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Ren Y, Chen J, Wang Y, Fu S, Bu W, Xue H. The lncRNA-mediated ceRNA network of Altica viridicyanea is involved in the regulation of the Toll/Imd signaling pathway under antibiotic treatment. Front Physiol 2023; 14:1244190. [PMID: 37664435 PMCID: PMC10470016 DOI: 10.3389/fphys.2023.1244190] [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: 06/22/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play significant roles in the regulation of mRNA expression or in shaping the competing endogenous RNA (ceRNA) network by targeting miRNA. The insect gut is one of the most important tissues due to direct contact with external pathogens and functions in the immune defense against pathogen infection through the innate immune system and symbionts, but there are limited observations on the role of the lncRNA-involved ceRNA network of the Toll/Imd pathway and correlation analysis between this network and bacterial microbiota in the Altica viridicyanea gut. In this research, we constructed and sequenced six RNA sequencing libraries using normal and antibiotic-reared samples, generating a total of 17,193 lncRNAs and 26,361 mRNAs from massive clean data by quality control and bioinformatic analysis. Furthermore, a set of 8,539 differentially expressed lncRNAs (DELs) and 13,263 differentially expressed mRNAs (DEMs), of which related to various immune signaling pathways, such as the Toll/Imd, JAK/STAT, NF-κB, and PI3K-Akt signaling pathways, were obtained between the two experimental groups in A. viridicyanea. In addition, numerous GO and KEGG enrichment analyses were used to annotate the DELs and their target genes. Moreover, six Toll family members and nineteen signal genes from the Toll/Imd signaling pathway were identified and characterized using online tools, and phylogenetic analyses of the above genes proved their classification. Next, a lncRNA-miRNA-mRNA network of the Toll/Imd pathway was built, and it contained different numbers of DEMs in this pathway and related DELs based on prediction and annotation. In addition, qRT-PCR validation and sequencing data were conducted to show the expression patterns of the above DELs and DEMs related to the Toll/Imd signaling pathway. Finally, the correlated investigations between DELs or DEMs of the Toll/Imd signaling pathway and most changes in the gut bacterial microbiota revealed significantly positive or negative relationships between them. The present findings provide essential evidence for innate immune ceRNAs in the beetle gut and uncover new potential relationships between innate immune pathways and the gut bacterial microbiota in insects.
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Affiliation(s)
| | | | | | | | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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2
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Zhu X, Song J, Wang M, Wang X, Lv L. Dysregulated ceRNA network modulated by copy number variation-driven lncRNAs in breast cancer: A comprehensive analysis. J Gene Med 2023; 25:e3471. [PMID: 36525372 DOI: 10.1002/jgm.3471] [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: 08/10/2022] [Revised: 11/09/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is a malignancy harmful to physical and mental health in women, with quite high mortality. Copy number variations (CNVs) are vital factors affecting the progression of breast cancer. Detecting CNVs in breast cancer to predict the prognosis of patients has become a promising approach to accurate treatment in recent years. The differential analysis was performed on CNVs of long noncoding RNAs (lncRNAs) as well as the expression of lncRNAs, microRNAs (miRNAs) and mRNAs in normal tissue and breast tumor tissue based on The Cancer Genome Atlas (TCGA) database. The CNV-driven lncRNAs were identified by the Kruskal-Wallis test. Meanwhile, a competitive endogenous RNA (ceRNA) network regulated by CNV-driven lncRNA was constructed. As the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed, the mRNAs in the dysregulated ceRNA network were mainly enriched in the biological functions and signaling pathways, including the Focal Adhesion-PI3K-Akt-mTOR-signaling pathway, the neuronal system, metapathway biotransformation Phase I and II and blood circulation, etc. The relationship between the CNVs of five lncRNAs and their gene expression in the ceRNA network was analyzed via a chi-square test, which confirmed that except for LINC00243, the expression of four lncRNAs was notably correlated with the CNVs. The survival analysis revealed that only the copy number gain of LINC00536 was evidently related to the poor prognosis of patients. The CIBERSORT algorithm showed that five lncRNAs were correlated with the abundance of immune cell infiltration and immune checkpoints. In a word, by analyzing CNV-driven lncRNAs and the ceRNA network regulated by these lncRNAs, this study explored the mechanism of breast cancer and provided novel insights into new biomarkers.
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Affiliation(s)
- Xiaotao Zhu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jialu Song
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mingzheng Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaohui Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Lin Lv
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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3
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Yu N, Qin H, Zhang F, Liu T, Cao K, Yang Y, Chen Y, Cai J. The role and mechanism of long non-coding RNAs in homologous recombination repair of radiation-induced DNA damage. J Gene Med 2023; 25:e3470. [PMID: 36537017 DOI: 10.1002/jgm.3470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022] Open
Abstract
DNA double-strand breaks can seriously damage the genetic information that organisms depend on for survival and reproduction. Therefore, cells require a robust DNA damage response mechanism to repair the damaged DNA. Homologous recombination (HR) allows error-free repair, which is key to maintaining genomic integrity. Long non-coding RNAs (lncRNAs) are RNA molecules that are longer than 200 nucleotides. In recent years, a number of studies have found that lncRNAs can act as regulators of gene expression and DNA damage response mechanisms, including HR repair. Moreover, they have significant effects on the occurrence, development, invasion and metastasis of tumor cells, as well as the sensitivity of tumors to radiotherapy and chemotherapy. These studies have therefore begun to expose the great potential of lncRNAs for clinical applications. In this review, we focus on the regulatory roles of lncRNAs in HR repair.
