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Lohani N, Golicz AA, Allu AD, Bhalla PL, Singh MB. Genome-wide analysis reveals the crucial role of lncRNAs in regulating the expression of genes controlling pollen development. PLANT CELL REPORTS 2023; 42:337-354. [PMID: 36653661 DOI: 10.1007/s00299-022-02960-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
The genomic location and stage-specific expression pattern of many long non-coding RNAs reveal their critical role in regulating protein-coding genes crucial in pollen developmental progression and male germ line specification. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 bp with no apparent protein-coding potential. Multiple investigations have revealed high expression of lncRNAs in plant reproductive organs in a cell and tissue-specific manner. However, their potential role as essential regulators of molecular processes involved in sexual reproduction remains largely unexplored. We have used developing field mustard (Brassica rapa) pollen as a model system for investigating the potential role of lncRNAs in reproductive development. Reference-based transcriptome assembly performed to update the existing genome annotation identified novel expressed protein-coding genes and long non-coding RNAs (lncRNAs), including 4347 long intergenic non-coding RNAs (lincRNAs, 1058 expressed) and 2,045 lncRNAs overlapping protein-coding genes on the opposite strand (lncNATs, 780 expressed). The analysis of expression profiles reveals that lncRNAs are significant and stage-specific contributors to the gene expression profile of developing pollen. Gene co-expression networks accompanied by genome location analysis identified 38 cis-acting lincRNA, 31 cis-acting lncNAT, 7 trans-acting lincRNA and 14 trans-acting lncNAT to be substantially co-expressed with target protein-coding genes involved in biological processes regulating pollen development and male lineage specification. These findings provide a foundation for future research aiming at developing strategies to employ lncRNAs as regulatory tools for gene expression control during reproductive development.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- School of Science, Western Sydney University, Richmond, Australia
| | - Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Gießen, Gießen, Germany
| | - Annapurna D Allu
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
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2
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Gao Y, Zhang N, Zeng Z, Wu Q, Jiang X, Li S, Sun W, Zhang J, Li Y, Li J, He F, Huang Z, Zhang J, Gong Y, Xie C. LncRNA PCAT1 activates SOX2 and suppresses radioimmune responses via regulating cGAS/STING signalling in non-small cell lung cancer. Clin Transl Med 2022; 12:e792. [PMID: 35415876 PMCID: PMC9005924 DOI: 10.1002/ctm2.792] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 01/03/2023] Open
Abstract
Background The expression of long non‐coding RNA (lncRNA) prostate cancer‐associated ncRNA transcripts 1 (PCAT1) is increased in non‐small cell lung cancer (NSCLC). It stimulates tumour growth and metastasis, but its role in the radioimmune responses remain unknown. We aimed to explore the impacts of PCAT1 on tumorigenesis and radioimmune responses and the underlying molecular mechanisms in NSCLC. Methods Comprehensive bioinformatics analysis was performed to identify immunosuppressive lncRNAs involved with tumour invasion in NSCLC. The expression levels of PCAT1 were analysed by in situ hybridisation in 55 paired NSCLC tissues and adjacent normal tissues. Both loss‐ and gain‐of‐function assays were performed to examine the effects of PCAT1 and SOX2 on NSCLC cell behaviours in vivo and in vitro. Bioinformatic analyses, chromatin isolation by RNA purification (ChIRP) and dual‐luciferase reporter assays were applied to validate the regulatory effects of PCAT1 on SOX2 expression. Chromatin immunoprecipitation, luciferase and rescue assays were utilised to identify the relationship between SOX2 and the cGAS/stimulator of interferon genes (STING) signalling. Results PCAT1 was immunosuppressive and related with NSCLC invasion. Increased PCAT1 was negatively correlated with immune cell infiltration in NSCLC. PCAT1 knockdown restrained proliferation, increased apoptosis, and repressed cell metastasis in vivo and in vitro. PCAT1 activated SOX2 that accelerated tumorigenesis and immunosuppression. SOX2 promoted tumour growth through inhibiting cytotoxic T‐cell immunity. Moreover, SOX2 restrained cGAS transcription and hampered downstream type I interferon (IFN)‐induced immune responses. Inhibition of PCAT1/SOX2 in collaboration with radiation further inhibited tumour growth, and initiated the cGAS/STING signalling pathway, which enhanced the immune responses of radiotherapy in NSCLC. Conclusions PCAT1/SOX2 axis promoted tumorigenesis and immunosuppression through inhibition of cGAS/STING signalling‐mediated T‐cell activation. Inhibition of PCAT1 and SOX2 synergised with radiotherapy to activate the immune response and could serve as potential therapeutic targets.
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Affiliation(s)
- Yanping Gao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Nannan Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zihang Zeng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xueping Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shuying Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wenjie Sun
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianguo Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyi Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiali Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fajian He
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengrong Huang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jinfang Zhang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
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3
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Wang Y, Jia L, Wang C, Du Z, Zhang S, Zhou L, Wen X, Li H, Chen H, Nie Y, Li D, Liu S, Figueroa DS, Ay F, Xu W, Zhang S, Li W, Cui J, Hoffman AR, Guo H, Hu JF. Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture. J Cell Biol 2022; 221:213009. [PMID: 35171230 PMCID: PMC8855478 DOI: 10.1083/jcb.202009134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/01/2021] [Accepted: 01/19/2022] [Indexed: 11/22/2022] Open
Abstract
The molecular circuitry that causes stem cells to exit from pluripotency remains largely uncharacterized. Using chromatin RNA in situ reverse transcription sequencing, we identified Peln1 as a novel chromatin RNA component in the promoter complex of Oct4, a stem cell master transcription factor gene. Peln1 was negatively associated with pluripotent status during somatic reprogramming. Peln1 overexpression caused E14 cells to exit from pluripotency, while Peln1 downregulation induced robust reprogramming. Mechanistically, we discovered that Peln1 interacted with the Oct4 promoter and recruited the DNA methyltransferase DNMT3A. By de novo altering the epigenotype in the Oct4 promoter, Peln1 dismantled the intrachromosomal loop that is required for the maintenance of pluripotency. Using RNA reverse transcription-associated trap sequencing, we showed that Peln1 targets multiple pathway genes that are associated with stem cell self-renewal. These findings demonstrate that Peln1 can act as a new epigenetic player and use a trans mechanism to induce an exit from the pluripotent state in stem cells.
