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Fan L, Sun W, Lyu Y, Ju F, Sun W, Chen J, Ma H, Yang S, Zhou X, Wu N, Yi W, Chen E, Villaseñor R, Baubec T, Yan J. Chrom-seq identifies RNAs at chromatin marks. SCIENCE ADVANCES 2024; 10:eadn1397. [PMID: 39083617 PMCID: PMC11290522 DOI: 10.1126/sciadv.adn1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Chromatin marks are associated with transcriptional regulatory activities. However, very few lncRNAs have been characterized with the role in regulating epigenetic marks, largely due to the technical difficulty in identifying chromatin-associating RNA. Current methods are largely limited by the availability of ChIP-grade antibody and the crosslinking, which generates high noise. Here, we developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin mark reader with APEX2, which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1, and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3, and H3K4me3, respectively. We demonstrated that Chrom-seq outperformed other equivalent methods in terms of sensitivity, efficiency, and cost of practice. It provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in epigenetic events.
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Affiliation(s)
- Ligang Fan
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | | | - Yitong Lyu
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Furong Ju
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
| | - Wenju Sun
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Jie Chen
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Haiqian Ma
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Shifei Yang
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Xiaomin Zhou
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Nan Wu
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Wenkai Yi
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Erfei Chen
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Rodrigo Villaseñor
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tuncay Baubec
- Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Jian Yan
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
- Department of Precision Diagnostic and Therapeutic Technology, The City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, China
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Musgrove MRB, Mikhaylova M, Bredy TW. Fundamental Neurochemistry Review: At the intersection between the brain and the immune system: Non-coding RNAs spanning learning, memory and adaptive immunity. J Neurochem 2024; 168:961-976. [PMID: 38339812 DOI: 10.1111/jnc.16071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
Non-coding RNAs (ncRNAs) are highly plastic RNA molecules that can sequester cellular proteins and other RNAs, serve as transporters of cellular cargo and provide spatiotemporal feedback to the genome. Mounting evidence indicates that ncRNAs are central to biology, and are critical for neuronal development, metabolism and intra- and intercellular communication in the brain. Their plasticity arises from state-dependent dynamic structure states that can be influenced by cell type and subcellular environment, which can subsequently enable the same ncRNA with discrete functions in different contexts. Here, we highlight different classes of brain-enriched ncRNAs, including microRNA, long non-coding RNA and other enigmatic ncRNAs, that are functionally important for both learning and memory and adaptive immunity, and describe how they may promote cross-talk between these two evolutionarily ancient biological systems.
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Affiliation(s)
- Mason R B Musgrove
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Marina Mikhaylova
- AG Optobiologie, Institute für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Timothy W Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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3
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López-Martínez A, Santos-Álvarez JC, Velázquez-Enríquez JM, Ramírez-Hernández AA, Vásquez-Garzón VR, Baltierrez-Hoyos R. lncRNA-mRNA Co-Expression and Regulation Analysis in Lung Fibroblasts from Idiopathic Pulmonary Fibrosis. Noncoding RNA 2024; 10:26. [PMID: 38668384 PMCID: PMC11054336 DOI: 10.3390/ncrna10020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease marked by abnormal accumulation of extracellular matrix (ECM) due to dysregulated expression of various RNAs in pulmonary fibroblasts. This study utilized RNA-seq data meta-analysis to explore the regulatory network of hub long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in IPF fibroblasts. The meta-analysis unveiled 584 differentially expressed mRNAs (DEmRNA) and 75 differentially expressed lncRNAs (DElncRNA) in lung fibroblasts from IPF. Among these, BCL6, EFNB1, EPHB2, FOXO1, FOXO3, GNAI1, IRF4, PIK3R1, and RXRA were identified as hub mRNAs, while AC008708.1, AC091806.1, AL442071.1, FAM111A-DT, and LINC01989 were designated as hub lncRNAs. Functional characterization revealed involvement in TGF-β, PI3K, FOXO, and MAPK signaling pathways. Additionally, this study identified regulatory interactions between sequences of hub mRNAs and lncRNAs. In summary, the findings suggest that AC008708.1, AC091806.1, FAM111A-DT, LINC01989, and AL442071.1 lncRNAs can regulate BCL6, EFNB1, EPHB2, FOXO1, FOXO3, GNAI1, IRF4, PIK3R1, and RXRA mRNAs in fibroblasts bearing IPF and contribute to fibrosis by modulating crucial signaling pathways such as FoxO signaling, chemical carcinogenesis, longevity regulatory pathways, non-small cell lung cancer, and AMPK signaling pathways.
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Affiliation(s)
- Armando López-Martínez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Jovito Cesar Santos-Álvarez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Juan Manuel Velázquez-Enríquez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Alma Aurora Ramírez-Hernández
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Verónica Rocío Vásquez-Garzón
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
- CONACYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico
| | - Rafael Baltierrez-Hoyos
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
- CONACYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico
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Wang S, Li J, Zhao Y. Construction and analysis of a network of exercise-induced mitochondria-related non-coding RNA in the regulation of diabetic cardiomyopathy. PLoS One 2024; 19:e0297848. [PMID: 38547044 PMCID: PMC10977711 DOI: 10.1371/journal.pone.0297848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/09/2024] [Indexed: 04/02/2024] Open
Abstract
Diabetic cardiomyopathy (DCM) is a major factor in the development of heart failure. Mitochondria play a crucial role in regulating insulin resistance, oxidative stress, and inflammation, which affect the progression of DCM. Regular exercise can induce altered non-coding RNA (ncRNA) expression, which subsequently affects gene expression and protein function. The mechanism of exercise-induced mitochondrial-related non-coding RNA network in the regulation of DCM remains unclear. This study seeks to construct an innovative exercise-induced mitochondrial-related ncRNA network. Bioinformatic analysis of RNA sequencing data from an exercise rat model identified 144 differentially expressed long non-coding RNA (lncRNA) with cutoff criteria of p< 0.05 and fold change ≥1.0. GSE6880 and GSE4745 were the differentially expressed mRNAs from the left ventricle of DCM rat that downloaded from the GEO database. Combined with the differentially expressed mRNA and MitoCarta 3.0 dataset, the mitochondrial located gene Pdk4 was identified as a target gene. The miRNA prediction analysis using miRanda and TargetScan confirmed that 5 miRNAs have potential to interact with the 144 lncRNA. The novel lncRNA-miRNA-Pdk4 network was constructed for the first time. According to the functional protein association network, the newly created exercise-induced ncRNA network may serve as a promising diagnostic marker and therapeutic target, providing a fresh perspective to understand the molecular mechanism of different exercise types for the prevention and treatment of diabetic cardiomyopathy.
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Affiliation(s)
- Shuo Wang
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Tianjin University of Sport, Tianjin, China
| | - Jiacong Li
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Tianjin University of Sport, Tianjin, China
| | - Yungang Zhao
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Tianjin University of Sport, Tianjin, China
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Chen X, Wang T, Guo W, Yan X, Kou H, Yu Y, Liu C, Gao W, Wang W, Wang R. Transcriptome reveals the roles and potential mechanisms of lncRNAs in the regulation of albendazole resistance in Haemonchus contortus. BMC Genomics 2024; 25:188. [PMID: 38368335 PMCID: PMC10873934 DOI: 10.1186/s12864-024-10096-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/07/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Haemonchus contortus (H. contortus) is the most common parasitic nematode in ruminants and is prevalent worldwide. H. contortus resistance to albendazole (ABZ) hinders the efficacy of anthelmintic drugs, but little is known about the molecular mechanisms that regulate this of drug resistance. Recent research has demonstrated that long noncoding RNAs (lncRNAs) can exert significant influence as pivotal regulators of the emergence of drug resistance. RESULTS In this study, transcriptome sequencing was conducted on both albendazole-sensitive (ABZ-sensitive) and albendazole-resistant (ABZ-resistant) H. contortus strains, with three biological replicates for each group. The analysis of lncRNA in the transcriptomic data revealed that there were 276 differentially expressed lncRNA (DElncRNA) between strains with ABZ-sensitive and ABZ-resistant according to the criteria of |log2Foldchange|≥ 1 and FDR < 0.05. Notably, MSTRG.12969.2 and MSTRG.9827.1 exhibited the most significant upregulation and downregulation, respectively, in the resistant strains. The potential roles of the DElncRNAs included catalytic activity, stimulus response, regulation of drug metabolism, and modulation of the immune response. Moreover, we investigated the interactions between DElncRNAs and other RNAs, specifically MSTRG.12741.1, MSTRG.11848.1, MSTRG.5895.1, and MSTRG.14070.1, involved in regulating drug stimulation through cis/trans/antisense/lncRNA‒miRNA-mRNA interaction networks. This regulation leads to a decrease (or increase) in the expression of relevant genes, consequently enhancing the resistance of H. contortus to albendazole. Furthermore, through comprehensive analysis of competitive endogenous RNAs (ceRNAs) involved in drug resistance-related pathways, such as the mTOR signalling pathway and ABC transporter signalling pathway, the relevance of the MSTRG.2499.1-novel-m0062-3p-HCON_00099610 interaction was identified to mainly involve the regulation of catalytic activity, metabolism, ubiquitination and transcriptional regulation of gene promoters. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) validation indicated that the transcription profiles of six DElncRNAs and six DEmRNAs were consistent with those obtained by RNA-seq. CONCLUSIONS The results of the present study allowed us to better understand the changes in the lncRNA expression profile of ABZ-resistant H. contortus. In total, these results suggest that the lncRNAs MSTRG.963.1, MSTRG.12741.1, MSTRG.11848.1 and MSTRG.2499.1 play important roles in the development of ABZ resistance and can serve as promising biomarkers for further study.
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Affiliation(s)
- Xindi Chen
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Tengyu Wang
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Wenrui Guo
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Xu Yan
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Huilin Kou
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Yu Yu
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Chunxia Liu
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Wa Gao
- Inner Mongolia Key Laboratory of Tick-Borne Zoonotic Infectious Disease, Department of Medicine, Hetao College, Bayan Nur, 015000, Inner Mongolia Autonomous Region, China
| | - Wenlong Wang
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China.
| | - Rui Wang
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China.
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Li P, Chen CZ, Liu L, Li ZH. Whole-Transcriptome Analysis Reveals the RNA Profiles in Mouse Bone Marrow Mesenchymal Stem Cells or Zebrafish Embryos After Exposure to Environmental Level of Tributyltin. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2024; 112:34. [PMID: 38342962 DOI: 10.1007/s00128-024-03861-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/19/2024] [Indexed: 02/13/2024]
Abstract
To understand the underlying molecular mechanisms, mouse bone marrow mesenchymal stem cells (BMSCs) and zebrafish embryos were exposed to the control group and Tributyltin (TBT) group (10 ng/L, environmental concentration) for 48 h, respectively. The expression profiles of RNAs were investigated using whole-transcriptome analysis in mouse BMSCs or zebrafish embryos after TBT exposure. For mouse BMSCs, the results showed 2,449 differentially expressed (DE) mRNAs, 59 DE miRNAs, 317 DE lncRNAs, and 15 circRNAs. Similarly, for zebrafish embryos, the results showed 1,511 DE mRNAs, 4 DE miRNAs, 272 DE lncRNAs, and 28 circRNAs. According to KEGG pathway analysis showed that DE RNAs were mainly associated with immune responses, signaling, and cellular interactions. Competing endogenous RNA (ceRNA) network analysis revealed that the regulatory network of miRNA-circRNA constructed in zebrafish embryos was more complex compared to that of mouse BMSCs.
