmental processes still presents a major challenge that must be addressed. This review assembles the main data regarding morpho-functional and intrinsic sperm features that are associated with male infertility, with a particular focus on microRNA (miRNA) molecules.
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Affiliation(s)
- Maíra Bianchi Rodrigues Alves
- CHU de Québec Research Center (CHUL), Department of Obstetrics, Gynecology and Reproduction, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.,Department of Animal Reproduction, Universidade de São Paulo, Pirassununga, Brazil
| | | | - Clémence Belleannée
- CHU de Québec Research Center (CHUL), Department of Obstetrics, Gynecology and Reproduction, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
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128
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Chen Q, Meng X, Liao Q, Chen M. Versatile interactions and bioinformatics analysis of noncoding RNAs. Brief Bioinform 2020; 20:1781-1794. [PMID: 29939215 DOI: 10.1093/bib/bby050] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Indexed: 02/07/2023] Open
Abstract
Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as inconsequential results of transcriptional promiscuity, ncRNAs were later found to exert great roles in various aspects of biological functions. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). Here, we provide an overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions. To better investigate the ncRNA-mediated regulation, it is necessary to make full use of innovative sequencing techniques and computational tools. We further describe a comprehensive workflow for in silico ncRNA analysis, providing up-to-date platforms, databases and tools dedicated to ncRNA identification and functional annotation.
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Affiliation(s)
- Qi Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Qi Liao
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Ming Chen
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University, Ningbo, Zhejiang, P. R. China
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129
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Gu H, Cheng X, Xu J, Zhou K, Bian C, Chen G, Yin X. Circular RNA circFAT1(e2) Promotes Osteosarcoma Progression and Metastasis by Sponging miR-181b and Regulating HK2 Expression. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3589871. [PMID: 32733938 PMCID: PMC7378629 DOI: 10.1155/2020/3589871] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/17/2020] [Indexed: 01/14/2023]
Abstract
As a subclass of noncoding RNAs, circular RNAs (circRNAs) have been demonstrated to play a critical role in regulating gene expression in eukaryotes. Recent studies have revealed the pivotal functions of circRNAs in cancer progression. Nevertheless, how circRNAs participate in osteosarcoma (OS) development and progression are not well understood. In the present study, we identified a circRNA circFAT1(e2) with an upregulated expression level in OS tissues. By functional experiments, we found that circFAT1(e2) depletion significantly suppressed the proliferation and reduced migration in OS. In terms of mechanism, we found that circFAT1(e2) inhibited miR-181b, while miR-181b targeted HK2. By releasing the inhibition of miR-181b on HK2 expression, leading to attenuated OS progression. Mechanistic investigations suggested that circFAT1(e2) served as a competing endogenous RNA (ceRNA) of miR-181b to enhance HK2 expression. On the whole, our study indicated that circFAT1(e2) exerted oncogenic roles in OS and suggested the circFAT1(e2)/miR-181b/HK2 axis might be a potential therapeutic target.
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Affiliation(s)
- Huijie Gu
- Department of Orthopaedics, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai 201199, China
| | - Xiangyang Cheng
- Department of Orthopaedics, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai 201199, China
| | - Jun Xu
- Department of Orthopaedics, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai 201199, China
| | - Kaifeng Zhou
- Department of Orthopaedics, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai 201199, China
| | - Chong Bian
- Department of Orthopaedics, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai 201199, China
| | - Guangnan Chen
- Department of Orthopaedics, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai 201199, China
| | - Xiaofan Yin
- Department of Orthopaedics, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai 201199, China
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130
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Liu Y, Cheng G, Huang Z, Bao L, Liu J, Wang C, Xiong Z, Zhou L, Xu T, Liu D, Yang H, Chen K, Zhang X. Long noncoding RNA SNHG12 promotes tumour progression and sunitinib resistance by upregulating CDCA3 in renal cell carcinoma. Cell Death Dis 2020; 11:515. [PMID: 32641718 PMCID: PMC7343829 DOI: 10.1038/s41419-020-2713-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022]
Abstract
Renal cell carcinoma (RCC) is one of the most frequently observed malignant tumours in the urinary system and targeted drug resistance is quite common in RCC. Long noncoding RNA SNHG12 (lncRNA SNHG12) has emerged as a key molecule in numerous human cancers, but its functions in renal cell carcinoma (RCC) sunitinib resistance remain unclear. In this study, we found SNHG12 was highly expressed in RCC tissues and in sunitinib-resistant RCC cells and was associated with a poor clinical prognosis. SNHG12 promoted RCC proliferation, migration, invasion and sunitinib resistance via CDCA3 in vitro. Mechanically, SNHG12 bound to SP1 and prevented the ubiquitylation-dependent proteolysis of SP1. Stabilised SP1 bound to a specific region in the promoter of CDCA3 and increased CDCA3 expression. Furthermore, in vivo experiments showed that SNHG12 increased tumour growth and that knocking down SNHG12 could reverse RCC sunitinib resistance. Our study revealed that the lncRNA SNHG12/SP1/CDCA3 axis promoted RCC progression and sunitinib resistance, which could provide a new therapeutic target for sunitinib-resistant RCC.
