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Aljabali AAA, Alkaraki AK, Gammoh O, Tambuwala MM, Mishra V, Mishra Y, Hassan SS, El-Tanani M. Deciphering Depression: Epigenetic Mechanisms and Treatment Strategies. BIOLOGY 2024; 13:638. [PMID: 39194576 DOI: 10.3390/biology13080638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
Depression, a significant mental health disorder, is under intense research scrutiny to uncover its molecular foundations. Epigenetics, which focuses on controlling gene expression without altering DNA sequences, offers promising avenues for innovative treatment. This review explores the pivotal role of epigenetics in depression, emphasizing two key aspects: (I) identifying epigenetic targets for new antidepressants and (II) using personalized medicine based on distinct epigenetic profiles, highlighting potential epigenetic focal points such as DNA methylation, histone structure alterations, and non-coding RNA molecules such as miRNAs. Variations in DNA methylation in individuals with depression provide opportunities to target genes that are associated with neuroplasticity and synaptic activity. Aberrant histone acetylation may indicate that antidepressant strategies involve enzyme modifications. Modulating miRNA levels can reshape depression-linked gene expression. The second section discusses personalized medicine based on epigenetic profiles. Analyzing these patterns could identify biomarkers associated with treatment response and susceptibility to depression, facilitating tailored treatments and proactive mental health care. Addressing ethical concerns regarding epigenetic information, such as privacy and stigmatization, is crucial in understanding the biological basis of depression. Therefore, researchers must consider these issues when examining the role of epigenetics in mental health disorders. The importance of epigenetics in depression is a critical aspect of modern medical research. These findings hold great potential for novel antidepressant medications and personalized treatments, which would significantly improve patient outcomes, and transform psychiatry. As research progresses, it is expected to uncover more complex aspects of epigenetic processes associated with depression, enhance our comprehension, and increase the effectiveness of therapies.
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Affiliation(s)
- Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid 21163, Jordan
| | - Almuthanna K Alkaraki
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid 21163, Jordan
| | - Omar Gammoh
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Yarmouk University, P.O. Box 566, Irbid 21163, Jordan
| | - Murtaza M Tambuwala
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah P.O. Box 11172, United Arab Emirates
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Yachana Mishra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India
| | - Mohamed El-Tanani
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah P.O. Box 11172, United Arab Emirates
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Gao J, Yu H, Pan Y, Wang X, Zhang H, Xu Y, Ma W, Zhang W, Fu L, Wang Y. Porcine cis-acting lnc-CAST positively regulates CXCL8 expression through histone H3K27ac. Vet Res 2024; 55:56. [PMID: 38715098 PMCID: PMC11077775 DOI: 10.1186/s13567-024-01296-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/26/2024] [Indexed: 05/12/2024] Open
Abstract
The chemokine CXCL8, also known as the neutrophil chemotactic factor, plays a crucial role in mediating inflammatory responses and managing cellular immune reactions during viral infections. Porcine reproductive and respiratory syndrome virus (PRRSV) primarily infects pulmonary alveolar macrophages (PAMs), leading to acute pulmonary infections. In this study, we explored a novel long non-coding RNA (lncRNA), termed lnc-CAST, situated within the Cxcl8 gene locus. This lncRNA was found to be highly expressed in porcine macrophages. We observed that both lnc-CAST and CXCL8 were significantly upregulated in PAMs following PRRSV infection, and after treatments with lipopolysaccharide (LPS) or lipoteichoic acid (LTA). Furthermore, we noticed a concurrent upregulation of lnc-CAST and CXCL8 expression in lungs of PRRSV-infected pigs. We then determined that lnc-CAST positively influenced CXCL8 expression in PAMs. Overexpression of lnc-CAST led to an increase in CXCL8 production, which in turn enhanced the migration of epithelial cells and the recruitment of neutrophils. Conversely, inhibiting lnc-CAST expression resulted in reduced CXCL8 production in PAMs, leading to decreased migration levels of epithelial cells and neutrophils. From a mechanistic perspective, we found that lnc-CAST, localized in the nucleus, facilitated the enrichment of histone H3K27ac in CXCL8 promoter region, thereby stimulating CXCL8 transcription in a cis-regulatory manner. In conclusion, our study underscores the pivotal critical role of lnc-CAST in regulating CXCL8 production, offering valuable insights into chemokine regulation and lung damage during PRRSV infection.
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Affiliation(s)
- Junxin Gao
- College of Veterinary Medicine, Southwest University, Chongqing, 400715, China
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Haidong Yu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Yu Pan
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xinrong Wang
- College of Veterinary Medicine, Southwest University, Chongqing, 400715, China
| | - He Zhang
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Yunfei Xu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
- Chongqing Academy of Animal Science, Chongqing, 408599, China
| | - Wenjie Ma
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Wenli Zhang
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Lizhi Fu
- Chongqing Academy of Animal Science, Chongqing, 408599, China.
- National Center of Technology Innovation for Pigs, Chongqing, 402460, China.
| | - Yue Wang
- College of Veterinary Medicine, Southwest University, Chongqing, 400715, China.
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
- National Center of Technology Innovation for Pigs, Chongqing, 402460, China.
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Xiao L, Zhang Y, Luo Q, Guo C, Chen Z, Lai C. DHRS4-AS1 regulate gastric cancer apoptosis and cell proliferation by destabilizing DHX9 and inhibited the association between DHX9 and ILF3. Cancer Cell Int 2023; 23:304. [PMID: 38041141 PMCID: PMC10693172 DOI: 10.1186/s12935-023-03151-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/18/2023] [Indexed: 12/03/2023] Open
Abstract
Gastric cancer (GC) causes millions of cancer-related deaths due to anti-apoptosis and rapid proliferation. However, the molecular mechanisms underlying GC cell proliferation and anti-apoptosis remain unclear. The expression levels of DHRS4-AS1 in GC were analyzed based on GEO database and recruited GC patients in our institution. We found that DHRS4-AS1 was significantly downregulated in GC. The expression of DHRS4-AS1 in GC tissues showed a significant correlation with tumor size, advanced pathological stage, and vascular invasion. Moreover, DHRS4-AS1 levels in GC tissues were significantly associated with prognosis. DHRS4-AS1 markedly inhibited GC cell proliferation and promotes apoptosis in vitro and in vivo assays. Mechanically, We found that DHRS4-AS1 bound to pro-oncogenic DHX9 (DExH-box helicase 9) and recruit the E3 ligase MDM2 that contributed to DHX9 degradation. We also confirmed that DHRS4-AS1 inhibited DHX9-mediated cell proliferation and promotes apoptosis. Furthermore, we found DHX9 interact with ILF3 (Interleukin enhancer Binding Factor 3) and activate NF-kB Signaling in a ILF3-dependent Manner. Moreover, DHRS4-AS1 can also inhibit the association between DHX9 and ILF3 thereby interfered the activation of the signaling pathway. Our results reveal new insights into mechanisms underlying GC progression and indicate that LncRNA DHRS4-AS1 could be a future therapeutic target and a biomarker for GC diagnosis.
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Affiliation(s)
- Lei Xiao
- Department of General Surgery, Xiangya Hospital of Central South University, Xiangya Road No. 87, Kaifu District, Changsha, 410000, Hunan Province, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumors, Xiangya Hospital of Central South University, Changsha, 410000, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yang Zhang
- Department of General Surgery, Xiangya Hospital of Central South University, Xiangya Road No. 87, Kaifu District, Changsha, 410000, Hunan Province, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumors, Xiangya Hospital of Central South University, Changsha, 410000, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qingqing Luo
- Department of Oncology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000, Hunan Province, China
| | - Cao Guo
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zihua Chen
- Department of General Surgery, Xiangya Hospital of Central South University, Xiangya Road No. 87, Kaifu District, Changsha, 410000, Hunan Province, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumors, Xiangya Hospital of Central South University, Changsha, 410000, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Chen Lai
- Department of General Surgery, Xiangya Hospital of Central South University, Xiangya Road No. 87, Kaifu District, Changsha, 410000, Hunan Province, China.
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumors, Xiangya Hospital of Central South University, Changsha, 410000, Hunan Province, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Gong HY, Zhou PC, Zhang HY, Chen LM, Zhou YM, Liu ZG. Transcriptional regulation of Glis2 in hepatic fibrosis. Exp Mol Med 2023:10.1038/s12276-023-01031-y. [PMID: 37394585 PMCID: PMC10393978 DOI: 10.1038/s12276-023-01031-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/21/2023] [Accepted: 04/12/2023] [Indexed: 07/04/2023] Open
Abstract
The role of Gli-similar 2 (Glis2) in hepatic fibrosis (HF) is controversial. In this study, we focused on the functional and molecular mechanisms involved in the Glis2-mediated activation of hepatic stellate cells (HSCs)-a milestone event leading to HF. The expression levels of Glis2 mRNA and protein were significantly decreased in the liver tissues of patients with severe HF and in mouse fibrotic liver tissues as well as HSCs activated by TGFβ1. Functional studies indicated that upregulated Glis2 significantly inhibited HSC activation and alleviated BDL-induced HF in mice. Downregulation of Glis2 was found to correlate significantly with DNA methylation of the Glis2 promoter mediated by methyltransferase 1 (DNMT1), which restricted the binding of hepatic nuclear factor 1-α (HNF1-α), a liver-specific transcription factor, to Glis2 promoters. In addition, the enrichment of DNMT1 in the Glis2 promoter region was mediated by metastasis-associated lung adenocarcinoma transcriptor-1 (MALAT1) lncRNA, leading to transcriptional silencing of Glis2 and activation of HSCs. In conclusion, our findings reveal that the upregulation of Glis2 can maintain the resting state of HSCs. The decreased expression of Glis2 under pathological conditions may lead to the occurrence and development of HF with the expression silencing of DNA methylation mediated by MALAT1 and DNMT1.
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Affiliation(s)
- Huan-Yu Gong
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
| | - Peng-Cheng Zhou
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China
| | - Hao-Ye Zhang
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
| | - Li-Min Chen
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
| | - Yang-Mei Zhou
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
| | - Zhen-Guo Liu
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China.
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China.
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Lin Z, Liu Y, Xu T, Su T, Yang Y, Liang R, Gu S, Li J, Song X, Liang B, Leng Z, Li Y, Meng L, Luo Y, Chang X, Huang D, Xie L. STAT3-Mediated Promoter-Enhancer Interaction Up-Regulates Inhibitor of DNA Binding 1 ( ID1) to Promote Colon Cancer Progression. Int J Mol Sci 2023; 24:10041. [PMID: 37373188 DOI: 10.3390/ijms241210041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/10/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND High expression of inhibitor of DNA binding 1 (ID1) correlates with poor prognosis in colorectal cancer (CRC). Aberrant enhancer activation in regulating ID1 transcription is limited. METHODS Immunohistochemistry (IHC), quantitative RT-PCR (RT-qPCR) and Western blotting (WB) were used to determine the expression of ID1. CRISPR-Cas9 was used to generate ID1 or enhancer E1 knockout cell lines. Dual-luciferase reporter assay, chromosome conformation capture assay and ChIP-qPCR were used to determine the active enhancers of ID1. Cell Counting Kit 8, colony-forming, transwell assays and tumorigenicity in nude mice were used to investigate the biological functions of ID1 and enhancer E1. RESULTS Human CRC tissues and cell lines expressed a higher level of ID1 than normal controls. ID1 promoted CRC cell proliferation and colony formation. Enhancer E1 actively regulated ID1 promoter activity. Signal transducer and activator of transcription 3 (STAT3) bound to ID1 promoter and enhancer E1 to regulate their activity. The inhibitor of STAT3 Stattic attenuated ID1 promoter and enhancer E1 activity and the expression of ID1. Enhancer E1 knockout down-regulated ID1 expression level and cell proliferation in vitro and in vivo. CONCLUSIONS Enhancer E1 is positively regulated by STAT3 and contributes to the regulation of ID1 to promote CRC cell progression and might be a potential target for anti-CRC drug studies.
