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Saleh RO, Al-Ouqaili MTS, Ali E, Alhajlah S, Kareem AH, Shakir MN, Alasheqi MQ, Mustafa YF, Alawadi A, Alsaalamy A. lncRNA-microRNA axis in cancer drug resistance: particular focus on signaling pathways. Med Oncol 2024; 41:52. [PMID: 38195957 DOI: 10.1007/s12032-023-02263-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024]
Abstract
Cancer drug resistance remains a formidable challenge in modern oncology, necessitating innovative therapeutic strategies. The convergence of intricate regulatory networks involving long non-coding RNAs, microRNAs, and pivotal signaling pathways has emerged as a crucial determinant of drug resistance. This review underscores the multifaceted roles of lncRNAs and miRNAs in orchestrating gene expression and cellular processes, mainly focusing on their interactions with specific signaling pathways. Dysregulation of these networks leads to the acquisition of drug resistance, dampening the efficacy of conventional treatments. The review highlights the potential therapeutic avenues unlocked by targeting these non-coding RNAs. Developing specific inhibitors or mimics for lncRNAs and miRNAs, alone or in combination with conventional chemotherapy, emerges as a promising strategy. In addition, epigenetic modulators, immunotherapies, and personalized medicine present exciting prospects in tackling drug resistance. While substantial progress has been made, challenges, including target validation and safety assessment, remain. The review emphasizes the need for continued research to overcome these hurdles and underscores the transformative potential of lncRNA-miRNA interplay in revolutionizing cancer therapy.
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Affiliation(s)
- Raed Obaid Saleh
- Department of Medical Laboratory Techniques, Al-Maarif University College, Al-Anbar, Iraq.
| | - Mushtak T S Al-Ouqaili
- Department of Microbiology, College of Medicine, University of Anbar, Ramadi, Anbar, Iraq
| | - Eyhab Ali
- College of Chemistry, Al-Zahraa University for Women, Karbala, Iraq
| | - Sharif Alhajlah
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, 11961, Shaqra, Saudi Arabia.
| | | | - Maha Noori Shakir
- Department of Medical Laboratories Technology, AL-Nisour University College, Baghdad, Iraq
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, 41001, Iraq
| | - Ahmed Alawadi
- College of Technical Engineering, The Islamic University, Najaf, Iraq
- College of Technical Engineering, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Technical Engineering, The Islamic University of Babylon, Babylon, Iraq
| | - Ali Alsaalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna, 66002, Iraq
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2
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Wang F, Yang K, Pan R, Xiang Y, Xiong Z, Li P, Li K, Sun H. A glycometabolic gene signature associating with immune infiltration and chemosensitivity and predicting the prognosis of patients with osteosarcoma. Front Med (Lausanne) 2023; 10:1115759. [PMID: 37293295 PMCID: PMC10244582 DOI: 10.3389/fmed.2023.1115759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/05/2023] [Indexed: 06/10/2023] Open
Abstract
Background Accumulating evidence has suggested that glycometabolism plays an important role in the pathogenesis of tumorigenesis. However, few studies have investigated the prognostic values of glycometabolic genes in patients with osteosarcoma (OS). This study aimed to recognize and establish a glycometabolic gene signature to forecast the prognosis, and provide therapeutic options for patients with OS. Methods Univariate and multivariate Cox regression, LASSO Cox regression, overall survival analysis, receiver operating characteristic curve, and nomogram were adopted to develop the glycometabolic gene signature, and further evaluate the prognostic values of this signature. Functional analyses including Gene Ontology (GO), kyoto encyclopedia of genes and genomes analyses (KEGG), gene set enrichment analysis, single-sample gene set enrichment analysis (ssGSEA), and competing endogenous RNA (ceRNA) network, were used to explore the molecular mechanisms of OS and the correlation between immune infiltration and gene signature. Moreover, these prognostic genes were further validated by immunohistochemical staining. Results A total of four genes including PRKACB, SEPHS2, GPX7, and PFKFB3 were identified for constructing a glycometabolic gene signature which had a favorable performance in predicting the prognosis of patients with OS. Univariate and multivariate Cox regression analyses revealed that the risk score was an independent prognostic factor. Functional analyses indicated that multiple immune associated biological processes and pathways were enriched in the low-risk group, while 26 immunocytes were down-regulated in the high-risk group. The patients in high-risk group showed elevated sensitivity to doxorubicin. Furthermore, these prognostic genes could directly or indirectly interact with other 50 genes. A ceRNA regulatory network based on these prognostic genes was also constructed. The results of immunohistochemical staining showed that SEPHS2, GPX7, and PFKFB3 were differentially expressed between OS tissues and adjacent normal tissues. Conclusion The preset study constructed and validated a novel glycometabolic gene signature which could predict the prognosis of patients with OS, identify the degree of immune infiltration in tumor microenvironment, and provide guidance for the selection of chemotherapeutic drugs. These findings may shed new light on the investigation of molecular mechanisms and comprehensive treatments for OS.
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Affiliation(s)
- Fengyan Wang
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Kun Yang
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Runsang Pan
- School of Basic Medicine, Guizhou Medical University, Guiyang, China
| | - Yang Xiang
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zhilin Xiong
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Pinhao Li
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Ke Li
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Hong Sun
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
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Li Y, Lu Y, Du K, Yin Y, Hu T, Fu Q, Zhang Y, Wen D, Wu X, Xia X. RNA-sequencing analysis reveals the long noncoding RNA profile in the mouse myopic retina. Front Genet 2022; 13:1014031. [PMID: 36313450 PMCID: PMC9606684 DOI: 10.3389/fgene.2022.1014031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2023] Open
Abstract
Aim: Myopia is a prevalent public health problem. The long noncoding RNA (lncRNA) mechanisms for dysregulated retinal signaling in the myopic eye have remained elusive. The aim of this study was to analyze the expression profiles and possible pathogenic roles of lncRNAs in mouse form-deprived myopia (FDM) retinas. Methods: A mouse FDM model was induced and retinas from the FDM right eyes and the contralateral eyes were collected for RNA sequencing. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and lncRNA-mRNA coexpression network analyses were conducted to explore the biological functions of the differentially expressed lncRNAs. In addition, the levels of differentially expressed lncRNAs in the myopic retinas were validated by quantitative real-time PCR (qRT-PCR). Fluorescence in situ hybridization (FISH) was used to detect the localization of lncRNAs in mouse retinas. Results: FDM eyes exhibited reduced refraction and increased ocular axial length compared to control fellow eyes. RNA sequencing revealed that there were 655 differentially expressed lncRNAs between the FDM and control retinas. Functional enrichment analysis indicated that the differentially expressed RNAs were mostly enriched in cellular processes, cytokine-cytokine receptor interactions, retinol metabolism, and rhythmic processes. Differentially expressed lncRNAs were validated by qRT-PCR. Additionally, RNA FISH showed that XR_384718.4 (Gm35369) localized in the ganglion cell (GCL) and inner nuclear layers (INL). Conclusion: This study identified the differential expression profiles of lncRNAs in myopic mouse retinas. Our results provide scientific evidence for investigations of myopia and the development of putative interventions in the future.