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Affiliation(s)
- Nanxi Yu
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China
| | - Hongran Qin
- Department of Nuclear Radiation, Shanghai Pulmonary Hospital,School of Medicine, Tongji University, Shanghai, China
| | - Fangxiao Zhang
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China
| | - Tingting Liu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Kun Cao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yanyong Yang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yuanyuan Chen
- South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China.,Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Jianming Cai
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China
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Zhang XJ, Xiao ZB, Gu JX, Chen K, Wang J, Xu SL, Xing KK, Chen T. Investigating the molecular mechanisms of delirium-like neuropsychiatric disorder induced by electromagnetic pulse based on bioinformatics analysis. Mol Brain 2023; 16:21. [PMID: 36750928 PMCID: PMC9906835 DOI: 10.1186/s13041-023-00998-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/03/2023] [Indexed: 02/09/2023] Open
Abstract
Electromagnetic pulse (EMP), a unique type of electromagnetic radiation, may induce diverse neuropsychiatric disorders, such as irritability, hyperkinesis, retardation of learning and memory. However, the underlying mechanism of EMP exposure on neuronal injury has not been elucidated. Here, we aimed to delineate the regulatory expression networks based on high-throughput sequencing data to explore the possible molecular mechanisms related to EMP-induced delirium-like neuropsychiatric disorder in rats. It's shown that EMP exposure induced anxiety, cognitive decline and short-term memory impairment. The expression profiles of the long noncoding RNAs (lncRNAs) and mRNAs, along with their biological function and regulatory network, were explored in rats after EMP exposure. We identified 41 differentially expressed lncRNAs (DELs) and 266 differentially expressed mRNAs (DEMs) between EMP and sham groups. Sixty-one co-expression relationships between 18 DELs and 56 DEMs were mostly associated with synapse- and metabolic-related pathways. We predicted 51 DEL-miRNA pairs and 290 miRNA-mRNA pairs using the miRanda database to constructed a DEL-miRNA-DEM network. LncRNA AABR07042999.1 and mRNA Tph2, Slc6a4, Dbh and Th were upregulated, and the contents of serotonin, dopamine and norepinephrine were increased in both PFC and HIP after EMP exposure. The current study provided a better understanding of the ceRNA network, which might reveal the pathological mechanism and provide more treatment options for the EMP-induced neurobehavioral disorder.
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Affiliation(s)
- Xia-Jing Zhang
- grid.440588.50000 0001 0307 1240Institute of Medical Research, Northwestern Polytechnical University, Xi’an, 710072 Shaanxi China ,grid.233520.50000 0004 1761 4404Department of Human Anatomy, Histology and Embryology & K.K. Leung Brain Research Centre, The Fourth Military Medical University, No. 169 Changle West Road, Xi’an, 710032 China
| | - Zhi-Bin Xiao
- grid.233520.50000 0004 1761 4404Department of Anesthesiology, The 986th Air Force Hospital, Xijing Hospital, The Fourth Military Medical University, Shaanxi 710032 Xi’an, China
| | - Jun-Xiang Gu
- grid.452672.00000 0004 1757 5804Department of Neurosurgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Kun Chen
- grid.233520.50000 0004 1761 4404Department of Human Anatomy, Histology and Embryology & K.K. Leung Brain Research Centre, The Fourth Military Medical University, No. 169 Changle West Road, Xi’an, 710032 China
| | - Jian Wang
- grid.460007.50000 0004 1791 6584Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, 710038 China
| | - Sheng-Long Xu
- grid.233520.50000 0004 1761 4404Department of Radiation Biology, Faculty of Preventive Medicine, The Fourth Military Medical University, Xi’an, 710032 China
| | - Ke-Ke Xing
- grid.233520.50000 0004 1761 4404Department of Human Anatomy, Histology and Embryology & K.K. Leung Brain Research Centre, The Fourth Military Medical University, No. 169 Changle West Road, Xi’an, 710032 China
| | - Tao Chen
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China. .,Department of Human Anatomy, Histology and Embryology & K.K. Leung Brain Research Centre, The Fourth Military Medical University, No. 169 Changle West Road, Xi'an, 710032, China.
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Fu Q, Li Y, Zhao S, Wang H, Zhao C, Zhang P, Cao M, Yang N, Li C. Comprehensive identification and expression profiling of immune-related lncRNAs and their target genes in the intestine of turbot (Scophthalmus maximus L.) in response to Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2022; 130:233-243. [PMID: 36084890 DOI: 10.1016/j.fsi.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/22/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Long non-coding RNA (lncRNA) play vital regulatory roles in various biological processes. Intestine is one of the most sensitive organs to environmental and homeostatic disruptions for fish. However, systematic profiles of lncRNAs in the intestine of teleost in responses to pathogen infections is still limited. Turbot (Scophthalmus maximus L.), an important commercial fish species in China, has been suffering with Vibrio anguillarum infection, resulted in dramatic economic loss. Hereinto, the intestinal tissues of turbot were sampled at 0 h, 2 h, 12 h, and 48 h following V. anguillarum infection. The histopathological analysis revealed that the pathological trauma was mainly present in intestinal tunica mucosal epithelium. After high-throughput sequencing and bioinformatic analysis, a total of 9722 lncRNAs and 21,194 mRNAs were obtained, and the average length and exon number of lncRNAs were both less than those of mRNAs. Among which, a set of 158 lncRNAs and 226 mRNAs were differentially expressed (DE-lncRNAs and DEGs) in turbot intestine at three time points, related to many immune-related genes such as complement, interleukin, chemokine, lysosome, and macrophage, indicating their potential critical roles in immune responses. In addition, 2803 and 1803 GO terms were enriched for DEGs and co-expressed target genes of DE-lncRNAs, respectively. Moreover, 127 and 50 KEGG pathways including cell adhesion molecules (CAMs), phagosome, JAK-STAT signaling pathway, cytokine-cytokine receptor interaction, and intestinal immune network for IgA production, were enriched for DEGs and co-expressed target genes of DE-lncRNAs, respectively. Finally, qRT-PCR was conducted to confirm the reliability of sequencing data. The present study will set the foundation for the future exploration of lncRNA functions in teleost in response to bacterial infection.