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Affiliation(s)
- Zhike Lin
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Ying Liu
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Tian Xu
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Ting Su
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Yingying Yang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Runhua Liang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Songgang Gu
- Department of Hepatobiliary Surgery, Cancer Hospital of Shantou University Medical College, Shantou 515041, China
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Jie Li
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Xuhong Song
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Bin Liang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Zhijun Leng
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Yangsihan Li
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Lele Meng
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Yijing Luo
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Xiaolan Chang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Dongyang Huang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
- Department of Central Laboratory, Cancer Hospital of Shantou University Medical College, Shantou 515041, China
| | - Lingzhu Xie
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
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Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, He Y. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022; 9:1067406. [PMID: 36533073 PMCID: PMC9755597 DOI: 10.3389/fmolb.2022.1067406] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Li
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yungang He
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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7
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Navigating the Multiverse of Antisense RNAs: The Transcription- and RNA-Dependent Dimension. Noncoding RNA 2022; 8:ncrna8060074. [PMID: 36412909 PMCID: PMC9680235 DOI: 10.3390/ncrna8060074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022] Open
Abstract
Evidence accumulated over the past decades shows that the number of identified antisense transcripts is continuously increasing, promoting them from transcriptional noise to real genes with specific functions. Indeed, recent studies have begun to unravel the complexity of the antisense RNA (asRNA) world, starting from the multidimensional mechanisms that they can exert in physiological and pathological conditions. In this review, we discuss the multiverse of the molecular functions of asRNAs, describing their action through transcription-dependent and RNA-dependent mechanisms. Then, we report the workflow and methodologies to study and functionally characterize single asRNA candidates.
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8
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Wang M, Wang Y, Yao W, Du X, Li Q. Lnc2300 is a cis-acting long noncoding RNA of CYP11A1 in ovarian granulosa cells. J Cell Physiol 2022; 237:4238-4250. [PMID: 36074900 DOI: 10.1002/jcp.30872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022]
Abstract
The high level of progesterone and 17β-estradiol ratio (P4/E2) in follicular fluid has been considered as a biomarker of follicular atresia. CYP11A1, the crucial gene encoding the rate-limiting enzyme for steroid hormone synthesis, has been reported differently expressed in the ovary during follicular atresia. However, the regulation mechanism of CYP11A1 expression during follicular atresia still remains unclear. Here, we have demonstrated that lnc2300, a novel pig ovary-specific highly expressed cis-acting long noncoding RNA (lncRNA) transcribed from chromosome 7, has the ability to induce the expression of CYP11A1 and inhibit the apoptosis of porcine granulosa cells (GCs). Mechanistically, lnc2300, mainly located in the cytoplasm of porcine GCs, sponges and suppresses the expression of miR-365-3p through acting as a competing endogenous RNA (ceRNA), which further relieves the inhibitory effects of miR-365-3p on the expression of CYP11A1. Besides, CYP11A1 is validated as a direct functional target of miR-365-3p in porcine GCs. Functionally, lnc2300 is an antiapoptotic lncRNA that reduces porcine GC apoptosis by inhibiting the proapoptotic function of miR-365-3p. In summary, our findings reveal a cis-acting regulation mechanism of CYP11A1 through lncRNA, and define a novel signaling pathway, lnc2300/miR-365-3p/CYP11A1 axis, which is involved in the regulation of GC apoptosis and follicular atresia.
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Affiliation(s)
- Miaomiao Wang
- Laboratory of Statistical Genetics and Epigenome, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yang Wang
- Laboratory of Statistical Genetics and Epigenome, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wang Yao
- Laboratory of Statistical Genetics and Epigenome, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xing Du
- Laboratory of Statistical Genetics and Epigenome, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qifa Li
- Laboratory of Statistical Genetics and Epigenome, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Yang K, Liang X, Wen K. Long non‑coding RNAs interact with RNA‑binding proteins to regulate genomic instability in cancer cells (Review). Oncol Rep 2022; 48:175. [PMID: 36004472 PMCID: PMC9478986 DOI: 10.3892/or.2022.8390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 11/05/2022] Open
Abstract
Genomic instability, a feature of most cancers, contributes to malignant cell transformation and cancer progression due to the accumulation of genetic alterations. Genomic instability is reflected at numerous levels, from single nucleotide to the chromosome levels. However, the exact molecular mechanisms and regulators of genomic instability in cancer remain unclear. Growing evidence indicates that the binding of long non-coding RNAs (lncRNAs) to protein chaperones confers a variety of regulatory functions, including managing of genomic instability. The aim of the present review was to examine the roles of mitosis, telomeres, DNA repair, and epigenetics in genomic instability, and the mechanisms by which lncRNAs regulate them by binding proteins in cancer cells. This review contributes to our understanding of the role of lncRNAs and genomic instability in cancer and can potentially provide entry points and molecular targets for cancer therapies.
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Affiliation(s)
- Kai Yang
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Xiaoxiang Liang
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Kunming Wen
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
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10
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Lee S, Fu F, Liao CJ, Mewa DB, Adeyanju A, Ejeta G, Lisch D, Mengiste T. Broad-spectrum fungal resistance in sorghum is conferred through the complex regulation of an immune receptor gene embedded in a natural antisense transcript. THE PLANT CELL 2022; 34:1641-1665. [PMID: 35018449 PMCID: PMC9048912 DOI: 10.1093/plcell/koab305] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/09/2021] [Indexed: 06/12/2023]
Abstract
Sorghum (Sorghum bicolor), the fifth most widely grown cereal crop globally, provides food security for millions of people. Anthracnose caused by the fungus Colletotrichum sublineola is a major disease of sorghum worldwide. We discovered a major fungal resistance locus in sorghum composed of the nucleotide-binding leucine-rich repeat receptor gene ANTHRACNOSE RESISTANCE GENE1 (ARG1) that is completely nested in an intron of a cis-natural antisense transcript (NAT) gene designated CARRIER OF ARG1 (CARG). Susceptible genotypes express CARG and two alternatively spliced ARG1 transcripts encoding truncated proteins lacking the leucine-rich repeat domains. In resistant genotypes, elevated expression of an intact allele of ARG1, attributed to the loss of CARG transcription and the presence of miniature inverted-repeat transposable element sequences, resulted in broad-spectrum resistance to fungal pathogens with distinct virulence strategies. Increased ARG1 expression in resistant genotypes is also associated with higher histone H3K4 and H3K36 methylation. In susceptible genotypes, lower ARG1 expression is associated with reduced H3K4 and H3K36 methylation and increased expression of NATs of CARG. The repressive chromatin state associated with H3K9me2 is low in CARG-expressing genotypes within the CARG exon and higher in genotypes with low CARG expression. Thus, ARG1 is regulated by multiple mechanisms and confers broad-spectrum, strong resistance to fungal pathogens.
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Affiliation(s)
| | | | - Chao-Jan Liao
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Demeke B Mewa
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Adedayo Adeyanju
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
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11
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Chen Y, Long W, Yang L, Zhao Y, Wu X, Li M, Du F, Chen Y, Yang Z, Wen Q, Yi T, Xiao Z, Shen J. Functional Peptides Encoded by Long Non-Coding RNAs in Gastrointestinal Cancer. Front Oncol 2021; 11:777374. [PMID: 34888249 PMCID: PMC8649637 DOI: 10.3389/fonc.2021.777374] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Gastrointestinal cancer is by far the most common malignancy and the most common cause of cancer-related deaths worldwide. Recent studies have shown that long non-coding RNAs (lncRNAs) play an important role in the epigenetic regulation of cancer cells and regulate tumor progression by affecting chromatin modifications, gene transcription, translation, and sponge to miRNAs. In particular, lncRNA has recently been found to possess open reading frame (ORF), which can encode functional small peptides or proteins. These peptides interact with its targets to regulate transcription or the signal axis, thus promoting or inhibiting the occurrence and development of tumors. In this review, we summarize the involvement of lncRNAs and the function of lncRNAs encoded small peptides in gastrointestinal cancer.
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Affiliation(s)
- Yao Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Weili Long
- School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Liqiong Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Zhihui Yang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Tao Yi
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong SAR, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
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12
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Xie W, Sun H, Li X, Lin F, Wang Z, Wang X. Ovarian cancer: epigenetics, drug resistance, and progression. Cancer Cell Int 2021; 21:434. [PMID: 34404407 PMCID: PMC8369623 DOI: 10.1186/s12935-021-02136-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/03/2021] [Indexed: 03/05/2023] Open
Abstract
Ovarian cancer (OC) is one of the most common malignant tumors in women. OC is associated with the activation of oncogenes, the inactivation of tumor suppressor genes, and the activation of abnormal cell signaling pathways. Moreover, epigenetic processes have been found to play an important role in OC tumorigenesis. Epigenetic processes do not change DNA sequences but regulate gene expression through DNA methylation, histone modification, and non-coding RNA. This review comprehensively considers the importance of epigenetics in OC, with a focus on microRNA and long non-coding RNA. These types of RNA are promising molecular markers and therapeutic targets that may support precision medicine in OC. DNA methylation inhibitors and histone deacetylase inhibitors may be useful for such targeting, with a possible novel approach combining these two therapies. Currently, the clinical application of such epigenetic approaches is limited by multiple obstacles, including the heterogeneity of OC, insufficient sample sizes in reported studies, and non-optimized methods for detecting potential tumor markers. Nonetheless, the application of epigenetic approaches to OC patient diagnosis, treatment, and prognosis is a promising area for future clinical investigation.
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Affiliation(s)
- Weiwei Xie
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China
| | - Huizhen Sun
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China
| | - Xiaoduan Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feikai Lin
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China
| | - Ziliang Wang
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China.
| | - Xipeng Wang
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China.
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13
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Ni J, Hong J, Li Q, Zeng Q, Xia R. Long non-coding RNA CRNDE suppressing cell proliferation is regulated by DNA methylation in chronic lymphocytic leukemia. Leuk Res 2021; 105:106564. [PMID: 33857783 DOI: 10.1016/j.leukres.2021.106564] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/03/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022]
Abstract
Long non-coding RNA CRNDE and DNA methylation play a vital role in the occurrence and development of chronic lymphocytic leukemia (CLL). This study attempted to investigate the biological role of CRNDE methylation in CLL. The expression and methylation levels of CRNDE in CLL cell lines (MEC-1 and HG3) before or after methylation inhibitor (5-Aza-2'-deoxycytidine, 5-Aza-CdR) treatment was detected by quantitative real-time PCR or methylation-Specific PCR. The relationship among CRNDE, miR-28 and NDRG2 was verified by luciferase reporter assay. The effect of CRNDE overexpression and 5-Aza-CdR treatment on cell proliferation and apoptosis of MEC-1 and HG3 cells were assessed by CCK8 and flow cytomery. Compared with normal B lymphocytes, CRNDE was down-regulated and the methylation level of CRNDE was increased in MEC-1 and HG3 cells. Then, 5-Aza-CdR treatment caused an increase of CRNDE expression in MEC-1 and HG3 cells by demethylation. The overexpression or demethylation of CRNDE inhibited cell proliferation and promoted apoptosis in MEC-1 and HG3 cells by up-regulating CRNDE expression. Moreover, CRNDE functioned as a competing endogenous RNA to repress miR-28, which controlled its down-stream target NDRG2. CRNDE overexpression inhibited cell proliferation and promoted apoptosis via miR-28/NDRG2 axis in CLL. In conclusion, our data elaborated that CRNDE expression was regulated by DNA methylation, and the protective effect of CRNDE on CLL was attributed to the inhibition of proliferation in CLL via miR-28/NDRG2 axis. Thus, this work highlights a novel competing endogenous RNA circuitry involving key regulators of CLL.