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Affiliation(s)
- Yuanjun Li
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ying Lu
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Kaixuan Du
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yewei Yin
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Tu Hu
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qiuman Fu
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yanni Zhang
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Dan Wen
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoying Wu
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaobo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Yang L, Yu J, Tao L, Huang H, Gao Y, Yao J, Liu Z. Cuproptosis-Related lncRNAs are Biomarkers of Prognosis and Immune Microenvironment in Head and Neck Squamous Cell Carcinoma. Front Genet 2022; 13:947551. [PMID: 35938003 PMCID: PMC9354258 DOI: 10.3389/fgene.2022.947551] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Cuproptosis is a new type of cell death that induces protein toxic stress and eventually leads to cell death. Hence, regulating cuproptosis in tumor cells is a new therapeutic approach. However, studies on cuproptosis-related long noncoding RNA (lncRNA) in head and neck squamous cell carcinoma (HNSC) have not been found. This study aimed to explore the cuproptosis-related lncRNAs prognostic marker and their relationship to immune microenvironment in HNSC by using bioinformatics methods. Methods: RNA sequencing, genomic mutations, and clinical data of TCGA_HNSC were downloaded from The Cancer Genome Atlas. HNSC patients were randomly assigned to either a training group or a validation cohort. The least absolute shrinkage and selection operator Cox regression and multivariate Cox regression models were used to determine the prognostic model in the training cohort, and its independent prognostic effect was further confirmed in the validation and entire cohorts. Results: Based on previous literature, we collected 19 genes associated with cuproptosis. Afterward, 783 cuproptosis-related lncRNAs were obtained through coexpression. Cox model revealed and constructed eight cuproptosis-related lncRNAs prognostic marker (AL132800.1, AC090587.1, AC079160.1, AC011462.4, AL157888.1, GRHL3-AS1, SNHG16, and AC021148.2). Patients were divided into high- and low-risk groups based on the median risk score. The Kaplan–Meier survival curve revealed that the overall survival between the high- and low-risk groups was statistically significant. The receiver operating characteristic curve and principal component analysis demonstrated the accurate prognostic ability of the model. Univariate and multivariate Cox regression analysis showed that risk score was an independent prognostic factor. In addition, we used multivariate Cox regression to establish a nomogram of the predictive power of prognostic markers. The tumor mutation burden showed significant differences between the high- and low-risk groups. HNSC patients in the high-risk group responded better to immunotherapy than those in the low-risk group. We also found that risk scores were significantly associated with drug sensitivity in HNSC. Conclusion: In summary, our study identified eight cuprotosis-related lncRNAs signature of HNSC as the prognostic predictor, which may be promising biomarkers for predicting the benefit of HNSC immunotherapy as well as drug sensitivity.
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Najari-Hanjani P, Farazmandfar T, Golalipour M. PER3P1 pseudogene modulates PER3 oscillation: a new player in the molecular clock network. BIOL RHYTHM RES 2022. [DOI: 10.1080/09291016.2022.2050978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Parisa Najari-Hanjani
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
| | - Touraj Farazmandfar
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
- Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran
| | - Masoud Golalipour
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
- Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran
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6
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Kong D, Hou Y, Li W, Ma X, Jiang J. LncRNA-ZXF1 stabilizes P21 expression in endometrioid endometrial carcinoma by inhibiting ubiquitination-mediated degradation and regulating the miR-378a-3p/PCDHA3 axis. Mol Oncol 2022; 16:813-829. [PMID: 33751805 PMCID: PMC8807357 DOI: 10.1002/1878-0261.12940] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/25/2021] [Accepted: 02/20/2021] [Indexed: 01/09/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have a profound effect on biological processes in various malignancies. However, few studies have investigated their functions and specific mechanisms in endometrial cancer. In this study, we focused on the role and mechanism of lncRNA-ZXF1 in endometrial cancer. Bioinformatics and in vitro and in vivo experiments were used to explore the expression and function of lncRNA-ZXF1. We found that lncRNA-ZXF1 altered the migration and invasion of endometrioid endometrial cancer (EEC) cells. Furthermore, our results suggest that lncRNA-ZXF1 regulates EEC cell proliferation. This regulation may be achieved by the lncRNA-ZXF1-mediated alteration in the expression of P21 through two mechanisms. One is that lncRNA-ZXF1 functions as a molecular sponge of miR-378a-3p to regulate PCDHA3 expression and then modulate the expression of P21. The other is that lncRNA-ZXF1 inhibits CDC20-mediated degradation of ubiquitination by directly binding to P21. To the best of our knowledge, this study is the first to explore lncRNA-ZXF1 functioning as a tumor-suppressing lncRNA in EEC. LncRNA-ZXF1 may become therapeutic, diagnostic, and prognostic indicator in the future.