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Affiliation(s)
- Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuqing Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shoucong Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Haojie Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Chunyan Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Pei Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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6
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Qiu M, Yu C, Zhu S, Liu S, Peng H, Xiong X, Chen J, Jiang X, Du H, Li Q, Zhang Z, Yang C. RNA sequencing reveals lncRNA-mediated non-mendelian inheritance of feather growth change in chickens. Genes Genomics 2022; 44:1323-1331. [PMID: 36087248 PMCID: PMC9569315 DOI: 10.1007/s13258-022-01304-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/07/2022] [Indexed: 11/29/2022]
Abstract
Background Long non-coding RNAs (lncRNAs) play an essential role in biological processes. However, the expression patterns of lncRNAs that regulate the non-Mendelian inheritance feather phenotypes remain unknown. Objective This study aimed to compare the expression profiles of lncRNAs in the follicles of the late-feathering cocks (LC) and late-feathering hens (LH) that followed genetic rules and the early-feathering hen (EH) and early-feathering cock (EC) that did not conform to the genetic laws. Methods We performed RNA sequencing and investigated the differentially expressed lncRNAs (DElncRNAs) between the early- and late-feathering chickens, which function by cis-acting or participate in the competing endogenous RNA (ceRNA) network. Results A total of 53 upregulated and 43 downregulated lncRNAs were identified in EC vs. LC, and 58 upregulated and 109 downregulated lncRNAs were identified in EH vs. LH. The target mRNAs regulated by lncRNAs in cis were enriched in the pentose phosphate pathway, TGF-β signaling pathway and Jak-STAT signaling pathway in EC vs. LC and were associated with the TGF-β signaling pathway, Wnt signaling pathway, p53 signaling pathway and Jak-STAT signaling pathway in EH vs. LH. In addition, the lncRNA-mediated ceRNA regulatory pathways of hair follicle formation were mainly enriched in the TGF-β signaling pathway, Wnt signaling pathway, melanogenesis, and calcium signaling pathways. The levels of ENSGALG00000047626 were significantly higher in the late-feathering chickens than in the early-feathering chickens, which regulated the expression of SSTR2 by gga-miR-1649-5p. Conclusion This study provides a novel molecular mechanism of lncRNA’s response to the feather rate that does not conform to the genetic laws in chickens. Supplementary Information The online version contains supplementary material available at 10.1007/s13258-022-01304-2.
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Affiliation(s)
- Mohan Qiu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China
| | - Chunlin Yu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Xinkang Road, 610066, Chengdu, China
| | - Shiliang Zhu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China
| | - Siyang Liu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China
| | - Han Peng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China
| | - Xia Xiong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China
| | - Jialei Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China
| | - Xiaosong Jiang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China
| | - Huarui Du
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China
| | - Qingyun Li
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China
| | - Zengrong Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China.
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, 7 Niusha Road, 610066, Chengdu, China.
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Construction and Analysis of lncRNA-Associated ceRNA Network in Atherosclerotic Plaque Formation. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4895611. [PMID: 35463977 PMCID: PMC9033352 DOI: 10.1155/2022/4895611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/05/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022]
Abstract
Atherosclerosis (AS) is a vascular disease with plaque formation. Unstable plaques can be expected to result in cardiovascular disease, such as myocardial infarction and stroke. Studies have verified that long noncoding RNAs (lncRNAs) play a critical role in atherosclerotic plaque formation (APF), including MALAT1, GAS5, and H19. A ceRNA network is a combination of these two interacting processes, which regulate the occurrence and progression of many diseases. However, lncRNA-associated ceRNA network in terms of APF is limited. This study sought to discover novel potential biomarkers and ceRNA network for APF. We designed a triple network based on the lncRNA-miRNA and mRNA-miRNA pairs obtained from lncRNASNP and starBase. Differentially expressed genes (DEGs) and lncRNAs in human vascular tissues derived from the Gene Expression Omnibus database (GSE43292, GSE97210) were systematically selected and analyzed. A ceRNA network was constructed by hypergeometric test, including 8 lncRNAs, 243 miRNAs, and 8 mRNAs. APF-related ceRNA structure was discovered for the first time by combining network analysis and statistical validation. Topological analysis determined the key lncRNAs with the highest centroid. GO and KEGG enrichment analysis indicated that the ceRNA network was primarily enriched in “regulation of platelet-derived growth factor receptor signaling pathway,” “negative regulation of leukocyte chemotaxis,” and “axonal fasciculation.” A functional lncRNA, HAND2-AS1, was identified in the ceRNA network, and the main miRNA (miRNA-570-3p) regulated by HAND2-AS1 was further screened. This present study elucidated the important function of lncRNA in the origination and progression of APF and indicated the potential use of these hub nodes as diagnostic biomarkers and therapeutic targets.
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Jain A, McCoy M, Coats C, Brown SZ, Addya S, Pelz C, Sears RC, Yeo CJ, Brody JR. HuR Plays a Role in Double-Strand Break Repair in Pancreatic Cancer Cells and Regulates Functional BRCA1-Associated-Ring-Domain-1(BARD1) Isoforms. Cancers (Basel) 2022; 14:cancers14071848. [PMID: 35406624 PMCID: PMC8997573 DOI: 10.3390/cancers14071848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/07/2022] [Accepted: 04/02/2022] [Indexed: 02/06/2023] Open
Abstract
Human Antigen R (HuR/ELAVL1) is known to regulate stability of mRNAs involved in pancreatic ductal adenocarcinoma (PDAC) cell survival. Although several HuR targets are established, it is likely that many remain currently unknown. Here, we identified BARD1 mRNA as a novel target of HuR. Silencing HuR caused a >70% decrease in homologous recombination repair (HRR) efficiency as measured by the double-strand break repair (pDR-GFP reporter) assay. HuR-bound mRNAs extracted from RNP-immunoprecipitation and probed on a microarray, revealed a subset of HRR genes as putative HuR targets, including the BRCA1-Associated-Ring-Domain-1 (BARD1) (p < 0.005). BARD1 genetic alterations are infrequent in PDAC, and its context-dependent upregulation is poorly understood. Genetic silencing (siRNA and CRISPR knock-out) and pharmacological targeting of HuR inhibited both full length (FL) BARD1 and its functional isoforms (α, δ, Φ). Silencing BARD1 sensitized cells to olaparib and oxaliplatin; caused G2-M cell cycle arrest; and increased DNA-damage while decreasing HRR efficiency in cells. Exogenous overexpression of BARD1 in HuR-deficient cells partially rescued the HRR dysfunction, independent of an HuR pro-oncogenic function. Collectively, our findings demonstrate for the first time that BARD1 is a bona fide HuR target, which serves as an important regulatory point of the transient DNA-repair response in PDAC cells.
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Affiliation(s)
- Aditi Jain
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.C.); (S.Z.B.); (C.J.Y.)
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA;
- Correspondence: (A.J.); (J.R.B.); Tel.: +1-215-955-2693 (A.J.); +1-443-812-1852 (J.R.B.)
| | - Matthew McCoy
- Department of Oncology, Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC 20007, USA;
| | - Carolyn Coats
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.C.); (S.Z.B.); (C.J.Y.)
| | - Samantha Z. Brown
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.C.); (S.Z.B.); (C.J.Y.)