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Affiliation(s)
- Yuenan Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Gong Cheng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Ziwei Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Lin Bao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Jingchong Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Cheng Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Zhiyong Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Lijie Zhou
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Tianbo Xu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Di Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China
| | - Hongmei Yang
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, No. 13 Hangkong Road, 430030, Wuhan, China
| | - Ke Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China.
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, 430022, Wuhan, China.
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131
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Yu Y, Chang Z, Han C, Zhuang L, Zhou C, Qi X, Peng Z. Long non-coding RNA MINCR aggravates colon cancer via regulating miR-708-5p-mediated Wnt/β-catenin pathway. Biomed Pharmacother 2020; 129:110292. [PMID: 32535381 DOI: 10.1016/j.biopha.2020.110292] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/11/2020] [Accepted: 05/16/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Increasing evidence has found that the dysregulation of long non-coding RNAs (lncRNAs) may be important indicators in tumorigenesis. MYC-induced long non-coding RNA (MINCR) has been found to be related with some cancers, such as non-small cell lung cancer and gallbladder cancer. Besides, MINCR has potentially prognostic value for colon cancer (CC) patients' prognosis, yet its function and molecular mechanism in CC are not explored. METHODS qRT-PCR evaluated gene expression, and western blot detected protein level. In vitro and in vivo experiments were adopted to understand the biological role of MINCR in CC. TOP/FOP Flash assay was performed to measure the activity of Wnt/β-catenin pathway. RNA pull down, luciferase reporter and RIP assays were utilized to analyze the relationship among genes. Immunohistochemistry and HE staining techniques were utilized to evaluate Ki67 staining in xenografts. RESULTS MINCR was up-regulated in CC cells. Knockdown of MINCR suppressed cell proliferation and migration. MINCR could up-regulate CTNNB1 via sequestering miR-708-5p, resulting in activated Wnt/β-catenin pathway. The addition of LiCl treatment, miR-708-5p inhibitor or pcDNA3.1/CTNNB1 abolished the inhibitory impacts induced by MINCR silence in CC progression. CONCLUSION MINCR sponges miR-708-5p to up-regulate CTNNB1 and activate Wnt/β-catenin pathway, thus promoting the development CC. Targeting MINCR might shed new light on the therapeutic strategies of CC.
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Affiliation(s)
- Yang Yu
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China.
| | - Zhuo Chang
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Chao Han
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Lingling Zhuang
- Department of Ultrasound, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Chongzhi Zhou
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Xiaosheng Qi
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Zhihai Peng
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China.
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132
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Nguyen TM, Alchalabi S, Oluwatoyosi A, Ropri AS, Herschkowitz JI, Rosen JM. New twists on long noncoding RNAs: from mobile elements to motile cancer cells. RNA Biol 2020; 17:1535-1549. [PMID: 32522127 DOI: 10.1080/15476286.2020.1760535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The purpose of this review is to highlight several areas of lncRNA biology and cancer that we hope will provide some new insights for future research. These include the relationship of lncRNAs and the epithelial to mesenchymal transition (EMT) with a focus on transcriptional and alternative splicing mechanisms and mRNA stability through miRNAs. In addition, we highlight the potential role of enhancer e-lncRNAs, the importance of transposable elements in lncRNA biology, and finally the emerging area of using antisense oligonucleotides (ASOs) and small molecules to target lncRNAs and their therapeutic implications.
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Affiliation(s)
- Tuan M Nguyen
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School , Boston, MA, USA.,Cancer Research Institute, Beth Israel Deaconess Medical Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston, MA, USA
| | - Sumayya Alchalabi
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, SUNY , Rensselaer, NY, USA
| | - Adewunmi Oluwatoyosi
- Department of Molecular & Cellular Biology, Baylor College of Medicine , Houston, TX, USA
| | - Ali S Ropri
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, SUNY , Rensselaer, NY, USA
| | - Jason I Herschkowitz
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, SUNY , Rensselaer, NY, USA
| | - Jeffrey M Rosen
- Department of Molecular & Cellular Biology, Baylor College of Medicine , Houston, TX, USA
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133
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Rusconi F, Battaglioli E, Venturin M. Psychiatric Disorders and lncRNAs: A Synaptic Match. Int J Mol Sci 2020; 21:ijms21093030. [PMID: 32344798 PMCID: PMC7246907 DOI: 10.3390/ijms21093030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
Psychiatric disorders represent a heterogeneous class of multifactorial mental diseases whose origin entails a pathogenic integration of genetic and environmental influences. Incidence of these pathologies is dangerously high, as more than 20% of the Western population is affected. Despite the diverse origins of specific molecular dysfunctions, these pathologies entail disruption of fine synaptic regulation, which is fundamental to behavioral adaptation to the environment. The synapses, as functional units of cognition, represent major evolutionary targets. Consistently, fine synaptic tuning occurs at several levels, involving a novel class of molecular regulators known as long non-coding RNAs (lncRNAs). Non-coding RNAs operate mainly in mammals as epigenetic modifiers and enhancers of proteome diversity. The prominent evolutionary expansion of the gene number of lncRNAs in mammals, particularly in primates and humans, and their preferential neuronal expression does represent a driving force that enhanced the layering of synaptic control mechanisms. In the last few years, remarkable alterations of the expression of lncRNAs have been reported in psychiatric conditions such as schizophrenia, autism, and depression, suggesting unprecedented mechanistic insights into disruption of fine synaptic tuning underlying severe behavioral manifestations of psychosis. In this review, we integrate literature data from rodent pathological models and human evidence that proposes the biology of lncRNAs as a promising field of neuropsychiatric investigation.
