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Hao L, Chen M, Li D, Lijavetzky D. Editorial: Plant RNA processing: discovery, mechanism and function. Front Plant Sci 2024; 15:1359415. [PMID: 38282821 PMCID: PMC10809176 DOI: 10.3389/fpls.2024.1359415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024]
Affiliation(s)
- Lili Hao
- China National Center for Bioinformation, Beijing, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dayong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Diego Lijavetzky
- Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (FCA-UNCuyo), Mendoza, Argentina
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2
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Zhu ZX, Liu Y, Wang J, Xie Y, Li RY, Ma Q, Tu Q, Melhem NA, Couldwell S, El-Araby RE, Tai A, Van Dyke TE, Karimbux N, Jeong YN, Chen JJ. A novel lncRNA-mediated epigenetic regulatory mechanism in periodontitis. Int J Biol Sci 2023; 19:5187-5203. [PMID: 37928259 PMCID: PMC10620817 DOI: 10.7150/ijbs.87977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/01/2023] [Indexed: 11/07/2023] Open
Abstract
Periodontitis is a highly prevalent chronic inflammatory disease with an exaggerated host immune response, resulting in periodontal tissue destruction and potential tooth loss. The long non-coding RNA, LncR-ANRIL, located on human chromosome 9p21, is recognized as a genetic risk factor for various conditions, including atherosclerosis, periodontitis, diabetes, and cancer. LncR-APDC is an ortholog of ANRIL located on mouse genome chr4. This study aims to comprehend the regulatory role of lncR-APDC in periodontitis progression. Our experimental findings, obtained from lncR-APDC gene knockout (KO) mice with induced experimental periodontitis (EP), revealed exacerbated bone loss and disrupted pro-inflammatory cytokine regulation. Downregulation of osteogenic differentiation occurred in bone marrow stem cells harvested from lncR-APDC-KO mice. Furthermore, single-cell RNA sequencing of periodontitis gingival tissue revealed alterations in the proportion and function of immune cells, including T and B cells, macrophages, and neutrophils, due to lncR-APDC silencing. Our findings also unveiled a previously unidentified epithelial cell subset that is distinctively presenting in the lncR-APDC-KO group. This epithelial subset, characterized by the positive expression of Krt8 and Krt18, engages in interactions with immune cells through a variety of ligand-receptor pairs. The expression of Tff2, now recognized for its role in chronic inflammatory conditions, exhibited a notable increase across various tissue and cell types in lncR-APDC deficient mice. Additionally, our investigation revealed the potential for a direct binding interaction between lncR-APDC and Tff2. Intra-gingival administration of AAV9-lncR-APDC was shown to have therapeutic effects in the EP model. In conclusion, our results suggest that lncR-APDC plays a critical role in the progression of periodontal disease and holds therapeutic potential for periodontitis. Furthermore, the presence of the distinctive epithelial subpopulation and significantly elevated Tff2 levels in the lncR-APDC-silenced EP model offer new perspectives on the epigenetic regulation of periodontitis pathogenesis.
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Affiliation(s)
- Zoe Xiaofang Zhu
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Yao Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jinghao Wang
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Ying Xie
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Rachel Yuantong Li
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Qian Ma
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Qisheng Tu
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Neiman A Melhem
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Sandrine Couldwell
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Rady E. El-Araby
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Albert Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
- Data Intensive Studies Center, Tufts University, Medford, MA, United States
| | - Thomas E. Van Dyke
- Clinical and Translational Research, Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Forsyth Institute, Boston, MA, United States
| | - Nadeem Karimbux
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Y. Natalie Jeong
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Jake Jinkun Chen
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
- Department of Genetics, Molecular and Cell Biology, Tufts University School of Medicine, Tufts School of Graduate Biomedical Sciences, 136 Harrison Ave, M&V Room 811, Boston, MA 02111, United States
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Horai Y, Shimizu T, Umeda M, Nishihata SY, Nakamura H, Kawakami A. Current Views on Pathophysiology and Potential Therapeutic Targets in Sjögren's Syndrome: A Review from the Perspective of Viral Infections, Toll-like Receptors, and Long-Noncoding RNAs. J Clin Med 2023; 12:5873. [PMID: 37762814 PMCID: PMC10531551 DOI: 10.3390/jcm12185873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Sjögren's syndrome (SS) is a rheumatic disease characterized by sicca and extraglandular symptoms, such as interstitial lung disease and renal tubular acidosis. SS potentially affects the prognosis of patients, especially in cases of complicated extraglandular symptoms; however, only symptomatic therapies against xerophthalmia and xerostomia are currently included in the practice guidelines as recommended therapies for SS. Considering that SS is presumed to be a multifactorial entity caused by genetic and environmental factors, a multidisciplinary approach is necessary to clarify the whole picture of its pathogenesis and to develop disease-specific therapies for SS. This review discusses past achievements and future prospects for pursuing the pathophysiology and therapeutic targets for SS, especially from the perspectives of viral infections, toll-like receptors (TLRs), long-noncoding RNAs (lncRNAs), and related signals. Based on the emerging roles of viral infections, TLRs, long-noncoding RNAs and related signals, antiviral therapy, hydroxychloroquine, and vitamin D may lower the risk of or mitigate SS. Janus-kinase (JAK) inhibitors are also potential novel therapeutic options for several rheumatic diseases involving the JAK-signal transducer and activator of transcription pathways, which are yet to be ascertained in a randomized controlled study targeting SS.
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Affiliation(s)
- Yoshiro Horai
- Department of Rheumatology, Sasebo City General Hospital, Sasebo 857-8511, Japan
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan; (T.S.); (M.U.); (A.K.)
| | - Toshimasa Shimizu
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan; (T.S.); (M.U.); (A.K.)
- Clinical Research Center, Nagasaki University Hospital, Nagasaki 852-8501, Japan
| | - Masataka Umeda
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan; (T.S.); (M.U.); (A.K.)
| | - Shin-Ya Nishihata
- Department of Rheumatology, National Hospital Organization Ureshino Medical Center, Ureshino 843-0393, Japan;
| | - Hideki Nakamura
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, Tokyo 173-8610, Japan;
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan; (T.S.); (M.U.); (A.K.)