- The Department of Surgery, Brenden-Colson Center for Pancreatic Care, The Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Sankar Addya
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Carl Pelz
- The Department of Molecular and Medical Genetics, Brenden-Colson Center for Pancreatic Care, The Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA; (C.P.); (R.C.S.)
| | - Rosalie C. Sears
- The Department of Molecular and Medical Genetics, Brenden-Colson Center for Pancreatic Care, The Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA; (C.P.); (R.C.S.)
| | - Charles J. Yeo
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.C.); (S.Z.B.); (C.J.Y.)
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Jonathan R. Brody
- The Department of Surgery, Brenden-Colson Center for Pancreatic Care, The Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
- Correspondence: (A.J.); (J.R.B.); Tel.: +1-215-955-2693 (A.J.); +1-443-812-1852 (J.R.B.)
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Wu S, Xu J, Zhang M, Lu X, Wang K, Sun S, Wang Y, Wu J. Analysis of Genetic Variants and the ceRNA Network of miR-9 in Non-Small Cell Lung Cancer. DNA Cell Biol 2022; 41:142-150. [PMID: 35143342 DOI: 10.1089/dna.2021.0549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Objective: To explore the role of single-nucleotide polymorphisms (SNPs) in hsa-miR-9 in non-small cell lung cancer (NSCLC). Methods: Log-rank and Cox regression analyses were conducted to assess the association of four functional SNPs of miR-9 with overall survival (OS) of Chinese patients with NSCLC. A reporter luciferase assay was performed to examine the relationship between the SNPs and transcriptional activity of miR-9. The expression of miR-9 in cells was detected by quantitative real-time PCR assay. Xenograft model was established in nude mice, which were treated with Lv-MiR-9-mimics or Lv-miR-9-inhibitor. A long noncoding RNA (lncRNA)-miR-9-messenger RNA (mRNA) competing endogenous RNA (ceRNA) network was established based on bioinformatics analyses. Results: We found that rs1501672 was associated with the prognosis of 1001 Chinese NSCLC patients (A>G, additive model: adjusted hazard ratio = 0.89, 95% confidence interval = 0.79-1.00, p = 0.056). Luciferase reporter assay showed higher luciferase activity with wild A allele than that with mutant G allele in 293T, SPC-A1, and A549 cell lines. The miR-9 level was significantly higher in lung cancer cells than normal lung cells. miR-9 was also over expressed in lung cancer tissue according to The Cancer Genome Atlas and gene expression omnibus databases. Xenograft models based on H1299 cells showed that lv-miR-9-inhibitor significantly decreased tumor growth compared with the lv-miR-9-NC group (p < 0.001). Bioinformatics analysis showed that one target gene leukemia inhibitory factor receptor and two lncRNAs (KIAA0087 and GVINP1) were associated with OS of NSCLC patients. Conclusion: The rs1501672 of miR-9 was associated with the prognosis of NSCLC patients in the Chinese population. The lncRNA-miR-9-mRNA ceRNA network revealed potential molecular biological regulation pathways and prognostic biomarkers for NSCLC.
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Affiliation(s)
- Shuangshuang Wu
- Jiangsu Provincial Key Laboratory of Geriatrics, Department of Geriatrics, the First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Jiali Xu
- Department of Oncology, the First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Mingjiong Zhang
- Jiangsu Provincial Key Laboratory of Geriatrics, Department of Geriatrics, the First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Xiao Lu
- Department of Oncology, Changshu No.1 People's Hospital, Suzhou, China
| | - Kai Wang
- Jiangsu Provincial Key Laboratory of Geriatrics, Department of Geriatrics, the First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Sibo Sun
- Jiangsu Provincial Key Laboratory of Geriatrics, Department of Geriatrics, the First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Yu Wang
- Jiangsu Provincial Key Laboratory of Geriatrics, Department of Geriatrics, the First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Jianqing Wu
- Jiangsu Provincial Key Laboratory of Geriatrics, Department of Geriatrics, the First Affiliated Hospital with Nanjing Medical University, Nanjing, China
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10
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Corrà F, Crudele F, Baldassari F, Bianchi N, Galasso M, Minotti L, Agnoletto C, Di Leva G, Brugnoli F, Reali E, Bertagnolo V, Vecchione A, Volinia S. UC.183, UC.110, and UC.84 Ultra-Conserved RNAs Are Mutually Exclusive with miR-221 and Are Engaged in the Cell Cycle Circuitry in Breast Cancer Cell Lines. Genes (Basel) 2021; 12:genes12121978. [PMID: 34946928 PMCID: PMC8701292 DOI: 10.3390/genes12121978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 12/13/2022] Open
Abstract
In the human genome, there are about 600 ultra-conserved regions (UCRs), long DNA sequences extremely conserved in vertebrates. We performed a large-scale study to quantify transcribed UCR (T-UCR) and miRNA levels in over 6000 cancer and normal tissue samples to find possible correlation between these kinds of regulatory molecules. Our analysis evidenced several non-coding RNAs showing negative co-regulation with miRNAs; among them, we focused on miR-221 to investigate any relationship with its pivotal role in the cell cycle. We have chosen breast cancer as model, using two cell lines with different phenotypes to carry out in vitro treatments with siRNAs against T-UCRs. Our results demonstrate that the expression of uc.183, uc.110, and uc.84 T-UCRs is mutually exclusive with miR-221 and is engaged in the regulation of CDKN1B expression. In addition, tests with a set of anticancer drugs, including BYL719, AZD5363, AZD8055, AZD7762, and XL765, revealed the modulation of specific T-UCRs without alteration of miR-221 levels.