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Affiliation(s)
- Jing Ni
- Department of Hematology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China
| | - Jian Hong
- Department of Hematology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China
| | - Qingsheng Li
- Department of Hematology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China
| | - Qingshu Zeng
- Department of Hematology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China
| | - Ruixiang Xia
- Department of Hematology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China.
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14
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Caglayan S, Hashim A, Cieslar-Pobuda A, Jensen V, Behringer S, Talug B, Chu DT, Pecquet C, Rogne M, Brech A, Brorson SH, Nagelhus EA, Hannibal L, Boschi A, Taskén K, Staerk J. Optic Atrophy 1 Controls Human Neuronal Development by Preventing Aberrant Nuclear DNA Methylation. iScience 2020; 23:101154. [PMID: 32450518 PMCID: PMC7251951 DOI: 10.1016/j.isci.2020.101154] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/03/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Optic atrophy 1 (OPA1), a GTPase at the inner mitochondrial membrane involved in regulating mitochondrial fusion, stability, and energy output, is known to be crucial for neural development: Opa1 heterozygous mice show abnormal brain development, and inactivating mutations in OPA1 are linked to human neurological disorders. Here, we used genetically modified human embryonic and patient-derived induced pluripotent stem cells and reveal that OPA1 haploinsufficiency leads to aberrant nuclear DNA methylation and significantly alters the transcriptional circuitry in neural progenitor cells (NPCs). For instance, expression of the forkhead box G1 transcription factor, which is needed for GABAergic neuronal development, is repressed in OPA1+/− NPCs. Supporting this finding, OPA1+/− NPCs cannot give rise to GABAergic interneurons, whereas formation of glutamatergic neurons is not affected. Taken together, our data reveal that OPA1 controls nuclear DNA methylation and expression of key transcription factors needed for proper neural cell specification. OPA1 haploinsufficiency impairs formation of DLX1/2-positive GABAergic neurons Reduced OPA1 levels significantly alter the transcriptional circuitry in neural cells Expression of the pioneer factor FOXG1 is decreased in OPA1+/− neural progenitor cells Impaired FOXG1 expression correlates with increased CpG methylation at its promoter
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Affiliation(s)
- Safak Caglayan
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Adnan Hashim
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Artur Cieslar-Pobuda
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Vidar Jensen
- GliaLab and Letten Centre, Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Sidney Behringer
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center, University of Freiburg, Mathildenstraße 1, 79106 Freiburg, Germany
| | - Burcu Talug
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Dinh Toi Chu
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Christian Pecquet
- Ludwig Institute for Cancer Research Brussels, 1200 Brussels, Belgium; Université Catholique de Louvain and de Duve Institute, 1200 Brussels, Belgium
| | - Marie Rogne
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Andreas Brech
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
| | | | - Erlend Arnulf Nagelhus
- GliaLab and Letten Centre, Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center, University of Freiburg, Mathildenstraße 1, 79106 Freiburg, Germany
| | - Antonella Boschi
- Department of Ophthalmology, Cliniques Universitaires Saint-Luc, UCL, 1200 Brussels, Belgium
| | - Kjetil Taskén
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway; Department for Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Judith Staerk
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway; Department of Haematology, Oslo University Hospital, 0424 Oslo, Norway.
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15
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Shang R, Wang M, Dai B, Du J, Wang J, Liu Z, Qu S, Yang X, Liu J, Xia C, Wang L, Wang D, Li Y. Long noncoding RNA SLC2A1-AS1 regulates aerobic glycolysis and progression in hepatocellular carcinoma via inhibiting the STAT3/FOXM1/GLUT1 pathway. Mol Oncol 2020; 14:1381-1396. [PMID: 32174012 PMCID: PMC7266282 DOI: 10.1002/1878-0261.12666] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/02/2020] [Accepted: 03/12/2020] [Indexed: 12/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal malignant diseases worldwide. Despite advances in the diagnosis and treatment of HCC, its overall prognosis remains poor. Recent studies have shown that long noncoding RNAs (lncRNAs) play crucial roles in various pathophysiological processes, including liver cancer. In the current study, we report that lncRNA SLC2A1-AS1 is frequently downregulated in HCC samples, as shown by quantitative real-time polymerase chain reaction analysis. SLC2A1-AS1 deletion is significantly associated with recurrence-free survival in HCC. By performing glucose uptake, lactate production and ATP detection assays, we found that SLC2A1-AS1-mediated glucose transporter 1 (GLUT1) downregulation significantly suppressed glycolysis of HCC. In vitro Cell Counting Kit-8, colony formation, transwell assays as well as in vivo tumorigenesis and metastasis assays showed that SLC2A1-AS1 overexpression significantly suppressed proliferation and metastasis in HCC through the transcriptional inhibition of GLUT1. Results from fluorescence in situ hybridization, ChIP and luciferase reporter assays demonstrated that SLC2A1-AS1 exerts its regulatory role on GLUT1 by competitively binding to transketolase and signal transducer and activator of transcription 3 (STAT3) and inhibits the transactivation of Forkhead box M1 (FOXM1) via STAT3, thus resulting in inactivation of the FOXM1/GLUT1 axis in HCC cells. Our findings will be helpful for understanding the function and mechanism of lncRNA in HCC. These data also highlight the crucial role of SLC2A1-AS1 in HCC aerobic glycolysis and progression and pave the way for further research regarding the potential of SLC2A1-AS1 as a valuable predictive biomarker for HCC recurrence.
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Affiliation(s)
- Runze Shang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Miao Wang
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Bin Dai
- Department of General Surgery, General Hospital of the Central Theater Command of the People's Liberation Army, Wuhan, China
| | - Jianbing Du
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Jianlin Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Zekun Liu
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Shibin Qu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Xisheng Yang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Jingjing Liu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Congcong Xia
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Lin Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Desheng Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Yu Li
- School of Life Science, Northwestern Polytechnical University, Xi'an, China
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16
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DNA methylation landscape of triple-negative ductal carcinoma in situ (DCIS) progressing to the invasive stage in canine breast cancer. Sci Rep 2020; 10:2415. [PMID: 32051475 PMCID: PMC7015930 DOI: 10.1038/s41598-020-59260-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/16/2020] [Indexed: 11/09/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a subtype of breast cancer unresponsive to traditional receptor-targeted treatments, leading to a disproportionate number of deaths. Invasive breast cancer is believed to evolve from non-invasive ductal carcinoma in situ (DCIS). Detection of triple-negative DCIS (TN-DCIS) is challenging, therefore strategies to study molecular events governing progression of pre-invasive TN-DCIS to invasive TNBC are needed. Here, we study a canine TN-DCIS progression and investigate the DNA methylation landscape of normal breast tissue, atypical ductal hyperplasia (ADH), DCIS and invasive breast cancer. We report hypo- and hypermethylation of genes within functional categories related to cancer such as transcriptional regulation, apoptosis, signal transduction, and cell migration. DNA methylation changes associated with cancer-related genes become more pronounced at invasive breast cancer stage. Importantly, we identify invasive-only and DCIS-specific DNA methylation alterations that could potentially determine which lesions progress to invasive cancer and which could remain as pre-invasive DCIS. Changes in DNA methylation during TN-DCIS progression in this canine model correspond with gene expression patterns in human breast tissues. This study provides evidence for utilizing methylation status of gene candidates to define late-stage (DCIS and invasive), invasive stage only or DCIS stage only of TN-DCIS progression.
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17
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Liu B, Zhao H, Zhang L, Shi X. Silencing of long-non-coding RNA ANCR suppresses the migration and invasion of osteosarcoma cells by activating the p38MAPK signalling pathway. BMC Cancer 2019; 19:1112. [PMID: 31727012 PMCID: PMC6857278 DOI: 10.1186/s12885-019-6335-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 11/05/2019] [Indexed: 12/25/2022] Open
Abstract
Background Osteosarcoma (OS) is a malignancy of the bone that has no clearly identified prognostic factors for diagnosis. In this study, we evaluated the regulatory role of long non-coding RNA (lncRNA) ANCR on the migration and invasion of OS cells as well as the possible mechanism involving the p38MAPK signalling pathway. Methods ANCR expression was determined in OS tissues and OS cell lines (MG-63, S1353, U2OS, and UMR-106) by qRT-PCR. It was observed that ANCR was down-regulated in MG-63 and U2OS cells by 48 h of siRNA-ANCR (si-ANCR) transfection. The proliferation of transfected cells was determined using the CCK-8 and the EdU assays. The migration and invasion of transfected cells were determined by the Transwell assay. The expression of E-cadherin, N-cadherin, and phosphorylated p38MAPK (p-p38MAPK) proteins was determined by Western blot. In addition, combinatorial treatment of cells with si-ANCR + SB203580 (p38MAPK inhibitor) was performed to investigate the association between ANCR and MAPK signalling in OS cells. Results ANCR was up-regulated in OS cells and tissues. ANCR silencing significantly inhibited the proliferation rate, decreased the percentage of migration and invasion cells, down-regulated N-cadherin, and up-regulated E-cadherin and p-p38MAPK in MG-63 and U2OS cells. Inhibition of the p38MAPK signalling pathway (SB203580) in MG-63 and U2OS cells rescued si-ANCR-induced inhibition of cell migration and invasion. Conclusions Silencing of ANCR inhibited the migration and invasion of OS cells through activation of the p38MAPK signalling pathway.
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Affiliation(s)
- Bo Liu
- The Third Department of Orthopedics, The No. 4 Hospital of Jinan, No. 50, Shifan Road, Tianqiao District, Jinan City, 250031, Shandong Province, China
| | - Hongyan Zhao
- Department of Community Section, The First People's Hospital of Jinan, No. 132, Daminghu Road, Lixia District, Jinan City, 250011, Shandong Province, China
| | - Lili Zhang
- Department of Gynecology, The No. 4 Hospital of Jinan, No. 50, Shifan Road, Tianqiao District, Jinan City, 250031, Shandong Province, China
| | - Xuefeng Shi
- Department of Orthopedic Trauma & Hand and Foot Surgery, Jinan Central Hospital Affiliated to Shandong University, No. 105, Jiefang Road, Jinan City, 250013, Shandong Province, China.
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18
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Vélez JI, Lopera F, Silva CT, Villegas A, Espinosa LG, Vidal OM, Mastronardi CA, Arcos-Burgos M. Familial Alzheimer's Disease and Recessive Modifiers. Mol Neurobiol 2019; 57:1035-1043. [PMID: 31664702 PMCID: PMC7031188 DOI: 10.1007/s12035-019-01798-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/22/2019] [Indexed: 12/15/2022]
Abstract
Alzheimer’s disease (AD) is progressive brain disorder that affects ~ 50 million people worldwide and has no current effective treatment. AD age of onset (ADAOO) has shown to be critical for the identification of genes that modify the appearance of AD signs and symptoms in a specific population. We clinically characterized and whole-exome genotyped 71 individuals with AD from the Paisa genetic isolate, segregating the (PSEN1) E280A dominant fully penetrant mutation, and analyzed the potential recessive effects of ~ 50,000 common functional genomic variants to the ADAOO. Standard quality control and filtering procedures were applied, and recessive single- and multi-locus linear mixed-effects models were used. We identified genetic variants in the SLC9C1, CSN1S1, and LOXL4 acting recessively to delay ADAOO up to ~ 11, ~ 6, and ~ 9 years on average, respectively. In contrast, the CC recessive genotype in marker DHRS4L2-rs2273946 accelerates ADAOO by ~ 8 years. This study, reports new recessive variants modifying ADAOO in PSEN1 E280A mutation carriers. This set of genes are implicated in important biological processes and molecular functions commonly affected by genes associated with the etiology of AD such as APP, APOE, and CLU. Future functional studies using modern techniques such as induced pluripotent stem cells will allow a better understanding of the over expression and down regulation of these recessive modifier variants and hence the pathogenesis of AD. These results are important for prediction of AD and ultimately, substantial to develop new therapeutic strategies for individuals at risk or affected by AD.