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Affiliation(s)
- Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Zhonghua Du
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Xue Wen
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Li
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Huiling Chen
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Yuanyuan Nie
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Dan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Shanshan Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | | | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Wei Xu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Andrew R Hoffman
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Guo
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
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Zhao SP, Yu C, Yang MS, Liu ZL, Yang BC, Xiao XF. Long Non-coding RNA FENDRR Modulates Autophagy Through Epigenetic Suppression of ATG7 via Binding PRC2 in Acute Pancreatitis. Inflammation 2021; 44:999-1013. [PMID: 33417179 DOI: 10.1007/s10753-020-01395-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/19/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022]
Abstract
Acute pancreatitis (AP) is an inflammatory, complicated pancreatic disease, carrying significant morbidity and mortality. However, the molecular and cellular mechanisms involved in AP pathogenesis remain to be elucidated. Here, we explore the role of FOXF1 adjacent non-coding developmental regulatory RNA (FENDRR) in AP progression. Caerulein with or without LPS- induced or taurolithocholic acid 3-sulfate (TLC-S)-induced AP mouse models and cell models were performed for the validation of FENDRR expression in vivo and in vitro, respectively. Histopathological examinations of pancreatic tissues were performed to evaluate the severity of AP. Transmission electron microscopy was utilized to visualize the autophagic vacuoles. siRNA specifically targeting FENDRR was further applied. Flow cytometry was employed to assess cell apoptosis. ELISA, immunoflureoscence, and western blotting analysis were also performed to determine the levels of inflammatory cytokines and autophagy activity. RNA immunoprecipitation (RIP) and chromatin immunoprecipitation (ChIP) assays were carried out to reveal the epigenetic regulation of FENDRR on ATG7. Additionally, silencing FENDRR was also verified in AP mouse models. Higher FENDRR and impaired autophagy were displayed in both AP mouse models and cell models. FENDRR knockdown dramatically attenuated caerulein- or TLC-S-induced AR42J cells apoptosis and autophagy suppression. Further mechanistic experiments implied that the action of FENDRR is moderately attributable to its repression of ATG7 via direct interaction with the epigenetic repressor PRC2. Moreover, the silencing of FENDRR significantly induced the promotion of ATG7, thus alleviating the development of AP in vivo. Our study highlights FENDRR as a novel target that may contribute to AP progression, suggesting a therapeutic target for AP treatment.
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Affiliation(s)
- Shang-Ping Zhao
- The Third Xiangya Hospital of Central South University, No. 138, Tongzipo Road, Yuelu District, Changsha, 410013, Hunan Province, People's Republic of China
| | - Can Yu
- The Third Xiangya Hospital of Central South University, No. 138, Tongzipo Road, Yuelu District, Changsha, 410013, Hunan Province, People's Republic of China
| | - Ming-Shi Yang
- The Third Xiangya Hospital of Central South University, No. 138, Tongzipo Road, Yuelu District, Changsha, 410013, Hunan Province, People's Republic of China
| | - Zuo-Liang Liu
- The Third Xiangya Hospital of Central South University, No. 138, Tongzipo Road, Yuelu District, Changsha, 410013, Hunan Province, People's Republic of China
| | - Bing-Chang Yang
- The Third Xiangya Hospital of Central South University, No. 138, Tongzipo Road, Yuelu District, Changsha, 410013, Hunan Province, People's Republic of China
| | - Xue-Fei Xiao
- The Third Xiangya Hospital of Central South University, No. 138, Tongzipo Road, Yuelu District, Changsha, 410013, Hunan Province, People's Republic of China.
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5
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Alam MN, Shapla UM, Shen H, Huang Q. Linking emerging contaminants exposure to adverse health effects: Crosstalk between epigenome and environment. J Appl Toxicol 2020; 41:878-897. [PMID: 33113590 DOI: 10.1002/jat.4092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022]
Abstract
Environmental epigenetic findings shed new light on the roles of epigenetic regulations in environmental exposure-induced toxicities or disease susceptibilities. Currently, environmental emerging contaminants (ECs) are in focus for further investigation due to the evidence of human exposure in addition to their environmental occurrences. However, the adverse effects of these environmental ECs on health through epigenetic mechanisms are still poorly addressed in many aspects. This review discusses the epigenetic mechanisms (DNA methylation, histone modifications, and microRNA expressions) linking ECs exposure to health outcomes. We emphasized on the recent literature describing how ECs can dysregulate epigenetic mechanisms and lead to downstream health outcomes. These up-to-date research outputs could provide novel insights into the toxicological mechanisms of ECs. However, the field still faces a demand for further studies on the broad spectrum of health effects, synergistic/antagonistic effects, transgenerational epigenetic effects, and epidemiologic and demographic data of ECs.
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Affiliation(s)
- Md Nur Alam
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ummay Mahfuza Shapla
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Dhaka, Bangladesh
| | - Heqing Shen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Qingyu Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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Zhang Z, Meng Y, Gao F, Xiao Y, Zheng Y, Wang HQ, Gao Y, Jiang H, Yuan B, Zhang JB. TGF-β1-Mediated FDNCR1 Regulates Porcine Preadipocyte Differentiation via the TGF-β Signaling Pathway. Animals (Basel) 2020; 10:ani10081399. [PMID: 32796679 PMCID: PMC7459525 DOI: 10.3390/ani10081399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023] Open
Abstract
Simple Summary Fat differentiation affects lipid deposition and is a complex metabolic process. It has been previously reported that multiple transcription factors regulate adipocyte formation. With the in-depth study of epigenetics, in recent years it has been reported that long noncoding RNA (lncRNA) can effectively affect the formation of lipid droplets and thus regulate fat deposition. lncRNA can regulate cell function through a variety of mechanisms, the most studied is the mechanism of action of lncRNA as a miRNA molecular sponge. The purpose of this article is to explore the role of transforming growth factor-beta (TGF-β1) mediated lncRNA in the formation of porcine adipocytes, from the perspective of lncRNA to reveal the effect of TGF-β1 on the differentiation of porcine adipocytes, and provide a new way to improve the quality of pork. Abstract Adipocyte differentiation and lipid metabolism have important regulatory effects on the quality of meat from livestock. A variety of transcription factors regulate preadipocyte differentiation. Several studies have revealed that transforming growth factor-beta (TGF-β1) may play a key role in epithelial–mesenchymal transition (EMT); however, little is known about the effects of TGF-β1 treatment on porcine preadipocytes. To explore the role of TGF-β1 in porcine adipocyte differentiation, porcine preadipocytes were treated with 10 ng/mL TGF-β1, and two libraries were constructed for RNA-seq. We chose an abundant and differentially expressed long noncoding RNA (lncRNA), which we named fat deposition-associated long noncoding RNA1 (FDNCR1), for further study. RT-qPCR was used to detect mRNA levels of genes related to adipocyte differentiation. Triglyceride assay kits were used to detect lipid droplet deposition. TGF-β1 significantly suppressed porcine preadipocyte differentiation. We identified 8158 lncRNAs in total and 39 differentially expressed lncRNAs. After transfection with FDNCR1 siRNA, the mRNA expression of aP2, C/EBPα, and PPARγ and triglyceride levels significantly increased. Transfection with FDNCR1 siRNA significantly decreased protein levels of p-Smad2/Smad2 and p-Smad3/Smad3. These results demonstrate that FDNCR1 suppresses porcine preadipocyte differentiation via the TGF-β signaling pathway.
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Affiliation(s)
- Zhe Zhang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Yu Meng
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
| | - Fei Gao
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
| | - Yue Xiao
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
| | - Yi Zheng
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
| | - Hao-Qi Wang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
| | - Yan Gao
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
| | - Hao Jiang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
| | - Bao Yuan
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
- Correspondence: (B.Y.); (J.-B.Z.); Tel.: +86-431-8783-6536 (B.Y.); +86-431-8783-6551 (J.-B.Z.)
| | - Jia-Bao Zhang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, Jilin 130062, China; (Z.Z.); (Y.M.); (F.G.); (Y.X.); (Y.Z.); (H.-Q.W.); (Y.G.); (H.J.)
- Correspondence: (B.Y.); (J.-B.Z.); Tel.: +86-431-8783-6536 (B.Y.); +86-431-8783-6551 (J.-B.Z.)