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Affiliation(s)
- Fabio Corrà
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (F.C.); (F.C.); (F.B.); (N.B.); (M.G.); (L.M.); (F.B.); (V.B.)
| | - Francesca Crudele
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (F.C.); (F.C.); (F.B.); (N.B.); (M.G.); (L.M.); (F.B.); (V.B.)
| | - Federica Baldassari
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (F.C.); (F.C.); (F.B.); (N.B.); (M.G.); (L.M.); (F.B.); (V.B.)
| | - Nicoletta Bianchi
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (F.C.); (F.C.); (F.B.); (N.B.); (M.G.); (L.M.); (F.B.); (V.B.)
| | - Marco Galasso
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (F.C.); (F.C.); (F.B.); (N.B.); (M.G.); (L.M.); (F.B.); (V.B.)
| | - Linda Minotti
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (F.C.); (F.C.); (F.B.); (N.B.); (M.G.); (L.M.); (F.B.); (V.B.)
| | - Chiara Agnoletto
- Advanced Translational Research Laboratory, Veneto Institute of Oncology IOV-IRCCS, 35127 Padua, Italy;
| | - Gianpiero Di Leva
- School of Pharmacy and Bioengineering, Guy Hilton Research Centre, Keele University, Stoke-on-Trent ST4 7QB, UK;
| | - Federica Brugnoli
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (F.C.); (F.C.); (F.B.); (N.B.); (M.G.); (L.M.); (F.B.); (V.B.)
| | - Eva Reali
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy;
| | - Valeria Bertagnolo
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (F.C.); (F.C.); (F.B.); (N.B.); (M.G.); (L.M.); (F.B.); (V.B.)
| | - Andrea Vecchione
- Department of Medical Surgical Science and Translational Medicine-c/o Azienda Ospedaliera Sant’Andrea, Via di Grottarossa 1035, 00189 Rome, Italy;
| | - Stefano Volinia
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (F.C.); (F.C.); (F.B.); (N.B.); (M.G.); (L.M.); (F.B.); (V.B.)
- Correspondence: ; Tel.: +39-0532-455-714
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11
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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12
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Wen J, Liu J, Wang X, Wang J. Triptolide promotes the apoptosis and attenuates the inflammation of fibroblast-like synoviocytes in rheumatoid arthritis by down-regulating lncRNA ENST00000619282. Phytother Res 2021; 35:4334-4346. [PMID: 34161642 DOI: 10.1002/ptr.7129] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/31/2022]
Abstract
Rheumatoid arthritis (RA), recognized as a common chronic autoimmune disease, is characterized by the excessive proliferation and inflammatory infiltration of fibroblast-like synoviocytes (FLS). In this study, our purpose is to elucidate the mechanisms of triptolide (TPL) in the treatment of RA by regulating the long non-coding RNA (lncRNA) ENST00000619282, which promoted apoptosis and reduced inflammatory infiltration of FLS in RA (RA-FLS). RA-FLS was treated with different concentrations of TPL at different time points. CCK-8 assay, ELISA, RT-qPCR, immunofluorescence, TUNEL assay, and the transmission electron microscopy were used to measure the changes of cell viability, apoptosis, and the release of inflammatory cytokines. Next, the involvement of ENST00000619282 in TPL-mediated protection against RA was explored. ENST00000619282 expression was significantly increased in the peripheral blood mononuclear cells (PBMCs) of RA patients. ENST0000061928 expression in RA PBMCs was positively associated with ESR, RF, CCP, and DAS28, while TPL treatment led to a downregulation of ENST00000619282. In addition, ENST00000619282 was significantly increased in RA-FLS. Furthermore, overexpression of ENST00000619282 elevated the levels of pro-apoptotic and pro-inflammatory factors, while reduced the levels of anti-apoptotic proteins and antiinflammatory factors. Besides, TPL treatment could reverse these effects by ENST00000619282 overexpression. The anti-RA potential of TPL might be achieved by downregulating ENST00000619282, thereby promoting apoptosis, and reducing the inflammatory response in RA.
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Affiliation(s)
- Jianting Wen
- College of Traditional Chinese Medicine, Anhui University of Traditional Chinese Medicine, Hefei, China.,Institute of Rheumatology, Anhui Academy of Traditional Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Jian Liu
- Institute of Rheumatology, Anhui Academy of Traditional Chinese Medicine, Hefei, China.,Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Xin Wang
- College of Traditional Chinese Medicine, Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Jie Wang
- College of Traditional Chinese Medicine, Anhui University of Traditional Chinese Medicine, Hefei, China
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13
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Regulatory and Functional Involvement of Long Non-Coding RNAs in DNA Double-Strand Break Repair Mechanisms. Cells 2021; 10:cells10061506. [PMID: 34203749 PMCID: PMC8232683 DOI: 10.3390/cells10061506] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Protection of genome integrity is vital for all living organisms, particularly when DNA double-strand breaks (DSBs) occur. Eukaryotes have developed two main pathways, namely Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR), to repair DSBs. While most of the current research is focused on the role of key protein players in the functional regulation of DSB repair pathways, accumulating evidence has uncovered a novel class of regulating factors termed non-coding RNAs. Non-coding RNAs have been found to hold a pivotal role in the activation of DSB repair mechanisms, thereby safeguarding genomic stability. In particular, long non-coding RNAs (lncRNAs) have begun to emerge as new players with vast therapeutic potential. This review summarizes important advances in the field of lncRNAs, including characterization of recently identified lncRNAs, and their implication in DSB repair pathways in the context of tumorigenesis.
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14
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Zhao H, Wang A, Zhang Z. LncRNA SDHAP1 confers paclitaxel resistance of ovarian cancer by regulating EIF4G2 expression via miR-4465. J Biochem 2021; 168:171-181. [PMID: 32211849 DOI: 10.1093/jb/mvaa036] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer has ranked as one of the leading causes of female morbidity and mortality around the world, which affects ∼239,000 patients and causes 152,000 deaths every year. Chemotherapeutic resistance of ovarian cancer remains a devastating actuality in clinic. The aberrant upregulation of long non-coding RNA succinate dehydrogenase complex flavoprotein subunit A pseudogene 1 (lncRNA SDHAP1) in the Paclitaxel (PTX)-resistant ovarian cancer cell lines has been reported. However, studies focussed on SDHAP1 in its regulatory function of chemotherapeutic resistance in ovarian cancer are limited, and the detailed mechanisms remain unclear. In this study, we demonstrated that SDHAP1 was upregulated in PTX-resistant SKOV3 and Hey-8 ovarian cancer cell lines while the level of miR-4465 was downregulated. Knocking-down SDHAP1 induced re-acquirement of chemo-sensitivity to PTX in ovarian cancer cells in vitro. Mechanically, SDHAP1 upregulated the expression of EIF4G2 by sponging miR-4465 and thus facilitated the PTX-induced apoptosis in ovarian cancer cells. The regulation network involving SDHAP1, miR-4465 and EIF4G2 could be a potential therapy target for the PTX-resistant ovarian cancer.