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4
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Saigusa H, Mimura I, Kurata Y, Tanaka T, Nangaku M. Hypoxia-inducible lncRNA MIR210HG promotes HIF1α expression by inhibiting miR-93-5p in renal tubular cells. FEBS J 2023; 290:4040-4056. [PMID: 37029581 DOI: 10.1111/febs.16794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 02/24/2023] [Accepted: 04/06/2023] [Indexed: 04/09/2023]
Abstract
Chronic hypoxia in the renal tubular interstitium has been reported to contribute to the progression of chronic kidney disease. Recently, long-noncoding RNAs have been shown to be involved in various pathological conditions, including hypoxia, one of which is the MIR210 host gene (MIR210HG). To elucidate the function of MIR210HG in renal hypoxia, we exposed primary cultured renal proximal tubular epithelial cells to hypoxia and examined the temporal profile of MIR210HG expression and the role of MIR210HG interaction with hypoxia-inducible factor1α (HIF1α, encoded by HIF1A). MIR210HG expression was induced by hypoxia. HIF1A silencing and cobalt chloride exposure showed that MIR210HG expression in hypoxia is HIF1α-dependent. MIR210HG silencing significantly reduced both the mRNA and protein levels of HIF1α, pointing to positive feedback regulation. To further investigate the details of this regulation, we turned to the in-silico miRNA targets of MIR210HG. We found that miR-93-5p levels increased when MIR210HG was knocked down. We then showed that miR-93-5p reduced the expression of HIF1A mRNA and MIR210HG. Furthermore, a dual luciferase assay confirmed that miR-93-5p binds to MIR210HG and HIF1A 3' UTR, inhibiting their expression. In conclusion, the long-noncoding RNA MIR210HG is induced shortly after hypoxia, and it promotes HIF1α expression by competing for miR-93-5p and inhibiting it. MIR210HG plays a crucial role in the biological response to hypoxia in renal tubular epithelial cells.
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Affiliation(s)
- Hanako Saigusa
- Division of Nephrology and Endocrinology, the University of Tokyo Graduate School of Medicine, Bunkyo-ku, Japan
| | - Imari Mimura
- Division of Nephrology and Endocrinology, the University of Tokyo Graduate School of Medicine, Bunkyo-ku, Japan
| | - Yu Kurata
- Division of Nephrology and Endocrinology, the University of Tokyo Graduate School of Medicine, Bunkyo-ku, Japan
| | - Tetsuhiro Tanaka
- Department of Nephrology, Rheumatology and Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, the University of Tokyo Graduate School of Medicine, Bunkyo-ku, Japan
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Tiwari S, Jain M, Singla-Pareek SL, Bhalla PL, Singh MB, Pareek A. Pokkali: A Naturally Evolved Salt-Tolerant Rice Shows a Distinguished Set of lncRNAs Possibly Contributing to the Tolerant Phenotype. Int J Mol Sci 2023; 24:11677. [PMID: 37511436 PMCID: PMC10380863 DOI: 10.3390/ijms241411677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 07/30/2023] Open
Abstract
Pokkali is a strong representation of how stress-tolerant genotypes have evolved due to natural selection pressure. Numerous omics-based investigations have indicated different categories of stress-related genes and proteins, possibly contributing to salinity tolerance in this wild rice. However, a comprehensive study towards understanding the role of long-noncoding RNAs (lncRNAs) in the salinity response of Pokkali has not been done to date. We have identified salt-responsive lncRNAs from contrasting rice genotypes IR64 and Pokkali. A total of 63 and 81 salinity-responsive lncRNAs were differentially expressed in IR64 and Pokkali, respectively. Molecular characterization of lncRNAs and lncRNA-miRNA-mRNA interaction networks helps to explore the role of lncRNAs in the stress response. Functional annotation revealed that identified lncRNAs modulate various cellular processes, including transcriptional regulation, ion homeostasis, and secondary metabolite production. Additionally, lncRNAs were predicted to bind stress-responsive transcription factors, namely ERF, DOF, and WRKY. In addition to salinity, expression profiling was also performed under other abiotic stresses and phytohormone treatments. A positive modulation in TCONS_00035411, TCONS_00059828, and TCONS_00096512 under both abiotic stress and phytohormone treatments could be considered as being of potential interest for the further functional characterization of IncRNA. Thus, extensive analysis of lncRNAs under various treatments helps to delineate stress tolerance mechanisms and possible cross-talk.
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Affiliation(s)
- Shalini Tiwari
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- National Agri-Food Biotechnology Institute, Sahibzada Ajit Singh Nagar 140306, India
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6
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Wang Y, Wang Z, Du Q, Wang K, Zou C, Li WX. The long-noncoding RNA PILNCR2 increases low phosphate tolerance in maize by interfering with miRNA399-guided cleavage of ZmPHT1s. Mol Plant 2023:S1674-2052(23)00145-4. [PMID: 37264570 DOI: 10.1016/j.molp.2023.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 03/26/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023]
Abstract
miR399 has target sites in the open reading region of ZmPHT1s (Pi transporters) in maize. However, the relation between miR399 and ZmPHT1s and its functional importance in responses to Pi deficiency remain to be explored. We show here that ZmPHT1;1, ZmPHT1;3, and ZmPHT1;13 are the targets of ZmmiRNA399. We characterized a long-noncoding RNA PILNCR2 (Pi-deficiency-induced lncRNA 2) transcribed from the opposing DNA strand of ZmPHT1;1. PILNCR2 was predominantly localized in the cytoplasm. A ribonuclease protection assay and an RNA-RNA binding assay showed that PILNCR2 and ZmPHT1s could form RNA/RNA duplexes in vivo and in vitro. A co-expression assay in N. benthamiana verified that the RNA/RNA duplex interfered with the miR399-guided cleavage of mRNAs of ZmPHT1s. Overexpression of PILNCR2 increased low-Pi tolerance in maize. Knock-out and -down of PILNCR2 decreased low-Pi tolerance in maize. We further show that PILNCR2 positively regulated the mRNA abundance of ZmPHT1; 3 and ZmPHT1;13 in maize. Thus, PILNCR2 is important for Pi homeostasis in maize by interfering miRNA399-guided cleavage of mRNAs of ZmPHT1s.