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Affiliation(s)
| | - Francisco Lopera
- Neuroscience Research Group, University of Antioquia, Medellín, Colombia
| | - Claudia T Silva
- Neuroscience Research Group, University of Antioquia, Medellín, Colombia
| | - Andrés Villegas
- Neuroscience Research Group, University of Antioquia, Medellín, Colombia
| | - Lady G Espinosa
- INPAC Research Group, Fundación Universitaria Sanitas, Bogotá, Colombia
| | | | | | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas (IIM), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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19
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Molecular programs underlying differences in the expression of mood disorders in males and females. Brain Res 2019; 1719:89-103. [DOI: 10.1016/j.brainres.2019.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 04/20/2019] [Accepted: 05/13/2019] [Indexed: 01/13/2023]
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20
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Chen Z, Song X, Li Q, Xie L, Guo T, Su T, Tang C, Chang X, Liang B, Huang D. Androgen Receptor-Activated Enhancers Simultaneously Regulate Oncogene TMPRSS2 and lncRNA PRCAT38 in Prostate Cancer. Cells 2019; 8:cells8080864. [PMID: 31405024 PMCID: PMC6721761 DOI: 10.3390/cells8080864] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/04/2019] [Accepted: 08/06/2019] [Indexed: 02/05/2023] Open
Abstract
Prostate cancer is a common carcinoma in males, the development of which involves the androgen receptor (AR) as a key regulator. AR transactivation induces the high expression of androgen-regulated genes, including transmembrane protease serine 2 (TMPRSS2) and long noncoding RNA prostate cancer-associated transcript 38 (PRCAT38). PRCAT38 and TMPRSS2 are both located on chromosome 21, separated by a series of enhancers. PRCAT38 is a prostate-specific long noncoding RNA that is highly expressed in cancer tissue as compared to normal tissue. Here, we show chromatin looping by enhancers E1 and E2 with the promoters for PRCAT38 and TMPRSS2, indicating the co-regulation of PRCAT38 and TMPRSS2 by the same enhancers. The knockout of enhancer E1 or E2 simultaneously impaired the transcription of PRCAT38 and TMPRSS2 and inhibited cell growth and migration. Moreover, the loop formation and enhancer activity were mediated by AR/FOXA1 binding and the activity of acetyltransferase p300. Our findings demonstrate the utilization of shared enhancers in the joint regulation of two oncogenes in prostate cancer cells.
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Affiliation(s)
- Zikai Chen
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xuhong Song
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Qidong Li
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Lingzhu Xie
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Tangfei Guo
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Ting Su
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Chang Tang
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xiaolan Chang
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Bin Liang
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China.
| | - Dongyang Huang
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China.
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LncRNAs and PRC2: Coupled Partners in Embryonic Stem Cells. EPIGENOMES 2019; 3:epigenomes3030014. [PMID: 34968226 PMCID: PMC8594682 DOI: 10.3390/epigenomes3030014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 02/07/2023] Open
Abstract
The power of embryonic stem cells (ESCs) lies in their ability to self-renew and differentiate. Behind these two unique capabilities is a fine-tuned molecular network that shapes the genetic, epigenetic, and epitranscriptomic ESC plasticity. Although RNA has been shown to be functionally important in only a small minority of long non-coding RNA genes, a growing body of evidence has highlighted the pivotal and intricate role of lncRNAs in chromatin remodeling. Due to their multifaceted nature, lncRNAs interact with DNA, RNA, and proteins, and are emerging as new modulators of extensive gene expression programs through their participation in ESC-specific regulatory circuitries. Here, we review the tight cooperation between lncRNAs and Polycomb repressive complex 2 (PRC2), which is intimately involved in determining and maintaining the ESC epigenetic landscape. The lncRNA-PRC2 partnership is fundamental in securing the fully pluripotent state of ESCs, which must be primed to differentiate properly. We also reflect on the advantages brought to this field of research by the advent of single-cell analysis.
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Xie X, Lin J, Liu J, Huang M, Zhong Y, Liang B, Song X, Gu S, Chang X, Huang D, Tang A. A novel lncRNA NR4A1AS up-regulates orphan nuclear receptor NR4A1 expression by blocking UPF1-mediated mRNA destabilization in colorectal cancer. Clin Sci (Lond) 2019; 133:1457-1473. [PMID: 31253658 DOI: 10.1042/cs20181061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/19/2019] [Accepted: 06/27/2019] [Indexed: 02/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in tumorigenesis and cancer progression. The orphan nuclear receptor subfamily 4 group A member 1 (NR4A1) acts as an oncogene, and is involved in colorectal cancer (CRC) development. However, the mechanism through which lncRNA regulates NR4A1 expression remains unknown. We aimed to identify lncRNAs that regulate NR4A1 and assess their underlying mechanisms in CRC. We first identified an antisense lncRNA of NR4A1 that was up-regulated in CRC tissues and cells with rapid amplification of cDNA ends (RACE), and designated it as NR4A1AS. Spearman correlation analysis showed that NR4A1AS was positively correlated with NR4A1 mRNA levels in 37 CRC tissues. Mechanistically, NR4A1AS stabilized NR4A1 mRNA by forming RNA-RNA complexes via partial base-pairing and up-regulated NR4A1 expression in CRC cells. RNA immunoprecipitation (RIP) assays revealed that knockdown of NR4A1AS expression by siRNA enhanced up-frameshift 1 (UPF1) recruitment to NR4A1 mRNA, thereby decreasing NR4A1 mRNA stability. Moreover, depletion of NR4A1AS was found to mimic the effect of NR4A1 knockdown, specifically by suppressing cell proliferation, migration and invasion, and inducing apoptosis and cell cycle arrest. Accordingly, restoring NR4A1 expression ameliorated the effects of NR4A1AS knockdown on tumor growth and metastasis of CRC cells in vitro and in vivo Thus, we conclude that NR4A1AS up-regulates NR4A1 expression by forming RNA-RNA complexes and blocking UPF1-mediated mRNA destabilization, and it functions in tumor growth and metastasis of CRC cells at least partly through regulating NR4A1, suggesting that NR4A1AS might be as a potential target for RNA-based anti-CRC drug studies.
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MESH Headings
- Animals
- Apoptosis
- Caco-2 Cells
- Cell Cycle Checkpoints
- Cell Movement
- Cell Proliferation
- Colorectal Neoplasms/enzymology
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Gene Expression Regulation, Neoplastic
- HCT116 Cells
- Humans
- Male
- Mice, Inbred BALB C
- Mice, Nude
- Neoplasm Invasiveness
- Nuclear Receptor Subfamily 4, Group A, Member 1/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 1/metabolism
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA Stability
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Signal Transduction
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Tumor Burden
- Up-Regulation
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Affiliation(s)
- Xina Xie
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Jiatian Lin
- Department of Minimally Invasive Intervention, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Jianlan Liu
- Department of Pathology, Shenzhen People's Hospital, Shenzhen 518000, China
| | - Meihui Huang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
- Department of Pathology and Central Laboratory, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Yuantang Zhong
- Department of Urinary Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen 518035, China
| | - Bin Liang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Xuhong Song
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Songgang Gu
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Xiaolan Chang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Dongyang Huang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Aifa Tang
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
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Identification and characterization of a novel group of natural anti-sense transcripts from RNA1.2 gene locus of human cytomegalovirus. Chin Med J (Engl) 2019; 132:1591-1598. [PMID: 31205077 PMCID: PMC6616230 DOI: 10.1097/cm9.0000000000000299] [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] [Indexed: 11/26/2022] Open
Abstract
Background: Natural anti-sense transcripts (NATs), which are transcribed from the complementary DNA strand of annotated genes, exert regulatory function of gene expression. Increasing studies recognized anti-sense transcription widespread throughout human cytomegalovirus (HCMV) genome, whereas the anti-sense transcription of RNA1.2 gene locus has never been investigated. In this study, the transcription of the RNA1.2 anti-sense strand was investigated in clinically isolated HCMV strain. Methods: Strand-specific high-through RNA-sequencing (RNA-seq) was performed to find possible anti-sense transcripts (ASTs). For analyzing and visualization of RNA-seq data sets, Integrative Genomics Viewer software was applied. To confirm these possibilities, Northern blotting and rapid amplification of cDNA ends (RACE) were used. Results: Transcription of the opposite strand of RNA1.2 gene locus was detected by RNA-sequencing using RNAs extracted from human embryonic lung fibroblasts infected with HCMV clinical isolate HAN. At least three HCMV NATs, named RNA1.2 AST 1, RNA1.2 AST2, and RNA1.2 AST3, were characterized by Northern blotting and RACE analyses. These RNA1.2 ASTs orientated from the complementary strand of RNA1.2 locus during the late phase of HCMV infection. The 5′- and 3′-termini of these transcripts were located within the opposite sequence of the predicted RNA1.2 gene. Conclusion: A cluster of novel NATs was transcribed from the opposite sequence of the HCMV RNA1.2 gene region.
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Liu W, Xu J, Zhang C. Clinical usefulness of gastric adenocarcinoma predictive long intergenic noncoding RNA in human malignancies: A meta-analysis. Pathol Res Pract 2019; 215:152387. [DOI: 10.1016/j.prp.2019.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 01/31/2023]
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Xie L, Song X, Lin H, Chen Z, Li Q, Guo T, Xu T, Su T, Xu M, Chang X, Wang LK, Liang B, Huang D. Aberrant activation of CYR61 enhancers in colorectal cancer development. J Exp Clin Cancer Res 2019; 38:213. [PMID: 31118064 PMCID: PMC6532222 DOI: 10.1186/s13046-019-1217-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/07/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND High expression of secreted matricellular protein cysteine-rich 61 (CYR61) correlates with poor prognosis in colorectal cancer (CRC). Aberrant enhancer activation has been shown to correlate with expression of key genes involved in cancer progression. However, such mechanisms in CYR61 transcription regulation remain unexplored. METHODS Expression of CYR61 was determined by immunohistochemistry (IHC), quantitative real-time PCR (qRT-PCR) and western blotting (WB) in CRC patients paraffin specimens and colon cell lines. ChIP-seq data of enhancer-characteristic histone modifications, in CRC tissues from the Gene Expression Omnibus (GEO) database, were reanalyzed to search for putative enhancers of CYR61. Dual-luciferase reporter assay was used to detected enhancer activity. Physical interactions between putative enhancers and CYR61 promoter were detected by chromosome conformation capture (3C) assay. Histone modification and transcription factors (TFs) enrichment were detected by ChIP-qPCR. Additionally, biological function of enhancers was investigated by transwell migration assays. RESULTS CRC tissues and cell lines expressed higher level of CYR61 than normal colon mucosa. Three putative enhancers located downstream of CYR61 were found in CRC tissues by ChIP-seq data reanalysis. Consistent with the ChIP-seq analysis results in the GEO database, the normal colon mucosal epithelial cell line NCM460 possessed no active CYR61 enhancers, whereas colon cancer cells exhibited different patterns of active CYR61 enhancers. HCT116 cells had an active Enhancer3, whereas RKO cells had both Enhancer1 and Enhancer3 active. Pioneer factor FOXA1 promoted CYR61 expression by recruiting CBP histone acetyltransferase binding and increasing promoter-enhancer looping frequencies and enhancer activity. CBP knockdown attenuated H3K27ac enrichment, promoter-enhancer looping frequencies, and enhancer activity. Small molecule compound 12-O-tetradecanoyl phorbol-13-acetate (TPA) treatment, which stimulated CYR61 expression, and verteporfin (VP) treatment, which inhibited CYR61 expression, confirmed that the enhancers regulated CYR61 expression. Knockdown and ectopic expression of CYR61 rescued cell migration changes induced by over-expressing and knockdown of FOXA1, respectively. CONCLUSIONS CYR61 enhancer activation, mediated by FOXA1 and CBP, occurs during CRC progression to up-regulate CYR61 expression and promote cell migration in CRC, suggesting inhibition of recruitment of FOXA1 and/or CBP to CYR61 enhancers may have therapeutic implications.