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Affiliation(s)
- Francesco Rusconi
- Correspondence: (F.R.); (M.V.); Tel.: +39-02-503-30445 (F.R.); +39-02-503-30443 (M.V.)
| | | | - Marco Venturin
- Correspondence: (F.R.); (M.V.); Tel.: +39-02-503-30445 (F.R.); +39-02-503-30443 (M.V.)
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134
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Chu LY, Peng YH, Weng XF, Xie JJ, Xu YW. Blood-based biomarkers for early detection of esophageal squamous cell carcinoma. World J Gastroenterol 2020; 26:1708-1725. [PMID: 32351288 PMCID: PMC7183865 DOI: 10.3748/wjg.v26.i15.1708] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 03/13/2020] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common malignant tumor of the digestive system worldwide, especially in China. Due to the lack of effective early detection methods, ESCC patients often present at an advanced stage at the time of diagnosis, which seriously affects the prognosis of patients. At present, early detection of ESCC mainly depends on invasive and expensive endoscopy and histopathological biopsy. Therefore, there is an unmet need for a non-invasive method to detect ESCC in the early stages. With the emergence of a large class of non-invasive diagnostic tools, serum tumor markers have attracted much attention because of their potential for detection of early tumors. Therefore, the identification of serum tumor markers for early detection of ESCC is undoubtedly one of the most effective ways to achieve early diagnosis and treatment of ESCC. This article reviews the recent advances in the discovery of blood-based ESCC biomarkers, and discusses the origins, clinical applications, and technical challenges of clinical validation of various types of biomarkers.
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Affiliation(s)
- Ling-Yu Chu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yu-Hui Peng
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Xue-Fen Weng
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Jian-Jun Xie
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yi-Wei Xu
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, Guangdong Province, China
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135
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Liao Y, Zhang B, Zhang T, Zhang Y, Wang F. LncRNA GATA6-AS Promotes Cancer Cell Proliferation and Inhibits Apoptosis in Glioma by Downregulating lncRNA TUG1. Cancer Biother Radiopharm 2020; 34:660-665. [PMID: 31809214 DOI: 10.1089/cbr.2019.2830] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: Long noncoding RNA (lncRNA) GATA6-AS regulates the growth of endothelial cells, indicating its involvement in human diseases. The present study aimed to investigate the roles of GATA6-AS in glioma. Results: GATA6-AS was significantly upregulated in glioma. GATA6-AS levels in plasma was positively and significantly correlated with its expression levels in glioma tissues. TUG1 was significantly downregulated in glioma and was inversely correlated with GATA6-AS. GATA6-AS overexpression led to TUG1 downregulation, whereas TUG1 overexpression failed to significantly affect GATA6-AS. GATA6-AS overexpression promoted glioma cell proliferation and inhibited apoptosis, TUG1 overexpression inhibited cell proliferation and attenuated the effects of GATA6-AS overexpression. Conclusions: Therefore, lncRNA GATA6-AS affects cell proliferation and apoptosis and regulates TUG1 expression in glioma.
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Affiliation(s)
- Yuzhi Liao
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
| | - Baozhong Zhang
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
| | - Ting Zhang
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
| | - Yiming Zhang
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
| | - Fei Wang
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
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136
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Fehlmann T, Sahay S, Keller A, Backes C. A review of databases predicting the effects of SNPs in miRNA genes or miRNA-binding sites. Brief Bioinform 2020; 20:1011-1020. [PMID: 29186316 DOI: 10.1093/bib/bbx155] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/23/2017] [Indexed: 12/16/2022] Open
Abstract
Modern precision medicine comprises the knowledge and understanding of individual differences in the genomic sequence of patients to provide tailor-made treatments. Regularly, such variants are considered in coding regions only, and their effects are predicted based on their impact on the amino acid sequence of expressed proteins. However, assessing the effects of variants in noncoding elements, in particular microRNAs (miRNAs) and their binding sites, is important as well, as a single miRNA can influence the expression patterns of many genes at the same time. To analyze the effects of variants in miRNAs and their target sites, several databases storing variant impact predictions have been published. In this review, we will compare the core functionalities and features of these databases and discuss the importance of up-to-date data resources in the context of web applications. Finally, we will outline some recommendations for future developments in the field.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Shashwat Sahay
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
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137
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Liu F, Hu L, Pei Y, Zheng K, Wang W, Li S, Qiu E, Shang G, Zhang J, Zhang X. Long non-coding RNA AFAP1-AS1 accelerates the progression of melanoma by targeting miR-653-5p/RAI14 axis. BMC Cancer 2020; 20:258. [PMID: 32228518 PMCID: PMC7106910 DOI: 10.1186/s12885-020-6665-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/20/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Melanoma is the most aggressive skin cancer that derived from pigment cells, accounting for the majority of the skin-cancer-related deaths. Despite great development and evolution have been made in surgery, radiotherapy and adjuvant chemotherapy, the prognosis of melanoma patients exhibited no significant improvement. Long noncoding RNAs (lncRNAs) are frequently dysregulated and involved in the development of cancers. LncRNA AFAP1-AS1 has been explored in various cancers, whereas its role and regulatory mechanism in melanoma are not well understood. METHODS The expression of AFAP1-AS1 was detected by qRT-PCR. CCK-8, colony formation, transwell and western blot assays were performed to investigate the biological role of AFAP1-AS1 in melanoma. Male BALB/c nude mice were applied for in vivo experiments. The interaction among AFAP1-AS1, miR-653-5p and RAI14 was investigated by RNA pull down, RIP and luciferase reporter assays. RESULTS AFAP1-AS1 was highly expressed in melanoma cell lines. Suppression of AFAP1-AS1 impaired cell proliferation, migration, invasion and EMT in melanoma. Moreover, AFAP1-AS1 was a ceRNA of RAI14 by competitively binding with miR-653-5p. Besides, miR-653-5p overexpression or RAI14 inhibition could repress tumor growth. Eventually, rescue assays indicated that the function of AFAP1-AS1 in the cellular process of melanoma was dependent on miR-653-5p and RAI14. CONCLUSIONS AFAP1-AS1 exerts its oncogenic function in melanoma by targeting miR-653-5p/RAI14 axis.