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Affiliation(s)
- Ping Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Cheng-Zhuang Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China.
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Aydın E, Saus E, Chorostecki U, Gabaldón T. A hybrid approach to assess the structural impact of long noncoding RNA mutations uncovers key
NEAT1
interactions in colorectal cancer. IUBMB Life 2023. [PMID: 36971476 DOI: 10.1002/iub.2710] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/25/2023] [Indexed: 03/29/2023]
Abstract
Long noncoding RNAs (lncRNAs) are emerging players in cancer and they entail potential as prognostic biomarkers or therapeutic targets. Earlier studies have identified somatic mutations in lncRNAs that are associated with tumor relapse after therapy, but the underlying mechanisms behind these associations remain unknown. Given the relevance of secondary structure for the function of some lncRNAs, some of these mutations may have a functional impact through structural disturbance. Here, we examined the potential structural and functional impact of a novel A > G point mutation in NEAT1 that has been recurrently observed in tumors of colorectal cancer patients experiencing relapse after treatment. Here, we used the nextPARS structural probing approach to provide first empirical evidence that this mutation alters NEAT1 structure. We further evaluated the potential effects of this structural alteration using computational tools and found that this mutation likely alters the binding propensities of several NEAT1-interacting miRNAs. Differential expression analysis on these miRNA networks shows upregulation of Vimentin, consistent with previous findings. We propose a hybrid pipeline that can be used to explore the potential functional effects of lncRNA somatic mutations.
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Affiliation(s)
- Efe Aydın
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Ester Saus
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, Barcelona, Spain
| | - Uciel Chorostecki
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, Barcelona, Spain
| | - Toni Gabaldón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
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Fu X, Guo M, Liu J, Li C. circRNA432 enhances the coelomocyte phagocytosis via regulating the miR-2008-ELMO1 axis in Vibrio splendidus-challenged Apostichopus japonicus. Commun Biol 2023; 6:115. [PMID: 36709365 PMCID: PMC9884281 DOI: 10.1038/s42003-023-04516-8] [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: 08/03/2022] [Accepted: 01/20/2023] [Indexed: 01/30/2023] Open
Abstract
Circular RNAs (circRNAs) are a kind of extensive and diverse covalently closed circular endogenous RNA, which exert crucial functions in immune regulation in mammals. However, the functions and mechanisms of circRNAs in invertebrates are largely unclarified. In our previous work, 261 differentially expressed circRNAs including circRNA432 (circ432) were identified from skin ulcer syndrome (SUS) diseased sea cucumber Apostichopus japonicus by RNA-seq. To better address the functional role of sea cucumber circRNAs, circ432 was first found to be significantly induced by Vibrio splendidus challenge and LPS exposure in this study. Knock-down circ432 could depress the V. splendidus-induced coelomocytes phagocytosis. Moreover, circ432 is validated to serve as the sponge of miR-2008, a differential expressed miRNA in SUS-diseased sea cucumbers, by Argonaute 2-RNA immunoprecipitation (AGO2-RIP) assay, luciferase reporter assay and RNA fluorescence in situ hybridization (FISH) in vitro. Engulfment and cell motility protein 1 (AjELMO1) is further demonstrated to be the target of miR-2008, and silencing AjELMO1 inhibits the V. splendidus-induced coelomocytes phagocytosis, and this phenomenon could be further suppressed by supplementing with miR-2008 mimics, suggesting that circ432 might regulate coelomocytes phagocytosis via miR-2008-AjELMO1 axis. We further confirm that the depressed coelomocytes' phagocytosis by circ432 silencing is consistent with the decreased abundance of AjELMO1, and could be recovered by miR-2008 inhibitors transfection. All our results provide the evidence that circ432 is involved in regulating pathogen-induced coelomocyte phagocytosis via sponge miR-2008 and promotes the abundance of AjELMO1. These findings will enrich the regulatory mechanism of phagocytosis in echinoderm and provide theoretical data for SUS disease prevention and control in sea cucumbers.
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Affiliation(s)
- Xianmu Fu
- grid.203507.30000 0000 8950 5267State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211 Ningbo, P. R. China
| | - Ming Guo
- grid.203507.30000 0000 8950 5267State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211 Ningbo, P. R. China
| | - Jiqing Liu
- grid.203507.30000 0000 8950 5267State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211 Ningbo, P. R. China
| | - Chenghua Li
- grid.203507.30000 0000 8950 5267State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211 Ningbo, P. R. China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266071 Qingdao, P. R. China
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9
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Marchetti L, Nifosì R, Martelli PL, Da Pozzo E, Cappello V, Banterle F, Trincavelli ML, Martini C, D’Elia M. Quantum computing algorithms: getting closer to critical problems in computational biology. Brief Bioinform 2022; 23:bbac437. [PMID: 36220772 PMCID: PMC9677474 DOI: 10.1093/bib/bbac437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022] Open
Abstract
The recent biotechnological progress has allowed life scientists and physicians to access an unprecedented, massive amount of data at all levels (molecular, supramolecular, cellular and so on) of biological complexity. So far, mostly classical computational efforts have been dedicated to the simulation, prediction or de novo design of biomolecules, in order to improve the understanding of their function or to develop novel therapeutics. At a higher level of complexity, the progress of omics disciplines (genomics, transcriptomics, proteomics and metabolomics) has prompted researchers to develop informatics means to describe and annotate new biomolecules identified with a resolution down to the single cell, but also with a high-throughput speed. Machine learning approaches have been implemented to both the modelling studies and the handling of biomedical data. Quantum computing (QC) approaches hold the promise to resolve, speed up or refine the analysis of a wide range of these computational problems. Here, we review and comment on recently developed QC algorithms for biocomputing, with a particular focus on multi-scale modelling and genomic analyses. Indeed, differently from other computational approaches such as protein structure prediction, these problems have been shown to be adequately mapped onto quantum architectures, the main limit for their immediate use being the number of qubits and decoherence effects in the available quantum machines. Possible advantages over the classical counterparts are highlighted, along with a description of some hybrid classical/quantum approaches, which could be the closest to be realistically applied in biocomputation.
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Affiliation(s)
- Laura Marchetti
- University of Pisa, Department of Pharmacy, via Bonanno 6, 56126 Pisa Italy
| | - Riccardo Nifosì
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, P.zza San Silvestro 12, 56127 Pisa Italy
| | - Pier Luigi Martelli
- University of Bologna, Department of Pharmacy and Biotechnology, via San Giacomo 9/2, 40126 Bologna Italy
| | - Eleonora Da Pozzo
- University of Pisa, Department of Pharmacy, via Bonanno 6, 56126 Pisa Italy
| | - Valentina Cappello
- Italian Institute of Technology, Center for Materials Interfaces, Viale Rinaldo Piaggio 34, 56025 Pontedera (PI), Italy
| | | | | | - Claudia Martini
- University of Pisa, Department of Pharmacy, via Bonanno 6, 56126 Pisa Italy
| | - Massimo D’Elia
- University of Pisa, Department of Physics, Largo Bruno Pontecorvo 3, 56127, Pisa Italy
- INFN, Sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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10
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Liao W, Du J, Wang Z, Feng Q, Liao M, Liu H, Yuan K, Zeng Y. The role and mechanism of noncoding RNAs in regulation of metabolic reprogramming in hepatocellular carcinoma. Int J Cancer 2022; 151:337-347. [PMID: 35460073 PMCID: PMC9325518 DOI: 10.1002/ijc.34040] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/24/2022] [Accepted: 04/05/2022] [Indexed: 02/05/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. Metabolic reprogramming is considered to be an important hallmark of cancer. Emerging studies have demonstrated that noncoding RNAs (ncRNAs) are closely associated with metabolic reprogramming of HCC. NcRNAs can directly regulate the expressions or functions of metabolic enzymes or indirectly regulate the metabolism of HCC cells through some vital signaling pathways. Until now, the mechanisms of HCC development and progression remain largely unclear, and understanding the regulatory mechanism of ncRNAs on metabolic reprogramming of HCC may provide an important basis for breakthrough progress in the treatment of HCC. In this review, we summarize the ncRNAs involved in regulating metabolic reprogramming of HCC. Specifically, the regulatory roles of ncRNAs in glucose, lipid and amino acid metabolism are elaborated. In addition, we discuss the molecular mechanism of ncRNAs in regulation of metabolic reprogramming and possible therapeutic strategies that target the metabolism of cancer cells by modulating the expressions of specific ncRNAs.
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Affiliation(s)
- Wenwei Liao
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Jinpeng Du
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Zhen Wang
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Qingbo Feng
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Mingheng Liao
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Huixian Liu
- Department of Postanesthesia Care Unit & Surgical Anesthesia Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Kefei Yuan
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yong Zeng
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
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11
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Zhang H, Liu Y, Li M, Peng G, Zhu T, Sun X. The Long Non-coding RNA SNHG12 Functions as a Competing Endogenous RNA to Modulate the Progression of Cerebral Ischemia/Reperfusion Injury. Mol Neurobiol 2022; 59:1073-1087. [PMID: 34839459 DOI: 10.1007/s12035-021-02648-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/11/2021] [Indexed: 01/22/2023]
Abstract
Increasing research has proved that long non-coding RNAs (lncRNAs) play a critical role in a variety of biological processes. However, their functions in cerebral ischemia are still unclear. We found that the small nucleolar RNA host gene 12 (SNHG12) is a new type of lncRNA induced by ischemia/reperfusion. Here, we show that the expression of SNHG12 was upregulated in the brain tissue of mice exposed to middle cerebral artery occlusion/reperfusion (MCAO/R) and primary mouse cerebral cortex neurons treated with oxygen-glucose deprivation/reoxygenation (OGD/R). Mechanistically, SNHG12 knockdown resulted in larger infarct sizes and worse neurological scores in MCAO/R mice. Consistent with the in vivo results, SNHG12 upregulation significantly increased the viability and prevented apoptosis of neurons cultured under OGD/R conditions. In addition, we found that SNHG12 acts as a competing endogenous RNA (ceRNA) with microRNA (miR)-136-5p, thereby regulating the inhibition of its endogenous target Bcl-2. Moreover, SNHG12 was proven to target miR-136-5p, increasing Bcl-2 expression, which finally led to the activation of PI3K/AKT signaling. In conclusion, we demonstrated that SNHG12 acts as a ceRNA of miR-136-5p, thereby targets and regulates the expression of Bcl-2, which attenuates cerebral ischemia/reperfusion injury via activation of the PI3K/AKT pathway. This knowledge helps to better understand the pathophysiology of cerebral ischemic stroke and may provide new treatment options for this disease.
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Affiliation(s)
- Hao Zhang
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yuan Liu
- Department of Pharmacy, The Third People's Hospital of Kunming, Kunming, 650000, China
| | - Meng Li
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Gongfeng Peng
- Department of Pharmacy, The Third People's Hospital of Kunming, Kunming, 650000, China
| | - Tao Zhu
- School of Life Science and Bioengineering, Henan University of Urban Construction, Pingdingshan, 467000, China
| | - Xiaoou Sun
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China.