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Affiliation(s)
- Lingzhu Xie
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
| | - Xuhong Song
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
| | - Hao Lin
- Department of Gastroenterology, Shantou Central Hospital, Shantou, 515041 China
| | - Zikai Chen
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
| | - Qidong Li
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
| | - Tangfei Guo
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
| | - Tian Xu
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
| | - Ting Su
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
| | - Man Xu
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
| | - Xiaolan Chang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
| | - Long-Kun Wang
- Department of Clinical Laboratory, Jiujiang First People’s Hospital, Jiujiang, 332000 China
| | - Bin Liang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
- Department of Cell Biology and Genetics, Shantou University Medical College, Complex Building, Room 602, No. 22 Xinling Road, Shantou, Guangdong China
| | - Dongyang Huang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041 China
- Department of Cell Biology and Genetics, Shantou University Medical College, Complex Building, Room 602, No. 22 Xinling Road, Shantou, Guangdong China
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26
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Zhu L, Zhu Y, Han S, Chen M, Song P, Dai D, Xu W, Jiang T, Feng L, Shin VY, Wang X, Jin H. Impaired autophagic degradation of lncRNA ARHGAP5-AS1 promotes chemoresistance in gastric cancer. Cell Death Dis 2019; 10:383. [PMID: 31097692 PMCID: PMC6522595 DOI: 10.1038/s41419-019-1585-2] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 04/08/2019] [Indexed: 01/08/2023]
Abstract
Chemoresistance remains the uppermost disincentive for cancer treatment on account of many genetic and epigenetic alterations. Long non-coding RNAs (lncRNAs) are emerging players in promoting cancer initiation and progression. However, the regulation and function in chemoresistance are largely unknown. Herein, we identified ARHGAP5-AS1 as a lncRNA upregulated in chemoresistant gastric cancer cells and its knockdown reversed chemoresistance. Meanwhile, high ARHGAP5-AS1 expression was associated with poor prognosis of gastric cancer patients. Intriguingly, its abundance is affected by autophagy and SQSTM1 is responsible for transporting ARHGAP5-AS1 to autophagosomes. Inhibition of autophagy in chemoresistant cells, thus, resulted in the upregulation of ARHGAP5-AS1. In turn, it activated the transcription of ARHGAP5 in the nucleus by directly interacting with ARHGAP5 promoter. Interestingly, ARHGAP5-AS1 also stabilized ARHGAP5 mRNA in the cytoplasm by recruiting METTL3 to stimulate m6A modification of ARHGAP5 mRNA. As a result, ARHGAP5 was upregulated to promote chemoresistance and its upregulation was also associated with poor prognosis in gastric cancer. In summary, impaired autophagic degradation of lncRNA ARHGAP5-AS1 in chemoresistant cancer cells promoted chemoresistance. It can activate the transcription of ARHGAP5 in the nucleus and stimulate m6A modification of ARHGAP5 mRNA to stabilize ARHGAP5 mRNA in the cytoplasm by recruiting METTL3. Therefore, targeting ARHGAP5-AS1/ARHGAP5 axis might be a promising strategy to overcome chemoresistance in gastric cancer.
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Affiliation(s)
- Liyuan Zhu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Yiran Zhu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Shuting Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Miaoqin Chen
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Ping Song
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Dongjun Dai
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Wenxia Xu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Tingting Jiang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Lifeng Feng
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Vivian Y Shin
- Department of Surgery, the University of Hong Kong, Hong Kong SAR, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China.
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Mei ZZ, Sun H, Ou X, Li L, Cai J, Hu S, Wang J, Luo H, Liu J, Jiang Y. The natural antisense transcript NATTD regulates the transcription of decapping scavenger (DcpS) enzyme. Int J Biochem Cell Biol 2019; 110:103-110. [PMID: 30858142 DOI: 10.1016/j.biocel.2019.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 12/25/2022]
Abstract
Natural antisense transcripts (NATs) are transcribed from the opposite strand of other genes. Most of them are noncoding RNAs. They have been reported to play important roles in a variety of biological processes. In this study, we identified a novel NAT, NATTD, which is partially complementary to both the TIRAP/Mal and DcpS genes. Interestingly, NATTD only positively regulates the expression of DcpS, a decapping scavenger enzyme which is a promising therapeutic target for spinal muscular atrophy. But it has no obvious effects on the expression of TIRAP/Mal gene. The NATTD transcript primarily resides in the nucleus and does not alter the mRNA stability of DcpS. Instead, it is required for the recruitment of RNA polymerase II at the mouse DcpS promoter. Chromatin immunoprecipitation assays revealed that knocking-down NATTD transcript with shRNA enhanced the H3K27-Me3 modification at the DcpS promoter. In summary, our studies identified NATTD as a regulator of DcpS transcription through epigenetic mechanisms.
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Affiliation(s)
- Zhu-Zhong Mei
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China.
| | - Hongwei Sun
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Xiaoli Ou
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Lei Li
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Junwei Cai
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Shuiwang Hu
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Juan Wang
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Haihua Luo
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Jinghua Liu
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China.
| | - Yong Jiang
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China.
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Lin S, Zhang Z, Xie T, Hu B, Ruan Z, Zhang L, Li C, Li C, Luo W, Nie Q, Zhang X. Identification of a novel antisense RNA that regulates growth hormone receptor expression in chickens. RNA Biol 2019; 16:626-638. [PMID: 30764709 PMCID: PMC6546403 DOI: 10.1080/15476286.2019.1572440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules of gene expression. However, studies on NATs in the chicken are relatively rare. We identified a novel antisense transcript in the chicken, designated GHR-AS-EST, transcribed from the growth hormone receptor (GHR) locus, which encodes a well-known regulatory molecule of muscle development and fat deposition. GHR-AS-EST is predominantly expressed in the chicken liver and muscle tissues. GHR-AS-EST sequence conservation among vertebrates is weak. GHR-AS-EST forms an RNA-RNA duplex with GHBP to increase its stability, and regulates the expression of GHR sense transcripts at both the mRNA and protein levels. Further, GHR-AS-EST promotes cell proliferation by stimulating the expression of signaling factors in the JAK2/STAT pathway, and contributes to fat deposition via downregulating the expression of signaling factors in the JAK2/SOCS pathway in LMH hepatocellular carcinoma cells. We expect that the discovery of a NAT for a regulatory gene associated with cell proliferation and lipolysis will further our understanding of the molecular regulation of both muscle development and fat deposition.
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Affiliation(s)
- Shudai Lin
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China.,b Animal Genomics and Improvement Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA.,c Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA
| | - Zihao Zhang
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Tingting Xie
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Bowen Hu
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Zhuohao Ruan
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Li Zhang
- d Agricultural College , Guangdong Ocean University , Zhanjiang , P.R. China
| | - Congjun Li
- b Animal Genomics and Improvement Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA
| | - Charles Li
- c Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA
| | - Wen Luo
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Qinghua Nie
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Xiquan Zhang
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
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Gu Y, Feng C, Liu T, Zhang B, Yang L. The downregulation of lncRNA EMX2OS might independently predict shorter recurrence-free survival of classical papillary thyroid cancer. PLoS One 2018; 13:e0209338. [PMID: 30576338 PMCID: PMC6303026 DOI: 10.1371/journal.pone.0209338] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/04/2018] [Indexed: 11/23/2022] Open
Abstract
Homeobox protein Emx2 is a transcription factor that is encoded by the EMX2 gene. In this study, using data from the Cancer Genome Atlas-Thyroid Cancer (TCGA-THCA), we aimed to examine the expression profile of EMX2 and its antisense transcript EMX2OS in papillary thyroid cancer (PTC), their prognostic value and potential regulatory networks. Results showed that in the three variants of PTC, EMX2 was significantly downregulated in classical PTC, while EMX2OS were significantly downregulated in follicular and classical PTC, compared with adjacent normal tissues. Kaplan-Meier survival curves showed that EMX2 and EMX2OS expression was not related to RFS in follicular PTC. In comparison, the high EMX2 or EMX2OS group were associated with better RFS compared with their respective low expression group in classical PTC (p = 0.007 and 0.004 respectively). Correlation analysis showed that EMX2 and EMX2OS were highly co-expressed in PTC tissues (Spearman’s r = 0.83). By performing stepwise regression, we found that EMX2OS was better than EMX2 in predicting RFS in classical PTC. Multivariate analysis confirmed that high EMX2OS expression was an independent indicator of favorable RFS in classical PTC (HR: 0.239, 95%CI: 0.100 = 0.569, p = 0.001), after adjustment of pathological stages and residual tumors. By performing in silico analysis, we found that the genes co-expressed with EMX2 or EMX2OS were highly overlapped. KEGG pathway analysis showed that these genes were enriched in the ECM-receptor interaction, focal adhesion, and PI3K-Akt signaling, protein digestion and absorption and proteoglycans in cancer pathways, which are closely related to cancer initiation and progression. Based on the findings, we infer that decreased EMX2OS expression might be a valuable prognostic biomarker of unfavorable RFS in classical PTC.
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Affiliation(s)
- Yi Gu
- Department of Vascular and Thyroid Surgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Chao Feng
- Department of Vascular and Thyroid Surgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Tong Liu
- Department of Vascular and Thyroid Surgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Bowei Zhang
- Department of Vascular and Thyroid Surgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Lan Yang
- Department of Anatomy, Histology and Embryology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- * E-mail:
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Elling R, Robinson EK, Shapleigh B, Liapis SC, Covarrubias S, Katzman S, Groff AF, Jiang Z, Agarwal S, Motwani M, Chan J, Sharma S, Hennessy EJ, FitzGerald GA, McManus MT, Rinn JL, Fitzgerald KA, Carpenter S. Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2. Cell Rep 2018; 25:1511-1524.e6. [PMID: 30404006 PMCID: PMC6291222 DOI: 10.1016/j.celrep.2018.10.027] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 09/04/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022] Open
Abstract
An inducible gene expression program is a hallmark of the host inflammatory response. Recently, long intergenic non-coding RNAs (lincRNAs) have been shown to regulate the magnitude, duration, and resolution of these responses. Among these is lincRNA-Cox2, a dynamically regulated gene that broadly controls immune gene expression. To evaluate the in vivo functions of this lincRNA, we characterized multiple models of lincRNA-Cox2-deficient mice. LincRNA-Cox2-deficient macrophages and murine tissues had altered expression of inflammatory genes. Transcriptomic studies from various tissues revealed that deletion of the lincRNA-Cox2 locus also strongly impaired the basal and inducible expression of the neighboring gene prostaglandin-endoperoxide synthase (Ptgs2), encoding cyclooxygenase-2, a key enzyme in the prostaglandin biosynthesis pathway. By utilizing different genetic manipulations in vitro and in vivo, we found that lincRNA-Cox2 functions through an enhancer RNA mechanism to regulate Ptgs2. More importantly, lincRNA-Cox2 also functions in trans, independently of Ptgs2, to regulate critical innate immune genes in vivo.
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Affiliation(s)
- Roland Elling
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA; Center for Pediatrics, Department of General Pediatrics, University of Freiburg, Freiburg, Germany
| | - Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Barbara Shapleigh
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Stephen C Liapis
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sol Katzman
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Abigail F Groff
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
| | - Zhaozhao Jiang
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shiuli Agarwal
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mona Motwani
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennie Chan
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shruti Sharma
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Elizabeth J Hennessy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Smilow, Philadelphia, PA 19104, USA
| | - Garret A FitzGerald
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Smilow, Philadelphia, PA 19104, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - John L Rinn
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Department of Biochemistry, BioFrontiers, University of Colorado Boulder, Boulder, CO 80301, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.