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Affiliation(s)
- Fei Liu
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110000, Liaoning, China
| | - Lanting Hu
- Department of Dermatology, the Seventh People's Hospital of Shenyang, Shenyang, 110000, Liaoning Province, China
| | - Yi Pei
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110000, Liaoning, China
| | - Ke Zheng
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110000, Liaoning, China
| | - Wei Wang
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110000, Liaoning, China
| | - Shenglong Li
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110000, Liaoning, China
| | - Enduo Qiu
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110000, Liaoning, China
| | - Guanning Shang
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110000, Liaoning, China
| | - Jiaming Zhang
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110000, Liaoning, China
| | - Xiaojing Zhang
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110000, Liaoning, China.
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138
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Chellini L, Frezza V, Paronetto MP. Dissecting the transcriptional regulatory networks of promoter-associated noncoding RNAs in development and cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:51. [PMID: 32183847 PMCID: PMC7079525 DOI: 10.1186/s13046-020-01552-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 02/25/2020] [Indexed: 12/31/2022]
Abstract
In-depth analysis of global RNA sequencing has enabled a comprehensive overview of cellular transcriptomes and revealed the pervasive transcription of divergent RNAs from promoter regions across eukaryotic genomes. These studies disclosed that genomes encode a vast repertoire of RNAs beyond the well-known protein-coding messenger RNAs. Furthermore, they have provided novel insights into the regulation of eukaryotic epigenomes, and transcriptomes, including the identification of novel classes of noncoding transcripts, such as the promoter-associated noncoding RNAs (pancRNAs). PancRNAs are defined as transcripts transcribed within few hundred bases from the transcription start sites (TSSs) of protein-coding or non-coding genes. Unlike the long trans-acting ncRNAs that regulate expression of target genes located in different chromosomal domains and displaying their function both in the nucleus and in the cytoplasm, the pancRNAs operate as cis-acting elements in the transcriptional regulation of neighboring genes. PancRNAs are very recently emerging as key players in the epigenetic regulation of gene expression programs in development and diseases. Herein, we review the complex epigenetic network driven by pancRNAs in eukaryotic cells, their impact on physiological and pathological states, which render them promising targets for novel therapeutic strategies.
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Affiliation(s)
- Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, 00143, Rome, Italy
| | - Valentina Frezza
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, 00143, Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, 00143, Rome, Italy. .,Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135, Rome, Italy.
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139
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O'Neill RJ. Seq'ing identity and function in a repeat-derived noncoding RNA world. Chromosome Res 2020; 28:111-127. [PMID: 32146545 PMCID: PMC7393779 DOI: 10.1007/s10577-020-09628-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 01/06/2023]
Abstract
Innovations in high-throughout sequencing approaches are being marshaled to both reveal the composition of the abundant and heterogeneous noncoding RNAs that populate cell nuclei and lend insight to the mechanisms by which noncoding RNAs influence chromosome biology and gene expression. This review focuses on some of the recent technological developments that have enabled the isolation of nascent transcripts and chromatin-associated and DNA-interacting RNAs. Coupled with emerging genome assembly and analytical approaches, the field is poised to achieve a comprehensive catalog of nuclear noncoding RNAs, including those derived from repetitive regions within eukaryotic genomes. Herein, particular attention is paid to the challenges and advances in the sequence analyses of repeat and transposable element-derived noncoding RNAs and in ascribing specific function(s) to such RNAs.
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Affiliation(s)
- Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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140
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Abbasifard M, Kamiab Z, Bagheri-Hosseinabadi Z, Sadeghi I. The role and function of long non-coding RNAs in osteoarthritis. Exp Mol Pathol 2020; 114:104407. [PMID: 32088191 DOI: 10.1016/j.yexmp.2020.104407] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 01/03/2020] [Accepted: 02/19/2020] [Indexed: 12/20/2022]
Abstract
Osteoarthiritis (OA) is the most prevalent disease of articulating joints in human that frequently results in joint pain, movement limitations, inflammation, and progressive degradation of articular cartilage. The etiology of OA is not completely clear and there is no full treatment for this disease. Molecular investigations have revealed the involvement of non-coding RNAs such as Long non-coding RNAs (lncRNAs) in OA pathogenesis. LncRNAs play roles in multiple cellular and biological processes. Moreover, numerous lncRNAs are differentially expressed in human OA cartilage. In this review, we underlie the increasing evidence for the critical role of lncRNAs in OA pathogenesis reviewing the latest researches.