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Affiliation(s)
- Hui Zhao
- Department of Obstetrics and Gynecology, Liaocheng People's Hospital, No. 67 of Dongchang West Road, Liaocheng 252000, Shandong, China
| | - Aixia Wang
- Department of Obstetrics and Gynecology, Liaocheng People's Hospital, No. 67 of Dongchang West Road, Liaocheng 252000, Shandong, China
| | - Zhiwei Zhang
- Department of Obstetrics and Gynecology, Liaocheng People's Hospital, No. 67 of Dongchang West Road, Liaocheng 252000, Shandong, China
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15
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Jasiak A, Krawczyńska N, Iliszko M, Czarnota K, Buczkowski K, Stefanowicz J, Adamkiewicz-Drożyńska E, Cichosz G, Iżycka-Świeszewska E. Expression of BARD1 β Isoform in Selected Pediatric Tumors. Genes (Basel) 2021; 12:genes12020168. [PMID: 33530592 PMCID: PMC7911681 DOI: 10.3390/genes12020168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 12/20/2022] Open
Abstract
Currently, many new possible biomarkers and mechanisms are being searched and tested to analyse pathobiology of pediatric tumours for the development of new treatments. One such candidate molecular factor is BARD1 (BRCA1 Associated RING Domain 1)—a tumour-suppressing gene involved in cell cycle control and genome stability, engaged in several types of adult-type tumours. The data on BARD1 significance in childhood cancer is limited. This study determines the expression level of BARD1 and its isoform beta (β) in three different histogenetic groups of pediatric cancer—neuroblastic tumours, and for the first time in chosen germ cell tumours (GCT), and rhabdomyosarcoma (RMS), using the qPCR method. We found higher expression of beta isoform in tumour compared to healthy tissue with no such changes concerning BARD1 full-length. Additionally, differences in expression of BARD1 β between histological types of neuroblastic tumours were observed, with higher levels in ganglioneuroblastoma and ganglioneuroma. Furthermore, a higher expression of BARD1 β characterized yolk sac tumours (GCT type) and RMS when comparing with non-neoplastic tissue. These tumours also showed a high expression of the TERT (Telomerase Reverse Transcriptase) gene. In two RMS cases we found deep decrease of BARD1 β in post-chemotherapy samples. This work supports the oncogenicity of the beta isoform in pediatric tumours, as well as demonstrates the differences in its expression depending on the histological type of neoplasm, and the level of maturation in neuroblastic tumours.
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Affiliation(s)
- Anna Jasiak
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
- Laboratory of Clinical Genetics, University Clinical Centre, 17 Smoluchowskiego St., 80-210 Gdansk, Poland
| | - Natalia Krawczyńska
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 407S Goodwin Ave, Urbana, IL 61801, USA;
| | - Mariola Iliszko
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
- Laboratory of Clinical Genetics, University Clinical Centre, 17 Smoluchowskiego St., 80-210 Gdansk, Poland
| | - Katarzyna Czarnota
- Department of Pathology and Neuropathology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (K.C.); (K.B.)
| | - Kamil Buczkowski
- Department of Pathology and Neuropathology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (K.C.); (K.B.)
- Department of Pathomorphology, Copernicus Hospitals, 1-6 Nowe Ogrody St., 80-803 Gdansk, Poland
| | - Joanna Stefanowicz
- Department of Pediatrics, Hematology, Oncology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (J.S.); (E.A.-D.)
| | - Elżbieta Adamkiewicz-Drożyńska
- Department of Pediatrics, Hematology, Oncology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (J.S.); (E.A.-D.)
| | - Grzegorz Cichosz
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
| | - Ewa Iżycka-Świeszewska
- Department of Pathology and Neuropathology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (K.C.); (K.B.)
- Department of Pathomorphology, Copernicus Hospitals, 1-6 Nowe Ogrody St., 80-803 Gdansk, Poland
- Correspondence:
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16
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Long noncoding RNA SNHG1 promotes human prostate cancer progression by sponging miR-383-5p. Anticancer Drugs 2021; 32:286-295. [PMID: 33470616 DOI: 10.1097/cad.0000000000000916] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Prostate cancer is the most common urinary malignancy in males. Long noncoding RNA small nucleolar RNA host gene 1 (lncRNA SNHG1) has been reported to play a crucial role in the development of various cancers. However, the understanding of SNHG1 in prostate cancer is still limited and needs further investigation. In this study, we found the level of SNHG1 was significantly upregulated in prostate cancer tissues and cells. Knockdown of SNHG1 significantly suppressed proliferation, migration and invasion and promoted cell apoptosis in prostate cancer cells. In addition, knockdown of SNHG1 significantly downregulated proliferating cell nuclear antigen and upregulated cleaved caspase-3. MiR-383-5p was identified to be a target of SNHG1 by bioinformatics analysis, dual-luciferase reporter assay, RNA immunoprecipitation assay and RNA pull-down assay. MiR-383-5p was significantly downregulated in prostate cancer tissues and cells. Inhibition of miR-383-5p could partially restore the effects of SNHG1 knockdown on prostate cancer cell proliferation, apoptosis, migration and invasion. Furthermore, murine xenograft models were established to investigate the effects of SNHG1 and miR-383-5p in tumorigenesis in vivo. We found SNHG1 knockdown or miR-383-5p overexpression repressed tumor growth in vivo. In conclusion, SNHG1 contributed to prostate cancer progression by targeting miR-383-5p, elucidating that SNHG1 might be a target for prostate cancer therapy.