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Wang Z, Xu H, Li T, Wu J, An L, Zhao Z, Xiao M, Adu-Asiamah P, Zhang X, Zhang L. Chicken GHR antisense transcript regulates its sense transcript in hepatocytes. Gene 2018; 682:101-110. [PMID: 30296567 DOI: 10.1016/j.gene.2018.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 07/29/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022]
Abstract
An increasing number of evidences indicated that long noncoding RNAs (LncRNAs) regulate a variety of biological progresses via different mechanisms. Our previous study had identified a chicken growth hormone receptor (GHR) antisense transcript (GHR-AS) which regulated GHR sense transcript (GHR-S) in LMH cells. In the present study, roles of GHR-AS and its regulatory mechanism were analyzed in chicken hepatocytes. The expression patterns of liver GHR-S, GHR-AS and Let-7b ascended with the development of chicken. The hepatocytes proliferation was promoted and more cells entered into DNA synthesis (S) phase when GHR-AS was overexpressed while the cell proliferation was slowed and fewer cells were in S phase when GHR-AS was interfered. Meanwhile, the GHR-S increased when we overexpressed GHR-AS while it reduced when GHR-AS was inhibited. The S1 Nuclease protection assay indicated that GHR-S and GHR-AS formed RNA duplex via GHR-S 3' untranslation regon (3'UTR). In hepatocytes or LMH cells, the half-time of GHR-S showed a delayed trend when GHR-AS or GHR-AS 5' untranslation regon (5'UTR) was overexpressed. Furthermore, the level of GHR-S can be decreased by Let-7b mimics whereas it was partially rescued when co-transfected pGHR-AS or pGHR-AS 5'UTR with Let-7b mimics. Based on our findings, GHR-AS affected hepatocytes proliferation and improved GHR-S stability possibly by forming RNA duplex between GHR-S and GHR-AS, competing with Let-7b.
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Affiliation(s)
- Zhang Wang
- Agricultural College, GuangDong Ocean University, ZhanJiang, China
| | - HaiDong Xu
- Agricultural College, GuangDong Ocean University, ZhanJiang, China
| | - Ting Li
- Agricultural College, GuangDong Ocean University, ZhanJiang, China
| | - Jiang Wu
- Agricultural College, GuangDong Ocean University, ZhanJiang, China
| | - LiLong An
- Agricultural College, GuangDong Ocean University, ZhanJiang, China
| | - ZhiHui Zhao
- Agricultural College, GuangDong Ocean University, ZhanJiang, China
| | - Mei Xiao
- Agricultural College, GuangDong Ocean University, ZhanJiang, China
| | | | - XiQuan Zhang
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Li Zhang
- Agricultural College, GuangDong Ocean University, ZhanJiang, China.
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32
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Wang C, Wang G, Zhang Z, Wang Z, Ren M, Wang X, Li H, Yu Y, Liu J, Cai L, Li Y, Zhang D, Zhang C. The downregulated long noncoding RNA DHRS4-AS1 is protumoral and associated with the prognosis of clear cell renal cell carcinoma. Onco Targets Ther 2018; 11:5631-5646. [PMID: 30254456 PMCID: PMC6141115 DOI: 10.2147/ott.s164984] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have been identified as important factors in cancer biology and are deregulated in many cancers. The present study aimed to determine the expression and roles of lncRNA DHRS4-AS1 in the progression of clear cell renal cell carcinoma (ccRCC). METHODS AND RESULTS Using high-throughput RNA-sequencing data of ccRCC tumors from the Cancer Genome Atlas project, we identified lncRNA DHRS4-AS1 as significantly associated with ccRCC patients' overall survival. We confirmed the downregulation of DHRS4-AS1 in ccRCC by assessing its expression levels in a cohort of 52 tumor and paired non-tumor samples. In addition, we found that low DHRS4-AS1 expression was significantly associated with a high tumor node metastasis stage, lymph node metastasis, advanced pathological grade and poor prognosis. Furthermore, DHRS4-AS1 overexpression inhibited the progression of cell cycles of ccRCC in vitro. These data indicate that DHRS4-AS1 functions by preventing the proliferation and invasion, inhibiting the cell cycle progression and promoting the apoptosis of ccRCC cells. CONCLUSION Taken together, our findings identify the role of DHRS4-AS1 as a tumor inhibitor in ccRCC for the first time, demonstrating that DHRS4-AS1 is a potential prognostic biomarker that could potentially be applied in ccRCC therapy.
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Affiliation(s)
- Changlin Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Gang Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Zijian Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Zichun Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Minghua Ren
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Xiaoxiong Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Haoming Li
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Yipeng Yu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Jing Liu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Licheng Cai
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Yong Li
- Department of PET/CT, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Daming Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,
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Pajares MA, Pérez-Sala D. Mammalian Sulfur Amino Acid Metabolism: A Nexus Between Redox Regulation, Nutrition, Epigenetics, and Detoxification. Antioxid Redox Signal 2018; 29:408-452. [PMID: 29186975 DOI: 10.1089/ars.2017.7237] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Transsulfuration allows conversion of methionine into cysteine using homocysteine (Hcy) as an intermediate. This pathway produces S-adenosylmethionine (AdoMet), a key metabolite for cell function, and provides 50% of the cysteine needed for hepatic glutathione synthesis. The route requires the intake of essential nutrients (e.g., methionine and vitamins) and is regulated by their availability. Transsulfuration presents multiple interconnections with epigenetics, adenosine triphosphate (ATP), and glutathione synthesis, polyol and pentose phosphate pathways, and detoxification that rely mostly in the exchange of substrates or products. Major hepatic diseases, rare diseases, and sensorineural disorders, among others that concur with oxidative stress, present impaired transsulfuration. Recent Advances: In contrast to the classical view, a nuclear branch of the pathway, potentiated under oxidative stress, is emerging. Several transsulfuration proteins regulate gene expression, suggesting moonlighting activities. In addition, abnormalities in Hcy metabolism link nutrition and hearing loss. CRITICAL ISSUES Knowledge about the crossregulation between pathways is mostly limited to the hepatic availability/removal of substrates and inhibitors. However, advances regarding protein-protein interactions involving oncogenes, identification of several post-translational modifications (PTMs), and putative moonlighting activities expand the potential impact of transsulfuration beyond methylations and Hcy. FUTURE DIRECTIONS Increasing the knowledge on transsulfuration outside the liver, understanding the protein-protein interaction networks involving these enzymes, the functional role of their PTMs, or the mechanisms controlling their nucleocytoplasmic shuttling may provide further insights into the pathophysiological implications of this pathway, allowing design of new therapeutic interventions. Antioxid. Redox Signal. 29, 408-452.
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Affiliation(s)
- María A Pajares
- 1 Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas (CSIC) , Madrid, Spain .,2 Molecular Hepatology Group, Instituto de Investigación Sanitaria La Paz (IdiPAZ) , Madrid, Spain
| | - Dolores Pérez-Sala
- 1 Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas (CSIC) , Madrid, Spain
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Guo W, Lv P, Liu S, Xu F, Guo Y, Shen S, Liang J, Kuang G, Dong Z. Aberrant methylation-mediated downregulation of long noncoding RNA C5orf66-AS1 promotes the development of gastric cardia adenocarcinoma. Mol Carcinog 2018; 57:854-865. [PMID: 29566283 DOI: 10.1002/mc.22806] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/28/2018] [Accepted: 03/20/2018] [Indexed: 02/01/2023]
Abstract
As a long non-coding RNA, C5orf66-AS1 is located at 5q31.1. Downregulation and aberrant hypermethylation of C5orf66-AS1 have been detected in a limited several tumors. However, the biological role and distribution of methylated CpG sites of C5orf66-AS1 in gastric cardia adenocarcinoma (GCA) development and prognosis are poorly clarified. The present study was to investigate the expression status and function of C5orf66-AS1 in GCA, and to detect the distribution of methylated CpG sites within the three CpG islands of the promoter and gene body of C5orf66-AS1, further to clarify its prognostic value in GCA patients. C5orf66-AS1 was significantly downregulated in GCA tissues and cell lines, and the expression level was associated with TNM stage, pathological differentiation, lymph node metastasis, and distant metastasis or recurrence. The expression level of C5orf66-AS1 was significantly increased in cancer cells after treated with 5-Aza-dC. Further methylation analysis demonstrated that the aberrant hypermethylation of the regions around the transcription start site of C5orf66-AS1 was more tumor specific and was associated with its expression. Moreover, Sp1 may upregulate C5orf66-AS1 expression and CpG sites hypermethylation within the binding sites may abrogate Sp1 binding. In addition, C5orf66-AS1 inhibited gastric cancer cell proliferation and invasion, and the dysregulation and hypermethylation of the regions around the transcription start site of C5orf66-AS1 were associated with poorer GCA patients' survival. These findings suggest that aberrant hypermethylation-mediated downregulation of C5orf66-AS1 may play important roles in GCA tumorigenesis and C5orf66-AS1 may serve as a potential prognostic marker in predicting GCA patients' survival.
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Affiliation(s)
- Wei Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Ping Lv
- Department of Histology and Embryology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shengnan Liu
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Fenglou Xu
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanli Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Supeng Shen
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jia Liang
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Gang Kuang
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhiming Dong
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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Fachrul M, Utomo DH, Parikesit AA. lncRNA-based study of epigenetic regulations in diabetic peripheral neuropathy. In Silico Pharmacol 2018; 6:7. [PMID: 30607320 DOI: 10.1007/s40203-018-0042-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/19/2018] [Indexed: 01/09/2023] Open
Abstract
Diabetes remains one of the most prevalent non-communicable diseases in the world, affecting over 400 million of people worldwide, causing serious complications leading to amputations and even death. Over the years, researchers have found that, in addition to genomic mutations, epigenetic mechanisms also play a role in the development of diabetes-specifically type-2 diabetes. Long noncoding RNAs (lncRNAs) have been linked to mediate epigenetic mechanisms, including those in late-stage diabetes. This study attempts to assess the unexplored topic of how lncRNAs could be used to assess the epigenetic mechanisms present in diabetic peripheral neuropathy (DPN); a serious complication of the disease often leading to amputation. Differential lncRNA expression analysis was done with a dataset containing DPN and healthy patients. Standard and corrected t test, and also LIMMA was applied. Results of this study indicates the usefulness of lncRNAs as an exploratory tool to elucidate the complexity of the epigenetic mechanisms of human DPN.
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Affiliation(s)
- Muhamad Fachrul
- Bioinformatics Department, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | - Didik H Utomo
- 2Biology Department, Faculty of Sciences, Brawijaya University, Malang, Indonesia
- Research and Education Center for Bioinformatics, Nusantara Institute for Life Science and Technology, Jakarta, Indonesia
| | - Arli A Parikesit
- Bioinformatics Department, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
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Zhang L, Lin S, An L, Ma J, Qiu F, Jia R, Nie Q, Zhang D, Luo Q, Li T, Wang Z, Zhang X. Chicken GHR natural antisense transcript regulates GHR mRNA in LMH cells. Oncotarget 2018; 7:73607-73617. [PMID: 27713155 PMCID: PMC5342002 DOI: 10.18632/oncotarget.12437] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/21/2016] [Indexed: 01/03/2023] Open
Abstract
Growth hormone receptor (GHR) played key roles in human and animal growth. Both human laron type dwarfism and sex linked dwarf chicken were caused by the mutation of GHR gene. In this study, we identified an endogenously expressed long non-coding natural antisense transcript, GHR-AS, which overlapped with the GHR mRNA (GHR-S) in a tail to tail manner. Spatial and temporal expression analyses indicated that GHR-AS were highly expressed in chicken liver and displayed ascending with the development of chicken from E10 to 3 w of age. Interfering GHR-AS caused GHR-S decreasing, accompanied with increasing of the inactive gene indicator, H3K9me2, in the GHR-S promoter regions in LMH cells. RNase A experiment exhibited that GHR-AS and GHR-S can form double strand RNAs at the last exon of GHR gene in vivo and in vitro, which hinted they could act on each other via the region. In addition, the levels of GHR-S and GHR-AS can be affected by DNA methylation. Compared the normal chicken with the dwarfs, the negative correlation trends were showed between the GHR-S promoter methylation status and the GHR-AS levels. This is the first report of that GHR gene possessed natural antisense transcript and the results presented here further highlight the fine and complicated regulating mechanism of GHR gene in chicken development.