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Affiliation(s)
- Deshui Kong
- Department of Obstetrics and GynecologyQilu Hospital of Shandong UniversityJinanChina
| | - Yixin Hou
- Department of Obstetrics and GynecologyQilu Hospital of Shandong UniversityJinanChina
| | - Wenzhi Li
- Department of Obstetrics and GynecologyQilu Hospital of Shandong UniversityJinanChina
| | - Xiaohong Ma
- Department of Obstetrics and GynecologyQilu Hospital of Shandong UniversityJinanChina
| | - Jie Jiang
- Department of Obstetrics and GynecologyQilu Hospital of Shandong UniversityJinanChina
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7
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Svensson SL, Sharma CM. RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist. eLife 2021; 10:69064. [PMID: 34843430 PMCID: PMC8687705 DOI: 10.7554/elife.69064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/28/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are important post-transcriptional regulators in stress responses and virulence. They can be derived from an expanding list of genomic contexts, such as processing from parental transcripts by RNase E. The role of RNase III in sRNA biogenesis is less well understood despite its well-known roles in rRNA processing, RNA decay, and cleavage of sRNA-mRNA duplexes. Here, we show that RNase III processes a pair of cis-encoded sRNAs (CJnc190 and CJnc180) of the food-borne pathogen Campylobacter jejuni. While CJnc180 processing by RNase III requires CJnc190, RNase III processes CJnc190 independent of CJnc180 via cleavage of an intramolecular duplex. We also show that CJnc190 directly represses translation of the colonization factor PtmG by targeting a G-rich ribosome-binding site, and uncover that CJnc180 is a cis-acting antagonist of CJnc190, indirectly affecting ptmG regulation. Our study highlights a role for RNase III in sRNA biogenesis and adds cis-encoded RNAs to the expanding diversity of transcripts that can antagonize bacterial sRNAs.
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Affiliation(s)
- Sarah Lauren Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Cynthia Mira Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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8
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Brinkman FSL, Winsor GL, Done RE, Filloux A, Francis VI, Goldberg JB, Greenberg EP, Han K, Hancock REW, Haney CH, Häußler S, Klockgether J, Lamont IL, Levesque RC, Lory S, Nikel PI, Porter SL, Scurlock MW, Schweizer HP, Tümmler B, Wang M, Welch M. The Pseudomonas aeruginosa whole genome sequence: A 20th anniversary celebration. Adv Microb Physiol 2021; 79:25-88. [PMID: 34836612 DOI: 10.1016/bs.ampbs.2021.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Toward the end of August 2000, the 6.3 Mbp whole genome sequence of Pseudomonas aeruginosa strain PAO1 was published. With 5570 open reading frames (ORFs), PAO1 had the largest microbial genome sequenced up to that point in time-including a large proportion of metabolic, transport and antimicrobial resistance genes supporting its ability to colonize diverse environments. A remarkable 9% of its ORFs were predicted to encode proteins with regulatory functions, providing new insight into bacterial network complexity as a function of network size. In this celebratory article, we fast forward 20 years, and examine how access to this resource has transformed our understanding of P. aeruginosa. What follows is more than a simple review or commentary; we have specifically asked some of the leaders in the field to provide personal reflections on how the PAO1 genome sequence, along with the Pseudomonas Community Annotation Project (PseudoCAP) and Pseudomonas Genome Database (pseudomonas.com), have contributed to the many exciting discoveries in this field. In addition to bringing us all up to date with the latest developments, we also ask our contributors to speculate on how the next 20 years of Pseudomonas research might pan out.
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Affiliation(s)
- Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Rachel E Done
- Department of Pediatrics, Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, United States
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Vanessa I Francis
- Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, United States
| | - E Peter Greenberg
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Kook Han
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | | | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Susanne Häußler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jens Klockgether
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Pavillon Charles-Eugène Marchand, Faculté of Médicine, Université Laval, Québec City, QC, Canada
| | - Stephen Lory
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Steven L Porter
- Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | | | - Herbert P Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Burkhard Tümmler
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Meng Wang
- Department of Biochemistry (Hopkins Building), University of Cambridge, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry (Hopkins Building), University of Cambridge, Cambridge, United Kingdom.
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Liu T, Shi Q, Yang L, Wang S, Song H, Wang Z, Xu X, Liu H, Zheng H, Shen Z. Long non-coding RNAs HERH-1 and HERH-4 facilitate cyclin A2 expression and accelerate cell cycle progression in advanced hepatocellular carcinoma. BMC Cancer 2021; 21:957. [PMID: 34445994 PMCID: PMC8390207 DOI: 10.1186/s12885-021-08714-7] [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: 01/11/2021] [Accepted: 08/18/2021] [Indexed: 12/11/2022] Open
Abstract
Background The advanced hepatocellular carcinoma (HCC), such as the recurrent tumor after liver transplantation (LT), is an obstacle of HCC treatment. The aim of this study was to discover the underlying mechanism of HCC progression caused by non-coding RNAs (ncRNAs). Methods To this end, we investigated the selected patient cohort of matching primary and recurrent HCC after receiving LT. The recurrent tumors after LT were regarded as clinical models of the advanced HCC. Microarrays were used to profile lncRNA and mRNA expression in HCC recurrent and primary tissue samples. The mRNA profile characteristics were analyzed by bioinformatics. Two cell lines, HepG2 and QGY-7703, were used as HCC cell models. The protein-coding potential, length, and subcellular location of the interested lncRNAs were examined by bioinformatics, Northern blot, fluorescent in situ hybridization (FISH), and quantitative RT-PCR (qRT-PCR) assays. HCC cell proliferation was detected by CCK-8, doubling time and proliferation marker gene quantitation assays. DNA replication during the cell cycle was measured by EdU/PI staining and flow cytometry analyses. Promoter activity was measured using a luciferase reporter assay. Interactions between DNA, RNA, and protein were examined by immunoprecipitation and pull-down assays. The miRNA-target regulation was validated by a fluorescent reporter assay. Results Both lncRNA and mRNA profiles exhibited characteristic alterations in the recurrent tumor cells compared with the primary HCC. The mRNA profile in the HCC recurrent tissues, which served as model of advanced HCC, showed an aberrant cell cycle regulation. Two lncRNAs, the highly expressed lncRNA in recurrent HCC (HERH)-1 and HERH-4, were upregulated in the advanced HCC cells. HERH-1/4 enhanced proliferation and promoted DNA replication and G1-S transition during the cell cycle in HCC cells. HERH-1 interacted with the transcription factor CREB1. CREB1 enhanced cyclin A2 (CCNA2) transcription, depending on HERH-1-CREB1 interaction. HERH-4 acted as an miR-29b/c sponge to facilitate CCNA2 protein translation through a competing endogenous RNA (ceRNA) pathway. Conclusions The oncogenic lncRNA HERH-1/4 promoted CCNA2 expression at the transcriptional and post-transcriptional levels and accelerated cell cycle progression in HCC cells. The HERH-1-CREB1-CCNA2 and HERH-4-miR-29b/c-CCNA2 axes served as molecular stimuli for HCC advance. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08714-7.