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12
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Jiang Z, Zhao J, Zou H, Cai K. CircRNA PTPRM Promotes Non-Small Cell Lung Cancer Progression by Modulating the miR-139-5p/SETD5 Axis. Technol Cancer Res Treat 2022; 21:15330338221090090. [PMID: 35491723 PMCID: PMC9066640 DOI: 10.1177/15330338221090090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Introduction: Circular RNAs (circRNAs) are important regulators in various cancers, especially hepatocellular carcinoma. However, the role of circ RNA PTPRM (circPTPRM) in the development of non-small-cell lung cancer (NSCLC) remains unclear. Methods: We collected 26 clinical specimens (corresponding to 26 normal lung tissues) of lung adenocarcinoma and the expression of mir-139-5p and circPTPRM were first detected. Cell proliferation was detected by EdU method, invasion/migration ability of cells was evaluated by transwell method. And the correlation between circPTPRM and mir-139-5p was detected by luciferase reporter gene and RNA pull-down assay. Finally, we verified our hypothesis with BALB/c nude mice. Results: Through bioinformatics software, we found that circPTPRM was negatively correlated with mir-139-5p, and then we used human adenocarcinoma tissue samples to further verify their relationship and get the same result. EdU method, transwell method, and luciferase assay, RNA pull-down assay were applied, and the results show that the knockdown of circPTPRM inhibit proliferation, migration, and invasion of cells can be reversed by mir-139-5p inhibitor. Next, we used Starbase v2.0 to identify the target site of miR-139-5p and focused on SET domain containing 5 (SETD5). We derive the hypothesis by verifying the relationship between miR-139-5p and SETD5 that circPTPRM may interact with miR-139-5p/SETD5 axis. At last, we evaluated the effects of circPTPRM, SETD5, and miR-139-5p on tumor growth in vivo using BALB/c nude mice to prove the hypothesis. Conclusion: We thus conclude that circPTPRM promotes the progression of NSCLC by regulating the miR-139-5p/SETD5 axis.
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Affiliation(s)
- Zeyong Jiang
- Nanfang Hospital, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Zhao
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Hanlin Zou
- People's Hospital of Chenghai, Shantou, China
| | - Kaican Cai
- Nanfang Hospital, 70570Southern Medical University, Guangzhou, Guangdong, China
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13
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The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model. Genes (Basel) 2021; 12:genes12101524. [PMID: 34680920 PMCID: PMC8535310 DOI: 10.3390/genes12101524] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/25/2021] [Accepted: 09/26/2021] [Indexed: 12/18/2022] Open
Abstract
The pericentric satellite III (SatIII or Sat3) and II tandem repeats recently appeared to be transcribed under stress conditions, and the transcripts were shown to play an essential role in the universal stress response. In this paper, we review the role of human-specific SatIII copy number variation (CNV) in normal stress response, aging and pathology, with a focus on 1q12 loci. We postulate a close link between transcription of SatII/III repeats and their CNV. The accrued body of data suggests a hypothetical universal mechanism, which provides for SatIII copy gain during the stress response, alongside with another, more hypothetical reverse mechanism that might reduce the mean SatIII copy number, likely via the selection of cells with excessively large 1q12 loci. Both mechanisms, working alternatively like swings of the pendulum, may ensure the balance of SatIII copy numbers and optimum stress resistance. This model is verified on the most recent data on SatIII CNV in pathology and therapy, aging, senescence and response to genotoxic stress in vitro.
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14
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Long Non-coding RNA PVT1 Inhibits miR-30c-5p to Upregulate Rock2 to Modulate Cerebral Ischemia/Reperfusion Injury Through MAPK Signaling Pathway Activation. Mol Neurobiol 2021; 58:6032-6048. [PMID: 34436749 DOI: 10.1007/s12035-021-02539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) play a key role in a variety of disease processes. Plasmacytoma variant translocation 1 (PVT1), a lncRNA, is known to regulate cell functions and play a key role in the pathogenesis of many malignant tumors. The function and molecular mechanisms of lncRNA-PVT1 in cerebral ischemia remain unknown. Real-time PCR (qRT-PCR) was used to detect lncRNA-PVT1 and microRNA-30c-5p (miR-30c-5p) expression in the brain tissues of mice underwent middle cerebral artery occlusion/reperfusion (MCAO/R) and oxygen-glucose deprivation/reperfusion (OGD/R)-treated mouse primary brain neurons. Gain- or loss-of-function approaches were used to manipulate PVT1, miR-30c-5p, and Rho-associated protein kinase 2 (Rock2). The mechanism of PVT1 in ischemic stroke was evaluated both in vivo and in vitro via bioinformatics analysis, CCK-8, flow cytometry, TUNEL staining, luciferase activity assay, RNA FISH, and Western blot. PVT1 was upregulated in the brain tissues of mice treated with MCAO/R and primary cerebral cortex neurons of mice treated with OGD/R. Mechanistically, PVT1 knockdown resulted in a lower infarct volume and ameliorated neurobehavior in MCAO mice. Consistent with in vivo results, PVT1 upregulation significantly decreased the viability and induced apoptosis of neurons cultured in OGD/R. Moreover, we demonstrated that PVT1 acts as a competitive endogenous RNA (ceRNA) that competes with miR-30c-5p, thereby negatively regulating its endogenous target Rock2. Overexpression of miR-30c-5p significantly promoted cell proliferation and inhibited apoptosis. Meanwhile, PVT1 was confirmed to target miR-30c-5p, thus activating Rock2 expression, which finally led to the activation of MAPK signaling. We demonstrated that PVT1, as a ceRNA of miR-30c-5p, could target and regulate the level of Rock2, which aggravates cerebral I/R injury via activation of the MAPK pathway. These findings reveal a new function of PVT1, which helps to broadly understand cerebral ischemic stroke and provide a new treatment strategy for this disease.
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15
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Wang X, Yang P, Zhang D, Lu M, Zhang C, Sun Y. LncRNA SNHG14 promotes cell proliferation and invasion in colorectal cancer through modulating miR-519b-3p/DDX5 axis. J Cancer 2021; 12:4958-4970. [PMID: 34234865 PMCID: PMC8247390 DOI: 10.7150/jca.55495] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/29/2021] [Indexed: 12/15/2022] Open
Abstract
Numbers of studies suggest that long non-coding RNAs (lncRNAs) exert an important role in cancer progression. It is reported that lncRNA SNHG14 (SNHG14) promotes cell proliferation and invasion in many cancers. However, the underlying molecular mechanism of SNHG14 in colorectal cancer (CRC) remains unclear. In our study, we found that SNHG14 is highly expressed in CRC tissues and cells, especially in SW480 and HT-29 cells. In addition, sh-SNHG14 inhibits cell proliferation, cell migration and invasion, promotes cell apoptosis in CRC cell lines. Furthermore, we found that SNHG14 functions as a sponge for miR-519b-3p, while the DEAD box protein 5 (DDX5) is a downstream target gene of miR-519b-3p, and the functions of miR-519b-3p inhibitors on the CRC progression could be rescued by downregulation of DDX5. Our findings suggest that SNHG14 promotes the CRC progression by miR-519b-3p/DDX5 axis, implying the promising therapeutic target of SNHG4 for CRC patients.
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Affiliation(s)
- Xiaoyuan Wang
- Department of General Surgery, The Second Affiliated Hospital Of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Department of General Surgery, The First Affiliated Hospital Of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Peng Yang
- Department of General Surgery, The First Affiliated Hospital Of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Dongsheng Zhang
- Department of General Surgery, The First Affiliated Hospital Of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Ming Lu
- Department of General Surgery, The Second Affiliated Hospital Of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Chi Zhang
- Department of General Surgery, The Second Affiliated Hospital Of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Yueming Sun
- Department of General Surgery, The First Affiliated Hospital Of Nanjing Medical University, Nanjing, Jiangsu Province, China
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16
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Pelayo MA, Yamaguchi N, Ito T. One factor, many systems: the floral homeotic protein AGAMOUS and its epigenetic regulatory mechanisms. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102009. [PMID: 33640614 DOI: 10.1016/j.pbi.2021.102009] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 05/15/2023]
Abstract
Tissue-specific transcription factors allow cells to specify new fates by exerting control over gene regulatory networks and the epigenetic landscape of a cell. However, our knowledge of the molecular mechanisms underlying cell fate decisions is limited. In Arabidopsis, the MADS-box transcription factor AGAMOUS (AG) plays a central role in regulating reproductive organ identity and meristem determinacy during flower development. During the vegetative phase, AG transcription is repressed by Polycomb complexes and intronic noncoding RNA. Once AG is transcribed in a spatiotemporally regulated manner during the reproductive phase, AG functions with chromatin regulators to change the chromatin structure at key target gene loci. The concerted actions of AG and the transcription factors functioning downstream of AG recruit general transcription machinery for proper cell fate decision. In this review, we describe progress in AG research that has provided important insights into the regulatory and epigenetic mechanisms underlying cell fate determination in plants.
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Affiliation(s)
- Margaret Anne Pelayo
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
| | - Toshiro Ito
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
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17
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Boti MA, Adamopoulos PG, Tsiakanikas P, Scorilas A. Nanopore Sequencing Unveils Diverse Transcript Variants of the Epithelial Cell-Specific Transcription Factor Elf-3 in Human Malignancies. Genes (Basel) 2021; 12:genes12060839. [PMID: 34072506 PMCID: PMC8227732 DOI: 10.3390/genes12060839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
The human E74-like ETS transcription factor 3 (Elf-3) is an epithelium-specific member of the ETS family, all members of which are characterized by a highly conserved DNA-binding domain. Elf-3 plays a crucial role in epithelial cell differentiation by participating in morphogenesis and terminal differentiation of the murine small intestinal epithelium, and also acts as an indispensable regulator of mesenchymal to epithelial transition, underlying its significant involvement in development and in pathological states, such as cancer. Although previous research works have deciphered the functional role of Elf-3 in normal physiology as well as in tumorigenesis, the present study highlights for the first time the wide spectrum of ELF3 mRNAs that are transcribed, providing an in-depth analysis of splicing events and exon/intron boundaries in a broad panel of human cell lines. The implementation of a versatile targeted nanopore sequencing approach led to the identification of 25 novel ELF3 mRNA transcript variants (ELF3 v.3–v.27) with new alternative splicing events, as well as two novel exons. Although the current study provides a qualitative transcriptional profile regarding ELF3, further studies must be conducted, so the biological function of all novel alternative transcript variants as well as the putative protein isoforms are elucidated.
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18
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Long non-coding RNA ARAP1-AS1 accelerates cell proliferation and migration in breast cancer through miR-2110/HDAC2/PLIN1 axis. Biosci Rep 2021; 40:222266. [PMID: 32110804 PMCID: PMC7197975 DOI: 10.1042/bsr20191764] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 12/16/2019] [Accepted: 01/22/2020] [Indexed: 02/07/2023] Open
Abstract
Breast cancer (BC) poses a great threaten to women health. Numerous evidences suggest the important role of long non-coding RNAs (lncRNAs) in BC development. In the present study, we intended to investigate the role of ARAP1-AS1 in BC progression. First of all, the GEPIA data suggested that ARAP1-AS1 was highly expressed in breast invasive carcinoma (BRAC) tissues compared with the normal breast tissues. Meanwhile, the expression of ARAP1-AS1 was greatly up-regulated in BC cell lines. ARAP1-AS1 knockdown led to repressed proliferation, strengthened apoptosis and blocked migration of BC cells. Moreover, ARAP1-AS1 could boost HDAC2 expression in BC through sponging miR-2110 via a ceRNA mechanism. Of note, the UCSC predicted that HDAC2 was a potential transcriptional regulator of PLIN1, an identified tumor suppressor in BC progression. Moreover, we explained that the repression of HDAC2 on PLIN1 was owing to its deacetylation on PLIN1 promoter. More importantly, depletion of PLIN1 attenuated the mitigation function of ARAP1-AS1 silence on the malignant phenotypes of BC cells. To sum up, ARAP1-AS1 serves a tumor-promoter in BC development through modulating miR-2110/HDAC2/PLIN1 axis, which may help to develop novel effective targets for BC treatment.