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GPRC5A: An Emerging Biomarker in Human Cancer. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1823726. [PMID: 30417009 PMCID: PMC6207857 DOI: 10.1155/2018/1823726] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/23/2018] [Accepted: 09/26/2018] [Indexed: 12/16/2022]
Abstract
Aberrant expression of G protein-coupled receptors (GPCRs) is frequently associated with tumorigenesis. G Protein-coupled receptor class C group 5 member A (GPRC5A) is a member of the GPCR superfamily, is expressed preferentially in lung tissues, and is regulated by various entities at multiple levels. GPRC5A exerts a tumor suppressive role in lung cancer and GPRC5A deletion promotes lung tumor initiation and progression. Recent advances have highlighted that GPRC5A dysregulation is found in various human cancers and is related to many tumor-associated signaling pathways, including the cyclic adenosine monophosphate (cAMP), nuclear factor (NF)-κB, signal transducer and activator of transcription (STAT) 3, and focal adhesion kinase (FAK)/Src signaling. This review aimed to summarize our updated view on the biology and regulation of GPRC5A, its expression in human cancers, and the linked signaling pathways. A better comprehension of the underlying cellular and molecular mechanisms of GPRC5A will provide novel insights into its potential diagnostic and therapeutic value.
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8
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Liu X, Yang Q, Yan J, Zhang X, Zheng M. LncRNA MNX1‐AS1 promotes the progression of cervical cancer through activating MAPK pathway. J Cell Biochem 2018; 120:4268-4277. [PMID: 30302806 DOI: 10.1002/jcb.27712] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/29/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Xiang Liu
- Department of Obstetrics and Gynecology The First People's Hospital of Wenling Wenling Zhejiang China
| | - Qian Yang
- Department of Obstetrics and Gynecology The First People's Hospital of Wenling Wenling Zhejiang China
| | - Jinyu Yan
- Department of Obstetrics and Gynecology The First People's Hospital of Wenling Wenling Zhejiang China
| | - Xiahui Zhang
- Department of Obstetrics and Gynecology The First People's Hospital of Wenling Wenling Zhejiang China
| | - Meiyun Zheng
- Department of Obstetrics and Gynecology The First People's Hospital of Wenling Wenling Zhejiang China
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9
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Laham-Karam N, Laitinen P, Turunen TA, Ylä-Herttuala S. Activating the Chromatin by Noncoding RNAs. Antioxid Redox Signal 2018; 29:813-831. [PMID: 28699365 DOI: 10.1089/ars.2017.7248] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE The extent and breadth of transcription have recently been uncovered and this has revealed an extensive array of noncoding RNAs (ncRNAs). The biological role and significance of these ncRNAs have been realized and to date it appears that ncRNAs may have many important regulatory functions. ncRNAs are multifaceted and they induce a complexity of different types of transcriptional and posttranscriptional regulation, including gene activation. Recent Advances: Association of ncRNAs with gene activation is an important finding. Not only enhancer RNA (eRNA) but other types of ncRNAs, including small RNA (sRNA), long-noncoding RNA (lncRNA), microRNA (miRNA), and PIWI-associated RNA (piRNA), have also been implicated in gene activation. Interestingly, they often coincide with histone modifications that favor an open chromatin. In addition, these ncRNAs can recruit key factors important for transcription, including RNA polymerase II. They may directly bind the genomic DNA or act as scaffolds; alternatively, they may loop the chromatin to enhance transcription. CRITICAL ISSUES Although the role of small activating (sa)RNAs has been considerably studied, the roles of miRNAs and piRNAs in gene activation still need to be substantiated and issues of specificity require further studies. FUTURE DIRECTIONS The ncRNA field is coming out of its infancy and we are gaining a global picture of the importance of ncRNAs. However, detailed mechanisms of action of the different ncRNAs are still to be determined. This may reveal novel ways of transcriptional regulation, which will facilitate our ability to utilize these regulatory pathways for research and therapeutic purposes. Antioxid. Redox Signal. 29, 813-831.
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Affiliation(s)
- Nihay Laham-Karam
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland
| | - Pia Laitinen
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland
| | - Tiia A Turunen
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland
| | - Seppo Ylä-Herttuala
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland .,2 Heart Center, Kuopio University Hospital , Kuopio, Finland .,3 Gene Therapy Unit, Kuopio University Hospital , Kuopio, Finland
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10
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A current view on long noncoding RNAs in yeast and filamentous fungi. Appl Microbiol Biotechnol 2018; 102:7319-7331. [PMID: 29974182 PMCID: PMC6097775 DOI: 10.1007/s00253-018-9187-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are crucial players in epigenetic regulation. They were initially discovered in human, yet they emerged as common factors involved in a number of central cellular processes in several eukaryotes. For example, in the past decade, research on lncRNAs in yeast has steadily increased. Several examples of lncRNAs were described in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Also, screenings for lncRNAs in ascomycetes were performed and, just recently, the first full characterization of a lncRNA was performed in the filamentous fungus Trichoderma reesei. In this review, we provide a broad overview about currently known fugal lncRNAs. We make an attempt to categorize them according to their functional context, regulatory strategies or special properties. Moreover, the potential of lncRNAs as a biotechnological tool is discussed.
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11
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Jayanthi S, Gonzalez B, McCoy MT, Ladenheim B, Bisagno V, Cadet JL. Methamphetamine Induces TET1- and TET3-Dependent DNA Hydroxymethylation of Crh and Avp Genes in the Rat Nucleus Accumbens. Mol Neurobiol 2018; 55:5154-5166. [PMID: 28842817 PMCID: PMC5948251 DOI: 10.1007/s12035-017-0750-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/15/2017] [Indexed: 12/30/2022]
Abstract
Methamphetamine (METH) addiction is a biopsychosocial disorder that is accompanied by multiple relapses even after prolonged abstinence, suggesting the possibilities of long-lasting maladaptive epigenetic changes in the brain. Here, we show that METH administration produced time-dependent increases in the expression of corticotropin-releasing hormone (Crh/Crf), arginine vasopressin (Avp), and cocaine- and amphetamine-regulated transcript prepropeptide (Cartpt) mRNAs in the rat nucleus accumbens (NAc). Chromatin immunoprecipitation (ChIP) assays revealed that METH increased the abundance of phosphorylated CREB (pCREB) at the promoter of Cartpt but not at Avp or Crh DNA sequences. In contrast, METH produced DNA hypomethylation at sites near the Crh transcription start site (TSS) and at intragenic Avp sequences. METH also increased DNA hydroxymethylation at the Crh TSS and at intragenic Avp sites. In addition, METH increased the protein expression of ten-eleven-translocation enzymes that catalyze DNA hydroxymethylation. Importantly, METH increased TET1 binding at the Crh promoter and increased TET3 binding at Avp intragenic regions. We further tested the role of TET enzymes in METH-induced changes in gene expression by using the TET inhibitor, 1,5-isoquinolinediol (IQD), and found that IQD blocked METH-induced increases in Crh and Avp mRNA expression. Together, these results indicate that METH produced changes in neuropeptide transcription by both activation of the cAMP/CREB pathway and stimulation of TET-dependent DNA hydroxymethylation. These results provide molecular evidence for epigenetic controls of METH-induced changes in the expression of neuropeptides.
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Affiliation(s)
- Subramaniam Jayanthi
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, USA
| | - Betina Gonzalez
- Instituto de Investigaciones Farmacológicas (Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Michael T McCoy
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, USA
| | - Bruce Ladenheim
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, USA
| | - Veronica Bisagno
- Instituto de Investigaciones Farmacológicas (Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, USA.