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Affiliation(s)
- Mitra Abbasifard
- Department of Internal Medicine, Ali-Ibn Abi-Talib Hospital, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Zahra Kamiab
- Department of Family Medicine, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Clinical Research Development Unit, Ali Ibn Abi Talib Hospital, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Zahra Bagheri-Hosseinabadi
- Department of Clinical Biochemistry, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.
| | - Iman Sadeghi
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain; CEINGE-biotecnologie avanzate, Naples, Italy.
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141
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Abstract
Liquid-liquid phase separation is emerging as the universal mechanism by which membraneless cellular granules form. Despite many previous studies on condensation of intrinsically disordered proteins and low complexity domains, we lack understanding about the role of RNA, which is the essential component of all ribonucleoprotein (RNP) granules. RNA, as an anionic polymer, is inherently an excellent platform for achieving multivalency and can accommodate many RNA binding proteins. Recent findings have highlighted the diverse function of RNA in tuning phase-separation propensity up or down, altering viscoelastic properties and thereby driving immiscibility between different condensates. In addition to contributing to the biophysical properties of droplets, RNA is a functionally critical constituent that defines the identity of cellular condensates and controls the temporal and spatial distribution of specific RNP granules. In this review, we summarize what we have learned so far about such roles of RNA in the context of in vitro and in vivo studies.
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Affiliation(s)
- Kevin Rhine
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Velinda Vidaurre
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA; .,Physics Frontier Center (Center for the Physics of Living Cells), University of Illinois, Urbana, Illinois 61801, USA
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142
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Haruna IL, Ekegbu UJ, Ullah F, Amirpour-Najafabadi H, Zhou H, Hickford JGH. Genetic variations and haplotypic diversity in the Myostatin gene of New Zealand cattle breeds. Gene 2020; 740:144400. [PMID: 31987910 DOI: 10.1016/j.gene.2020.144400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 01/02/2023]
Abstract
Myostatin (MSTN) is a circulating factor that is secreted by muscle cells, and that acts upon those cells to inhibit the proliferation of muscle fibres during pre-natal muscle growth. The Polymerase Chain Reaction (PCR) coupled with Single Strand Conformational Polymorphism (SSCP) analysis, was used to reveal variation in the bovine MSTN gene (MSTN) in 722 cattle from a variety of breeds farmed in New Zealand (NZ). These included Hereford, Angus, Charolais, Simmental, Red Poll, South Devon, Shorthorn, Murray Grey, cross-bred Holstein-Friesian × Jersey cattle, and other composite breeds of cattle. Sequence analysis of five regions of MSTN that encompassed coding and non-coding regions of the gene, revealed a total of twelve single-nucleotide substitutions (7 in intron 1 and 5 in a region spanning the intron 2 - exon 3 boundary), and a single nucleotide deletion. Of these 12 substitutions, five are reported here for the first time, whereas seven have been previously described. The deletion c.748-78del, was located in the intron 2 - exon 3 boundary region, and has been reported previously. No nucleotide variation was identified in exons 1, 2 and 3. A total of 18 extended haplotypes were resolved spanning two variable regions (intron 1 and the intron 2 - exon 3 boundary), some of which were common across the breeds, while others were peculiar to particular breeds. The genetic variations identified provide insight into the conserved and polymorphic nature of the coding and non-coding sequences of bovine MSTN respectively, and thus provides a baseline for further study into how variation in the gene might affect growth and carcass traits in NZ cattle.
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Affiliation(s)
- Ishaku L Haruna
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Ugonna J Ekegbu
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Farman Ullah
- Department of Biotechnology, University of Malakand, Dir lower 18800, Chakdara, Pakistan
| | | | - Huitong Zhou
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jon G H Hickford
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
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143
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LncRNA RP11-19E11 is an E2F1 target required for proliferation and survival of basal breast cancer. NPJ Breast Cancer 2020; 6:1. [PMID: 31934613 PMCID: PMC6944689 DOI: 10.1038/s41523-019-0144-4] [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: 07/17/2019] [Accepted: 11/20/2019] [Indexed: 12/31/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play key roles in the regulation of breast cancer initiation and progression. LncRNAs are differentially expressed in breast cancer subtypes. Basal-like breast cancers are generally poorly differentiated tumors, are enriched in embryonic stem cell signatures, lack expression of estrogen receptor, progesterone receptor, and HER2 (triple-negative breast cancer), and show activation of proliferation-associated factors. We hypothesized that lncRNAs are key regulators of basal breast cancers. Using The Cancer Genome Atlas, we identified lncRNAs that are overexpressed in basal tumors compared to other breast cancer subtypes and expressed in at least 10% of patients. Remarkably, we identified lncRNAs whose expression correlated with patient prognosis. We then evaluated the function of a subset of lncRNA candidates in the oncogenic process in vitro. Here, we report the identification and characterization of the chromatin-associated lncRNA, RP11-19E11.1, which is upregulated in 40% of basal primary breast cancers. Gene set enrichment analysis in primary tumors and in cell lines uncovered a correlation between RP11-19E11.1 expression level and the E2F oncogenic pathway. We show that this lncRNA is chromatin-associated and an E2F1 target, and its expression is necessary for cancer cell proliferation and survival. Finally, we used lncRNA expression levels as a tool for drug discovery in vitro, identifying protein kinase C (PKC) as a potential therapeutic target for a subset of basal-like breast cancers. Our findings suggest that lncRNA overexpression is clinically relevant. Understanding deregulated lncRNA expression in basal-like breast cancer may lead to potential prognostic and therapeutic applications.