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Affiliation(s)
- Yafei Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhonghua Wang
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development; Key Laboratory of Plant-Soil Interactions, Ministry of Education; China Agricultural University, Beijing 100193, PR China
| | - Qingguo Du
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunqin Zou
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development; Key Laboratory of Plant-Soil Interactions, Ministry of Education; China Agricultural University, Beijing 100193, PR China
| | - Wen-Xue Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Shi H, Nguyen T, Zhao Q, Cheng P, Sharma D, Kim HJ, Kim JB, Wirka R, Weldy CS, Monteiro JP, Quertermous T. Discovery of Transacting Long Noncoding RNAs That Regulate Smooth Muscle Cell Phenotype. Circ Res 2023; 132:795-811. [PMID: 36852690 PMCID: PMC11056793 DOI: 10.1161/circresaha.122.321960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
BACKGROUND Smooth muscle cells (SMC), the major cell type in atherosclerotic plaques, are vital in coronary artery diseases (CADs). SMC phenotypic transition, which leads to the formation of various cell types in atherosclerotic plaques, is regulated by a network of genetic and epigenetic mechanisms and governs the risk of disease. The involvement of long noncoding RNAs (lncRNAs) has been increasingly identified in cardiovascular disease. However, SMC lncRNAs have not been comprehensively characterized, and their regulatory role in SMC state transition remains unknown. METHODS A discovery pipeline was constructed and applied to deeply strand-specific RNA sequencing from perturbed human coronary artery SMC with different disease-related stimuli, to allow for the detection of novel lncRNAs. The functional relevance of a select few novel lncRNAs were verified in vitro. RESULTS We identified 4579 known and 13 655 de novo lncRNAs in human coronary artery SMC. Consistent with previous long noncoding RNA studies, these lncRNAs overall have fewer exons, are shorter in length than protein-coding genes (pcGenes), and have relatively low expression level. Genomic location of these long noncoding RNA is disproportionately enriched near CAD-related TFs (transcription factors), genetic loci, and gene regulators of SMC identity, suggesting the importance of their function in disease. Two de novo lncRNAs, ZIPPOR (ZEB-interacting suppressor) and TNS1-AS2 (TNS1-antisense 2), were identified by our screen. Combining transcriptional data and in silico modeling along with in vitro validation, we identified CAD gene ZEB2 as a target through which these lncRNAs exert their function in SMC phenotypic transition. CONCLUSIONS Expression of a large and diverse set of lncRNAs in human coronary artery SMC are highly dynamic in response to CAD-related stimuli. The dynamic changes in expression of these lncRNAs correspond to alterations in transcriptional programs that are relevant to CAD, suggesting a critical role for lncRNAs in SMC phenotypic transition and human atherosclerotic disease.
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Affiliation(s)
- Huitong Shi
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
| | - Trieu Nguyen
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
| | - Quanyi Zhao
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
| | - Paul Cheng
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
| | - Disha Sharma
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
| | - Hyun-Jung Kim
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
| | - Juyong Brian Kim
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
| | - Robert Wirka
- Departments of Medicine and Cell Biology and Physiology, and McAllister Heart Institute, University of North Carolina at Chapel Hill
| | - Chad S Weldy
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
| | - João P. Monteiro
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University
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Plasil SL, Collins VJ, Baratta AM, Farris SP, Homanics GE. Hippocampal ceRNA networks from chronic intermittent ethanol vapor-exposed male mice and functional analysis of top-ranked lncRNA genes for ethanol drinking phenotypes. Adv Drug Alcohol Res 2022; 2:10831. [PMID: 36908580 PMCID: PMC10004261 DOI: 10.3389/adar.2022.10831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular mechanisms regulating the development and progression of alcohol use disorder (AUD) are largely unknown. While noncoding RNAs have previously been implicated as playing key roles in AUD, long-noncoding RNA (lncRNA) remains understudied in relation to AUD. In this study, we first identified ethanol-responsive lncRNAs in the mouse hippocampus that are transcriptional network hub genes. Microarray analysis of lncRNA, miRNA, circular RNA, and protein coding gene expression in the hippocampus from chronic intermittent ethanol vapor- or air- (control) exposed mice was used to identify ethanol-responsive competing endogenous RNA (ceRNA) networks. Highly interconnected lncRNAs (genes that had the strongest overall correlation to all other dysregulated genes identified) were ranked. The top four lncRNAs were novel, previously uncharacterized genes named Gm42575, 4930413E15Rik, Gm15767, and Gm33447, hereafter referred to as Pitt1, Pitt2, Pitt3, and Pitt4, respectively. We subsequently tested the hypothesis that CRISPR/Cas9 mutagenesis of the putative promoter and first exon of these lncRNAs in C57BL/6J mice would alter ethanol drinking behavior. The Drinking in the Dark (DID) assay was used to examine binge-like drinking behavior, and the Every-Other-Day Two-Bottle Choice (EOD-2BC) assay was used to examine intermittent ethanol consumption and preference. No significant differences between control and mutant mice were observed in the DID assay. Female-specific reductions in ethanol consumption were observed in the EOD-2BC assay for Pitt1, Pitt3, and Pitt4 mutant mice compared to controls. Male-specific alterations in ethanol preference were observed for Pitt1 and Pitt2. Female-specific increases in ethanol preference were observed for Pitt3 and Pitt4. Total fluid consumption was reduced in Pitt1 and Pitt2 mutants at 15% v/v ethanol and in Pitt3 and Pitt4 at 20% v/v ethanol in females only. We conclude that all lncRNAs targeted altered ethanol drinking behavior, and that lncRNAs Pitt1, Pitt3, and Pitt4 influenced ethanol consumption in a sex-specific manner. Further research is necessary to elucidate the biological mechanisms for these effects. These findings add to the literature implicating noncoding RNAs in AUD and suggest lncRNAs also play an important regulatory role in the disease.