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19
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Zheng W, Chu Q, Yang L, Sun L, Xu T. Circular RNA circDtx1 regulates IRF3-mediated antiviral immune responses through suppression of miR-15a-5p-dependent TRIF downregulation in teleost fish. PLoS Pathog 2021; 17:e1009438. [PMID: 33735323 PMCID: PMC8009406 DOI: 10.1371/journal.ppat.1009438] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/30/2021] [Accepted: 03/01/2021] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) represent a class of widespread and diverse covalently closed circular endogenous RNAs that exert crucial functions in regulating gene expression in mammals. However, the function and regulation mechanism of circRNAs in lower vertebrates are still unknown. Here, we discovered a novel circRNA derived from Deltex E3 ubiquitin ligase 1 (Dtx1) gene, namely, circDtx1, which was related to the antiviral responses in teleost fish. Results indicated that circDtx1 played essential roles in host antiviral immunity and inhibition of SCRV replication. Our study also found a microRNA miR-15a-5p, which could inhibit antiviral immune response and promote viral replication by targeting TRIF. Moreover, we also found that the antiviral effect inhibited by miR-15a-5p could be reversed with the circDtx1. In mechanism, our data revealed that circDtx1 was a competing endogenous RNA (ceRNA) of TRIF by sponging miR-15a-5p, leading to activation of the NF-κB/IRF3 pathway, and then enhancing the innate antiviral responses. Our results indicated that circRNAs played a regulatory role in immune responses in teleost fish. Increasing evidence indicates that circRNAs participate in innate and adaptive immunity. However, the relationship between circRNAs and host antiviral responses remains unknown, particularly in lower vertebrates. Our results provided direct evidence that a circRNA, namely, circDtx1, is related to the antiviral responses in lower vertebrates. In addition, our study also found a microRNA, namely, miR-15a-5p, which could inhibit an antiviral immune response and promote viral replication by targeting TRIF. Moreover, circRNAs can serve as competing endogenous RNAs (ceRNAs) and cross-talk with mRNAs by competing shared miRNAs. Such ceRNAs regulate the distribution of miRNA molecules on their targets and apply an additional level of post-transcriptional regulation. In our study, circDtx1 functions as a ceRNA for miR-15a-5p to control protein abundance of fish TRIF, thereby inhibiting viral replication and promoting antiviral responses. Our study demonstrates the ceRNA regulatory networks existing in lower vertebrates, which can provide new insights into understanding the effects of circRNAs on host-virus interactions.
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Affiliation(s)
- Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qing Chu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liyuan Yang
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Lingping Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- * E-mail:
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20
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Huang Y, Wang J, Zhao Y, Wang H, Liu T, Li Y, Cui T, Li W, Feng Y, Luo J, Gong J, Ning L, Zhang Y, Wang D, Zhang Y. cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function. Nucleic Acids Res 2021; 49:D65-D70. [PMID: 33010163 PMCID: PMC7778915 DOI: 10.1093/nar/gkaa791] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/30/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
RNA endowed with both protein-coding and noncoding functions is referred to as 'dual-function RNA', 'binary functional RNA (bifunctional RNA)' or 'cncRNA (coding and noncoding RNA)'. Recently, an increasing number of cncRNAs have been identified, including both translated ncRNAs (ncRNAs with coding functions) and untranslated mRNAs (mRNAs with noncoding functions). However, an appropriate database for storing and organizing cncRNAs is still lacking. Here, we developed cncRNAdb, a manually curated database of experimentally supported cncRNAs, which aims to provide a resource for efficient manipulation, browsing and analysis of cncRNAs. The current version of cncRNAdb documents about 2600 manually curated entries of cncRNA functions with experimental evidence, involving more than 2,000 RNAs (including over 1300 translated ncRNAs and over 600 untranslated mRNAs) across over 20 species. In summary, we believe that cncRNAdb will help elucidate the functions and mechanisms of cncRNAs and develop new prediction methods. The database is available at http://www.rna-society.org/cncrnadb/.
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MESH Headings
- 3' Untranslated Regions
- 5' Untranslated Regions
- Animals
- Databases, Nucleic Acid/organization & administration
- Drosophila melanogaster/genetics
- Humans
- Mice
- MicroRNAs/classification
- MicroRNAs/genetics
- Pan troglodytes/genetics
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Messenger/classification
- RNA, Messenger/genetics
- RNA, Ribosomal/classification
- RNA, Ribosomal/genetics
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Transfer/classification
- RNA, Transfer/genetics
- Software
- Zebrafish/genetics
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Affiliation(s)
- Yan Huang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Jing Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yue Zhao
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310053, China
| | - Huafeng Wang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Tianyuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuhe Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Weiyi Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yige Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaqi Gong
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yong Zhang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Dong Wang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yang Zhang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
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21
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Shulenina LV, Mikhailov VF, Zasukhina GD. Long Noncoding RNAs in Radiation Response. BIOL BULL+ 2020. [DOI: 10.1134/s1062359020120092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Tito C, Ganci F, Sacconi A, Masciarelli S, Fontemaggi G, Pulito C, Gallo E, Laquintana V, Iaiza A, De Angelis L, Benedetti A, Cacciotti J, Miglietta S, Bellenghi M, Carè A, Fatica A, Diso D, Anile M, Petrozza V, Facciolo F, Alessandrini G, Pescarmona E, Venuta F, Marino M, Blandino G, Fazi F. LINC00174 is a novel prognostic factor in thymic epithelial tumors involved in cell migration and lipid metabolism. Cell Death Dis 2020; 11:959. [PMID: 33161413 PMCID: PMC7648846 DOI: 10.1038/s41419-020-03171-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs are emerging as new molecular players involved in many biological processes, such as proliferation, apoptosis, cell cycle, migration, and differentiation. Their aberrant expression has been reported in variety of diseases. The aim of this study is the identification and functional characterization of clinically relevant lncRNAs responsible for the inhibition of miR-145-5p, a key tumor suppressor in thymic epithelial tumors (TETs). Starting from gene expression analysis by microarray in a cohort of fresh frozen thymic tumors and normal tissues, we identified LINC00174 as upregulated in TET. Interestingly, LINC00174 expression is positively correlated with a 5-genes signature in TETs. Survival analyses, performed on the TCGA dataset, showed that LINC00174 and its associated 5-genes signature are prognostic in TETs. Specifically, we show that LINC00174 favors the expression of SYBU, FEM1B, and SCD5 genes by sponging miR-145-5p, a well-known tumor suppressor microRNA downregulated in a variety of tumors, included TETs. Functionally, LINC00174 impacts on cell migration and lipid metabolism. Specifically, SCD5, one of the LINC00174-associated genes, is implicated in the control of lipid metabolism and promotes thymic cancer cells migration. Our study highlights that LINC00174 and its associated gene signature are relevant prognostic indicators in TETs. Of note, we here show that a key controller of lipid metabolism, SCD5, augments the migration ability of TET cells, creating a link between lipids and motility, and highlighting these pathways as relevant targets for the development of novel therapeutic approaches for TET.
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Affiliation(s)
- Claudia Tito
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Federica Ganci
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Andrea Sacconi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Silvia Masciarelli
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy.,Istituto di Istologia ed Embriologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Claudio Pulito
- Molecular Chemoprevention Unit, "Regina Elena" National Cancer Institute - IFO, Rome, Italy
| | - Enzo Gallo
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Valentina Laquintana
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Alessia Iaiza
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Luciana De Angelis
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Anna Benedetti
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Jessica Cacciotti
- Pathology Unit, ICOT, Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Selenia Miglietta
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Human Anatomy, Sapienza University of Rome, Rome, Italy
| | - Maria Bellenghi
- Center for Gender-Specific Medicine, Oncology Unit-Istituto Superiore di Sanita', Rome, Italy
| | - Alessandra Carè
- Center for Gender-Specific Medicine, Oncology Unit-Istituto Superiore di Sanita', Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Daniele Diso
- Department of Thoracic Surgery, Sapienza University of Rome, Rome, Italy
| | - Marco Anile
- Department of Thoracic Surgery, Sapienza University of Rome, Rome, Italy
| | - Vincenzo Petrozza
- Pathology Unit, ICOT, Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Francesco Facciolo
- Thoracic Surgery, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Edoardo Pescarmona
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Federico Venuta
- Department of Thoracic Surgery, Sapienza University of Rome, Rome, Italy
| | - Mirella Marino
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy.
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23
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Lawrie RD, Mitchell RD, Dhammi A, Wallace A, Hodgson E, Roe RM. Role of long non-coding RNA in DEET- and fipronil-mediated alteration of transcripts associated with Phase I and Phase II xenobiotic metabolism in human primary hepatocytes. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 167:104607. [PMID: 32527422 DOI: 10.1016/j.pestbp.2020.104607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
Human exposure to environmental chemicals both individually and in combination occurs frequently world-wide most often with unknown consequences. Use of molecular approaches to aide in the assessment of risk involved in chemical exposure is a growing field in toxicology. In this study, we examined the impact of two environmental chemicals used in and around homes, the insect repellent DEET (N,N-diethyl-m-toluamide) and the phenylpyrazole insecticide fipronil (fluocyanobenpyrazole) on transcript levels of enzymes potentially involved in xenobiotic metabolism and on long non-coding RNAs (lncRNAs). Primary human hepatocytes were treated with these two chemicals both individually and in combination. Using RNA-Seq, we found that 10 major enzyme categories involved in phase 1 and phase 2 xenobiotic metabolism were significantly (α = 0.05) up- and down-regulated (i.e., 100 μM DEET-19 transcripts, 89% up and 11% down; 10 μM fipronil-52 transcripts, 53% up and 47% down; and 100 μM DEET +10 μM fipronil-69 transcripts, 43% up and 57% down). The altered genes were then mapped to the human genome and their proximity (within 1,000,000 bp) to lncRNAs examined. Unique proximities were discovered between altered lncRNA and altered P450s (CYP) and other enzymes (DEET, 2 CYP; Fipronil, 6 CYP and 15 other; and DEET + fipronil, 7 CYP and 21 other). Many of the altered P450 transcripts were in multiple clusters in the genome with proximal altered lncRNAs, suggesting a regulator function for the lncRNA. At the gene level there was high percent identity for lncRNAs near P450 clusters, but this relationship was not found at the transcript level. The role of these altered lncRNAs associated with xenobiotic induction, human diseases and chemical mixtures is discussed.