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144
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Mulati M, Kobayashi Y, Takahashi A, Numata H, Saito M, Hiraoka Y, Ochi H, Sato S, Ezura Y, Yuasa M, Hirai T, Yoshii T, Okawa A, Inose H. The long noncoding RNA Crnde regulates osteoblast proliferation through the Wnt/β-catenin signaling pathway in mice. Bone 2020; 130:115076. [PMID: 31622775 DOI: 10.1016/j.bone.2019.115076] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 12/13/2022]
Abstract
In the past decade, a growing importance has been placed on understanding the significance of long noncoding RNAs (lncRNAs) in regulating development, metabolism, and homeostasis. Osteoblast proliferation and differentiation are essential elements in skeletal development, bone metabolism, and homeostasis. However, the underlying mechanisms of lncRNAs in the process of osteoblast proliferation and differentiation remain largely unknown. Through comprehensive analysis of lncRNAs during bone formation, we show that colorectal neoplasia differentially expressed (Crnde), previously viewed as a cancer-related lncRNA, is an important regulator of osteoblast proliferation and differentiation. Crnde was found to be expressed in osteoblasts, and its expression was induced by parathyroid hormone. Furthermore, Crnde knockout mice developed a low bone mass phenotype due to impaired osteoblast proliferation and differentiation. Overexpression of Crnde in osteoblasts promoted their proliferation, and conversely, reduced Crnde expression inhibited osteoblast proliferation. Although ablation of Crnde inhibited osteoblast differentiation, overexpression of Crnde restored it. Finally, we provided evidence that Crnde modulates bone formation through Wnt/β-catenin signaling. Therefore, our data suggest that Crnde is a novel regulator of bone metabolism.
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Affiliation(s)
- Mieradili Mulati
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Yutaka Kobayashi
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Akira Takahashi
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Hoashi Numata
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Masanori Saito
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Yuichi Hiraoka
- Laboratory of Molecular Neuroscience, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan; Laboratory of Genome Editing for Biomedical Research, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hiroki Ochi
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Shingo Sato
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Yoichi Ezura
- Department of Molecular Pharmacology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masato Yuasa
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takashi Hirai
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Toshitaka Yoshii
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Atsushi Okawa
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Hiroyuki Inose
- Department of Orthopedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan.
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145
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Liu Y, Liu Q, Li Z, Acharya A, Chen D, Chen Z, Mattheos N, Chen Z, Huang B. Long non-coding RNA and mRNA expression profiles in peri-implantitis vs periodontitis. J Periodontal Res 2019; 55:342-353. [PMID: 31853997 DOI: 10.1111/jre.12718] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND OBJECTIVE Peri-implantitis is a biofilm-mediated infectious disease that results in progressive loss of implant-supporting bone. As compared to its analogue periodontitis, peri-implantitis is generally known to be more aggressive, with comparatively rapid progression and less predictable treatment outcomes, especially when advanced. An understanding of molecular mechanisms underpinning the similarities and differences between peri-implantitis and periodontitis is essential to develop novel management strategies. This study aimed to compare long non-coding RNAs (lncRNAs) and messenger RNA (mRNA) expression profiles between peri-implantitis and periodontitis. METHODS Inflamed soft tissue from peri-implantitis and periodontitis lesions, and healthy gingival tissue controls were analyzed by microarray. Cluster graphs, gene ontology (GO) analysis, and pathway analysis were performed. Quantitative real-time PCR was employed to verify microarray results. The expression levels of RANKL and OPG in the three tissue types were also evaluated, using qRT-PCR. Coding non-coding (CNC) network analyses were performed. RESULTS Microarray analyses revealed 1079 lncRNAs and 1003 mRNAs as differentially expressed in peri-implantitis when compared to periodontitis. The cyclooxygenase-2 pathway was the most up-regulated biological process in peri-implantitis as compared to periodontitis, whereas hemidesmosome assembly was the most down-regulated pathway. Osteoclast differentiation was relatively up-regulated, and RANKL/OPG ratio was higher in peri-implantitis than in periodontitis. CONCLUSIONS The study demonstrated that peri-implantitis and periodontitis exhibit significantly different lncRNA and mRNA expression profiles, suggesting that osteoclast differentiation-related pathways are comparatively more active in peri-implantitis. These data highlight potential molecular targets for periodontitis and peri-implantitis therapy development.