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Affiliation(s)
- SL Plasil
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - VJ Collins
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - AM Baratta
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - SP Farris
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - GE Homanics
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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9
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Dadafarin S, Rodríguez TC, Carnazza MA, Tiwari RK, Moscatello A, Geliebter J. MEG3 Expression Indicates Lymph Node Metastasis and Presence of Cancer-Associated Fibroblasts in Papillary Thyroid Cancer. Cells 2022; 11:cells11193181. [PMID: 36231143 PMCID: PMC9562881 DOI: 10.3390/cells11193181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Papillary thyroid cancer is the most common endocrine malignancy, occurring at an incidence rate of 12.9 per 100,000 in the US adult population. While the overall 10-year survival of PTC nears 95%, the presence of lymph node metastasis (LNM) or capsular invasion indicates the need for extensive neck dissection with possible adjuvant radioactive iodine therapy. While imaging modalities such as ultrasound and CT are currently in use for the detection of suspicious cervical lymph nodes, their sensitivities for tumor-positive nodes are low. Therefore, advancements in preoperative detection of LNM may optimize the surgical and medical management of patients with thyroid cancer. To this end, we analyzed bulk RNA-sequencing datasets to identify candidate markers highly predictive of LNM. We identified MEG3, a long-noncoding RNA previously described as a tumor suppressor when expressed in malignant cells, as highly associated with LNM tissue. Furthermore, the expression of MEG3 was highly predictive of tumor infiltration with cancer-associated fibroblasts, and single-cell RNA-sequencing data revealed the expression of MEG3 was isolated to cancer-associated fibroblasts (CAFs) in the most aggressive form of thyroid cancers. Our findings suggest that MEG3 expression, specifically in CAFs, is highly associated with LNM and may be a driver of aggressive disease.
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Affiliation(s)
- Sina Dadafarin
- Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, WA 98195, USA
- Correspondence: (S.D.); (J.G.)
| | - Tomás C. Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Michelle A. Carnazza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Raj K. Tiwari
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | | | - Jan Geliebter
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
- Correspondence: (S.D.); (J.G.)
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10
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Shi L, Chen W, Zhang Z, Chen J, Xue M. N1-methyladenosine profiling of long non-coding RNA in colorectal cancer. IUBMB Life 2021; 73:1235-1243. [PMID: 34314547 DOI: 10.1002/iub.2534] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 11/05/2022]
Abstract
N1-methyladenosine (m1A), is a unique methyl group that confers post-transcriptional modification of gene expression, and plays important roles in various human diseases. However, the abundance of this modification and its effects on long non-coding RNAs (lncRNAs) in human colorectal cancer (CRC) remain unclear. In this study, methylated RNA immunoprecipitation sequencing was performed in three pairs of human CRC and nontumorous tissues to identify m1A peaks and its correlation with differential alterations of lncRNA expression in CRC. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment pathway analyses were applied to predict the potential roles of m1A on gene expression. We found that CRC and adjacent tissues had a noticeable difference in m1A distribution. Notably, HGGAGRA and WGGANGA were recognized as the most significantly enriched motifs, respectively. Co-analysis of methylation and RNA sequencing demonstrated downregulated lncRNAs along with m1A modification in CRC. GO and KEGG pathway analyses revealed that the unique distribution of m1A sites in lncRNAs had a significant correlation with CRC signaling pathways. In conclusion, our results delineated the distribution pattern of m1A methylation on lncRNAs, and provided potential roles of this modification in different pathways and tumor progression of CRC.
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Affiliation(s)
- Liuhong Shi
- Department of Ultrasound, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Wenwen Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Zizhen Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Jingyu Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Meng Xue
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
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11
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Abstract
Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs
BIRC5 (Survivin) and
YBX1,
as well as long-noncoding RNAs
HOTAIR,
ZFAS1, and
AGAP2-AS1 were detected in BT-474 EVs by quantitative RT-PCR. Bioinformatics meta-analyses showed that
BIRC5 and
HOTAIR RNAs were substantially upregulated in breast tumours compared to non-tumour breast tissue, warranting further studies to explore their usefulness as biomarkers in patient EV samples. We envision this effective procedure for obtaining large amounts of cancer-specific EVs will accelerate discovery of EV-associated RNA biomarkers for cancers including HER2+ breast cancer.
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Affiliation(s)
- Colin L Hisey
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand.,Hub for Extracellular Vesicle Investigations, University of Auckland, Auckland, New Zealand
| | - Petr Tomek
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Yohanes N S Nursalim
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
| | - Lawrence W Chamley
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand.,Hub for Extracellular Vesicle Investigations, University of Auckland, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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12
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Abstract
In recent years, emerging evidence has suggested that noncoding RNAs (ncRNAs) participate in nearly every aspect of biological processes and play a crucial role in the genesis and progression of numerous tumors, including B-cell lymphoma. The exploration of ncRNA dysregulations and their functions in B-cell lymphoma provides new insights into lymphoma pathogenesis and is essential for indicating future clinical trials and optimizing the diagnostic and therapeutic strategies. In this review, we summarize the role of ncRNAs in B-cell lymphoma and discuss their potential in clinical applications.