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Fang J, Huang C, Ke J, Li J, Zhang W, Xue H, Chen J. lncRNA TTN-AS1 facilitates proliferation, invasion, and epithelial-mesenchymal transition of breast cancer cells by regulating miR-139-5p/ZEB1 axis. J Cell Biochem 2020; 121:4772-4784. [PMID: 32100921 DOI: 10.1002/jcb.29700] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/10/2020] [Indexed: 12/22/2022]
Abstract
Breast cancer is a common malignant tumor suffered predominantly by women worldwide, which results in serious levels of morbidity and mortality. To control the effects of the cancer, it is critically important to elucidate the pathophysiological processes by which it occurs and develops. Reports have demonstrated that long noncoding RNAs perform a critical role in the development and metastasis of cancers. The lncRNA TTN-AS1 is considered carcinogenic. Nevertheless, the importance and biological functions of TTN-AS1 in breast cancer require greater exploration. In the current paper, we observed that TTN-AS1 expression was significantly upregulated in breast cancer tissues/cells compared with those that are healthy. TTN-AS1 enhanced the proliferation, migration, invasion, and epithelial-mesenchymal transformation of breast cancer cells. Furthermore, a direct target of TTN-AS1, miR-139-5p was negatively regulated. In addition, zinc finger E-box binding homeobox 1 (ZEB1) is an important nuclear transcription factor, the expression of which is increased in multiple tumors. Here, we also found that ZEB1 is a target of miR-139-5p, of which TTN-AS1 could regulate the expression through competition with miR-139-5p. That is, TTN-AS1 promoted proliferation and invasion of breast cancer cells by interaction with the miR-139-5p/ZEB1 axis. In conclusion, the present study aimed to illustrate the significance of TTN-AS1 in breast cancer metastasis and contribute to potentially innovative strategies for its treatment.
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Affiliation(s)
- Jun Fang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Chen Huang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jing Ke
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jia Li
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Wei Zhang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Huimin Xue
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jinpeng Chen
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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18
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Li Z, Wang J, Yang J. TUG1 knockdown promoted viability and inhibited apoptosis and cartilage ECM degradation in chondrocytes via the miR-17-5p/FUT1 pathway in osteoarthritis. Exp Ther Med 2020; 20:154. [PMID: 33093892 PMCID: PMC7571376 DOI: 10.3892/etm.2020.9283] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Osteoarthritis (OA) is a degenerative disease characterized by cartilage destruction. Previous research has demonstrated that long non-coding RNAs serve a role in OA progression. The current study aimed to determine the function and mechanism of taurine upregulated gene (TUG) 1 in OA. The results of reverse transcription quantitative PCR revealed that TUG1 was elevated in OA cartilage tissues and interleukin (IL)-1β-induced chondrocytes. Cell Counting kit-8 and flow cytometry analysis revealed that TUG1 knockdown promoted cell viability and inhibited cell apoptosis. Furthermore, matrix metalloprotein (MMP) 13, collagen II and aggrecan expression was determined by western blotting, of which the results demonstrated that TUG1 knockdown significantly decreased MMP13 expression and increased collagen II and aggrecan expression in IL-1β-stimulated chondrocytes, indicating that extracellular matrix (ECM) damage was inhibited. Additionally, using bioinformatics analysis, dual-luciferase reporter and RNA immunoprecipitation assays, TUG1 was revealed to upregulate fucosyltransferase (FUT) 1 by targeting miR-17-5p. Furthermore, miR-17-5p was downregulated and FUT1 upregulated in OA cartilage tissues and IL-1β-induced chondrocytes. TUG1 overexpression reversed the aforementioned effects on cell viability, cell apoptosis and ECM degradation mediated by miR-17-5p in IL-1β-activated chondrocytes. Additionally, the effects of FUT1 knockdown on cell viability, apoptosis and ECM degradation mediated by FUT1 knockdown were reversed by miR-17-5p inhibition. In conclusion, TUG1 knockdown inhibited OA progression by downregulating FUT1 via miR-17-5p.
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Affiliation(s)
- Zhichao Li
- Department of Hand, Foot and Vascular Surgery, Hanyang Hospital, Wuhan University of Science and Technology, Wuhan, Hubei 430050, P.R. China
| | - Jin Wang
- Department of Hand, Foot and Vascular Surgery, Hanyang Hospital, Wuhan University of Science and Technology, Wuhan, Hubei 430050, P.R. China
| | - Jing Yang
- Department of Cardiology, Renmin Hospital, Wuhan University, Wuhan, Hubei 430060, P.R. China
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19
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Shen W, Yu L, Cong A, Yang S, Wang P, Han G, Gu B, Zhang W. Silencing lncRNA AFAP1-AS1 Inhibits the Progression of Esophageal Squamous Cell Carcinoma Cells via Regulating the miR-498/VEGFA Axis. Cancer Manag Res 2020; 12:6397-6409. [PMID: 32801880 PMCID: PMC7402668 DOI: 10.2147/cmar.s254302] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/11/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose In view of the continuous increase of the mortality rate, esophageal squamous cell carcinoma (ESCC) develops into a major health concern. In this study, we aimed to investigate the underlying mechanism of long noncoding RNA (lncRNA) actin filament-associated protein 1 antisense RNA (AFAP1-AS1)/microRNA-498 (miR-498)/vascular endothelial growth factor A (VEGFA) in ESCC cells. Methods The expression levels of AFAP1-AS1, miR-498 and VEGFA in ESCC tissues and cells were detected using quantitative real-time polymerase chain reaction (qRT-PCR). The effects of AFAP1-AS1 on ESCC cells proliferation and apoptosis were measured by methyl thiazolyl tetrazolium (MTT) and flow cytometry, respectively. Transwell assay was carried out to determine cell migration. In addition, VEGFA and cell behaviors-related proteins were determined by Western blot analysis. The targeted relationships of AFAP1-AS1 were verified by dual-luciferase reporter and RNA pull-down assays. Results The expression levels of lncRNA AFAP1-AS1 and VEGFA mRNA were upregulated, but miR-498 was downregulated in ESCC tissues and cells. Moreover, miR-498 was directly targeted by AFAP1-AS1 and there was a negative correlation between miR-498 and AFAP1-AS1. Functionally, AFAP1-AS1 silencing inhibited the proliferation and migration and induced apoptosis of ESCC cells. Interestingly, miR-498 inhibition rescued the effects of AFAP1-AS1 knockdown on cell proliferation, apoptosis and migration and restored the expression levels of tumor-developing marker proteins of AFAP1-AS1 silencing in Eca109 and KYSE-30 cells. Furthermore, VEGFA was verified as a direct target of miR-498 and reversed the effects of miR-498 overexpression on cell behaviors of ESCC in vitro. Conclusion Downregulation of AFAP1-AS1 impeded the proliferation and migration and induced apoptosis of ESCC cells by regulating miR-498/VEGFA axis, which might serve as a novel biomarker for the diagnosis and treatment of ESCC.