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Affiliation(s)
- Roger D Lawrie
- Toxicology Program, Department of Biology, North Carolina State University, Raleigh, NC 27695, USA; Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Robert D Mitchell
- Toxicology Program, Department of Biology, North Carolina State University, Raleigh, NC 27695, USA; United States Department of Agriculture, Agricultural Research Service, U.S. Livestock Insects Research Lab, Kerrville, TX 78028, USA
| | - Anirudh Dhammi
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Andrew Wallace
- Toxicology Program, Department of Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Ernest Hodgson
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
| | - R Michael Roe
- Toxicology Program, Department of Biology, North Carolina State University, Raleigh, NC 27695, USA; Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
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24
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Casarotto M, Fanetti G, Guerrieri R, Palazzari E, Lupato V, Steffan A, Polesel J, Boscolo-Rizzo P, Fratta E. Beyond MicroRNAs: Emerging Role of Other Non-Coding RNAs in HPV-Driven Cancers. Cancers (Basel) 2020; 12:cancers12051246. [PMID: 32429207 PMCID: PMC7281476 DOI: 10.3390/cancers12051246] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
Persistent infection with high-risk Human Papilloma Virus (HPV) leads to the development of several tumors, including cervical, oropharyngeal, and anogenital squamous cell carcinoma. In the last years, the use of high-throughput sequencing technologies has revealed a number of non-coding RNA (ncRNAs), distinct from micro RNAs (miRNAs), that are deregulated in HPV-driven cancers, thus suggesting that HPV infection may affect their expression. However, since the knowledge of ncRNAs is still limited, a better understanding of ncRNAs biology, biogenesis, and function may be challenging for improving the diagnosis of HPV infection or progression, and for monitoring the response to therapy of patients affected by HPV-driven tumors. In addition, to establish a ncRNAs expression profile may be instrumental for developing more effective therapeutic strategies for the treatment of HPV-associated lesions and cancers. Therefore, this review will address novel classes of ncRNAs that have recently started to draw increasing attention in HPV-driven tumors, with a particular focus on ncRNAs that have been identified as a direct target of HPV oncoproteins.
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Affiliation(s)
- Mariateresa Casarotto
- Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (M.C.); (R.G.); (A.S.)
| | - Giuseppe Fanetti
- Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (G.F.); (E.P.)
| | - Roberto Guerrieri
- Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (M.C.); (R.G.); (A.S.)
| | - Elisa Palazzari
- Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (G.F.); (E.P.)
| | - Valentina Lupato
- Division of Otolaryngology, General Hospital “Santa Maria degli Angeli”, 33170 Pordenone, Italy;
| | - Agostino Steffan
- Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (M.C.); (R.G.); (A.S.)
| | - Jerry Polesel
- Division of Cancer Epidemiology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy;
| | - Paolo Boscolo-Rizzo
- Section of Otolaryngology, Department of Neurosciences, University of Padova, 31100 Treviso, Italy;
| | - Elisabetta Fratta
- Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (M.C.); (R.G.); (A.S.)
- Correspondence: ; Tel.: +390434659569
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25
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Zhang Z, Li A, Song G, Geng S, Gill BS, Faris JD, Mao L. Comprehensive analysis of Q gene near-isogenic lines reveals key molecular pathways for wheat domestication and improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:299-310. [PMID: 31778224 DOI: 10.1111/tpj.14624] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/14/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
The wheat AP2-like transcription factor gene Q has played a major role in domestication by conferring the free-threshing character and pleiotropically affecting numerous other traits. However, little information is known regarding the molecular mechanisms associated with the regulation of these traits by Q, especially for the structural determination of threshability. Here, transcriptome analysis of immature spike tissues in three lines nearly isogenic for Q revealed over 3000 differentially expressed genes (DEGs) involved in a number of pathways. Using phenotypic, microscopic, transcriptomic, and tissue-specific gene expression analyses, we demonstrated that Q governs threshability through extensive modification of wheat glumes including their structure, cell wall thickness, and chemical composition. Critical DEGs and pathways involved in secondary cell wall synthesis and regulation of the chemical composition of glumes were identified. We also showed that the mutation giving rise to the Q allele synchronized the expression of genes for micro-sporogenesis that affected pollen fertility, and may determine the final grain number for wheat spikes. Transcriptome dissection of genes and genetic pathways regulated by Q should further our understanding of wheat domestication and improvement.
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Affiliation(s)
- Zengcui Zhang
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Aili Li
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Gaoyuan Song
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Shuaifeng Geng
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, 66506, KS, USA
| | - Justin D Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Long Mao
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
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26
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Pereira IT, Spangenberg L, Cabrera G, Dallagiovanna B. Polysome-associated lncRNAs during cardiomyogenesis of hESCs. Mol Cell Biochem 2020; 468:35-45. [PMID: 32125578 DOI: 10.1007/s11010-020-03709-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/22/2020] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been found to be involved in many biological processes, including the regulation of cell differentiation, but a complete characterization of lncRNA is still lacking. Additionally, there is evidence that lncRNAs interact with ribosomes, raising questions about their functions in cells. Here, we used a developmentally staged protocol to induce cardiogenic commitment of hESCs and then investigated the differential association of lncRNAs with polysomes. Our results identified lncRNAs in both the ribosome-free and polysome-bound fractions during cardiogenesis and showed a very well-defined temporal lncRNA association with polysomes. Clustering of lncRNAs was performed according to the gene expression patterns during the five timepoints analyzed. In addition, differential lncRNA recruitment to polysomes was observed when comparing the differentially expressed lncRNAs in the ribosome-free and polysome-bound fractions or when calculating the polysome-bound vs ribosome-free ratio. The association of lncRNAs with polysomes could represent an additional cytoplasmic role of lncRNAs, e.g., in translational regulation of mRNA expression.
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Affiliation(s)
- Isabela Tiemy Pereira
- Basic Stem-Cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Lucia Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Guillermo Cabrera
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Bruno Dallagiovanna
- Basic Stem-Cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil.
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27
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Liu Y, Yin L, Chen C, Zhang X, Wang S. Long non-coding RNA GAS5 inhibits migration and invasion in gastric cancer via interacting with p53 protein. Dig Liver Dis 2020; 52:331-338. [PMID: 31530437 DOI: 10.1016/j.dld.2019.08.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/30/2019] [Accepted: 08/04/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND The rapid progress of gastric cancer (GC) is mainly due to metastasis. Long non-coding RNA (lncRNA) GAS5 has been identified as a tumor suppressor in numerous cancers, and its downregulation in GC has already been reported. AIMS In this study, we planned to investigate the role of GAS5 in GC metastasis. METHODS Gene expressions were detected by qRT-PCR. ISH staining was applied to assess GAS5 level in clinical tissues. Gain-of-function assays were conducted to evaluate the function of GAS5 in GC metastasis. RNA pull down, RIP and cycloheximide assays were performed to confirm the relationship between GAS5 and p53 protein. RESULTS GAS5 expression was markedly decreased in GC tissues and cell lines, and its low expression was strongly related to GC metastasis and unsatisfactory prognosis. GAS5 overexpression repressed GC cell migration and invasion by targeting p53. Intriguingly, GAS5 relied on the exon 12 to interact with and stabilize p53 protein. CONCLUSION Our data implied that GAS5 is a suppressor in GC metastasis via modulating p53 signaling, suggesting GAS5 as a potential therapeutic target for GC, especially for patients with metastasis.
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Affiliation(s)
- Yongchao Liu
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Lu Yin
- Center for Diffcult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Chunqiu Chen
- Center for Diffcult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Xiangyu Zhang
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China.
| | - Sheng Wang
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China.
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28
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Kazimierczyk M, Kasprowicz MK, Kasprzyk ME, Wrzesinski J. Human Long Noncoding RNA Interactome: Detection, Characterization and Function. Int J Mol Sci 2020; 21:E1027. [PMID: 32033158 PMCID: PMC7037361 DOI: 10.3390/ijms21031027] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 01/17/2023] Open
Abstract
The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter" belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.
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Affiliation(s)
| | | | | | - Jan Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland (M.K.K.); (M.E.K.)
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29
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Rojano E, Seoane P, Ranea JAG, Perkins JR. Regulatory variants: from detection to predicting impact. Brief Bioinform 2019; 20:1639-1654. [PMID: 29893792 PMCID: PMC6917219 DOI: 10.1093/bib/bby039] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/18/2018] [Indexed: 02/01/2023] Open
Abstract
Variants within non-coding genomic regions can greatly affect disease. In recent years, increasing focus has been given to these variants, and how they can alter regulatory elements, such as enhancers, transcription factor binding sites and DNA methylation regions. Such variants can be considered regulatory variants. Concurrently, much effort has been put into establishing international consortia to undertake large projects aimed at discovering regulatory elements in different tissues, cell lines and organisms, and probing the effects of genetic variants on regulation by measuring gene expression. Here, we describe methods and techniques for discovering disease-associated non-coding variants using sequencing technologies. We then explain the computational procedures that can be used for annotating these variants using the information from the aforementioned projects, and prediction of their putative effects, including potential pathogenicity, based on rule-based and machine learning approaches. We provide the details of techniques to validate these predictions, by mapping chromatin-chromatin and chromatin-protein interactions, and introduce Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein 9 (CRISPR-Cas9) technology, which has already been used in this field and is likely to have a big impact on its future evolution. We also give examples of regulatory variants associated with multiple complex diseases. This review is aimed at bioinformaticians interested in the characterization of regulatory variants, molecular biologists and geneticists interested in understanding more about the nature and potential role of such variants from a functional point of views, and clinicians who may wish to learn about variants in non-coding genomic regions associated with a given disease and find out what to do next to uncover how they impact on the underlying mechanisms.
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Affiliation(s)
- Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Juan A G Ranea
- CIBER de Enfermedades Raras, ISCIII, Madrid, Spain and Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - James R Perkins
- Research laboratory, IBIMA-Regional University Hospital of Malaga, UMA, Malaga 29009, Spain
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30
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Iadevaia V, Wouters MD, Kanitz A, Matia-González AM, Laing EE, Gerber AP. Tandem RNA isolation reveals functional rearrangement of RNA-binding proteins on CDKN1B/p27Kip1 3'UTRs in cisplatin treated cells. RNA Biol 2019; 17:33-46. [PMID: 31522610 PMCID: PMC6948961 DOI: 10.1080/15476286.2019.1662268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Post-transcriptional control of gene expression is mediated via RNA-binding proteins (RBPs) that interact with mRNAs in a combinatorial fashion. While recent global RNA interactome capture experiments expanded the repertoire of cellular RBPs quiet dramatically, little is known about the assembly of RBPs on particular mRNAs; and how these associations change and control the fate of the mRNA in drug-treatment conditions. Here we introduce a novel biochemical approach, termed tobramycin-based tandem RNA isolation procedure (tobTRIP), to quantify proteins associated with the 3ʹUTRs of cyclin-dependent kinase inhibitor 1B (CDKN1B/p27Kip1) mRNAs in vivo. P27Kip1 plays an important role in mediating a cell’s response to cisplatin (CP), a widely used chemotherapeutic cancer drug that induces DNA damage and cell cycle arrest. We found that p27Kip1 mRNA is stabilized upon CP treatment of HEK293 cells through elements in its 3ʹUTR. Applying tobTRIP, we further compared the associated proteins in CP and non-treated cells, and identified more than 50 interacting RBPs, many functionally related and evoking a coordinated response. Knock-downs of several of the identified RBPs in HEK293 cells confirmed their involvement in CP-induced p27 mRNA regulation; while knock-down of the KH-type splicing regulatory protein (KHSRP) further enhanced the sensitivity of MCF7 adenocarcinoma cancer cells to CP treatment. Our results highlight the benefit of specific in vivo mRNA-protein interactome capture to reveal post-transcriptional regulatory networks implicated in cellular drug response and adaptation.