- Molecular Neuropsychiatry Research Branch, DHHS/NIH/NIDA IRP, 251 Bayview Boulevard, Baltimore, MD, 21224, USA.
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12
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Targeting the IGF1R Pathway in Breast Cancer Using Antisense lncRNA-Mediated Promoter cis Competition. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:105-117. [PMID: 30195750 PMCID: PMC6023958 DOI: 10.1016/j.omtn.2018.04.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023]
Abstract
Aberrant insulin-like growth factor I receptor (IGF1R) signaling pathway serves as a well-established target for cancer drug therapy. The intragenic antisense long noncoding RNA (lncRNA) IRAIN, a putative tumor suppressor, is downregulated in breast cancer cells, while IGF1R is overexpressed, leading to an abnormal IGF1R/IRAIN ratio that promotes tumor growth. To precisely target this pathway, we developed an “antisense lncRNA-mediated intragenic cis competition” (ALIC) approach to therapeutically correct the elevated IGF1R/IRAIN bias in breast cancer cells. We used CRISPR-Cas9 gene editing to target the weak promoter of IRAIN antisense lncRNA and showed that in targeted clones, intragenic activation of the antisense lncRNA potently competed in cis with the promoter of the IGF1R sense mRNA. Notably, the normalization of IGF1R/IRAIN transcription inhibited the IGF1R signaling pathway in breast cancer cells, decreasing cell proliferation, tumor sphere formation, migration, and invasion. Using “nuclear RNA reverse transcription-associated trap” sequencing, we uncovered an IRAIN lncRNA-specific interactome containing gene targets involved in cell metastasis, signaling pathways, and cell immortalization. These data suggest that aberrantly upregulated IGF1R in breast cancer cells can be precisely targeted by cis transcription competition, thus providing a useful strategy to target disease genes in the development of novel precision medicine therapies.
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13
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Arroyo AB, de Los Reyes-García AM, Teruel-Montoya R, Vicente V, González-Conejero R, Martínez C. microRNAs in the haemostatic system: More than witnesses of thromboembolic diseases? Thromb Res 2018; 166:1-9. [PMID: 29649766 DOI: 10.1016/j.thromres.2018.03.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are small endogenous RNAs that post-transcriptionally regulate gene expression. In the last few years, these molecules have been implicated in the regulation of haemostasis, and an increasing number of studies have investigated their relationship with the development of thrombosis. In this review, we discuss the latest developments regarding the role of miRNAs in the regulation of platelet function and secondary haemostasis. We also discuss the genetic and environmental factors that regulate miRNAs. Finally, we address the potential use of miRNAs as prognostic and diagnostic tools in thrombosis.
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Affiliation(s)
- Ana B Arroyo
- Department of Hematology and Medical Oncology, Morales Meseguer University Hospital, Centro Regional de Hemodonación, University of Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Ascensión M de Los Reyes-García
- Department of Hematology and Medical Oncology, Morales Meseguer University Hospital, Centro Regional de Hemodonación, University of Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Raúl Teruel-Montoya
- Department of Hematology and Medical Oncology, Morales Meseguer University Hospital, Centro Regional de Hemodonación, University of Murcia, IMIB-Arrixaca, Murcia, Spain; Red CIBERER CB15/00055, Murcia, Spain
| | - Vicente Vicente
- Department of Hematology and Medical Oncology, Morales Meseguer University Hospital, Centro Regional de Hemodonación, University of Murcia, IMIB-Arrixaca, Murcia, Spain; Red CIBERER CB15/00055, Murcia, Spain
| | - Rocío González-Conejero
- Department of Hematology and Medical Oncology, Morales Meseguer University Hospital, Centro Regional de Hemodonación, University of Murcia, IMIB-Arrixaca, Murcia, Spain.
| | - Constantino Martínez
- Department of Hematology and Medical Oncology, Morales Meseguer University Hospital, Centro Regional de Hemodonación, University of Murcia, IMIB-Arrixaca, Murcia, Spain.
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14
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Li Y, Wang Z, Wang Y, Zhao Z, Zhang J, Lu J, Xu J, Li X. Identification and characterization of lncRNA mediated transcriptional dysregulation dictates lncRNA roles in glioblastoma. Oncotarget 2018; 7:45027-45041. [PMID: 26943771 PMCID: PMC5216703 DOI: 10.18632/oncotarget.7801] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/27/2016] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) modulate gene expression, and lncRNA misregulation is associated with cancer. However, precise functional roles in biological and disease processes have been described for only a few lncRNAs. Identification of genome-wide lncRNA-mediated transcriptional dysregulations may improve cancer treatments. In the present study, we used a computational framework that combined lncRNA and gene expression profiles with transcription factor (TF)-target relationships to comprehensively identify dysregulatory lncRNA-TF-gene triplets. In glioblastoma (GBM), we found that most lncRNAs affect multiple targets and primarily affect TF activity in trans. Six different classes of lncRNA-mediated transcriptional dysregulations were identified, with most lncRNAs either enhancing or attenuating target gene expression. Functional analysis of lncRNAs via their dysregulated targets implicated lncRNA modulators in some hallmarks of cancer, providing a new way to predict lncRNA function. Finally, we identified several lncRNA-TF-gene triplets (including HOTAIR-MXI1-CD58/PRKCE and HOTAIR-ATF5-NCAM1) that are associated with glioblastoma prognosis. The integration of lncRNA modulators into transcriptional regulatory networks will further enhance our understanding of lncRNA functions in cancer.
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Affiliation(s)
- Yongsheng Li
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Zishan Wang
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Yuan Wang
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Zheng Zhao
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Jinwen Zhang
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Jianping Lu
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
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15
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DNA-RNA interactions are critical for chromosome condensation in Escherichia coli. Proc Natl Acad Sci U S A 2017; 114:12225-12230. [PMID: 29087325 DOI: 10.1073/pnas.1711285114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial chromosome (nucleoid) conformation dictates faithful regulation of gene transcription. The conformation is condition-dependent and is guided by several nucleoid-associated proteins (NAPs) and at least one nucleoid-associated noncoding RNA, naRNA4. Here we investigated the molecular mechanism of how naRNA4 and the major NAP, HU, acting together organize the chromosome structure by establishing multiple DNA-DNA contacts (DNA condensation). We demonstrate that naRNA4 uniquely acts by forming complexes that may not involve long stretches of DNA-RNA hybrid. Also, uncommonly, HU, a chromosome-associated protein that is essential in the DNA-RNA interactions, is not present in the final complex. Thus, HU plays a catalytic (chaperone) role in the naRNA4-mediated DNA condensation process.