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Affiliation(s)
- Yudong Liu
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Qifan Liu
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Zhipeng Li
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Aneesha Acharya
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China.,Department of Periodontology, Dr D Y Patil Vidyapeeth, Pune, India
| | - Danying Chen
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Zetao Chen
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Nikos Mattheos
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Zhuofan Chen
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Baoxin Huang
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
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146
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Liu T, Wang H, Yu H, Bi M, Yan Z, Hong S, Li S. The Long Non-coding RNA HOTTIP Is Highly Expressed in Colorectal Cancer and Enhances Cell Proliferation and Invasion. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 19:612-618. [PMID: 31945724 PMCID: PMC6965499 DOI: 10.1016/j.omtn.2019.12.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 11/30/2022]
Abstract
Long non-coding RNAs (lncRNAs) are associated with a spectrum of biological processes such as gene regulation on transcriptional and post-transcriptional levels. The HOXA transcript at the distal tip (HOTTIP) lncRNA plays an important role in carcinogenesis; however, the underlying role of HOTTIP in colorectal carcinoma (CRC) remains unknown. The aim of the present study was to evaluate the expression and function of HOTTIP in CRC. In the present study, we analyzed HOTTIP expression levels of CRC patients in tumor and adjacent normal tissue by real-time quantitative PCR. Knockdown of HOTTIP by RNA interference was performed to explore its roles in cell proliferation, migration, and invasion. Our results found that HOTTIP was upregulated in human primary CRC tissues. Knockdown of HOTTIP inhibited CRC cell proliferation, migration, and invasion. Above all, knockdown of HOTTIP could represent a rational therapeutic strategy for CRC.
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Affiliation(s)
- Tao Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Helei Wang
- Department of Gastrointestinal Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Haiyao Yu
- Changchun Food and Drug Inspection Center, Changchun, Jilin 130021, China
| | - Miaomiao Bi
- Department of Ophthalmology, The China-Japan Union Hospital of Jilin University, Jilin University, Changchun, Jilin 130021, China
| | - Zhenkun Yan
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Sen Hong
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
| | - Shiquan Li
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
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147
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Wang S, Mao C, Liu S. Peptides encoded by noncoding genes: challenges and perspectives. Signal Transduct Target Ther 2019; 4:57. [PMID: 31871775 PMCID: PMC6908703 DOI: 10.1038/s41392-019-0092-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/17/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023] Open
Abstract
In recent years, noncoding gene (NCG) translation events have been frequently discovered. The resultant peptides, as novel findings in the life sciences, perform unexpected functions of increasingly recognized importance in many fundamental biological and pathological processes. The emergence of these novel peptides, in turn, has advanced the field of genomics while indispensably aiding living organisms. The peptides from NCGs serve as important links between extracellular stimuli and intracellular adjustment mechanisms. These peptides are also important entry points for further exploration of the mysteries of life that may trigger a new round of revolutionary biotechnological discoveries. Insights into NCG-derived peptides will assist in understanding the secrets of life and the causes of diseases, and will also open up new paths to the treatment of diseases such as cancer. Here, a critical review is presented on the action modes and biological functions of the peptides encoded by NCGs. The challenges and future trends in searching for and studying NCG peptides are also critically discussed.
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Affiliation(s)
- Shuo Wang
- Changhai Hospital, Shanghai, 200433 China
| | - Chuanbin Mao
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, Institute for Biomedical Engineering, Science and Technology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5300 USA
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148
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Hung J, Scanlon JP, Mahmoud AD, Rodor J, Ballantyne M, Fontaine MAC, Temmerman L, Kaczynski J, Connor KL, Bhushan R, Biessen EAL, Newby DE, Sluimer JC, Baker AH. Novel Plaque Enriched Long Noncoding RNA in Atherosclerotic Macrophage Regulation (PELATON). Arterioscler Thromb Vasc Biol 2019; 40:697-713. [PMID: 31826651 PMCID: PMC7043732 DOI: 10.1161/atvbaha.119.313430] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Long noncoding RNAs (lncRNAs) are an emergent class of molecules with diverse functional roles, widely expressed in human physiology and disease. Although some lncRNAs have been identified in cardiovascular disease, their potential as novel targets in the prevention of atherosclerosis is unknown. We set out to discover important lncRNAs in unstable plaque and gain insight into their functional relevance. Approach and Results: Analysis of RNA sequencing previously performed on stable and unstable atherosclerotic plaque identified a panel of 47 differentially regulated lncRNAs. We focused on LINC01272, a lncRNA upregulated in unstable plaque previously detected in inflammatory bowel disease, which we termed PELATON (plaque enriched lncRNA in atherosclerotic and inflammatory bowel macrophage regulation). Here, we demonstrate that PELATON is highly monocyte- and macrophage-specific across vascular cell types, and almost entirely nuclear by cellular fractionation (90%-98%). In situ hybridization confirmed enrichment of PELATON in areas of plaque inflammation, colocalizing with macrophages around the shoulders and necrotic core of human plaque sections. Consistent with its nuclear localization, and despite containing a predicted open reading frame, PELATON did not demonstrate any protein-coding potential in vitro. Functionally, knockdown of PELATON significantly reduced phagocytosis, lipid uptake and reactive oxygen species production in high-content analysis, with a significant reduction in phagocytosis independently validated. Furthermore, CD36, a key mediator of phagocytic oxLDL (oxidized low-density lipoprotein) uptake was significantly reduced with PELATON knockdown. CONCLUSIONS PELATON is a nuclear expressed, monocyte- and macrophage-specific lncRNA, upregulated in unstable atherosclerotic plaque. Knockdown of PELATON affects cellular functions associated with plaque progression.