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Affiliation(s)
- Jingwen Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Zou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyue Wan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Peng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangbo Chu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
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13
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Zhou Z, Wang B. Identification of male infertility-related long non-coding RNAs and their functions based on a competing endogenous RNA network. J Int Med Res 2020; 48:300060520961277. [PMID: 33054493 PMCID: PMC7580164 DOI: 10.1177/0300060520961277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE To identify male infertility-related long non-coding (lnc)RNAs and an lncRNA-related competing endogenous (ce)RNA network. METHODS Expression data including 13 normospermic and eight teratozoospermic samples from postmortem donors were downloaded from the GEO database (GSE6872). The limma R package was used to discriminate dysregulated lncRNA and micro (m)RNA profiles. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of differentially expressed (DE) mRNAs were performed using the clusterProfiler R package. The ceRNA network of dysregulated genes was visualized by Cytoscape. RESULTS A total of 101 DE lncRNAs and 1722 mRNAs were identified as male infertility-specific RNAs with thresholds of |log2FoldChange| >2.0 and adjusted P-value <0.05. GO and KEGG pathways were analyzed for DE mRNAs. Gene set enrichment analysis revealed that DE genes were enriched in embryonic skeletal system development and cytokine-cytokine receptor interactions. A ceRNA network was constructed with 26 key lncRNAs, 33 microRNAs, and 133 mRNAs. DE lncRNAs in male sterility were mainly associated with transferring phosphorus-containing groups and complexes of histone methyltransferases, methyltransferases, PcG proteins, and serine/threonine protein kinases. CONCLUSION This provides a novel perspective to study lncRNA-related ceRNA networks in male infertility and assist in identifying new potential biomarkers for diagnostic purposes.
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Affiliation(s)
- Zuo Zhou
- Department of Obstetrics, Maternal and Child Health Hospital of Zibo City, Shandong Province, China
| | - Bing Wang
- Center of Reproductive Medicine, Maternal and Child Health Hospital of Zibo City, Shandong Province, China
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14
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Kciuk M, Bukowski K, Marciniak B, Kontek R. Advances in DNA Repair-Emerging Players in the Arena of Eukaryotic DNA Repair. Int J Mol Sci 2020; 21:E3934. [PMID: 32486270 DOI: 10.3390/ijms21113934] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA is constantly damaged by factors produced during natural metabolic processes as well as agents coming from the external environment. Considering such a wide array of damaging agents, eukaryotic cells have evolved a DNA damage response (DRR) that opposes the influence of deleterious factors. Despite the broad knowledge regarding DNA damage and repair, new areas of research are emerging. New players in the field of DDR are constantly being discovered. The aim of this study is to review current knowledge regarding the roles of sirtuins, heat shock proteins, long-noncoding RNAs and the circadian clock in DDR and distinguish new agents that may have a prominent role in DNA damage response and repair.
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15
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Bekric D, Neureiter D, Ritter M, Jakab M, Gaisberger M, Pichler M, Kiesslich T, Mayr C. Long Non-Coding RNAs in Biliary Tract Cancer-An Up-to-Date Review. J Clin Med 2020; 9:jcm9041200. [PMID: 32331331 PMCID: PMC7231154 DOI: 10.3390/jcm9041200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
The term long non-coding RNA (lncRNA) describes non protein-coding transcripts with a length greater than 200 base pairs. The ongoing discovery, characterization and functional categorization of lncRNAs has led to a better understanding of the involvement of lncRNAs in diverse biological and pathological processes including cancer. Aberrant expression of specific lncRNA species was demonstrated in various cancer types and associated with unfavorable clinical characteristics. Recent studies suggest that lncRNAs are also involved in the development and progression of biliary tract cancer, a rare disease with high mortality and limited therapeutic options. In this review, we summarize current findings regarding the manifold roles of lncRNAs in biliary tract cancer and give an overview of the clinical and molecular consequences of aberrant lncRNA expression as well as of underlying regulatory functions of selected lncRNA species in the context of biliary tract cancer.
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Affiliation(s)
- Dino Bekric
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria;
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Markus Ritter
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Paracelsus Medical University, 5020 Salzburg, Austria
- Gastein Research Institute, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Martin Jakab
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
| | - Martin Gaisberger
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Paracelsus Medical University, 5020 Salzburg, Austria
- Gastein Research Institute, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Martin Pichler
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Clinical Oncology, Department of Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria;
| | - Tobias Kiesslich
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria
| | - Christian Mayr
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria
- Correspondence:
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16
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Zhang PF, Wu J, Luo JH, Li KS, Wang F, Huang W, Wu Y, Gao SP, Zhang XM, Zhang PN. SNHG22 overexpression indicates poor prognosis and induces chemotherapy resistance via the miR-2467/Gal-1 signaling pathway in epithelial ovarian carcinoma. Aging (Albany NY) 2019; 11:8204-8216. [PMID: 31581131 PMCID: PMC6814594 DOI: 10.18632/aging.102313] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/21/2019] [Indexed: 12/13/2022]
Abstract
Recently, an increasing number of studies have reported that dysregulation of long noncoding RNAs (lncRNAs) plays an important role in cancer initiation and progression, including in epithelial ovarian carcinoma (EOC). However, little is known about the detailed biological functions of the lncRNA small nucleolar RNA host gene 22 (SNHG22) during the progression of EOC. Here, we found that SNHG22 was significantly increased in EOC tissues and was significantly associated with a low level of differentiation. Forced SNHG22 expression promoted chemotherapy resistance in EOC cells. Knockdown of SNHG22 expression increased the sensitivity of EOC cells to cisplatin and paclitaxel. Importantly, we found that SNHG22 could directly interact with miR-2467 and lead to the release of miR-2467-targeted Gal-1 mRNA. Moreover, SNHG22 overexpression induced EOC cell resistance to chemotherapy agents via PI3K/AKT and ERK cascade activation. In summary, our findings demonstrate that SNHG22 plays a critical role in the chemotherapy resistance of EOC by mediating the miR-2467/Gal-1 regulatory axis.