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16
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Dong Y, Yoshitomi T, Hu JF, Cui J. Long noncoding RNAs coordinate functions between mitochondria and the nucleus. Epigenetics Chromatin 2017; 10:41. [PMID: 28835257 PMCID: PMC5569521 DOI: 10.1186/s13072-017-0149-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 08/17/2017] [Indexed: 11/23/2022] Open
Abstract
In animal cells, mitochondria are the primary powerhouses and metabolic factories. They also contain genomes and can produce mitochondrial-specific nucleic acids and proteins. To maintain homeostasis of the entire cell, an intense cross-talk between mitochondria and the nucleus, mediated by encoded noncoding RNAs (ncRNAs), as well as proteins, is required. Long ncRNAs (lncRNAs) contain characteristic structures, and they are involved in the regulation of almost every stage of gene expression, as well as being implicated in a variety of disease states, such as cancer. In the coordinated signaling system, several lncRNAs, transcribed in the nucleus but residing in mitochondria, play a key role in regulating mitochondrial functions or dynamics. For example, RMRP, a component of the mitochondrial RNase MRP, is important for mitochondrial DNA replication and RNA processing, and the steroid receptor RNA activator, SRA, is a key modulator of hormone signaling and is present in both the nucleus and mitochondria. Some RNA-binding proteins maybe play a role in the lncRNAs transport system, such as HuR, GRSF1, SHARP, SLIRP, PPR, and PNPASE. Furthermore, a series of nuclear DNA-encoded lncRNAs were implicated in mitochondria-mediated apoptosis, mitochondrial bioenergetics and biosynthesis, and glutamine metabolism. The mitochondrial genome can also encode a set of lncRNAs, and they are divided into three categories: (1) lncND5, lncND6, and lncCyt b RNA; (2) chimeric mitochondrial DNA-encoded lncRNAs; and (3) putative mitochondrial DNA-encoded lncRNAs. It has been reported that the mitochondrial DNA-encoded lncRNAs appear to operate in the nucleus. The molecular mechanisms underlying trafficking of the mitochondrial DNA-encoded lncRNAs to the nucleus in mammals are only now beginning to emerge. In conclusion, both nuclear- and mitochondrial DNA-encoded lncRNAs mediate an intense intercompartmental cross-talk, which opens a rich field for investigation of the mechanism underlying the intercompartmental coordination and the maintenance of whole cell homeostasis.
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Affiliation(s)
- Yaru Dong
- Department of Ophthalmology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA, 94304, USA
| | - Takeshi Yoshitomi
- Department of Ophthalmology, Akita University School of Medicine, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Ji-Fan Hu
- Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA, 94304, USA. .,Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, 130061, Jilin, China.
| | - Jizhe Cui
- Department of Ophthalmology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China.
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17
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Yang ZY, Yang F, Zhang YL, Liu B, Wang M, Hong X, Yu Y, Zhou YH, Zeng H. LncRNA-ANCR down-regulation suppresses invasion and migration of colorectal cancer cells by regulating EZH2 expression. Cancer Biomark 2017; 18:95-104. [PMID: 27983539 DOI: 10.3233/cbm-161715] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our study aimed to explore the effects of long noncoding RNA (lncRNA)-ANCR on the invasion and migration of colorectal cancer (CRC) cells by regulating enhancer of zeste homolog 2 (EZH2) expression. CRC tissues and adjacent normal tissues were collected and CRC SW620 cells line and normal human intestinal epithelial cells (HIECs) were incubated. CRC SW620 cells line was transfected with ANCR-siRNA. The expressions of ANCR and EZH2 mRNA were measured by real-time quantitative polymerase chain reaction (RT-qPCR). EZH2 and trimethylation of H3K27 (H3K27me3) protein expressions were detected using Western blotting. The relationship between ANCR and EZH2 was determined through RNA pull-down and co-immunoprecipitation (co-IP) assays. Cell invasion and migration were determined by Trans-well and cell scratch assays. ANCR, EZH2 and H3K27me3 expressions were up-regulated in CRC tissues and SW620 cells (all P < 0.05). After transfected with ANCR-siRNA, SW620 cells showed decreased ANCR expression and EZH2 mRNA and protein expressions (all P < 0.05). According to the results of RNA pull-down and co-IP assays, ANCR could specifically bind to EZH2. The results of Trans-well and cell scratch tests showed that when ANCR expression was decreased, the invasion and migration abilities of SW620 cells significantly declined (both P < 0.05). In conclusion, these results suggest that lncRNA-ANCR could influence the invasion and migration of CRC cells by specifically binding to EZH2.
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Affiliation(s)
- Zhao-Yang Yang
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Fang Yang
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Ying-Li Zhang
- Department of Internal Medicine, Harbin Red Cross Central Hospital, Harbin, Heilongjiang, China
| | - Bao Liu
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Meng Wang
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Xuan Hong
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yan Yu
- Department of Sixth Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yao-Hui Zhou
- Department of Internal Medicine, The First Hospital of Harbin, Harbin, Heilongjiang, China
| | - Hai Zeng
- Department of Internal Medicine, The First Hospital of Harbin, Harbin, Heilongjiang, China
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18
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Zhao X, Wei X, Zhao L, Shi L, Cheng J, Kang S, Zhang H, Zhang J, Li L, Zhang H, Zhao W. The rs6983267 SNP and long non-coding RNA CARLo-5 are associated with endometrial carcinoma. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:508-515. [PMID: 27432114 DOI: 10.1002/em.22031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 06/14/2016] [Accepted: 06/17/2016] [Indexed: 06/06/2023]
Abstract
The single nucleotide polymorphism (SNP) rs6983267 and cancer-associated region long non-coding RNA (CARLo-5) are associated with various human cancers. This study aimed to investigate the expression of CARLo-5 in endometrial carcinoma (EC) and its relationship with clinicopathological features and patient survival. The association of the rs6983267 SNP with EC risk and its involvement in the regulation of CARLo-5 expression in EC were investigated. The rs6983267 SNP was genotyped by polymerase chain reaction (PCR) and ligase detection reaction in 543 EC patients and 584 controls. The expression of CARLo-5 in 108 EC tissues and 66 normal endometrial tissues (NETs) was determined using quantitative real-time PCR. The genotype and allele distributions of the rs6983267 SNP differed significantly between patients and controls. There was a significant correlation between the rs6983267 genotypes and lymph node metastasis of EC patients (P = 0.026). CARLo-5 expression was significantly higher in EC tissues than in NETs (P < 0.001) and significantly associated with FIGO stage (P = 0.029) and lymph node metastasis (P = 0.030). Patients with high CARLo-5 expression had significantly shorter overall survival than those with low CARLo-5 expression (P = 0.003). The rs6983267 genotype was significantly correlated with CARLo-5 expression (P < 0.05). In conclusion, CARLo-5 was identified as a pro-oncogenic lncRNA that may play an important role in EC progression and represent a prognostic marker for EC. The expression of CARLo-5 was significantly correlated with the rs6983267 genotype associated with increased susceptibility to EC. Environ. Mol. Mutagen. 57:508-515, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiwa Zhao
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Xurui Wei
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Lianmei Zhao
- Tumor Research Institute, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Li Shi
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Jianxin Cheng
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Shan Kang
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Hui Zhang
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Li Li
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Haibo Zhang
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Wei Zhao
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
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19
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Antisense technologies in the studying of Toxoplasma gondii. J Microbiol Methods 2015; 138:93-99. [PMID: 26724749 DOI: 10.1016/j.mimet.2015.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/13/2015] [Accepted: 12/17/2015] [Indexed: 11/23/2022]
Abstract
This review covers a brief history of antisense RNAs and its applications, and summarizes the current stage of antisense technologies used in Toxoplasma gondii, a fascinating model organism with a unique characteristic blend of genetic regulatory systems normally found in plants or animals. Based on the current knowledge of regulatory RNAs and non-coding RNA (ncRNA), the antisense technologies are reviewed according to the classification of ncRNAs, which are roughly categorized into small, ranging from ~20-200 nucleotides in length, and long >200 nucleotides. Techniques utilizing small regulatory RNAs such as siRNA, miRNA, antagomirs, ribozymes and morpholino oligomers are discussed along with long non-coding RNA (lncRNA) including antisense and double stranded. These antisense technologies can be used in forward and reverse genetics studies. The future of technologies is limitless, particularly by combining these technologies with conventional methods, and should allow for ever greater understanding of gene regulation of the organism and related pathogenic microorganisms.