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Affiliation(s)
- John Hung
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.)
| | - Jessica P Scanlon
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.)
| | - Amira D Mahmoud
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.)
| | - Julie Rodor
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.)
| | - Margaret Ballantyne
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.)
| | - Margaux A C Fontaine
- Maastricht University Medical Center, Maastricht, the Netherlands (M.A.C.F., L.T., E.A.L.B., J.C.S., A.H.B.)
| | - Lieve Temmerman
- Maastricht University Medical Center, Maastricht, the Netherlands (M.A.C.F., L.T., E.A.L.B., J.C.S., A.H.B.)
| | - Jakub Kaczynski
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.)
| | - Katie L Connor
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.)
| | - Raghu Bhushan
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.)
| | - Erik A L Biessen
- Maastricht University Medical Center, Maastricht, the Netherlands (M.A.C.F., L.T., E.A.L.B., J.C.S., A.H.B.)
| | - David E Newby
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.)
| | - Judith C Sluimer
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.).,Maastricht University Medical Center, Maastricht, the Netherlands (M.A.C.F., L.T., E.A.L.B., J.C.S., A.H.B.)
| | - Andrew H Baker
- From the Centre for Cardiovascular Science, University of Edinburgh, United Kingdom (J.H., J.P.S., A.D.M., J.R., M.B., J.K., K.L.C., R.B., D.E.N., J.C.S., A.H.B.).,Maastricht University Medical Center, Maastricht, the Netherlands (M.A.C.F., L.T., E.A.L.B., J.C.S., A.H.B.)
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149
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Zhou T, Wu L, Zong Z, Ma N, Li Y, Jiang Z, Wang Q, Chen S. Long non-coding RNA mortal obligate RNA transcript inhibits the migration and invasion of colon cancer cells by inactivating transforming growth factor β1. Oncol Lett 2019; 19:1131-1136. [PMID: 31966041 PMCID: PMC6955648 DOI: 10.3892/ol.2019.11189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 09/26/2019] [Indexed: 12/14/2022] Open
Abstract
Long non-coding (lnc)RNA mortal obligate RNA transcript (MORT) is inhibited in numerous types of cancer in humans, indicating its role as a tumor suppressor. The present study demonstrated downregulation of lncRNA MORT in the tumor tissues of patients with colon cancer. The expression of MORT in tumor tissues was linearly associated with its expression levels in plasma. Low MORT expression was associated with low overall survival rate. Moreover, the overexpression of MORT resulted in decreased, whereas treatment with transforming growth factor β1 (TGF-β1) resulted in increased, invasion and migration rates of colon cancer cells. In addition, TGF-β1 treatment attenuated the inhibitory effect of MORT overexpression on the invasion and migration rates of colon cancer cells. The overexpression of MORT inhibited TGF-β1 expression in colon cancer cells, whereas treatment with TGF-β1 failed to affect the expression of the lncRNA. Therefore, it is postulated that MORT inhibits invasion and migration colon cancer cells by inactivating TGF-β1.
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Affiliation(s)
- Taicheng Zhou
- Department of Gastroenterological Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, Guangzhou, Guangdong 510655, P.R. China
| | - Lili Wu
- Department of Ultrasonology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Zhen Zong
- Department of Gastroenterological Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 510655, P.R. China
| | - Ning Ma
- Department of Gastroenterological Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, Guangzhou, Guangdong 510655, P.R. China
| | - Yingru Li
- Department of Gastroenterological Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, Guangzhou, Guangdong 510655, P.R. China
| | - Zhipeng Jiang
- Department of Gastroenterological Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, Guangzhou, Guangdong 510655, P.R. China
| | - Qirui Wang
- Department of Molecular Biology, State Administration of Traditional Chinese Medicine of the People's Republic of China, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Shuang Chen
- Department of Gastroenterological Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, Guangzhou, Guangdong 510655, P.R. China
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150
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Zhang K, Li S, Kappel K, Pintilie G, Su Z, Mou TC, Schmid MF, Das R, Chiu W. Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Nat Commun 2019; 10:5511. [PMID: 31796736 PMCID: PMC6890682 DOI: 10.1038/s41467-019-13494-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/03/2019] [Indexed: 01/17/2023] Open
Abstract
Specimens below 50 kDa have generally been considered too small to be analyzed by single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it difficult to obtain high-resolution structures by cryo-EM. In bacteria, riboswitches regulate sulfur metabolism through binding to the S-adenosylmethionine (SAM) ligand and offer compelling targets for new antibiotics. SAM-I, SAM-I/IV, and SAM-IV are the three most commonly found SAM riboswitches, but the structure of SAM-IV is still unknown. Here, we report the structures of apo and SAM-bound SAM-IV riboswitches (119-nt, ~40 kDa) to 3.7 Å and 4.1 Å resolution, respectively, using cryo-EM. The structures illustrate homologies in the ligand-binding core but distinct peripheral tertiary contacts in SAM-IV compared to SAM-I and SAM-I/IV. Our results demonstrate the feasibility of resolving small RNAs with enough detail to enable detection of their ligand-binding pockets and suggest that cryo-EM could play a role in structure-assisted drug design for RNA.
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Affiliation(s)
- Kaiming Zhang
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Shanshan Li
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Grigore Pintilie
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Zhaoming Su
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Tung-Chung Mou
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, 59812, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Department of Physics, Stanford University, Stanford, CA, 94305, USA.
| | - Wah Chiu
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA.
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
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