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Affiliation(s)
- Li Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, P.R. China.,Agricultural College, Guangdong Ocean University, Zhanjiang 524088, P.R. China
| | - Shudai Lin
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, P.R. China
| | - Lilong An
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, P.R. China
| | - Jinge Ma
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, P.R. China
| | - Fengfang Qiu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, P.R. China
| | - Rumin Jia
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, P.R. China
| | - Qinghua Nie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, P.R. China
| | - Dexiang Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, P.R. China
| | - Qingbin Luo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, P.R. China
| | - Ting Li
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, P.R. China
| | - Zhang Wang
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, P.R. China
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, P.R. China
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Magnani E, Macchi F, Mancini M, Lomazzi V, Cogliati S, Pistore C, Mandruzzato M, Dock-Bregeon AC, Bonapace IM. UHRF1 regulates CDH1 via promoter associated non-coding RNAs in prostate cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:258-270. [PMID: 29466696 DOI: 10.1016/j.bbagrm.2018.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/01/2018] [Accepted: 02/15/2018] [Indexed: 01/07/2023]
Abstract
Non-coding RNAs (ncRNAs) transcribed from the promoter and the downstream region can affect the expression of the corresponding coding genes. It has been shown that sense-directed ncRNAs arising from the promoter region of the E-cadherin gene (CDH1) mediate its repression. Here, we show that an antisense-directed ncRNA (paRCDH1-AS) transcribed from the CDH1 promoter is necessary for its expression. paRCDH1-AS acts as a hooking scaffold by recruiting the epigenetic regulators, UHRF1, DNMT3A, SUV39H1 and SUZ12, involved in CDH1 repression. The binding of epigenetic regulators to paCRDH1-AS, indeed, prevents their localization to the chromatin on CDH1 promoter. Moreover, paRCDH1-AS silencing induces CDH1 repression and a switch of the epigenetic profile on the promoter towards a more closed chromatin. Using bioinformatic and experimental approaches we defined that the promoter of the paRCDH1-AS is shared with the E-cadherin gene, showing a bidirectional promoter activity. We found that UHRF1 controls both CDH1 and paRCDH1-AS by directly binding this bidirectional promoter region. Our study provides evidences, for the first time, that UHRF1 recruitment can be affected by promoter-associated non-coding RNAs, opening new perspective regarding the role of UHRF1 in these complex regulatory networks.
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Affiliation(s)
- Elena Magnani
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Filippo Macchi
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Monica Mancini
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Vanessa Lomazzi
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Sara Cogliati
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy; IGBMC, BP10142, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Christian Pistore
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Martina Mandruzzato
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | | | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy.
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Sun Q, Hao Q, Prasanth KV. Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression. Trends Genet 2018; 34:142-157. [PMID: 29249332 PMCID: PMC6002860 DOI: 10.1016/j.tig.2017.11.005] [Citation(s) in RCA: 388] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023]
Abstract
A significant portion of the human genome encodes genes that transcribe long nonprotein-coding RNAs (lncRNAs). A large number of lncRNAs localize in the nucleus, either enriched on the chromatin or localized to specific subnuclear compartments. Nuclear lncRNAs participate in several biological processes, including chromatin organization, and transcriptional and post-transcriptional gene expression, and also act as structural scaffolds of nuclear domains. Here, we highlight recent studies demonstrating the role of lncRNAs in regulating gene expression and nuclear organization in mammalian cells. In addition, we update current knowledge about the involvement of the most-abundant and conserved lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), in gene expression control.
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Affiliation(s)
- Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
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Mehra M, Chauhan R. Long Noncoding RNAs as a Key Player in Hepatocellular Carcinoma. BIOMARKERS IN CANCER 2017; 9:1179299X17737301. [PMID: 29147078 PMCID: PMC5673005 DOI: 10.1177/1179299x17737301] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Indexed: 12/16/2022]
Abstract
Hepatocellular carcinoma (HCC) is a major malignancy in the liver and has emerged as one of the main cancers in the world with a high mortality rate. However, the molecular mechanisms of HCC are still poorly understood. Long noncoding RNAs (lncRNAs) have recently come to the forefront as functional non-protein-coding RNAs that are involved in a variety of cellular processes ranging from maintaining the structural integrity of chromosomes to gene expression regulation in a spatiotemporal manner. Many recent studies have reported the involvement of lncRNAs in HCC which has led to a better understanding of the underlying molecular mechanisms operating in HCC. Long noncoding RNAs have been shown to regulate development and progression of HCC, and thus, lncRNAs have both diagnostic and therapeutic potentials. In this review, we present an overview of the lncRNAs involved in different stages of HCC and their potential in clinical applications which have been studied so far.
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Affiliation(s)
- Mrigaya Mehra
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Academy of Scientific & Innovative Research, Chennai, India
| | - Ranjit Chauhan
- Department of Hepatology, Loyola University Chicago, Chicago, IL, USA
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Health Sciences Center, Memorial University, St John’s, Newfoundland and Labrador, Canada
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40
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Expression Profiling of Long Noncoding RNA Splice Variants in Human Microvascular Endothelial Cells: Lipopolysaccharide Effects In Vitro. Mediators Inflamm 2017; 2017:3427461. [PMID: 29147069 PMCID: PMC5632992 DOI: 10.1155/2017/3427461] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/22/2017] [Indexed: 12/02/2022] Open
Abstract
Endothelial cell interactions with lipopolysaccharide (LPS) involve both activating and repressing signals resulting in pronounced alterations in their transcriptome and proteome. Noncoding RNAs are now appreciated as posttranscriptional and translational regulators of cellular signaling and responses, but their expression status and roles during endothelial interactions with LPS are not well understood. We report on the expression profile of long noncoding (lnc) RNAs of human microvascular endothelial cells in response to LPS. We have identified a total of 10,781 and 8310 lncRNA transcripts displaying either positive or negative regulation of expression, respectively, at 3 and 24 h posttreatment. A majority of LPS-induced lncRNAs are multiexonic and distributed across the genome as evidenced by their presence on all chromosomes. Present among these are a total of 44 lncRNAs with known regulatory functions, of which 41 multiexonic lncRNAs have multiple splice variants. We have further validated splice variant-specific expression of EGO (NONHSAT087634) and HOTAIRM1 (NONHSAT119666) at 3 h and significant upregulation of lnc-IL7R at 24 h. This study illustrates the genome-wide regulation of endothelial lncRNA splice variants in response to LPS and provides a foundation for further investigations of differentially expressed lncRNA transcripts in endothelial responses to LPS and pathophysiology of sepsis/septic shock.
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41
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Chu SK, Yang HC. Interethnic DNA methylation difference and its implications in pharmacoepigenetics. Epigenomics 2017; 9:1437-1454. [PMID: 28882057 DOI: 10.2217/epi-2017-0046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
AIM This is the first systematic study to examine the population differentiation effect of DNA methylation on the treatment response and drug absorption, distribution, metabolism and excretion in multiple tissue types and cancer types. MATERIALS & METHODS We analyzed the whole methylome and transcriptome data of primary tumor tissues of four cancer types (breast, colon, head & neck and uterine corpus) and lymphoblastoid cell lines for African and European ancestry populations. RESULTS Ethnicity-associated CpG sites exhibited similar methylation patterns in the two studied populations, but the patterns differed between tumor tissues and lymphoblastoid cell lines. Ethnicity-associated CpG sites may have triggered gene expression, influenced drug absorption, distribution, metabolism and excretion, and showed tumor-specific patterns of methylation and gene regulation. CONCLUSION Ethnicity should be carefully accounted for in future pharmacoepigenetics research.
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Affiliation(s)
- Shih-Kai Chu
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan
| | - Hsin-Chou Yang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan.,Department of Statistics, National Cheng Kung University, Tainan 701, Taiwan.,Institute of Statistics, National Tsing Hua University, Hsinchu 300, Taiwan.,Instutite of Public Health, National Yang-Ming University, Taipei 112, Taiwan.,School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
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42
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Wang J, Zhou Y, Li D, Sun X, Deng Y, Zhao Q. TSPAN
31 is a critical regulator on transduction of survival and apoptotic signals in hepatocellular carcinoma cells. FEBS Lett 2017; 591:2905-2918. [DOI: 10.1002/1873-3468.12737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Jianglin Wang
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
| | - Yuting Zhou
- Department of Molecular & Cellular Biochemistry College of Medicine University of Kentucky Lexington KY USA
| | - Dan Li
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
| | - Xuemeng Sun
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
| | - Yuanfei Deng
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
| | - Qing Zhao
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
- Sino‐French Hoffmann Institute Guangzhou Medical University China
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43
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Peng B, Liu A, Yu X, Xu E, Dai J, Li M, Yang Q. Silencing of lncRNA AFAP1-AS1 suppressed lung cancer development by regulatory mechanism in cis and trans. Oncotarget 2017; 8:93608-93623. [PMID: 29212176 PMCID: PMC5706822 DOI: 10.18632/oncotarget.20549] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
Although the long noncoding RNA AFAP1-AS1 has been shown to be involved in various types of cancer, its involvement in lung cancer remains poorly understood. In the current study, we found that AFAP1-AS1 was substantially over expressed in lung cancer tissues and cell lines. In addition, AFAP1-AS1 expression level was proven to be associated with the malignant features of lung cancer. Knockdown of AFAP1-AS1 significantly suppressed cell proliferation by increasing cell apoptosis and G0/G1 phase retardation of cell cycle in lung cancer cells. Furthermore, AFAP1-AS1 knockdown could suppress tumor growth of lung cancer in BALB/c nude mice. We also identified that AFAP1-AS1 silencing could influence the expression of AFAP1 and KRT1 on mRNA and protein level by cis and trans regulatory mechanism. Moreover, the oncogenic activities of AFAP1-AS1 on cell proliferation are partially mediated by KRT1. In summary, these findings demonstrate that AFAP1-AS1 plays an essential role in promoting lung cancer development in vitro and vivo. It indicated that AFAP1-AS1 is a promising prognostic predictor for patients with lung cancer.
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Affiliation(s)
- Baoying Peng
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Yuexiu District, Guangzhou 510120, PR China.,The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Anfei Liu
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Xuanwei Yu
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of Chinese People's Liberation Army, Guangzhou 510010, China
| | - Jiabin Dai
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Mengcheng Li
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Qiaoyuan Yang
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Yuexiu District, Guangzhou 510120, PR China.,The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
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44
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Gatto S, Gagliardi M, Franzese M, Leppert S, Papa M, Cammisa M, Grillo G, Velasco G, Francastel C, Toubiana S, D’Esposito M, Angelini C, Matarazzo MR. ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing. Nucleic Acids Res 2017; 45:5739-5756. [PMID: 28334849 PMCID: PMC5449610 DOI: 10.1093/nar/gkx163] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 02/07/2017] [Accepted: 02/28/2017] [Indexed: 12/11/2022] Open
Abstract
Hypomorphic mutations in DNA-methyltransferase DNMT3B cause majority of the rare disorder Immunodeficiency, Centromere instability and Facial anomalies syndrome cases (ICF1). By unspecified mechanisms, mutant-DNMT3B interferes with lymphoid-specific pathways resulting in immune response defects. Interestingly, recent findings report that DNMT3B shapes intragenic CpG-methylation of highly-transcribed genes. However, how the DNMT3B-dependent epigenetic network modulates transcription and whether ICF1-specific mutations impair this process remains unknown. We performed a transcriptomic and epigenomic study in patient-derived B-cell lines to investigate the genome-scale effects of DNMT3B dysfunction. We highlighted that altered intragenic CpG-methylation impairs multiple aspects of transcriptional regulation, like alternative TSS usage, antisense transcription and exon splicing. These defects preferentially associate with changes of intragenic H3K4me3 and at lesser extent of H3K27me3 and H3K36me3. In addition, we highlighted a novel DNMT3B activity in modulating the self-regulatory circuit of sense-antisense pairs and the exon skipping during alternative splicing, through interacting with RNA molecules. Strikingly, altered transcription affects disease relevant genes, as for instance the memory-B cell marker CD27 and PTPRC genes, providing us with biological insights into the ICF1-syndrome pathogenesis. Our genome-scale approach sheds light on the mechanisms still poorly understood of the intragenic function of DNMT3B and DNA methylation in gene expression regulation.