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20
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Zhou L, Sun K, Zhao Y, Zhang S, Wang X, Li Y, Lu L, Chen X, Chen F, Bao X, Zhu X, Wang L, Tang LY, Esteban MA, Wang CC, Jauch R, Sun H, Wang H. Linc-YY1 promotes myogenic differentiation and muscle regeneration through an interaction with the transcription factor YY1. Nat Commun 2015; 6:10026. [PMID: 26658965 DOI: 10.1038/ncomms10026] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/28/2015] [Indexed: 12/22/2022] Open
Abstract
Little is known how lincRNAs are involved in skeletal myogenesis. Here we describe the discovery of Linc-YY1 from the promoter of the transcription factor (TF) Yin Yang 1 (YY1) gene. We demonstrate that Linc-YY1 is dynamically regulated during myogenesis in vitro and in vivo. Gain or loss of function of Linc-YY1 in C2C12 myoblasts or muscle satellite cells alters myogenic differentiation and in injured muscles has an impact on the course of regeneration. Linc-YY1 interacts with YY1 through its middle domain, to evict YY1/Polycomb repressive complex (PRC2) from target promoters, thus activating the gene expression in trans. In addition, Linc-YY1 also regulates PRC2-independent function of YY1. Finally, we identify a human Linc-YY1 orthologue with conserved function and show that many human and mouse TF genes are associated with lincRNAs that may modulate their activity. Altogether, we show that Linc-YY1 regulates skeletal myogenesis and uncover a previously unappreciated mechanism of gene regulation by lincRNA.
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Affiliation(s)
- Liang Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kun Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Suyang Zhang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Xuecong Wang
- Genome Regulation Laboratory, Drug Discovery Pipeline, Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Yuying Li
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Leina Lu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaona Chen
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Fengyuan Chen
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Xichen Bao
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Xihua Zhu
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Lijun Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ling-Yin Tang
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Miguel A Esteban
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Chi-Chiu Wang
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Hao Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Orthopedics and Traumatology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Increased expression of long noncoding RNAs LOC100652951 and LOC100506036 in T cells from patients with rheumatoid arthritis facilitates the inflammatory responses. Immunol Res 2015; 64:576-83. [DOI: 10.1007/s12026-015-8756-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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22
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Baer B, Millar AH. Proteomics in evolutionary ecology. J Proteomics 2015; 135:4-11. [PMID: 26453985 DOI: 10.1016/j.jprot.2015.09.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 01/09/2023]
Abstract
Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein modifications and protein interactions of interest with high accuracy and assess protein diversity and function. Therefore, proteomic technologies can be viewed as providing evolutionary biologist with exciting novel opportunities to understand very early events in functional variation of cellular molecular machinery that are acting as part of evolutionary processes.
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Affiliation(s)
- B Baer
- Centre for Integrative Bee Research (CIBER) and ARC Centre of Excellence in Plant Energy Biology, Bayliss Building, The University of Western Australia, 6009 Crawley, Australia.
| | - A H Millar
- Centre for Integrative Bee Research (CIBER) and ARC Centre of Excellence in Plant Energy Biology, Bayliss Building, The University of Western Australia, 6009 Crawley, Australia
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23
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Dietrich A, Wallet C, Iqbal RK, Gualberto JM, Lotfi F. Organellar non-coding RNAs: Emerging regulation mechanisms. Biochimie 2015; 117:48-62. [DOI: 10.1016/j.biochi.2015.06.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
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24
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Liu Y, Zhao J, Zhang W, Gan J, Hu C, Huang G, Zhang Y. lncRNA GAS5 enhances G1 cell cycle arrest via binding to YBX1 to regulate p21 expression in stomach cancer. Sci Rep 2015; 5:10159. [PMID: 25959498 PMCID: PMC4426700 DOI: 10.1038/srep10159] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 03/31/2015] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs), which have evolved as important gene expression modulators, are involved in human malignancies. The down-regulation of lncRNA growth arrest specific transcript 5 (GAS5) has been reported in several cancers, however, the underlying mechanism of lncRNA GAS5 in stomach cancer is poorly understood. In this study, we found that lncRNA GAS5 had lower expression in stomach cancer tissues than the normal counterparts. lncRNA GAS5 was shown to interact with Y-box binding protein 1 (YBX1), and lncRNA GAS5 knockdown was shown to accelerate YBX1 protein turnover without affecting YBX1 transcription. lncRNA GAS5 down-regulation reduced the YBX1 protein level, which decreased YBX1-transactivated p21 expression and abolished G1 phase cell cycle arrest in stomach cancer. These results delineate a novel mechanism of lncRNA GAS5 in suppressing stomach carcinogenesis, and the lncRNA GAS5/YBX1/p21 pathway we discovered may provide useful targets for developing lncRNA-based therapies for stomach cancer.
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Affiliation(s)
- Yongchao Liu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Zhao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jun Gan
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Chengen Hu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Guangjian Huang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- 1] Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China [2] Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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25
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Murakami K. Non-coding RNAs and hypertension-unveiling unexpected mechanisms of hypertension by the dark matter of the genome. Curr Hypertens Rev 2015; 11:80-90. [PMID: 25828869 PMCID: PMC5384352 DOI: 10.2174/1573402111666150401105317] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/05/2015] [Accepted: 03/30/2015] [Indexed: 12/23/2022]
Abstract
Hypertension is a major risk factor of cardiovascular diseases and a most important health problem in developed countries. Investigations on pathophysiology of hypertension have been based on gene products from coding region that occupies only about 1% of total genome region. On the other hand, non-coding region that occupies almost 99% of human genome has been regarded as "junk" for a long time and went unnoticed until these days. But recently, it turned out that noncoding region is extensively transcribed to non-coding RNAs and has various functions. This review highlights recent updates on the significance of non-coding RNAs such as micro RNAs and long non-coding RNAs (lncRNAs) on the pathogenesis of hypertension, also providing an introduction to basic biology of noncoding RNAs. For example, microRNAs are associated with hypertension via neuro-fumoral factor, sympathetic nerve activity, ion transporters in kidneys, endothelial function, vascular smooth muscle phenotype transformation, or communication between cells. Although reports of lncRNAs on pathogenesis of hypertension are scarce at the moment, new lncRNAs in relation to hypertension are being discovered at a rapid pace owing to novel techniques such as microarray or next-generation sequencing. In the clinical settings, clinical use of non-coding RNAs in identifying cardiovascular risks or developing novel tools for treating hypertension such as molecular decoy or mimicks is promising, although improvement in chemical modification or drug delivery system is necessary.
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Affiliation(s)
- Kazuo Murakami
- Department of Health Care and Preventive Medicine, Matsuyama Red Cross Hospital, 1 Bunkyo-cho, Matsuyama, Ehime, 790-8524, Japan.