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Affiliation(s)
- Valentina Iadevaia
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Maikel D Wouters
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | | | - Ana M Matia-González
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Emma E Laing
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - André P Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
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31
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Ding L, Feng Z, Bai Y. Clustering analysis of microRNA and mRNA expression data from TCGA using maximum edge-weighted matching algorithms. BMC Med Genomics 2019; 12:117. [PMID: 31382962 PMCID: PMC6683425 DOI: 10.1186/s12920-019-0562-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/26/2019] [Indexed: 12/21/2022] Open
Abstract
Background microRNA (miRNA) is a short RNA (~ 22 nt) that regulates gene expression at the posttranscriptional level. Aberration of miRNA expressions could affect their targeting mRNAs involved in cancer-related signaling pathways. We conduct clustering analysis of miRNA and mRNA using expression data from the Cancer Genome Atlas (TCGA). We combine the Hungarian algorithm and blossom algorithm in graph theory. Data analysis is done using programming language R and Python. Methods We first quantify edge-weights of the miRNA-mRNA pairs by combining their expression correlation coefficient in tumor (T_CC) and correlation coefficient in normal (N_CC). We thereby introduce a bipartite graph partition procedure to identify cluster candidates. Specifically, we propose six weight formulas to quantify the change of miRNA-mRNA expression T_CC relative to N_CC, and apply the traditional hierarchical clustering to subjectively evaluate the different weight formulas of miRNA-mRNA pairs. Among these six different weight formulas, we choose the optimal one, which we define as the integrated mean value weights, to represent the connections between miRNA and mRNAs. Then the Hungarian algorithm and the blossom algorithm are employed on the miRNA-mRNA bipartite graph to passively determine the clusters. The combination of Hungarian and the blossom algorithms is dubbed maximum weighted merger method (MWMM). Results MWMM identifies clusters of different sizes that meet the mathematical criterion that internal connections inside a cluster are relatively denser than external connections outside the cluster and biological criterion that the intra-cluster Gene Ontology (GO) term similarities are larger than the inter-cluster GO term similarities. MWMM is developed using breast invasive carcinoma (BRCA) as training data set, but can also applies to other cancer type data sets. MWMM shows advantage in GO term similarity in most cancer types, when compared to other algorithms. Conclusions miRNAs and mRNAs that are likely to be affected by common underlying causal factors in cancer can be clustered by MWMM approach and potentially be used as candidate biomarkers for different cancer types and provide clues for targets of precision medicine in cancer treatment. Electronic supplementary material The online version of this article (10.1186/s12920-019-0562-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lizhong Ding
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA
| | - Zheyun Feng
- Department of Mathematics and Computer Science, Indiana State University, Terre Haute, IN, 47809, USA
| | - Yongsheng Bai
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA. .,Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA.
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Long noncoding RNA SNHG14 facilitates colorectal cancer metastasis through targeting EZH2-regulated EPHA7. Cell Death Dis 2019; 10:514. [PMID: 31273190 PMCID: PMC6609685 DOI: 10.1038/s41419-019-1707-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/28/2019] [Indexed: 12/24/2022]
Abstract
Accumulating evidence suggested the participation of long noncoding RNAs (lncRNAs) in regulating various biological processes so as to affecting cancer progression. However, the functional role of most lncRNAs in colorectal carcer (CRC) is still largely covered. In the present study, we disclosed SNHG14 as a carcinogene in CRC development, as it was low-expressed in normal colon tissues but markedly upregulated in CRC cell lines. Besides, SNHG14 contributed to CRC cell proliferation, motility and EMT in vitro, and inhibition of it confined CRC tumor growth and liver metastasis in vivo. Next, the mechanistic investigations confirmed that SNHG14-promoted CRC progression was mediated by EPHA7, which was negatively regulated by SNHG14 in CRC via an EZH2-dependent way. Importantly, EZH2 was proved as a transcription factor of EPHA7 and functioned as a repressor in EPHA7 transcription by enhancing methylation on EPHA7 promoter. Meanwhile, SNHG14 increased EZH2 expression in CRC via stabilizing its mRNA by interacting with FUS, and via freeing its mRNA from miR-186-5p-induced silence. All in all, our observations demonstrated that SNHG14 serves as a facilitator in CRC through targeting EZH2-repressed EPHA7 by enhancing EZH2 via recruiting FUS and absorbing miR-186-5p, indicating a promising new road for CRC diagnosis and treatment.
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Zou X, Wang J, Tang L, Wen Q. LncRNA TUG1 contributes to cardiac hypertrophy via regulating miR-29b-3p. In Vitro Cell Dev Biol Anim 2019; 55:482-490. [PMID: 31183682 DOI: 10.1007/s11626-019-00368-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/05/2019] [Indexed: 12/19/2022]
Abstract
Cardiac hypertrophy with maladjusted cardiac remodeling is the leading cause of heart failure. In the past decades, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been proved to exert multiple functions in cellular biological behaviors; however, their role in cardiac hypertrophy remains largely unclear. Presently, we first obtained hypertrophic H9c2 cells by treating with angiotensin II (Ang II) and uncovered upregulation of lncRNA taurine upregulated gene 1 (TUG1) in such H9c2 cells. Then, we demonstrated that silencing TUG1 attenuated Ang II-induced cardiac hypertrophy. Besides, a strong interactivity of TUG1 with miR-29b-3p at the putative sites was validated, suggesting that TUG1 was an endogenous sponge of miR-29b-3p in H9c2 cells. Additionally, the expression of miR-29b-3p was strikingly reduced by TUG1 upregulation and also inhibited under Ang II treatment, whereas it was restored after silencing TUG1 in hypertrophic cells. Also, we proved miR-29b-3p as a negative regulator in cardiac hypertrophy. Finally, miR-29b-3p inhibition abolished the anti-hypertrophy effect of TUG1 depletion in Ang II-treated H9c2 cells. Collectively, our findings confirmed that TUG1 functioned as a positive modulator of cardiac hypertrophy via sponging miR-29b-3p, indicating that TUG1 might serve as a potential target for the treatment of cardiac hypertrophy and even heart failure.
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Affiliation(s)
- Xue Zou
- Department of Cardiology, Daping Hospital, The Third Military Medical University, No.10 Changjiangzhilu, Daping, Yuzhong District, Chongqing, 40042, People's Republic of China
| | - Jialiang Wang
- Department of Cardiology, Daping Hospital, The Third Military Medical University, No.10 Changjiangzhilu, Daping, Yuzhong District, Chongqing, 40042, People's Republic of China
| | - Li Tang
- Department of Cardiology, Daping Hospital, The Third Military Medical University, No.10 Changjiangzhilu, Daping, Yuzhong District, Chongqing, 40042, People's Republic of China
| | - Qian Wen
- Department of Cardiology, Daping Hospital, The Third Military Medical University, No.10 Changjiangzhilu, Daping, Yuzhong District, Chongqing, 40042, People's Republic of China.
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Umuhire Juru A, Patwardhan NN, Hargrove AE. Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions. ACS Chem Biol 2019; 14:824-838. [PMID: 31042354 DOI: 10.1021/acschembio.8b00945] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The implication of RNA in multiple cellular processes beyond protein coding has revitalized interest in the development of small molecules for therapeutically targeting RNA and for further probing its cellular biology. However, the process of rationally designing such small molecule probes is hampered by the paucity of information about fundamental molecular recognition principles of RNA. In this Review, we summarize two important and often underappreciated aspects of RNA-small molecule recognition: RNA conformational dynamics and the biophysical properties of interactions of small molecules with RNA, specifically thermodynamics and kinetics. While conformational flexibility is often said to impede RNA ligand development, the ability of small molecules to influence the RNA conformational landscape can have a significant effect on the cellular functions of RNA. An analysis of the conformational landscape of RNA and the interactions of individual conformations with ligands can thus guide the development of new small molecule probes, which needs to be investigated further. Additionally, while it is common practice to quantify the binding affinities ( Ka or Kd) of small molecules for biomacromolecules as a measure of their activity, further biophysical characterization of their interaction can provide a deeper understanding. Studies that focus on the thermodynamic and kinetic parameters for interaction between RNA and ligands are next discussed. Finally, this Review provides the reader with a perspective on how such in-depth analysis of biophysical characteristics of the interaction of RNA and small molecules can impact our understanding of these interactions and how they will benefit the future design of small molecule probes.
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Affiliation(s)
- Aline Umuhire Juru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Neeraj N. Patwardhan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Amanda E. Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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Dempsey JL, Cui JY. Regulation of Hepatic Long Noncoding RNAs by Pregnane X Receptor and Constitutive Androstane Receptor Agonists in Mouse Liver. Drug Metab Dispos 2019; 47:329-339. [PMID: 30593543 PMCID: PMC6382996 DOI: 10.1124/dmd.118.085142] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/21/2018] [Indexed: 12/28/2022] Open
Abstract
Altered expression of long noncoding RNAs (lncRNAs) by environmental chemicals modulates the expression of xenobiotic biotransformation-related genes and may serve as therapeutic targets and novel biomarkers of exposure. The pregnane X receptor (PXR/NR1I2) is a critical xenobiotic-sensing nuclear receptor that regulates the expression of many drug-processing genes, and it has similar target-gene profiles and DNA-binding motifs with another xenobiotic-sensing nuclear receptor, namely, constitutive andronstrane receptor (CAR/Nr1i3). To test our hypothesis that lncRNAs are regulated by PXR in concert with protein-coding genes (PCGs) and to compare the PXR-targeted lncRNAs with CAR-targeted lncRNAs, RNA-Seq was performed from livers of adult male C57BL/6 mice treated with corn oil, the PXR agonist PCN, or the CAR agonist 1, 4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP). Among 125,680 known lncRNAs, 3843 were expressed in liver, and 193 were differentially regulated by PXR (among which 40% were also regulated by CAR). Most PXR- or CAR-regulated lncRNAs were mapped to the introns and 3'-untranslated regions (UTRs) of PCGs, as well as intergenic regions. Combining the RNA-Seq data with a published PXR chromatin immunoprecipitation coupled with high-throughput sequencing; cytochrome P450 (P450; ChIP-Seq) data set, we identified 774 expressed lncRNAs with direct PXR-DNA binding sites, and 26.8% of differentially expressed lncRNAs had changes in PXR-DNA binding after PCN exposure. De novo motif analysis identified colocalization of PXR with liver receptor homolog (LRH-1), which regulates bile acid synthesis after PCN exposure. There was limited overlap of PXR binding with an epigenetic mark for transcriptional activation (histone-H3K4-di-methylation, H3K4me2) but no overlap with epigenetic marks for transcriptional silencing [H3 lysine 27 tri-methylation (H3K27me3) and DNA methylation]. Among differentially expressed lncRNAs, 264 were in proximity of PCGs, and the lncRNA-PCG pairs displayed a high coregulatory pattern by PXR and CAR activation. This study was among the first to demonstrate that lncRNAs are regulated by PXR and CAR activation and that they may be important regulators of PCGs involved in xenobiotic metabolism.
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Affiliation(s)
- Joseph L Dempsey
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
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Song J, Huang S, Wang K, Li W, Pao L, Chen F, Zhao X. Long Non-coding RNA MEG3 Attenuates the Angiotensin II-Induced Injury of Human Umbilical Vein Endothelial Cells by Interacting With p53. Front Genet 2019; 10:78. [PMID: 30838022 PMCID: PMC6389612 DOI: 10.3389/fgene.2019.00078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 01/28/2019] [Indexed: 01/01/2023] Open
Abstract
Angiotensin II (Ang II)-induced damage to endothelial cells (ECs) plays a crucial role in the pathogenesis of cardiovascular disease. This study aimed to investigate the role of maternally expressed gene 3 (Meg3) in endothelial cell injury. A lncRNA human gene expression microarray analysis was used to identify differentially expressed lncRNAs in human umbilical vein endothelial cell (HUVECs). Cell viability, apoptosis, and migration were then assessed Ang II-treated HUVECs. qRT-PCR and western blotting were performed to detect the expression level of p53 after Meg3 knockdown and overexpression. We observed that Ang II treatment decreased the Meg3 level in HUVECs. Next, both knockdown of Meg3 and Ang II decreased cell viability, increased apoptotic cell rate and impair migration function in HUVECs. Furthermore, overexpression of Meg3 inhibited cell apoptosis, and increased cell migration by enhancing p53 transcription on its target genes, including CRP, ICAM-1, VEGF, and HIF-1α. Our findings indicate that Meg3 might be associated with cardiovascular disease development.