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Affiliation(s)
- Tao Liu
- National Health Commission's Key Laboratory of Critical Care Medicine, Tianjin First Central Hospital, School of Medicine, Nankai University, No. 24 Fukang Road, Nankai District, Tianjin, 300192, China. .,Key Laboratory of Transplant Medicine, Chinese Academy of Medical Sciences, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China.
| | - Qiao Shi
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Lei Yang
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Shusen Wang
- National Health Commission's Key Laboratory of Critical Care Medicine, Tianjin First Central Hospital, School of Medicine, Nankai University, No. 24 Fukang Road, Nankai District, Tianjin, 300192, China.,Key Laboratory of Transplant Medicine, Chinese Academy of Medical Sciences, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China.,Organ Transplant Center, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Hongli Song
- Organ Transplant Center, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Zhenglu Wang
- Biological Sample Resource Sharing Center (BSRSC), Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Xinnv Xu
- National Health Commission's Key Laboratory of Critical Care Medicine, Tianjin First Central Hospital, School of Medicine, Nankai University, No. 24 Fukang Road, Nankai District, Tianjin, 300192, China
| | - Hongsheng Liu
- National Health Commission's Key Laboratory of Critical Care Medicine, Tianjin First Central Hospital, School of Medicine, Nankai University, No. 24 Fukang Road, Nankai District, Tianjin, 300192, China
| | - Hong Zheng
- National Health Commission's Key Laboratory of Critical Care Medicine, Tianjin First Central Hospital, School of Medicine, Nankai University, No. 24 Fukang Road, Nankai District, Tianjin, 300192, China.,Key Laboratory of Transplant Medicine, Chinese Academy of Medical Sciences, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China.,Organ Transplant Center, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Zhongyang Shen
- National Health Commission's Key Laboratory of Critical Care Medicine, Tianjin First Central Hospital, School of Medicine, Nankai University, No. 24 Fukang Road, Nankai District, Tianjin, 300192, China. .,Key Laboratory of Transplant Medicine, Chinese Academy of Medical Sciences, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China. .,Organ Transplant Center, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China.
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10
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Peng C, Wang Y, Ji L, Kuang L, Yu Z, Li H, Zhang J, Zhao J. LncRNA-MALAT1/miRNA-204-5p/Smad4 Axis Regulates Epithelial-Mesenchymal Transition, Proliferation and Migration of Lens Epithelial Cells. Curr Eye Res 2021; 46:1137-1147. [PMID: 33327804 DOI: 10.1080/02713683.2020.1857778] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
MATERIALS AND METHODS LECs were cultured and induced with TGF-β2 (10 ng/mL). SiRNA against MALAT1 (Si-MALAT1) was transfected into LECs to knockdown the expression of MALAT1. To overexpress or knockdown miR-204-5p, miR-204-5p mimics (miR-204-5p mimics) and anti-miR-204-5p (miR-204-5p inhibitor) were transfected into LECs. We used RNA FISH to identify the location of MALAT1. RNA levels of MALAT1 and miR-204-5p were analyzed by RT-qPCR. Additionally, target protein levels of Smad4, epithelial differentiation and mesenchymal markers were analyzed with Western blot. We employed EdU Labeling to measured cell proliferation and performed Transwell Assay to analyze the cell migration. Dual-luciferase reporter assays in LECs were conducted to verify whether miRNA-204-5p was negatively regulated by MALAT1 and Smad4 was a direct target of miR-204-5p. RESULTS The expression of MALAT1 was upregulated in PCO specimens. MALAT1 was overexpressed in TGF-β2 induced LECs, and the knockdown of MALAT1 could attenuate TGF-β2 induced EMT. Besides, the upregulation of MALAT1 was correlated with the downregulation of miR-204-5p and upregulation of Smad4. Importantly, MALAT1 was revealed to be located in the cytoplasm of LECs. Furthermore, luciferase reporter assays confirmed that MALAT1 could negatively regulate the expression of miR-204-5p and then regulate its direct target Smad4. Finally, the knockdown of MALAT1 could inhibit the EMT, proliferation, and migration of LECs; however, those can be reversed by anti-miR-204-5p. CONCLUSIONS Our findings reveal that MALAT1 may regulate EMT, proliferation, and migration of LECs as a ceRNA by "sponging" miR-204-5p and targeting Smad4, and serve as a promising therapeutic target in preventing PCO.