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Affiliation(s)
- Sole Gatto
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- Sanford Burnham Prebys Medical Discovery Research Institute, La Jolla, CA, USA
| | - Miriam Gagliardi
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- Institute for Applied Mathematics ‘Mauro Picone’, CNR, Naples 80131, Italy
| | - Monica Franzese
- Institute for Applied Mathematics ‘Mauro Picone’, CNR, Naples 80131, Italy
| | - Sylwia Leppert
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
| | - Mariarosaria Papa
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
| | - Marco Cammisa
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta 81100, Italy
| | - Giacomo Grillo
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France
| | - Guillame Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France
| | - Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Maurizio D’Esposito
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Claudia Angelini
- Institute for Applied Mathematics ‘Mauro Picone’, CNR, Naples 80131, Italy
| | - Maria R. Matarazzo
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
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45
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Abstract
Long noncoding RNAs (lncRNAs) are a relatively well-characterized class of noncoding RNA (ncRNA) molecules, involved in the regulation of various cell processes, including transcription, intracellular trafficking, and chromosome remodeling. Their deregulation has been associated with the development and progression of various cancer types, the fact which makes them suitable as biomarkers for cancer diagnosis and prognosis. In recent years, detection of cancer-associated lncRNAs in body fluids of cancer patients has proven itself as an especially valuable method to effectively diagnose cancer. Cancer diagnosis and prognosis employing circulating lncRNAs are preferential when compared to classical biopsies of tumor tissues, especially due to their noninvasiveness, and have great potential for routine usage in clinical practice. Thus, this review focuses on summarizing the perspectives of lncRNAs as biomarkers in cancer, based on evaluating their expression profiles determined in body fluids of cancer patients.
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46
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Strategies to identify natural antisense transcripts. Biochimie 2017; 132:131-151. [DOI: 10.1016/j.biochi.2016.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022]
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47
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Dang Y, Cheng J, Sun X, Zhou Z, Liu Y. Antisense transcription licenses nascent transcripts to mediate transcriptional gene silencing. Genes Dev 2016; 30:2417-2432. [PMID: 27856616 PMCID: PMC5131781 DOI: 10.1101/gad.285791.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/21/2016] [Indexed: 12/21/2022]
Abstract
In this study, Dang et al. use Neurospora to demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism. In eukaryotes, antisense transcription can regulate sense transcription by induction of epigenetic modifications. We showed previously that antisense transcription triggers Dicer-independent siRNA (disiRNA) production and disiRNA locus DNA methylation (DLDM) in Neurospora crassa. Here we show that the conserved exonuclease ERI-1 (enhanced RNAi-1) is a critical component in this process. Antisense transcription and ERI-1 binding to target RNAs are necessary and sufficient to trigger DLDM. Convergent transcription causes stalling of RNA polymerase II during transcription, which permits ERI-1 to bind nascent RNAs in the nucleus and recruit a histone methyltransferase complex that catalyzes chromatin modifications. Furthermore, we show that, in the cytoplasm, ERI-1 targets hundreds of transcripts from loci without antisense transcription to regulate RNA stability. Together, our results demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism.
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Affiliation(s)
- Yunkun Dang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianyun Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Beijing 100080, China
| | - Zhipeng Zhou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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48
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Xu Y, Qiu M, Chen Y, Wang J, Xia W, Mao Q, Yang L, Li M, Jiang F, Xu L, Yin R. Long noncoding RNA, tissue differentiation-inducing nonprotein coding RNA is upregulated and promotes development of esophageal squamous cell carcinoma. Dis Esophagus 2016; 29:950-958. [PMID: 26833746 DOI: 10.1111/dote.12436] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the major causes of cancer death worldwide, especially in Eastern Asia. Due to the poor prognosis, it is necessary to further dissect the underlying mechanisms and explore therapeutic targets of ESCC. Recently, studies show that long noncoding RNAs (lncRNAs) have critical roles in diverse biological processes, including tumorigenesis. Increasing evidence indicates that some lncRNAs are widely involved in the development and progression of ESCC, such as HOTAIR, SPRY4-IT1 and POU3F3. An emerging lncRNA, tissue differentiation-inducing nonprotein coding RNA (TINCR), has been studied in human cutaneous squamous cell carcinoma and has critical biological function, but its role in ESCC remains unknown. Here, we evaluated the expression profile of TINCR and its biological function in ESCC. In a cohort of 56 patients, TINCR was significantly overexpressed in ESCC tissues compared with paired adjacent normal tissues. Further, in vitro silencing TINCR via small interfering RNA (siRNA) inhibited the proliferation, migration and invasion of ESCC cells. Meantime, siRNA treatment induced apoptosis and blocked the progression of cell cycle. Taken together, our study suggests that TINCR promotes proliferation, migration and invasion of ESCC cells, acting as a potential oncogene of ESCC.
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Affiliation(s)
- Y Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,The First Clinical College of Nanjing Medical University, Nanjing, China
| | - M Qiu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Y Chen
- Department of Thoracic Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China
| | - J Wang
- Department of Scientific Research, Nanjing Medical University, Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing, China
| | - W Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Q Mao
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - L Yang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing, China
| | - M Li
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - F Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - L Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - R Yin
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
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49
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Qi D, Li J, Que B, Su J, Li M, Zhang C, Yang M, Zhou G, Ji W. Long non-coding RNA DBCCR1-003 regulate the expression of DBCCR1 via DNMT1 in bladder cancer. Cancer Cell Int 2016; 16:81. [PMID: 27777512 PMCID: PMC5069854 DOI: 10.1186/s12935-016-0356-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 10/03/2016] [Indexed: 01/17/2023] Open
Abstract
Background Many long non coding RNAs have been identified as key modulators in cancer development. A lncRNA, DBCCR1-003, derived from the locus of tumor suppressor gene DBCCR1 (deleted in bladder cancer chromosome region 1), has unknown function. In the present study, we explored function and molecular mechanism of DBCCR1-003 in bladder cancer (BC) development. Methods We evaluated the expression levels of DBCCR1-003 in tissues and cells with western blot and quantitative real-time polymerase chain reaction. Multiple approaches including chromatin immunoprecipitation assay and RNA immunoprecipitation were used to confirm the direct binding of DBCCR1-003 to DNMT1. The recombinant vector overexpressing DBCCR1-003 was constructed. Cell proliferation assay, colony formation assay and flow cytometric analysis were employed to measure the role of DBCCR1-003 in regulation of cell proliferation, cycle and apoptosis. Results Firstly we detected the expression of DBCCR1-003, DBCCR1, DNMT1 (DNA methyltransferase 1) and DNA methylation in the promoter of DBCCR1. We found low expression of DBCCR1-003, same as DBCCR1, while high expression of DNMT1 and hypermethylation of DBCCR1 gene promoter in BC tissues and T24 cells line. Further studies revealed that treatment of DNMT inhibitor, 5-aza-2-deoxycytidine(DAC), or overexpression of DBCCR1-003 led to increased DBCCR1 expression by reversion of promoter hypermethylation and DNMT1 binding to DBCCR1 promoter in T24 cells. Importantly, RNA immunoprecipitation (RIP) showed that DBCCR1-003 physically associates with DNMT1. The binding of them was increased with the inhibition of DBCCR1 promoter methylation, indicating that DBCCR1-003 may bind to DNMT1 and prevent DNMT1-mediated the methylation of DBCCR1. Furthermore, overexpression of DBCCR1-003 resulted in significant inhibition of T24 cells growth through the inducing G0/G1 arrest and apoptosis. Conclusions Taken together, these findings demonstrated that a novel tumor suppressor DBCCR1-003 regulates the expression of DBCCR1 via binding to DNMT1 and preventing DNMT1-mediated the methylation of DBCCR1 in BC. LncRNA DBCCR1-003 may serve as a novel biomarker and therapeutic target for BC in future cancer clinic. Electronic supplementary material The online version of this article (doi:10.1186/s12935-016-0356-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Defeng Qi
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Jinhui Li
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China.,The Affiliated Hospital of School of Medicine of Ningbo University, Zhejiang, 315000 China
| | - Biao Que
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Jialin Su
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China.,The First Affiliated Hospital, Center for Translational Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Mengxi Li
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Chaofeng Zhang
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Mei Yang
- Breast Disease Center, Guangdong Women and Children Hospital of Guangzhou Medical University, Guangzhou, 510010 Guangdong China.,Department of General Surgery, General Hospital of Guangzhou Military Command of PLA, Guangzhou, 510010 Guangdong China
| | - Guoren Zhou
- Department of Medical Oncology, Jiangsu Cancer Hospital, Nanjing, 210009 Jiangsu China
| | - Weidong Ji
- The First Affiliated Hospital, Center for Translational Medicine, Sun Yat-sen University, Guangzhou, 510080 China
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50
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Li Z, Hou P, Fan D, Dong M, Ma M, Li H, Yao R, Li Y, Wang G, Geng P, Mihretab A, Liu D, Zhang Y, Huang B, Lu J. The degradation of EZH2 mediated by lncRNA ANCR attenuated the invasion and metastasis of breast cancer. Cell Death Differ 2016; 24:59-71. [PMID: 27716745 DOI: 10.1038/cdd.2016.95] [Citation(s) in RCA: 248] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 07/19/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022] Open
Abstract
EZH2 (the Enhancer of Zeste Homolog 2), as a key epigenetic regulator and EMT inducer, participates in a variety of cancer metastasis. EZH2 stability is regulated by several types of post-translational modifications (PTMs).The long non-coding RNAs (lncRNA) have been implicated to have critical roles in multiple carcinogenesis through a wide range of mechanisms, including modulating the stability of proteins. To date, whether the stability of EZH2 protein is regulated by lncRNAs remains unexplored. Here we report the discovery of ANCR modulating the stability of EZH2, and hence in the invasion and metastasis of breast cancer cells. We determined that ANCR potentiated the CDK1-EZH2 interaction, which then increased the intensity of phosphorylation at Thr-345 and Thr-487 sites of EZH2, facilitating EZH2 ubiquitination and hence its degradation. Moreover, we also uncover ANCR is an important player in breast cancer progression and metastasis mainly through decreasing EZH2 stability. More specifically, we initially found that ANCR level was lower in breast cancer tissues and breast cancer cell lines, in contrast to their normal counterparts. We then demonstrated that knockdown of ANCR induced an EMT program and promoted cell migration and invasion in MCF10A (epithelial cells), whereas ectopic expression of ANCR repressed breast cancer cells migration and invasion. Furthermore, we validated in a nude mouse model that overexpression of ANCR in highly malignant and invasive MDA-MB-231 breast cancer cells significantly reduced the ability of the cells to form tumors and prevented the lung metastasis in vivo. Based on these data, our findings define a new mechanism underlying modulation of EZH2 stability by linking ANCR interaction with EZH2 to promote its phosphorylation that facilitates EZH2 degradation and suppresses breast cancer progression.
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Affiliation(s)
- Zhongwei Li
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Pingfu Hou
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Dongmei Fan
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Meichen Dong
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Musong Ma
- The Breast Surgery, The Tumor Hospital of Jilin Province, Changchun, China
| | - Hongyuan Li
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Ruosi Yao
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yuxin Li
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, China
| | - Guannan Wang
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, China
| | - Pengyu Geng
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Adhanom Mihretab
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Dongxu Liu
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Yu Zhang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Baiqu Huang
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jun Lu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
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