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Affiliation(s)
- Jingwen Song
- Department of Cardiovascularology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Songqun Huang
- Department of Cardiovascularology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Kaizhong Wang
- Department of Cardiovascularology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wei Li
- Institute of Tumor, Second Military Medical University, Shanghai, China
| | - Lizhi Pao
- Department of Cardiovascularology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Feng Chen
- Department of Cardiovascularology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xianxian Zhao
- Department of Cardiovascularology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
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37
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Long noncoding RNAs in cancer cells. Cancer Lett 2019; 419:152-166. [PMID: 29414303 DOI: 10.1016/j.canlet.2018.01.053] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/15/2018] [Accepted: 01/18/2018] [Indexed: 12/11/2022]
Abstract
Long noncoding RNA (lncRNA) has recently been investigated as key modulators that regulate many biological processes in human cancers via diverse mechanisms. LncRNAs can interact with macromolecules such as DNA, RNA, or protein to exert cellular effects and to act as either tumor promoters or tumor suppressors in various malignancies. Moreover, the aberrant expression of lncRNAs may be detected in multiple cancer phenotypes by employing the rapidly developing modern gene chip technology and bioinformatics analysis. Herein, we highlight the mechanisms of action of lncRNAs, their functional cellular roles and their involvement in cancer progression. Finally, we provide an overview of recent progress in the lncRNA field and future potential for lncRNAs as cancer diagnostic markers and therapeutics.
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Huang C, Leng D, Sun S, Zhang XD. Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection. BMC Genomics 2019; 20:48. [PMID: 30651068 PMCID: PMC6335708 DOI: 10.1186/s12864-019-5429-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 01/02/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and accelerating devastation due to bleaching. The fact that the breakdown of symbiosis between coral and the dinoflagellate, zooxanthellae, has been well elucidated as the main cause of bleaching, implying the establishment of symbiosis with zooxanthellae plays a crucial role in maintaining coral survival. However, the relevant molecular and cellular mechanisms have not been well studied yet. In this study, based on the deep RNA-sequencing data derived from Mohamed, A. R. et al., an integrated transcriptome analysis was performed to deeply investigate global transcriptome changes of the coral Acropora digitifera in response to infection by dinoflagellate of the genus Symbiodinium. RESULTS The results revealed that compared to RefTranscriptome_v1.0 (A. digitifera transcriptome assembly v1.0), numerous novel transcripts and isoforms were identified, the Symbiodinium-infected coral larvae at 4 h generated the highest proportion of specific isoforms. Alternative splicing analysis showed that intron retention predominated in all alternative transcripts among six statuses. Additionally, 8117 lncRNAs were predicted via a stringent stepwise filtering pipeline. A complex lncRNAs-mRNAs network including 815 lncRNAs and 6395 mRNAs were established, in which 21 lncRNAs were differentially expressed at 4 h post infection. Functional clustering analysis for those differentially lncRNAs-coexpressed mRNAs demonstrated that several biological processes and pathways related to protein kinase activity, metabolic pathways, mitochondrion, ribosome, etc. were enriched. CONCLUSIONS Our study not only refined A. digitifera transcriptome via identification of novel transcripts and isoforms, but also predicted a high-confidence dataset of lncRNAs. Functional study based on the construction of lncRNAs-mRNAs co-expression network has disclosed a complex lncRNA-mediated regulation in response to Symbiodinium infection exhibited in A. digitifera. Once validated, these lncRNAs could be good potential targets for treatment and prevention of bleaching in coral.
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Affiliation(s)
- Chen Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Dongliang Leng
- Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Shixue Sun
- Faculty of Health Sciences, University of Macau, Taipa, Macau
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Zhang Y, Huang Z, Sheng F, Yin Z. MYC upregulated LINC00319 promotes human acute myeloid leukemia (AML) cells growth through stabilizing SIRT6. Biochem Biophys Res Commun 2018; 509:314-321. [PMID: 30587342 DOI: 10.1016/j.bbrc.2018.12.133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been identified by accumulating studies as critical regulator in tumorigenesis and tumor development in human cancers, including in acute myeloid leukemia (AML). This study investigated the function and the underlying mechanism of LINC00319 in AML progression. Firstly, the low expression level of LINC00319 in whole blood of healthy individuals was obtained from UCSC, and its upregulation was detected in AML patients as well as AML cell lines. Besides, the prognostic significance of LINC00319 was revealed in AML patients. Functionally, the loss-of-function assays revealed that LINC00319 silence restrained proliferation but stimulated apoptosis in AML cells. Furthermore, LINC00319 expression was demonstrated proportional to MYC level in AML samples and transcriptionally regulated by MYC. Mechanistically, we identified FUS as a shared RNA binding protein (RBP) interacting with both LINC00319 and SIRT6. And LINC00319 regulated SIRT6 expression at post-transcriptional level through FUS-dependent pathway. Last but not least, SIRT6 overexpression rescued the suppressive effect of LINC00319 knockdown on AML cells growth. Overall, our findings unveiled that LINC00319 contributed to AML leukemogenesis via elevating SIRT6 expression, indicating a possible molecular target of LINC00319 for AML treatment.
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Affiliation(s)
- Yanni Zhang
- Department of Neonatal Department, Ankang Maternal and Child Health Hospital, Ankang, Shaanxi, 725000, China
| | - Zongxuan Huang
- Department of Paediatrics, Affiliated Hospital of JiNing Medical Universrty, Jining, Shandong, 272029, China
| | - Fen Sheng
- Department of Intensive Care Unit, First People's Hospital of Jining City, Shandong Province, Jining, Shandong, 272000, China
| | - Zhaoyang Yin
- Department of Pediatrics, Central Hospital of Shangluo City, Shanxi province, 726000, China.
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Zhang L, Deng X, Shi X, Dong X. Silencing H19 regulated proliferation, invasion, and autophagy in the placenta by targeting miR-18a-5p. J Cell Biochem 2018; 120:9006-9015. [PMID: 30536700 PMCID: PMC6587755 DOI: 10.1002/jcb.28172] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022]
Abstract
Fetal growth restriction (FGR) is a serious pregnancy complication associated with increased perinatal mortality and morbidity. It may lead to neurodevelopmental impairment and adulthood onset disorders. Recently, long noncoding RNAs (lncRNAs) were found to be associated with the pathogenesis of FGR. Here we report that the lncRNAH19 is significantly decreased in placentae from pregnancies with FGR. Downregulation of H19 leads to reduced proliferation and invasion of extravillous trophoblast cells. This is identified with reduced trophoblast invasion, which has been discovered in FGR. Autophagy is exaggerated in FGR. Downregulation of H19 promotes autophagy via the PI3K/AKT/mTOR and MAPK/ERK/mTOR pathways of extravillous trophoblast cells in FGR. We also found that the expression level of microRNAs miR-18a-5p was negatively correlated with that of H19. H19 can act as an endogenous sponge by directly binding to miR-18a-5p, which targets IRF2. The expression of miR-18a-5p was upregulated, but IRF2 expression was downregulated after the H19 knockdown. In conclusion, our study revealed that H19 downexpressed could inhibit proliferation and invasion, and promote autophagy by targeting miR-18a-5pin HTR8 and JEG3 cells. We propose that aberrant regulation of H19/miR-18a-5p-mediated regulatory pathway may contribute to the molecular mechanism of FGR. We indicated that H19 may be a potential predictive, diagnostic, and therapeutic modality for FGR.
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Affiliation(s)
- Lei Zhang
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Xinru Deng
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Xian Shi
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Xiaojing Dong
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
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Wu HW, Deng S, Xu H, Mao HZ, Liu J, Niu QW, Wang H, Chua NH. A noncoding RNA transcribed from the AGAMOUS (AG) second intron binds to CURLY LEAF and represses AG expression in leaves. THE NEW PHYTOLOGIST 2018; 219:1480-1491. [PMID: 29862530 DOI: 10.1111/nph.15231] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/23/2018] [Indexed: 05/25/2023]
Abstract
Dispersed H3K27 trimethylation (H3K27me3) of the AGAMOUS (AG) genomic locus is mediated by CURLY LEAF (CLF), a component of the Polycomb Repressive Complex (PRC) 2. Previous reports have shown that the AG second intron, which confers AG tissue-specific expression, harbors sequences targeted by several positive and negative regulators. Using RACE reverse transcription polymerase chain reaction, we found that the AG intron 2 encodes several noncoding RNAs. RNAi experiment showed that incRNA4 is needed for CLF repressive activity. AG-incRNA4RNAi lines showed increased leaf AG mRNA levels associated with a decrease of H3K27me3 levels; these plants displayed AG overexpression phenotypes. Genetic and biochemical analyses demonstrated that the AG-incRNA4 can associate with CLF to repress AG expression in leaf tissues through H3K27me3-mediated repression and to autoregulate its own expression level. The mechanism of AG-incRNA4-mediated repression may be relevant to investigations on tissue-specific expression of Arabidopsis MADS-box genes.
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MESH Headings
- AGAMOUS Protein, Arabidopsis/genetics
- AGAMOUS Protein, Arabidopsis/metabolism
- Arabidopsis/genetics
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Co-Repressor Proteins/metabolism
- Flowers/genetics
- Gene Expression Regulation, Plant
- Glucuronidase/metabolism
- Histones/metabolism
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Introns/genetics
- Organ Specificity/genetics
- Plant Leaves/genetics
- Plants, Genetically Modified
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Seedlings/genetics
- Transcription, Genetic
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Affiliation(s)
- Hui-Wen Wu
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
| | - Shulin Deng
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
| | - Haiying Xu
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
| | - Hui-Zhu Mao
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
| | - Jun Liu
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
| | - Qi-Wen Niu
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
| | - Huan Wang
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
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Yau MYC, Xu L, Huang CL, Wong CM. Long Non-Coding RNAs in Obesity-Induced Cancer. Noncoding RNA 2018; 4:E19. [PMID: 30154386 PMCID: PMC6162378 DOI: 10.3390/ncrna4030019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/22/2018] [Accepted: 08/27/2018] [Indexed: 01/17/2023] Open
Abstract
Many mechanisms of obesity-induced cancers have been proposed. However, it remains unclear whether or not long non-coding RNAs (lncRNAs) play any role in obesity-induced cancers. In this article, we briefly discuss the generally accepted hypotheses explaining the mechanisms of obesity-induced cancers, summarize the latest evidence for the expression of a number of well-known cancer-associated lncRNAs in obese subjects, and propose the potential contribution of lncRNAs to obesity-induced cancers. We hope this review can serve as an inspiration to scientists to further explore the regulatory roles of lncRNAs in the development of obesity-induced cancers. Those findings will be fundamental in the development of effective therapeutics or interventions to combat this life-threatening adverse effect of obesity.
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Affiliation(s)
- Mabel Yin-Chun Yau
- School of Medical and Health Sciences, Tung Wah College, Hong Kong, China.
| | - Lu Xu
- Department of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Chi-Ming Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China.