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Affiliation(s)
- Cheng Peng
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Department of Ophthalmology, Eye Hospital of China Medical University, Shenyang, China
- Key Laboratory of Lens Research of Liaoning Province, Shenyang, China
| | - Yuchi Wang
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Department of Ophthalmology, Eye Hospital of China Medical University, Shenyang, China
- Key Laboratory of Lens Research of Liaoning Province, Shenyang, China
| | - Liyang Ji
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Department of Ophthalmology, Eye Hospital of China Medical University, Shenyang, China
- Key Laboratory of Lens Research of Liaoning Province, Shenyang, China
| | - Liangju Kuang
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Ziyan Yu
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Department of Ophthalmology, Eye Hospital of China Medical University, Shenyang, China
- Key Laboratory of Lens Research of Liaoning Province, Shenyang, China
| | - Hanrong Li
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Department of Ophthalmology, Eye Hospital of China Medical University, Shenyang, China
- Key Laboratory of Lens Research of Liaoning Province, Shenyang, China
| | - Jinsong Zhang
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Department of Ophthalmology, Eye Hospital of China Medical University, Shenyang, China
- Key Laboratory of Lens Research of Liaoning Province, Shenyang, China
| | - Jiangyue Zhao
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Department of Ophthalmology, Eye Hospital of China Medical University, Shenyang, China
- Key Laboratory of Lens Research of Liaoning Province, Shenyang, China
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11
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Zhan J, Steglich C, Scholz I, Hess WR, Kirilovsky D. Inverse regulation of light harvesting and photoprotection is mediated by a 3'-end-derived sRNA in cyanobacteria. THE PLANT CELL 2021; 33:358-380. [PMID: 33793852 PMCID: PMC8136909 DOI: 10.1093/plcell/koaa030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Phycobilisomes (PBSs), the principal cyanobacterial antenna, are among the most efficient macromolecular structures in nature, and are used for both light harvesting and directed energy transfer to the photosynthetic reaction center. However, under unfavorable conditions, excess excitation energy needs to be rapidly dissipated to avoid photodamage. The orange carotenoid protein (OCP) senses light intensity and induces thermal energy dissipation under stress conditions. Hence, its expression must be tightly controlled; however, the molecular mechanism of this regulation remains to be elucidated. Here, we describe the discovery of a posttranscriptional regulatory mechanism in Synechocystis sp. PCC 6803 in which the expression of the operon encoding the allophycocyanin subunits of the PBS is directly and in an inverse fashion linked to the expression of OCP. This regulation is mediated by ApcZ, a small regulatory RNA that is derived from the 3'-end of the tetracistronic apcABC-apcZ operon. ApcZ inhibits ocp translation under stress-free conditions. Under most stress conditions, apc operon transcription decreases and ocp translation increases. Thus, a key operon involved in the collection of light energy is functionally connected to the expression of a protein involved in energy dissipation. Our findings support the view that regulatory RNA networks in bacteria evolve through the functionalization of mRNA 3'-UTRs.
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Affiliation(s)
- Jiao Zhan
- Université Paris-Saclay, Commissariat à l’Énergie Atomiques et aux Énergies Alternatives, Centre National de la Recherche Scientifique (CEA, CNRS), Institute for Integrative Biology of the Cell (I2BC), 91198 Gif sur Yvette, France
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Claudia Steglich
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg im Breisgau, Germany
| | - Ingeborg Scholz
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg im Breisgau, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg im Breisgau, Germany
| | - Diana Kirilovsky
- Université Paris-Saclay, Commissariat à l’Énergie Atomiques et aux Énergies Alternatives, Centre National de la Recherche Scientifique (CEA, CNRS), Institute for Integrative Biology of the Cell (I2BC), 91198 Gif sur Yvette, France
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12
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Adams PP, Baniulyte G, Esnault C, Chegireddy K, Singh N, Monge M, Dale RK, Storz G, Wade JT. Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping. eLife 2021; 10:62438. [PMID: 33460557 PMCID: PMC7815308 DOI: 10.7554/elife.62438] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs. In most organisms, specific segments of a cell’s genetic information are copied to form single-stranded molecules of various sizes and purposes. Each of these RNA molecules, as they are known, is constructed as a chain that starts at the 5´ end and terminates at the 3´ end. Certain RNAs carry the information present in a gene, which provides the instructions that a cell needs to build proteins. Some, however, are ‘non-coding’ and instead act to fine-tune the activity of other RNAs. These regulatory RNAs can be separate from the RNAs they control, or they can be embedded in the very sequences they regulate; new evidence also shows that certain regulatory RNAs can act in both ways. Many regulatory RNAs are yet to be catalogued, even in simple, well-studied species such as the bacterium Escherichia coli. Here, Adams et al. aimed to better characterize the regulatory RNAs present in E. coli by mapping out the 3´ ends of every RNA molecule in the bacterium. This revealed many new regulatory RNAs and offered insights into where these sequences are located. For instance, the results show that several of these RNAs were embedded within RNA produced from larger genes. Some were nested in coding RNAs, and were parts of a longer RNA sequence that is adjacent to the protein coding segment. Others, however, were present within the instructions that code for a protein. The work by Adams et al. reveals that regulatory RNAs can be located in unexpected places, and provides a method for identifying them. This can be applied to other types of bacteria, in particular in species with few known RNA regulators.
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Affiliation(s)
- Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States.,Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, United States
| | - Gabriele Baniulyte
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Kavya Chegireddy
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Molly Monge
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, United States.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
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13
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Long Non-Coding RNAs in Liver Cancer and Nonalcoholic Steatohepatitis. Noncoding RNA 2020; 6:ncrna6030034. [PMID: 32872482 PMCID: PMC7549373 DOI: 10.3390/ncrna6030034] [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: 07/03/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022] Open
Abstract
This review aims to highlight the recent findings of long non-coding RNAs (lncRNAs) in liver disease. In particular, we focus on the functions of lncRNAs in hepatocellular carcinoma (HCC) and non-alcoholic steatohepatitis (NASH). We summarize the current research trend in lncRNAs and their potential as biomarkers and therapeutic targets for the treatment of HCC and NASH.
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14
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Denham EL. The Sponge RNAs of bacteria - How to find them and their role in regulating the post-transcriptional network. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194565. [PMID: 32475775 DOI: 10.1016/j.bbagrm.2020.194565] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
In bacteria small regulatory RNAs (sRNAs) interact with their mRNA targets through non-consecutive base-pairing. The loose base-pairing specificity allows sRNAs to regulate large numbers of genes, either affecting the stability and/or the translation of mRNAs. Mechanisms enabling post-transcriptional regulation of the sRNAs themselves have also been described involving so-called sponge RNAs. Sponge RNAs modulate free sRNA levels in the cell through RNA-RNA interactions that sequester ("soak up") the sRNA and/or promote degradation of the target sRNA or the sponge RNA-sRNA complex. The development of complex RNA sequencing strategies for the detection of RNA-RNA interactions has enabled identification of several sponge RNAs, as well as previously known regulatory RNAs able to act as both regulators and sponges. This review highlights techniques that have enabled the identification of these sponge RNAs, the origins of sponge RNAs and the mechanisms by which they function in the post-transcriptional network.