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Affiliation(s)
- Peng-Fei Zhang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jing Wu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jin-Hong Luo
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ke-Sang Li
- Department of Hematology and Oncology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Fei Wang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Huang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yin Wu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shui-Ping Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xue-Mei Zhang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Peng-Nan Zhang
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
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17
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Xu F, Zhao Y, Qin G, Huan Y, Li L, Gao W. Comprehensive analysis of competing endogenous RNA networks associated with cholangiocarcinoma. Exp Ther Med 2019; 18:4103-4112. [PMID: 31641385 DOI: 10.3892/etm.2019.8052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/12/2019] [Indexed: 12/14/2022] Open
Abstract
Cholangiocarcinoma (CCA) is the second most common type of primary malignancy of the liver. Certain long non-coding RNAs (lncRNAs) have been demonstrated to have key roles in tumor pathogenesis by binding to microRNAs (miRNAs). However, the competing endogenous RNA (ceRNA) network of CCA remains to be fully determined. In the present study, the RNA expression profiles for CCA were downloaded from The Cancer Genome Atlas and further analyzed. A total of 318 differentially expressed (DE) lncRNAs, 87 DE miRNAs and 3,851 DE mRNAs were identified from 36 CCA samples and 9 adjacent non-tumor samples (for lncRNAs and miRNAs, fold change ≥2.5 and P<0.01; for mRNAs, fold change ≥2 and P<0.01). Further bioinformatics analyses were performed and the ceRNA network for CCA was constructed, which included 16 lncRNAs, 55 miRNAs and 373 mRNAs. Survival analysis of all genes in the network revealed that high expression of the mRNAs fucosyltransferase 4 (P<0.005) and huntingtin-interacting protein 1 related (P<0.001) has a positive impact on the overall survival of patients with CAA. Furthermore, the lncRNAs H19 and PVT1, and the miRNAs Homo sapiens (hsa)-miR-16-5p and hsa-miR-424-5p, together with peroxisome proliferator-activated receptors, may also have important roles in the pathogenesis of CCA. The present study provided data to further the understanding of and research into the molecular mechanisms implicated in CCA.
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Affiliation(s)
- Fangting Xu
- Department of Anesthesia, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yuchong Zhao
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Gang Qin
- Department of Anesthesia, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Ye Huan
- Department of Anesthesia, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Longyan Li
- Department of Anesthesia, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Wei Gao
- Department of Anesthesia, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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18
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Liang Z, Wang Y, Li H, Sun Y, Gong Y. lncRNAs combine and crosstalk with NSPc1 in ATRA-induced differentiation of U87 glioma cells. Oncol Lett 2019; 17:5821-5829. [PMID: 31186810 DOI: 10.3892/ol.2019.10254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 02/04/2019] [Indexed: 12/24/2022] Open
Abstract
Nervous system polycomb 1 (NSPc1) is a member of the polycomb group (PcG) family of proteins and has been demonstrated to maintain the differentiation and pluripotency of stem cells. Long non-coding RNAs (lncRNAs) have been demonstrated to be involved in the control of pluripotency and differentiation in embryonic and pluripotent cells. In the present study, the expression levels of NSPc1 were associated with the malignant potential of various glioma cell lines. Additionally, lncRNAs were differentially expressed in glioblastoma cell lines. Following induced differentiation of U87 glioblastoma cells with all-trans retinoic acid, the expression levels of NSPc1 decreased initially, reaching its lowest point on day 6, but then subsequently increased until day 10. The expression of lncRNA candidates decreased in the cell differentiation stage. Additionally, the expression of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), sex-determining region of the Y chromosome-box 2 overlapping transcript (SOX2OT) and antisense non-coding RNA in the INK4 locus (ANRIL) was significantly altered relative to the expression levels of NSPc1. RNA immunoprecipitation (RIP) assays demonstrated that MALAT1, SOX2OT and ANRIL bind to NSPc1 in U87 glioblastoma cells and the enrichment of ANRIL in anti-NSPc1 antibody group was associated with the expression levels of NSPc1 during U87 cell differentiation. Small interfering RNA mediated downregulation of NSPc1 expression with MALAT1, SOX2OT and ANRIL, inhibited the proliferation, and promoted apoptosis in U87 cells. The results of the present study demonstrate that MALAT1, SOX2OT and ANRIL combine and crosstalk with NSPc1 in U87 cells to affect proliferation and apoptosis.
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Affiliation(s)
- Zhikong Liang
- Department of Immunology, Logistics University of Chinese People's Armed Police Force, Tianjin 300309, P.R. China.,Jiangsu Provincial Corps Hospital of Chinese People's Armed Police Force, Yangzhou 225003, P.R. China
| | - Yuliang Wang
- Department of Biochemistry and Molecular Biology, Logistics University of Chinese People's Armed Police Force, Tianjin 300309, P.R. China.,Sixth Detachment of Second Mobile Corps of Chinese People's Armed Police Force, Guangzhou 510812, P.R. China
| | - Hui Li
- Department of Histology and Embryology, Logistics University of Chinese People's Armed Police Force, Tianjin 300309, P.R. China
| | - Yi Sun
- Department of Immunology, Logistics University of Chinese People's Armed Police Force, Tianjin 300309, P.R. China
| | - Yanhua Gong
- Department of Biochemistry and Molecular Biology, Logistics University of Chinese People's Armed Police Force, Tianjin 300309, P.R. China.,Institute of Disaster Medicine, Tianjin University, Tianjin 300072, P.R. China
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19
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Almenar-Pérez E, Ovejero T, Sánchez-Fito T, Espejo JA, Nathanson L, Oltra E. Epigenetic Components of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Uncover Potential Transposable Element Activation. Clin Ther. 2019;41:675-698. [PMID: 30910331 DOI: 10.1016/j.clinthera.2019.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Studies to determine epigenetic changes associated with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) remain scarce; however, current evidence clearly shows that methylation patterns of genomic DNA and noncoding RNA profiles of immune cells differ between patients and healthy subjects, suggesting an active role of these epigenetic mechanisms in the disease. The present study compares and contrasts the available ME/CFS epigenetic data in an effort to evidence overlapping pathways capable of explaining at least some of the dysfunctional immune parameters linked to this disease. METHODS A systematic search of the literature evaluating the ME/CFS epigenome landscape was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. Differential DNA methylation and noncoding RNA differential expression patterns associated with ME/CFS were used to screen for the presence of transposable elements using the Dfam browser, a search program nurtured with the Repbase repetitive sequence database and the RepeatMasker annotation tool. FINDINGS Unexpectedly, particular associations of transposable elements and ME/CFS epigenetic hallmarks were uncovered. A model for the disease emerged involving transcriptional induction of endogenous dormant transposons and structured cellular RNA interactions, triggering the activation of the innate immune system without a concomitant active infection. IMPLICATIONS Repetitive sequence filters (ie, RepeatMasker) should be avoided when analyzing transcriptomic data to assess the potential participation of repetitive sequences ("junk repetitive DNA"), representing >45% of the human genome, in the onset and evolution of ME/CFS. In addition, transposable element screenings aimed at designing cost-effective, focused empirical assays that can confirm or disprove the suspected involvement of transposon transcriptional activation in this disease, following the pilot strategy presented here, will require databases gathering large ME/CFS epigenetic datasets.