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44
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Filatova EN, Utkin OV. The Role of Noncoding mRNA Isoforms in the Regulation of Gene Expression. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418080057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Zhong F, Zhu M, Gao K, Xu P, Yang H, Hu D, Cui D, Wang M, Xie X, Wei Y, Zhang H, Du H. Low expression of the long non-coding RNA NR_026827 in gastric cancer. Am J Transl Res 2018; 10:2706-2711. [PMID: 30210707 PMCID: PMC6129519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
AIM The contribution of long non-coding RNAs (lncRNAs) to gastric cancer associated with Helicobacter pylori (H. pylori) infection remains largely unknown. Therefore, the present study aimed to investigate the expression of a lncRNA NR_026827 in gastric epithelial cells infected with H. pylori, and demonstrate its expression characteristic in gastric cancer. MATERIALS AND METHODS Gastric epithelial cell line cells, GES-1, were cultured and infected with H. pylori. A microarray was used to analyze the lncRNA profile of gastric epithelial cells. Eighty fresh gastric cancer tissues and the paired adjacent non-cancerous tissue samples were randomly selected from patients. The expression of the lncRNA NR_026827 was investigated using quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS The expression of several lncRNAs was significantly altered in GES-1 cells following infection with H. pylori. Of these lncRNAs, NR_026827 was dramatically down-regulated in GES-1 cells infected with H. pylori. In addition, the expression of NR_026827 was decreased in gastric cancer tissues in comparison to the corresponding adjacent non-cancerous tissues. Moreover, the expression of NR_026827 did not change significantly in different gastric cancer stages. CONCLUSION The lncRNA, NR_026827, is down-regulated in all stages of gastric cancer associated with H. pylori infection and could represent a potential biomarker for the diagnosis of gastric cancer.
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Affiliation(s)
- Fengyun Zhong
- Department of General Surgery, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
| | - Meili Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
| | - Kaijian Gao
- Department of General Surgery, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
| | - Ping Xu
- Department of Clinical Laboratory, The Fifth People’s Hospital of SuzhouSuzhou 215007, Jiangsu, PR China
| | - Huan Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
| | - Duanmin Hu
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
| | - Dawei Cui
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhejiang UniversityHangzhou 310006, Zhejiang, PR China
| | - Min Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
| | - Xiaofang Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
| | - Yan Wei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, PR China
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Oliva R, Jansen B, Benscheidt F, Sandbichler AM, Egg M. Nuclear magnetic resonance affects the circadian clock and hypoxia-inducible factor isoforms in zebrafish. BIOL RHYTHM RES 2018. [DOI: 10.1080/09291016.2018.1498194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Regina Oliva
- Institute of Zoology, University Innsbruck, Innsbruck, Austria
| | - Bianca Jansen
- Institute of Zoology, University Innsbruck, Innsbruck, Austria
| | | | | | - Margit Egg
- Institute of Zoology, University Innsbruck, Innsbruck, Austria
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47
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Zhao W, Fu H, Zhang S, Sun S, Liu Y. LncRNA SNHG16 drives proliferation, migration, and invasion of hemangioma endothelial cell through modulation of miR-520d-3p/STAT3 axis. Cancer Med 2018; 7:3311-3320. [PMID: 29845747 PMCID: PMC6051179 DOI: 10.1002/cam4.1562] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/16/2018] [Accepted: 04/27/2018] [Indexed: 12/19/2022] Open
Abstract
It has been verified that long noncoding RNAs (lncRNAs) have great effects on various biological behaviors of human diseases. Although more and more lncRNAs have been studied in human cancers, countless lncRNAs still need to be excavated. This study aims to investigate the impacts of lncRNA SNHG16 on proliferation and metastasis of human hemangioma endothelial cell (HemECs). qRT-PCR analysis was carried out to explore the expression pattern of SNHG16, miR-520d-3p, and STAT3. The effect of SNHG16 on cell proliferation was detected by MTT and colony formation assay. Flow cytometry analysis was performed to test the apoptosis of HemECs cells. Migration and invasion of HemECs cells were determined and examined by transwell assays. Tube formation assay helped to observe the influence of SNHG16 expression on the vasoformation of HemECs cells. The correlations among SNHG16, miR-520d-3p, and STAT3 were certified by bioinformatics analysis, pull-down assay, and dual-luciferase reporter assay. Finally, rescue assays were conducted to demonstrate the effects of SNHG16-miR-520d-3p-STAT3 axis on biological behaviors of HemECs cell. SNHG16 was strongly expressed in proliferating phase hemangioma tissues and HemECs cells. Silenced SNHG16 negatively affected proliferation, migration, and invasion of HemECs cell. LncRNA SNHG16 acted as a ceRNA to upregulate STAT3 through binding with miR-520d-3p in HemECs cell. LncRNA SNHG16 acted as a ceRNA to drive proliferation, vasoformation, migration, and invasion of HemECs cells through modulating miR-520d-3p/STAT3 axis.
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Affiliation(s)
| | - Hao Fu
- The Affiliated Hospital of Logistics University of PAPTianjinChina
| | | | - Shengkai Sun
- The Affiliated Hospital of Logistics University of PAPTianjinChina
| | - Yang Liu
- Shanghai Fourth People's HospitalShanghaiChina
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48
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Liu S, Zhou B, Wang L, Hu H, Yao C, Cai Z, Cui X. Therapeutic Antidepressant Potential of NONHSAG045500 in Regulating Serotonin Transporter in Major Depressive Disorder. Med Sci Monit 2018; 24:4465-4473. [PMID: 29955033 PMCID: PMC6055515 DOI: 10.12659/msm.908543] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Major depressive disorder (MDD) is a chronic, life-threatening, highly disabling disease. Standardized treatment with fewer adverse effects, quick onset, and long-term maintenance of the effects of brief treatment for MDD is always being pursued. Long non-coding RNAs (lncRNAs) are highly expressed in the central nervous system and are involved in the occurrence and development of neurodegenerative and psychiatric diseases. This study aimed to investigate whether the overexpression and interference of 3 differentially down-regulated lncRNAs (NONHSAT142707, NONHSAG045500, and ENST00000517573) in MDD can affect the expression of central neurotransmitter serotonin (5-hydroxytryptamine) transporter (SERT) in vitro. Material/Methods First, we synthesized and validated the effect of 3 lncRNA plasmids and small interfering RNAs (siRNAs); next, we transfected the plasmids and siRNAs that caused significant overexpression or interference in SK-N-SH cells, and tested the expression of SERT by qRT-PCR. Results The results showed that 3 lncRNA plasmids and siRNAs2 caused overexpression and interference, respectively. Only the overexpression of NONHSAG045500 could significantly inhibit the expression of SERT; interference with NONHSAG045500 could significantly strengthen the expression of SERT. Conclusions This study indicated that the expression of SERT could be regulated by up-regulating or down-regulating NONHSAG045500 expression and suggested that NONHSAG045500 could potentially be established as a new therapeutic target of MDD. Future work may be needed to definitively determine the correlation between NONHSAG045500 and SERT in vivo.
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Affiliation(s)
- Song Liu
- College of Economy and Management, Changzhou Institute of Technology, Changzhou, Jiangsu, China (mainland)
| | - Beibei Zhou
- Department of Health, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Li Wang
- Department of Medical Section, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Huiwen Hu
- Department of Health, Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Chanjuan Yao
- Department of Health, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Zhengmao Cai
- Department of Administration, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Xuelian Cui
- Department of Health, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
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Qi Y, Ooi HS, Wu J, Chen J, Zhang X, Tan S, Yu Q, Li YY, Kang Y, Li H, Xiong Z, Zhu T, Liu B, Shao Z, Zhao X. MALAT1 long ncRNA promotes gastric cancer metastasis by suppressing PCDH10. Oncotarget 2017; 7:12693-703. [PMID: 26871474 PMCID: PMC4914315 DOI: 10.18632/oncotarget.7281] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/23/2016] [Indexed: 01/01/2023] Open
Abstract
EZH2, the catalytic component of polycomb repressive complex 2 (PRC2), is frequently overexpressed in human cancers and contributes to tumor initiation and progression, in part through transcriptional silencing of tumor suppressor genes. A number of noncoding RNAs (ncRNAs) recruit EZH2 to specific chromatin loci, where they modulate gene expression. Here, we used RNA immunoprecipitation sequencing (RIP-seq) to profile EZH2-associated transcripts in human gastric cancer cell lines. We identified 8,256 transcripts, including both noncoding and coding transcripts, some of which were derived from cancer-related loci. In particular, we found that long noncoding RNA (lncRNA) MALAT1 binds EZH2, suppresses the tumor suppressor PCDH10, and promotes gastric cellular migration and invasion. Our work thus provides a global view of the EZH2-associated transcriptome and offers new insight into the function of EZH2 in gastric tumorigenesis.
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Affiliation(s)
- Ying Qi
- School of Biomedical Engineering, Bio-ID Research Center, State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Sain Ooi
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jun Wu
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Chen
- School of Biomedical Engineering, Bio-ID Research Center, State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Zhang
- School of Biomedical Engineering, Bio-ID Research Center, State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
| | - Sheng Tan
- Laboratory of Molecular Tumor Pathology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Qing Yu
- Laboratory of Molecular Tumor Pathology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformatics Technology, Shanghai, China.,Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China
| | - Yani Kang
- School of Biomedical Engineering, Bio-ID Research Center, State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Li
- School of Biomedical Engineering, Bio-ID Research Center, State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
| | - Zirui Xiong
- Laboratory of Molecular Tumor Pathology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Tao Zhu
- Laboratory of Molecular Tumor Pathology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Bingya Liu
- School of Biomedical Engineering, Bio-ID Research Center, State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China.,Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhifeng Shao
- School of Biomedical Engineering, Bio-ID Research Center, State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaodong Zhao
- School of Biomedical Engineering, Bio-ID Research Center, State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
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50
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Teng W, Qiu C, He Z, Wang G, Xue Y, Hui X. Linc00152 suppresses apoptosis and promotes migration by sponging miR-4767 in vascular endothelial cells. Oncotarget 2017; 8:85014-85023. [PMID: 29156700 PMCID: PMC5689590 DOI: 10.18632/oncotarget.18777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/22/2017] [Indexed: 12/12/2022] Open
Abstract
Dysfunction of vascular endothelial cells (VECs), such as increased apoptosis and diminished migration, is closely connected with most cardiovascular diseases and angiogenesis-related events. LncRNAs have been involved in regulation of many pathological processes, but their roles in vascular endothelial function are hardly underreported. Here, we explore the role of a intergenic lncRNA named linc00152 in the apoptosis and migration of VECs. We found that linc00152 was downregulated in human umbilical vein VECs (HUVECs) in a dose- and time-dependent manner following treatment with oxLDL, which is a typical proinflammatory factor in the initiation and progression of vascular endothelial dysfunction. Gain- and loss-function experiments indicated that linc00152 distinctly inhibited apoptosis and improved migration in oxLDL-treated HUVECs. By sponging miR-4767, linc00152 positively regulated the expression of Bcl2L12 and EGFR proteins. Moreover, blocking miR-4767 rescued the decrease of Bcl2L12 and EGFR caused by linc00152 knockdown, as well as the changes in cell apoptosis and migration. Our findings propose a novel role of linc00152 in the improvement of vascular endothelial function and a potential target for the therapy of some cardiovascular diseases.
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Affiliation(s)
- Wei Teng
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
| | - Chunguang Qiu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhaohui He
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
| | - Guoliang Wang
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
| | - Yongliang Xue
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
| | - Xuezhi Hui
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
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