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Affiliation(s)
- Emma L Denham
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom.
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15
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Wang C, Chao Y, Matera G, Gao Q, Vogel J. The conserved 3' UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration. Nucleic Acids Res 2020; 48:2126-2143. [PMID: 31863581 PMCID: PMC7038943 DOI: 10.1093/nar/gkz1168] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022] Open
Abstract
Small noncoding RNAs (sRNAs) from mRNA 3′ UTRs seem to present a previously unrecognized layer of bacterial post-transcriptional control whereby mRNAs influence each other's expression, independently of transcriptional control. Studies in Escherichia coli and Salmonella enterica showed that such sRNAs are natural products of RNase E-mediated mRNA decay and associate with major RNA-binding proteins (RBPs) such as Hfq and ProQ. If so, there must be additional sRNAs from mRNAs that accumulate only under specific physiological conditions. We test this prediction by characterizing candidate NarS that represents the 3′ UTR of nitrate transporter NarK whose gene is silent during standard aerobic growth. We find that NarS acts by Hfq-dependent base pairing to repress the synthesis of the nitrite transporter, NirC, resulting in mRNA cross-regulation of nitrate and nitrite transporter genes. Interestingly, the NarS-mediated repression selectively targets the nirC cistron of the long nirBDC-cysG operon, an observation that we rationalize as a mechanism to protect the bacterial cytoplasm from excessive nitrite toxicity during anaerobic respiration with abundant nitrate. Our successful functional assignment of a 3′ UTR sRNA from a non-standard growth condition supports the notion that mRNA crossregulation is more pervasive than currently appreciated.
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Affiliation(s)
- Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200033, PR China.,Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Yanjie Chao
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,Howard Hughes Medical Institute, Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Gianluca Matera
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200033, PR China
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany
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16
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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17
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Zhou YH, Cui YH, Wang T, Luo Y. Long non-coding RNA HOTAIR in cervical cancer: Molecular marker, mechanistic insight, and therapeutic target. Adv Clin Chem 2020; 97:117-140. [PMID: 32448431 DOI: 10.1016/bs.acc.2019.12.004] [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] [Indexed: 02/07/2023]
Abstract
Cervical cancer is a common gynecologic malignant tumor with high mortality. HOX transcript antisense RNA (HOTAIR), a trans-acting long non-coding RNA (lncRNA) containing six exons in humans, is transcribed from the antisense strand of homeobox gene C cluster. This lncRNA serves as a modular scaffold for gene silencing and protein ubiquitination. In patients with cervical cancer, elevated HOTAIR levels are significantly associated with poor prognosis. HOTAIR plays an oncogenic role in cervical cancer by promoting cell proliferation, migration, invasion and autophagy, inhibiting cell apoptosis, stimulating angiogenesis, accelerating cell cycle progression, and inducing epithelial-mesenchymal transition. Moreover, blockade of HOTAIR by artesunate or propofol shows promise for further development of this lncRNA as a potential therapeutic target in cervical cancer. In this review, we summarized the latest advances regarding the role of HOTAIR in cervical cancer with an emphasis on its diagnostic and prognostic values.
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Affiliation(s)
- Yan-Hui Zhou
- Xiangya Nursing School, Central South University, Changsha, Hunan, China
| | - Yan-Hui Cui
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Ting Wang
- Xiangya Nursing School, Central South University, Changsha, Hunan, China
| | - Yang Luo
- Xiangya Nursing School, Central South University, Changsha, Hunan, China.
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18
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Mu W, Provaznik J, Hackert T, Zöller M. Tspan8-Tumor Extracellular Vesicle-Induced Endothelial Cell and Fibroblast Remodeling Relies on the Target Cell-Selective Response. Cells 2020; 9:cells9020319. [PMID: 32013145 PMCID: PMC7072212 DOI: 10.3390/cells9020319] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/17/2020] [Accepted: 01/26/2020] [Indexed: 12/12/2022] Open
Abstract
Tumor cell-derived extracellular vesicles (TEX) expressing tetraspanin Tspan8-alpha4/beta1 support angiogenesis. Tspan8-alpha6/beta4 facilitates lung premetastatic niche establishment. TEX-promoted target reprogramming is still being disputed, we explored rat endothelial cell (EC) and lung fibroblast (Fb) mRNA and miRNA profile changes after coculture with TEX. TEX were derived from non-metastatic BSp73AS (AS) or metastatic BSp73ASML (ASML) rat tumor lines transfected with Tspan8 (AS-Tspan8) or Tspan8-shRNA (ASML-Tspan8kd). mRNA was analyzed by deep sequencing and miRNA by array analysis of EC and Fb before and after coculture with TEX. EC and Fb responded more vigorously to AS-Tspan8- than AS-TEX. Though EC and Fb responses differed, both cell lines predominantly responded to membrane receptor activation with upregulation and activation of signaling molecules and transcription factors. Minor TEX-initiated changes in the miRNA profile relied, at least partly, on long noncoding RNA (lncRNA) that also affected chromosome organization and mRNA processing. These analyses uncovered three important points. TEX activate target cell autonomous programs. Responses are initiated by TEX targeting units and are target cell-specific. The strong TEX-promoted lncRNA impact reflects lncRNA shuttling and location-dependent distinct activities. These informations urge for an in depth exploration on the mode of TEX-initiated target cell-specific remodeling including, as a major factor, lncRNA.
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Affiliation(s)
- Wei Mu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of General, Visceral and Transplantation Surgery, Pancreas Section, University of Heidelberg, 69120 Heidelberg, Germany
- Correspondence: (W.M.); (M.Z.); Tel.: +86-021-6384-6590 (W.M.); +49-6221-484-730 (M.Z.)
| | - Jan Provaznik
- EMBL Genomics Core Facility, 69117 Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Pancreas Section, University of Heidelberg, 69120 Heidelberg, Germany
| | - Margot Zöller
- Department of General, Visceral and Transplantation Surgery, Pancreas Section, University of Heidelberg, 69120 Heidelberg, Germany
- Correspondence: (W.M.); (M.Z.); Tel.: +86-021-6384-6590 (W.M.); +49-6221-484-730 (M.Z.)