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20
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Abstract
Over many years, extensive efforts have focused on the development and improvement of diagnostic and therapeutic strategies to reduce stroke-associated neurovascular damage, such as blood-brain barrier dysfunction, brain edema, parenchymal inflammation, and neural cell death. However, the only clinically applied pharmacological therapy to date for the treatment of acute ischemic stroke is thrombolysis. Because of the short therapeutic window of current thrombolytic therapy and the activation of various pathophysiological signaling cascades triggered after ischemic stroke, the development of new therapies is urgently required. Noncoding RNAs (ncRNAs) are defined as untranslated regulatory RNA molecules. Although ncRNAs with biological roles have been known for almost 60 years, they have within the past decade emerged as key mediators of posttranscriptional gene expression/function in pathological aspects of ischemic stroke. With properties of relative stability, specificity, and reproducibility, ncRNAs are considered to be promising as biomarkers and better candidates than proteins and genes for early recognition of the onset of disease. In this update, we summarized the current knowledge for three groups of ncRNAs in stroke, focusing on the role of long noncoding RNAs and circular RNAs as biomarkers for stroke and as targets for regulating large sets of genes in related pathways after ischemic stroke.
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Affiliation(s)
- Xuejing Zhang
- Pittsburgh Institute of Brain Disorders & Recovery, Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Milton H. Hamblin
- Department of Pharmacology, Tulane University School of Medicine, 1430 Tulane Avenue SL83, New Orleans, LA 70112, USA
| | - Ke-Jie Yin
- Pittsburgh Institute of Brain Disorders & Recovery, Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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21
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Lyu Q, Xu S, Lyu Y, Choi M, Christie CK, Slivano OJ, Rahman A, Jin ZG, Long X, Xu Y, Miano JM. SENCR stabilizes vascular endothelial cell adherens junctions through interaction with CKAP4. Proc Natl Acad Sci U S A 2019; 116:546-55. [PMID: 30584103 DOI: 10.1073/pnas.1810729116] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
SENCR is a human-specific, vascular cell-enriched long-noncoding RNA (lncRNA) that regulates vascular smooth muscle cell and endothelial cell (EC) phenotypes. The underlying mechanisms of action of SENCR in these and other cell types is unknown. Here, levels of SENCR RNA are shown to be elevated in several differentiated human EC lineages subjected to laminar shear stress. Increases in SENCR RNA are also observed in the laminar shear stress region of the adult aorta of humanized SENCR-expressing mice, but not in disturbed shear stress regions. SENCR loss-of-function studies disclose perturbations in EC membrane integrity resulting in increased EC permeability. Biotinylated RNA pull-down and mass spectrometry establish an abundant SENCR-binding protein, cytoskeletal-associated protein 4 (CKAP4); this ribonucleoprotein complex was further confirmed in an RNA immunoprecipitation experiment using an antibody to CKAP4. Structure-function studies demonstrate a noncanonical RNA-binding domain in CKAP4 that binds SENCR Upon SENCR knockdown, increasing levels of CKAP4 protein are detected in the EC surface fraction. Furthermore, an interaction between CKAP4 and CDH5 is enhanced in SENCR-depleted EC. This heightened association appears to destabilize the CDH5/CTNND1 complex and augment CDH5 internalization, resulting in impaired adherens junctions. These findings support SENCR as a flow-responsive lncRNA that promotes EC adherens junction integrity through physical association with CKAP4, thereby stabilizing cell membrane-bound CDH5.
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22
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Villamizar O, Chambers CB, Riberdy JM, Persons DA, Wilber A. Long noncoding RNA Saf and splicing factor 45 increase soluble Fas and resistance to apoptosis. Oncotarget 2017; 7:13810-26. [PMID: 26885613 PMCID: PMC4924680 DOI: 10.18632/oncotarget.7329] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/29/2016] [Indexed: 12/21/2022] Open
Abstract
In multicellular organisms, cell growth and differentiation is controlled in part by programmed cell death or apoptosis. One major apoptotic pathway is triggered by Fas receptor (Fas)-Fas ligand (FasL) interaction. Neoplastic cells are frequently resistant to Fas-mediated apoptosis, evade Fas signals through down regulation of Fas and produce soluble Fas proteins that bind FasL thereby blocking apoptosis. Soluble Fas (sFas) is an alternative splice product of Fas pre-mRNA, commonly created by exclusion of transmembrane spanning sequences encoded within exon 6 (FasΔEx6). Long non-coding RNAs (lncRNAs) interact with other RNAs, DNA, and proteins to regulate gene expression. One lncRNA, Fas-antisense or Saf, was shown to participate in alternative splicing of Fas pre-mRNA through unknown mechanisms. We show that Saf is localized in the nucleus where it interacts with Fas receptor pre-mRNA and human splicing factor 45 (SPF45) to facilitate alternative splicing and exclusion of exon 6. The product is a soluble Fas protein that protects cells against FasL-induced apoptosis. Collectively, these studies reveal a novel mechanism to modulate this critical cell death program by an lncRNA and its protein partner.