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26
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He H, Li W, Liyanarachchi S, Jendrzejewski J, Srinivas M, Davuluri RV, Nagy R, de la Chapelle A. Genetic predisposition to papillary thyroid carcinoma: involvement of FOXE1, TSHR, and a novel lincRNA gene, PTCSC2. J Clin Endocrinol Metab 2015; 100:E164-72. [PMID: 25303483 PMCID: PMC4283026 DOI: 10.1210/jc.2014-2147] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
CONTEXT By genome-wide association studies, the risk allele [A] of SNP rs965513 predisposes strongly to papillary thyroid carcinoma (PTC). It is located in a gene-poor region of 9q22, some 60 kb from the FOXE1 gene. The underlying mechanisms remain to be discovered. OBJECTIVE Our objective was to identify novel transcripts in the 9q22 locus and correlate gene expression levels with the genotypes of rs965513. DESIGN We performed 3' and 5' rapid amplification of cDNA ends and RT-PCR to detect novel transcripts. One novel transcript was forcibly expressed in a cell line followed by gene expression array analysis. We genotyped rs965513 from PTC patients and measured gene expression levels by real-time RT-PCR in unaffected thyroid tissue and matched tumor. SETTING This was a laboratory-based study using cells from clinical tissue samples and a cancer cell line. MAIN OUTCOME MEASURES We detected previously uncharacterized transcripts and evaluated the gene expression levels and the correlation with the risk allele of rs965513, age, gender, chronic lymphocyte thyroiditis (CLT), and TSH levels. RESULTS We found a novel long intergenic noncoding RNA gene and named it papillary thyroid cancer susceptibility candidate 2 (PTCSC2). Transcripts of PTCSC2 are down-regulated in PTC tumors. The risk allele [A] of rs965513 was significantly associated with low expression of unspliced PTCSC2, FOXE1, and TSHR in unaffected thyroid tissue. We also observed a significant association of age and CLT with PTCSC2 unspliced transcript levels. The correlation between the rs965513 genotype and the PTCSC2 unspliced transcript levels remained significant after adjusting for age, gender, and CLT. Forced expression of PTCSC2 in the BCPAP cell line affected the expression of a subset of noncoding and coding transcripts with enrichment of genes functionally involved in cell cycle and cancer. CONCLUSIONS Our data suggest a role for PTCSC2, FOXE1, and TSHR in the predisposition to PTC.
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Affiliation(s)
- Huiling He
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology, and Medical Genetics (H.H., W.L., S.L., J.J., M.S., R.N., A.d.l.C), and Department of Internal Medicine (R.N.), Ohio State University Comprehensive Cancer Center, the Ohio State University, Columbus, Ohio 43210; and Division of Health and Biomedical Informatics, Department of Preventive Medicine, Robert H. Lurie Comprehensive Cancer Center (R.V.D.), Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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27
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Zhou H, Rigoutsos I. The emerging roles of GPRC5A in diseases. Oncoscience 2014; 1:765-76. [PMID: 25621293 PMCID: PMC4303886 DOI: 10.18632/oncoscience.104] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 12/14/2022] Open
Abstract
The ‘Retinoic Acid-Inducible G-protein-coupled receptors’ or RAIG are a group comprising the four orphan receptors GPRC5A, GPRC5B, GPRC5C and GPRC5D. As the name implies, their expression is induced by retinoic acid but beyond that very little is known about their function. In recent years, one member, GPRC5A, has been receiving increasing attention as it was shown to play important roles in human cancers. As a matter of fact, dysregulation of GPRC5A has been associated with several cancers including lung cancer, breast cancer, colorectal cancer, and pancreatic cancer. Here we review the current state of knowledge about the heterogeneity and evolution of GPRC5A, its regulation, its molecular functions, and its involvement in human disease.
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Affiliation(s)
- Honglei Zhou
- Computational Medicine Center, Jefferson Alumni Hall, Thomas Jefferson University, Philadelphia, PA
| | - Isidore Rigoutsos
- Computational Medicine Center, Jefferson Alumni Hall, Thomas Jefferson University, Philadelphia, PA
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28
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Maruyama A, Mimura J, Itoh K. Non-coding RNA derived from the region adjacent to the human HO-1 E2 enhancer selectively regulates HO-1 gene induction by modulating Pol II binding. Nucleic Acids Res 2014; 42:13599-614. [PMID: 25404134 PMCID: PMC4267629 DOI: 10.1093/nar/gku1169] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Recent studies have disclosed the function of enhancer RNAs (eRNAs), which are long non-coding RNAs transcribed from gene enhancer regions, in transcriptional regulation. However, it remains unclear whether eRNAs are involved in the regulation of human heme oxygenase-1 gene (HO-1) induction. Here, we report that multiple nuclear-enriched eRNAs are transcribed from the regions adjacent to two human HO-1 enhancers (i.e. the distal E2 and proximal E1 enhancers), and some of these eRNAs are induced by the oxidative stress-causing reagent diethyl maleate (DEM). We demonstrated that the expression of one forward direction (5′ to 3′) eRNA transcribed from the human HO-1 E2 enhancer region (named human HO-1enhancer RNA E2-3; hereafter called eRNA E2-3) was induced by DEM in an NRF2-dependent manner in HeLa cells. Conversely, knockdown of BACH1, a repressor of HO-1 transcription, further increased DEM-inducible eRNA E2-3 transcription as well as HO-1 expression. In addition, we showed that knockdown of eRNA E2-3 selectively down-regulated DEM-induced HO-1 expression. Furthermore, eRNA E2-3 knockdown attenuated DEM-induced Pol II binding to the promoter and E2 enhancer regions of HO-1 without affecting NRF2 recruitment to the E2 enhancer. These findings indicate that eRNAE2-3 is functional and is required for HO-1 induction.
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Affiliation(s)
- Atsushi Maruyama
- Department of Stress Response Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
| | - Junsei Mimura
- Department of Stress Response Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
| | - Ken Itoh
- Department of Stress Response Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
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29
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Saini Y, Dang H, Livraghi-Butrico A, Kelly EJ, Jones LC, O'Neal WK, Boucher RC. Gene expression in whole lung and pulmonary macrophages reflects the dynamic pathology associated with airway surface dehydration. BMC Genomics 2014; 15:726. [PMID: 25204199 PMCID: PMC4247008 DOI: 10.1186/1471-2164-15-726] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 08/15/2014] [Indexed: 12/28/2022] Open
Abstract
Background Defects in airway mucosal defense, including decreased mucus clearance, contribute to the pathogenesis of human chronic obstructive pulmonary diseases. Scnn1b-Tg mice, which exhibit chronic airway surface dehydration from birth, can be used as a model to study the pathogenesis of muco-obstructive lung disease across developmental stages. To identify molecular signatures associated with obstructive lung disease in this model, gene expression analyses were performed on whole lung and purified lung macrophages collected from Scnn1b-Tg and wild-type (WT) littermates at four pathologically relevant time points. Macrophage gene expression at 6 weeks was evaluated in mice from a germ-free environment to understand the contribution of microbes to disease development. Results Development- and disease-specific shifts in gene expression related to Scnn1b over-expression were revealed in longitudinal analyses. While the total number of transgene-related differentially expressed genes producing robust signals was relatively small in whole lung (n = 84), Gene Set Enrichment Analysis (GSEA) revealed significantly perturbed biological pathways and interactions between normal lung development and disease initiation/progression. Purified lung macrophages from Scnn1b-Tg mice exhibited numerous robust and dynamic gene expression changes. The expression levels of Classically-activated (M1) macrophage signatures were significantly altered at post-natal day (PND) 3 when Scnn1b-Tg mice lung exhibit spontaneous bacterial infections, while alternatively-activated (M2) macrophage signatures were more prominent by PND 42, producing a mixed M1-M2 activation profile. While differentially-regulated, inflammation-related genes were consistently identified in both tissues in Scnn1b-Tg mice, there was little overlap between tissues or across time, highlighting time- and tissue-specific responses. Macrophages purified from adult germ-free Scnn1b-Tg mice exhibited signatures remarkably similar to non-germ-free counterparts, indicating that the late-phase macrophage activation profile was not microbe-dependent. Conclusions Whole lung and pulmonary macrophages respond independently and dynamically to local stresses associated with airway mucus stasis. Disease-specific responses interact with normal developmental processes, influencing the final state of disease in this model. The robust signatures observed in Scnn1b-Tg lung macrophages highlight their critical role in disease pathogenesis. These studies emphasize the importance of region-, cell-type-, and time-dependent analyses to fully dissect the natural history of disease and the consequences of disease on normal lung development. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-726) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yogesh Saini
- Marsico Lung Institute/University of North Carolina Cystic Fibrosis Center, School of Medicine, University of North Carolina at Chapel Hill, 7011 Thurston Bowles Building, Chapel Hill, NC 27599-7248, USA.