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19
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LncRNA CAR10 Upregulates PDPK1 to Promote Cervical Cancer Development by Sponging miR-125b-5p. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4351671. [PMID: 32025520 PMCID: PMC6984746 DOI: 10.1155/2020/4351671] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/18/2019] [Accepted: 10/26/2019] [Indexed: 02/07/2023]
Abstract
Cervical cancer is one of the malignant tumors that seriously threaten women's health. The mechanism of development needs to be deeply studied. In recent years, lncRNA has been identified as one of the important factors affecting the malignant progression of tumors. In this study, we illustrated the important mechanism of lncRNA CAR10 in the development of cervical cancer. We found that CAR10 is significantly increased in4 cervical cancer tissues and cells, which can promote the proliferation of cervical cancer cells in vitro and in vivo, indicating that CAR10 is involved in the progression of cervical cancer as an oncogene. Further studies showed that CAR10 is a target gene of miR-125b-5p, and miR-125b-5p can inhibit the effect of CAR10 on the proliferation of cervical cancer cells. In addition, we also found that 3-phosphoinositide-dependent protein kinase 1 (PDPK1) is also a target gene of miR-125b-5p, and CAR10 can upregulate the expression level of PDPK1. The results showed that CAR10 acts as a ceRNA to upregulate the expression of PDPK1 by sponging miR-125b-5p. Knockdown of PDPK1 can inhibit the effect of CAR10 on cervical cancer cells. Our study demonstrates that, based on ceRNA mechanism, CAR10/miR-125b-5p/PDPK1 network can regulate the proliferation of cervical cancer cells and play an important role in the development of cervical cancer. In addition, our study also suggests that intervention of CAR10/miR-125b-5p/PDPK1 network may be a new strategy for targeted therapy of cervical cancer.
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20
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Yang M, Wei W. SNHG16: A Novel Long-Non Coding RNA in Human Cancers. Onco Targets Ther 2019; 12:11679-11690. [PMID: 32021246 PMCID: PMC6942535 DOI: 10.2147/ott.s231630] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/13/2019] [Indexed: 01/27/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have recently been considered as central regulators in diverse biological processes controlling tumorigenesis. Small nucleolar RNA host gene 16 (SNHG16) is an important tumor-associated lncRNA mainly involved in tumorigenesis and progression by competing with endogenous RNA (ceRNA) which sponges tumor-suppressive microRNA (miRNA), and by its recruitment mechanism. SNHG16 is overexpressed in tumor tissues and cell lines of different kinds of cancers, and its presence is associated with a poor clinical prognosis. Reviewing all publications about SNHG16 revealed that it plays a key role in the different hallmarks that define human cancer, including promoting proliferation, activating migration and invasion, inhibiting apoptosis, affecting lipid metabolism and chemoresistance. This review highlights the role that the aberrant expression of SNHG16 plays in the development and progression of cancer, and suggests that SNHG16 may function as a potential biomarker and therapeutic target for human cancers.
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Affiliation(s)
- Ming Yang
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology and Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing100730, People’s Republic of China
| | - Wenbin Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology and Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing100730, People’s Republic of China
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21
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Schreiner WP, Pagliuso DC, Garrigues JM, Chen JS, Aalto AP, Pasquinelli AE. Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock. Nucleic Acids Res 2019; 47:9829-9841. [PMID: 31396626 PMCID: PMC6765114 DOI: 10.1093/nar/gkz693] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023] Open
Abstract
Elevated temperatures activate a heat shock response (HSR) to protect cells from the pathological effects of protein mis-folding, cellular mis-organization, organelle dysfunction and altered membrane fluidity. This response includes activation of the conserved transcription factor heat shock factor 1 (HSF-1), which binds heat shock elements (HSEs) in the promoters of genes induced by heat shock (HS). The upregulation of protein-coding genes (PCGs), such as heat shock proteins and cytoskeletal regulators, is critical for cellular survival during elevated temperatures. While the transcriptional response of PCGs to HS has been comprehensively analyzed in a variety of organisms, the effect of this stress on the expression of non-coding RNAs (ncRNAs) has not been systematically examined. Here we show that in Caenorhabditis elegans HS induces up- and downregulation of specific ncRNAs from multiple classes, including miRNA, piRNA, lincRNA, pseudogene and repeat elements. Moreover, some ncRNA genes appear to be direct targets of the HSR, as they contain HSF-1 bound HSEs in their promoters and their expression is regulated by this factor during HS. These results demonstrate that multiple ncRNA genes respond to HS, some as direct HSF-1 targets, providing new candidates that may contribute to organismal survival during this stress.
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Affiliation(s)
- William P Schreiner
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Delaney C Pagliuso
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Jacob M Garrigues
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Jerry S Chen
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Antti P Aalto
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
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22
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Georg J, Lalaouna D, Hou S, Lott SC, Caldelari I, Marzi S, Hess WR, Romby P. The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs. Mol Microbiol 2019; 113:603-612. [PMID: 31705780 PMCID: PMC7154689 DOI: 10.1111/mmi.14420] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 12/17/2022]
Abstract
Trans‐acting small regulatory RNAs (sRNAs) are key players in the regulation of gene expression in bacteria. There are hundreds of different sRNAs in a typical bacterium, which in contrast to eukaryotic microRNAs are more heterogeneous in length, sequence composition, and secondary structure. The vast majority of sRNAs function post‐transcriptionally by binding to other RNAs (mRNAs, sRNAs) through rather short regions of imperfect sequence complementarity. Besides, every single sRNA may interact with dozens of different target RNAs and impact gene expression either negatively or positively. These facts contributed to the view that the entirety of the regulatory targets of a given sRNA, its targetome, is challenging to identify. However, recent developments show that a more comprehensive sRNAs targetome can be achieved through the combination of experimental and computational approaches. Here, we give a short introduction into these methods followed by a description of two sRNAs, RyhB, and RsaA, to illustrate the particular strengths and weaknesses of these approaches in more details. RyhB is an sRNA involved in iron homeostasis in Enterobacteriaceae, while RsaA is a modulator of virulence in Staphylococcus aureus. Using such a combined strategy, a better appreciation of the sRNA‐dependent regulatory networks is now attainable.