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Affiliation(s)
- Olga Villamizar
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, USA.,Department of Microbiology, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Christopher B Chambers
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Janice M Riberdy
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Derek A Persons
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Andrew Wilber
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, USA
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Stafford DA, Dichmann DS, Chang JK, Harland RM. Deletion of the sclerotome-enriched lncRNA PEAT augments ribosomal protein expression. Proc Natl Acad Sci U S A 2017; 114:101-6. [PMID: 27986952 DOI: 10.1073/pnas.1612069113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To define a complete catalog of the genes that are activated during mouse sclerotome formation, we sequenced RNA from embryonic mouse tissue directed to form sclerotome in culture. In addition to well-known early markers of sclerotome, such as Pax1, Pax9, and the Bapx2/Nkx3-2 homolog Nkx3-1, the long-noncoding RNA PEAT (Pax1 enhancer antisense transcript) was induced in sclerotome-directed samples. Strikingly, PEAT is located just upstream of the Pax1 gene. Using CRISPR/Cas9, we generated a mouse line bearing a complete deletion of the PEAT-transcribed unit. RNA-seq on PEAT mutant embryos showed that loss of PEAT modestly increases bone morphogenetic protein target gene expression and also elevates the expression of a large subset of ribosomal protein mRNAs.
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Fan Y, Yang J, Mathioni SM, Yu J, Shen J, Yang X, Wang L, Zhang Q, Cai Z, Xu C, Li X, Xiao J, Meyers BC, Zhang Q. PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice. Proc Natl Acad Sci U S A 2016; 113:15144-9. [PMID: 27965387 DOI: 10.1073/pnas.1619159114] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Phased small-interfering RNAs (phasiRNAs) are a special class of small RNAs, which are generated in 21- or 24-nt intervals from transcripts of precursor RNAs. Although phasiRNAs have been found in a range of organisms, their biological functions in plants have yet to be uncovered. Here we show that phasiRNAs generated by the photopheriod-sensetive genic male sterility 1 (Pms1) locus were associated with photoperiod-sensitive male sterility (PSMS) in rice, a germplasm that started the two-line hybrid rice breeding. The Pms1 locus encodes a long-noncoding RNA PMS1T that was preferentially expressed in young panicles. PMS1T was targeted by miR2118 to produce 21-nt phasiRNAs that preferentially accumulated in the PSMS line under long-day conditions. A single nucleotide polymorphism in PMS1T nearby the miR2118 recognition site was critical for fertility change, likely leading to differential accumulation of the phasiRNAs. This result suggested possible roles of phasiRNAs in reproductive development of rice, demonstrating the potential importance of this RNA class as regulators in biological processes.
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Zhu KP, Zhang CL, Shen GQ, Zhu ZS. Long noncoding RNA expression profiles of the doxorubicin-resistant human osteosarcoma cell line MG63/DXR and its parental cell line MG63 as ascertained by microarray analysis. Int J Clin Exp Pathol 2015; 8:8754-8773. [PMID: 26464619 PMCID: PMC4583851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/21/2015] [Indexed: 06/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) are emerging in molecular biology as crucial regulators of cancer. The efficacy of doxorubicin--based chemotherapy in osteosarcoma (OS) is usually limited by acquired drug resistance. To explore the mechanism of chemoresistance of OS in terms of lncRNA, using a human lncRNA-mRNA combined microarray, we identified 3,465 lncRNAs (1,761 up and 1,704 down) and 3,278 mRNAs (1,607 up and 1,671 down) aberrantly expressed in all three sets of doxorubicin-resistant MG63/DXR and their paired parental MG63 cells (fold-change >2.0, P<0.05 and FDR <0.05). Fifteen randomly selected lncRNAs were dysregulated in MG63/DXR cells relative to MG63 cells by qRT-PCR detection, which were consistent with our microarray data. Bioinformatics analysis identified that classical genes and pathways involved in cell proliferation, apoptosis, and drug metabolism were differently expressed in these cell lines. A lncRNA-mRNA co-expression network identified lncRNAs, including ENST00000563280 and NR-036444, may play a critical role in doxorubicin-resistance of OS by interacting with important genes such as ABCB1, HIF1A and FOXC2. Besides, we found that lncRNA ENST00000563280 was distinctly increased in specimens of OS patients with a poor chemoresponse compared to those with a good chemoresponse and the patients of lower expression of it may survive longer than those of higher expression, which suggest that it may serve as a biomarker to predict the chemoresponse and prognosis of osteosarcoma patients. These results provide important insights about the lncRNAs involved in osteosarcoma chemoresistance and lay a solid foundation for uncovering the mechanism ultimately.
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Affiliation(s)
- Kun-Peng Zhu
- Department of Orthopaedic Surgery, The Sixth People’s Hospital Affiliated to Shanghai Jiaotong UniversityShanghai 200233, PR China
| | - Chun-Lin Zhang
- Department of Orthopaedic Surgery, Shanghai Tenth People’s Hospital Affiliated to Tongji UniversityShanghai 200072, PR China
| | - Guo-Qi Shen
- Department of Orthopaedic Surgery, Shanghai Sixth People’s Hospital, Soochow UniversityShanghai 200233, PR China
| | - Zhong-Sheng Zhu
- Department of Orthopaedic Surgery, Shanghai Tenth People’s Hospital Affiliated to Tongji UniversityShanghai 200072, PR China
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Vickers KC, Roteta LA, Hucheson-Dilks H, Han L, Guo Y. Mining diverse small RNA species in the deep transcriptome. Trends Biochem Sci 2014; 40:4-7. [PMID: 25435401 DOI: 10.1016/j.tibs.2014.10.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/27/2014] [Accepted: 10/30/2014] [Indexed: 11/26/2022]
Abstract
Transcriptomes of many species are proving to be exquisitely diverse, and many investigators are now using high-throughput sequencing to quantify non-protein-coding RNAs, namely small RNAs (sRNA). Unfortunately, most studies are focused solely on microRNA changes, and many investigators are not analyzing the full compendium of sRNA species present in their large datasets. We provide here a rationale to include all types of sRNAs in sRNA sequencing analyses, which will aid in the discovery of their biological functions and physiological relevance.
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Affiliation(s)
- Kasey C Vickers
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Leslie A Roteta
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Leng Han
- M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yan Guo
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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