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Takebayashi H, Yamamoto N, Umino A, Nishikawa T. Identification of developmentally regulated PCP-responsive non-coding RNA, prt6, in the rat thalamus. PLoS One 2014; 9:e97955. [PMID: 24886782 PMCID: PMC4041572 DOI: 10.1371/journal.pone.0097955] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 04/26/2014] [Indexed: 12/19/2022] Open
Abstract
Schizophrenia and similar psychoses induced by NMDA-type glutamate receptor antagonists, such as phencyclidine (PCP) and ketamine, usually develop after adolescence. Moreover, adult-type behavioral disturbance following NMDA receptor antagonist application in rodents is observed after a critical period at around 3 postnatal weeks. These observations suggest that the schizophrenic symptoms caused by and psychotomimetic effects of NMDA antagonists require the maturation of certain brain neuron circuits and molecular networks, which differentially respond to NMDA receptor antagonists across adolescence and the critical period. From this viewpoint, we have identified a novel developmentally regulated phencyclidine-responsive transcript from the rat thalamus, designated as prt6, as a candidate molecule involved in the above schizophrenia-related systems using a DNA microarray technique. The transcript is a non-coding RNA that includes sequences of at least two microRNAs, miR132 and miR212, and is expressed strongly in the brain and testis, with trace or non-detectable levels in the spleen, heart, liver, kidney, lung and skeletal muscle, as revealed by Northern blot analysis. The systemic administration of PCP (7.5 mg/kg, subcutaneously (s.c.)) significantly elevated the expression of prt6 mRNA in the thalamus at postnatal days (PD) 32 and 50, but not at PD 8, 13, 20, or 24 as compared to saline-treated controls. At PD 50, another NMDA receptor antagonist, dizocilpine (0.5 mg/kg, s.c.), and a schizophrenomimetic dopamine agonist, methamphetamine (4.8 mg/kg, s.c.), mimicked a significant increase in the levels of thalamic prt6 mRNAs, while a D2 dopmamine receptor antagonist, haloperidol, partly inhibited the increasing influence of PCP on thalamic prt6 expression without its own effects. These data indicate that prt6 may be involved in the pathophysiology of the onset of drug-induced schizophrenia-like symptoms and schizophrenia through the possible dysregulation of target genes of the long non-coding RNA or microRNAs in the transcript.
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Affiliation(s)
- Hironao Takebayashi
- Department of Psychiatry and Behavioral Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Naoki Yamamoto
- Department of Psychiatry and Behavioral Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Asami Umino
- Department of Psychiatry and Behavioral Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Toru Nishikawa
- Department of Psychiatry and Behavioral Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
- * E-mail:
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Li K, Wu D, Chen X, Zhang T, Zhang L, Yi Y, Miao Z, Jin N, Bi X, Wang H, Xu J, Wang D. Current and emerging biomarkers of cell death in human disease. BIOMED RESEARCH INTERNATIONAL 2014; 2014:690103. [PMID: 24949464 PMCID: PMC4052120 DOI: 10.1155/2014/690103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/17/2014] [Indexed: 01/18/2023]
Abstract
Cell death is a critical biological process, serving many important functions within multicellular organisms. Aberrations in cell death can contribute to the pathology of human diseases. Significant progress made in the research area enormously speeds up our understanding of the biochemical and molecular mechanisms of cell death. According to the distinct morphological and biochemical characteristics, cell death can be triggered by extrinsic or intrinsic apoptosis, regulated necrosis, autophagic cell death, and mitotic catastrophe. Nevertheless, the realization that all of these efforts seek to pursue an effective treatment and cure for the disease has spurred a significant interest in the development of promising biomarkers of cell death to early diagnose disease and accurately predict disease progression and outcome. In this review, we summarize recent knowledge about cell death, survey current and emerging biomarkers of cell death, and discuss the relationship with human diseases.
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Affiliation(s)
- Kongning Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Deng Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xi Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ting Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ying Yi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Zhengqiang Miao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Nana Jin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiaoman Bi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hongwei Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jianzhen Xu
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
| | - Dong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Pang Q, Ge J, Shao Y, Sun W, Song H, Xia T, Xiao B, Guo J. Increased expression of long intergenic non-coding RNA LINC00152 in gastric cancer and its clinical significance. Tumour Biol 2014; 35:5441-7. [PMID: 24523021 DOI: 10.1007/s13277-014-1709-3] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 01/29/2014] [Indexed: 12/12/2022] Open
Abstract
It has been known that differential expression of long non-coding RNA (lncRNA) plays critical roles in carcinogenesis. However, the significance of lncRNA, especially long intergenic ncRNA (lincRNA, the main type of lncRNA family), in the diagnosis of gastric cancer is largely unknown. The aim of this study was to determine the expression level of LINC00152, a newfound lincRNA, in gastric carcinoma and its clinical association. The expression of LINC00152 in 71 pairs of tumorous and adjacent normal tissues from patients with gastric cancer was detected by quantitative real-time reverse transcription-polymerase chain reaction. And then, the potential associations between its level in gastric cancer tissue and the clinicopathological features were analyzed. Finally, a receiver operating characteristic (ROC) curve was constructed for differentiating patients with gastric cancer from patients with benign gastric diseases. The results showed that the expression level of LINC00152 in gastric carcinoma was significantly increased, compared with matched normal tissue (P=0.045) and normal mucosa from health control (P=0.004), respectively. Levels of LINC00152 in gastric cancer cell lines, BGC-823, MGC-803, and SGC-7901, were significantly higher than those in human normal gastric epithelial cell line GES-1. In addition, high expression of LINC00152 was correlated with invasion (P=0.042). LINC00152 levels in gastric juice from patients with gastric cancer were further found significantly higher than those from normal controls (P=0.002). Moreover, the area under the ROC curve (AUC) was up to 0.645 (95 % CI=0.559-0.740, P=0.003). This study highlights that lincRNA LINC00152 might be a novel biomarker for predicting gastric cancer.
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Affiliation(s)
- Qianqian Pang
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, 818 Fenghua Road, Ningbo, 315211, China
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