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Affiliation(s)
- Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - David Lalaouna
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Shengwei Hou
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Steffen C Lott
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
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23
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Ding LB, Li Y, Liu GY, Li TH, Li F, Guan J, Wang HJ. Long non-coding RNA PVT1, a molecular sponge of miR-26b, is involved in the progression of hyperglycemia-induced collagen degradation in human chondrocytes by targeting CTGF/TGF- β signal ways. Innate Immun 2019; 26:204-214. [PMID: 31625803 PMCID: PMC7144035 DOI: 10.1177/1753425919881778] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The current study was conducted to investigate the role of long non-coding RNA
PVT1 in hyperglycemia-triggered human osteoarthritis (OA) chondrocytes.
Cartilage from knee OA patients with and without diabetes, as well as normal
cartilage, was obtained. Isolated human chondrocytes were treated with 30 nM of
Glc with or without pioglitazone. The expression levels of PVT1, miR-26b, and
type II collagen were determined by RT-PCR. Type II collagen was detected by
immunocytochemistry and chondrocytes were stained with Alcian blue. Moreover,
the interaction among PVT1, miR-26b, and CTGF was examined using bioinformatics,
FISH, RIP, RNA-pull down, and luciferase reporter assays. Over-expression of
PVT1 and miR-26b were performed and expressions of CTGF, TGF-β1, SMAD3, MMP-13,
and type II collagen proteins were examined. Significantly higher expression of
PVT1 was observed in diabetic OA. High Glc induced the elevated expression of
PVT1, CTGF, TGF-β1, IL-6, and MMP-13, as well as decreased expression of type II
collagen and miR-26b. These alterations could be reversed by pioglitazone. PVT1
acted as a sponge for miR-26b to facilitate CTGF expression. Over-expression of
PVT1 increased the expressions of CTGF, TGF-β1, SMAD3, and MMP-13 and decreased
expression of type II collagen. Our findings confirmed that PVT1 is involved in
the hyperglycemia-induced collagen degradation, via the
miR-26b-CTGF-TGF-β1-axis.
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Affiliation(s)
- Luo-Bin Ding
- Department of Orthopedic Surgery, Third Hospital of Shijiazhuang, Shijiazhuang, HeBei Province, China
| | - Yao Li
- Department of Orthopedic Surgery, Third Hospital of Shijiazhuang, Shijiazhuang, HeBei Province, China
| | - Guang-Yuan Liu
- Department of Orthopedic Surgery, Third Hospital of Shijiazhuang, Shijiazhuang, HeBei Province, China
| | - Tai-Hang Li
- Department of Orthopedic Surgery, Third Hospital of Shijiazhuang, Shijiazhuang, HeBei Province, China
| | - Feng Li
- Department of Orthopedic Surgery, Third Hospital of Shijiazhuang, Shijiazhuang, HeBei Province, China
| | - Jian Guan
- Department of Orthopedic Surgery, Third Hospital of Shijiazhuang, Shijiazhuang, HeBei Province, China
| | - Hua-Jun Wang
- Department of Orthopedic Surgery and Sports Medicine Center, First Affiliated Hospital of Jinan University, Guangzhou, GuangDong Province, China
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24
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The Pancreatic Cancer-Initiating Cell Marker CD44v6 Affects Transcription, Translation, and Signaling: Consequences for Exosome Composition and Delivery. JOURNAL OF ONCOLOGY 2019; 2019:3516973. [PMID: 31485223 PMCID: PMC6702834 DOI: 10.1155/2019/3516973] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/20/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022]
Abstract
Pancreatic cancer-initiating cells (PaCIC) express CD44v6 and Tspan8. A knockdown (kd) of these markers hinders the metastatic capacity, which can be rescued, if the cells are exposed to CIC-exosomes (TEX). Additional evidence that CD44v6 regulates Tspan8 expression prompted us to explore the impact of these PaCIC markers on nonmetastatic PaCa and PaCIC-TEX. We performed proteome, miRNA, and mRNA deep sequencing analyses on wild-type, CD44v6kd, and Tspan8kd human PaCIC and TEX. Database comparative analyses were controlled by qRT-PCR, Western blot, flow cytometry, and confocal microscopy. Transcriptome analysis of CD44 versus CD44v6 coimmunoprecipitating proteins in cells and TEX revealed that Tspan8, several signal-transducing molecules including RTK, EMT-related transcription factors, and proteins engaged in mRNA processing selectively associate with CD44v6 and that the membrane-attached CD44 intracytoplasmic tail supports Tspan8 and NOTCH transcription. Deep sequencing uncovered a CD44v6 contribution to miRNA processing. Due to the association of CD44v6 with Tspan8 in internalization prone tetraspanin-enriched membrane domains (TEM) and the engagement of Tspan8 in exosome biogenesis, most CD44v6-dependent changes were transferred into TEX such that the input of CD44v6 to TEX activities becomes largely waved in both a CD44v6kd and a Tspan8kd. Few differences between CD44v6kd- and Tspan8kd-TEX rely on CD44v6 being also recovered in non-TEM derived TEX, highlighting distinct TEX delivery from individual cells that jointly account for TEX-promoted target modulation. This leads us to propose a model in which CD44v6 strongly supports tumor progression by cooperating with signaling molecules, altering transcription of key molecules, and through its association with the mRNA processing machinery. The association of CD44v6 with Tspan8, which plays a crucial role in vesicle biogenesis, promotes metastases by transferring CD44v6 activities into TEM and TEM-independently derived TEX. Further investigations of the lead position of CD44v6 in shifting metastasis-promoting activities into CIC-TEX may offer a means of targeting TEX-CD44v6 in therapeutic applications.
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