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Affiliation(s)
- Wenhao Shen
- Department of Oncology, Taizhou People's Hospital, Taizhou, Jiangsu, People's Republic of China.,Medical School of Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Lei Yu
- Department of Oncology, Taizhou People's Hospital, Taizhou, Jiangsu, People's Republic of China.,Medical School of Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Aihua Cong
- Department of Oncology, Taizhou People's Hospital, Taizhou, Jiangsu, People's Republic of China.,Medical School of Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Song Yang
- Department of Oncology, Taizhou People's Hospital, Taizhou, Jiangsu, People's Republic of China.,Medical School of Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Peng Wang
- Department of Oncology, Taizhou People's Hospital, Taizhou, Jiangsu, People's Republic of China.,Medical School of Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Gaohua Han
- Department of Oncology, Taizhou People's Hospital, Taizhou, Jiangsu, People's Republic of China.,Medical School of Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Bin Gu
- Medical School of Nantong University, Nantong, Jiangsu, People's Republic of China.,Department of Emergency, Taizhou People's Hospital, Taizhou, Jiangsu, People's Republic of China
| | - Wei Zhang
- Medical School of Nantong University, Nantong, Jiangsu, People's Republic of China.,Department of Infectious Disease, Taizhou People's Hospital, Taizhou, Jiangsu, People's Republic of China
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20
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The Effects of Genetic and Epigenetic Alterations of BARD1 on the Development of Non-Breast and Non-Gynecological Cancers. Genes (Basel) 2020; 11:genes11070829. [PMID: 32708251 PMCID: PMC7396976 DOI: 10.3390/genes11070829] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023] Open
Abstract
Breast Cancer 1 (BRCA1) gene is a well-characterized tumor suppressor gene, mutations of which are primarily found in women with breast and ovarian cancers. BRCA1-associated RING domain 1 (BARD1) gene has also been identified as an important tumor suppressor gene in breast, ovarian, and uterine cancers. Underscoring the functional significance of the BRCA1 and BARD1 interactions, prevalent mutations in the BRCA1 gene are found in its RING domain, through which it binds the RING domain of BARD1. BARD1-BRCA1 heterodimer plays a crucial role in a variety of DNA damage response (DDR) pathways, including DNA damage checkpoint and homologous recombination (HR). However, many mutations in both BARD1 and BRCA1 also exist in other domains that significantly affect their biological functions. Intriguingly, recent genome-wide studies have identified various single nucleotide polymorphisms (SNPs), genetic alterations, and epigenetic modifications in or near the BARD1 gene that manifested profound effects on tumorigenesis in a variety of non-breast and non-gynecological cancers. In this review, we will briefly discuss the molecular functions of BARD1, including its BRCA1-dependent as well as BRCA1-independent functions. We will then focus on evaluating the common BARD1 related SNPs as well as genetic and epigenetic changes that occur in the non-BRCA1-dominant cancers, including neuroblastoma, lung, and gastrointestinal cancers. Furthermore, the pro- and anti-tumorigenic functions of different SNPs and BARD1 variants will also be discussed.
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21
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Shan Q, Qu F, Yang W, Chen N. Effect of LINC00657 on Apoptosis of Breast Cancer Cells by Regulating miR-590-3p. Cancer Manag Res 2020; 12:4561-4571. [PMID: 32606949 PMCID: PMC7305342 DOI: 10.2147/cmar.s249576] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Objective To investigate the effect of LINC00657 on breast carcinoma by regulating miR-590-3p. Methods Ninety-seven cases with breast carcinoma who were admitted to Qingdao Chengyang People’s Hospital were collected. The breast carcinoma (n=97) and tumor-adjacent tissues (n=97) of patients were collected during the operation with the permission of the patients. The expressions of LINC00657 and miR-590-3p were detected in breast carcinoma cells and tissues. The breast carcinoma cells were transfected and their proliferation, migration, invasion and apoptosis were detected. Results LINC00657 was highly expressed in breast carcinoma tissues, while miR-590-3p was reduced (P<0.05). The proliferation, invasion and migration of cells transfected with si-LINC00657 or miR-590-3p-mimics were significantly inhibited, and the apoptosis rate increased, resulting in the up-regulation of the expressions of apoptosis-related proteins Bax and Caspase-3 and the reduction of Bcl-2 (P<0.05). After si-LINC00657 or miR-590-3p-mimics, the level of GOLPH3 decreased. Through double luciferase report and RIP experiment, it was confirmed that LINC00657 could act as a sponge of miR-590-3p to negatively regulate its expression. After correlation analysis, it was concluded that there was a negative correlation between LINC00657 and miR-590-3p. Rescue experiments concluded that co-transfection of si-LINC00657+miR-590-3P-inhibitor could reverse the inhibitory action of si-LINC00657 on breast carcinoma cells. Conclusion LINC00657 can participate in the biological behavior process of breast carcinoma by regulating miR-590-3p/GOLPH3 signal.
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Affiliation(s)
- Qiuli Shan
- College of Biological Science and Technology, University of Jinan, Jinan 250022, People's Republic of China
| | - Fan Qu
- College of Biological Science and Technology, University of Jinan, Jinan 250022, People's Republic of China
| | - Weiping Yang
- Department of Thyroid Breast Surgery, Qingdao Chengyang People's Hospital, Qingdao, People's Republic of China
| | - Ningning Chen
- College of Biological Science and Technology, University of Jinan, Jinan 250022, People's Republic of China
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22
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Advances in DNA Repair-Emerging Players in the Arena of Eukaryotic DNA Repair. Int J Mol Sci 2020; 21:ijms21113934. [PMID: 32486270 PMCID: PMC7313471 DOI: 10.3390/ijms21113934] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA is constantly damaged by factors produced during natural metabolic processes as well as agents coming from the external environment. Considering such a wide array of damaging agents, eukaryotic cells have evolved a DNA damage response (DRR) that opposes the influence of deleterious factors. Despite the broad knowledge regarding DNA damage and repair, new areas of research are emerging. New players in the field of DDR are constantly being discovered. The aim of this study is to review current knowledge regarding the roles of sirtuins, heat shock proteins, long-noncoding RNAs and the circadian clock in DDR and distinguish new agents that may have a prominent role in DNA damage response and repair.
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23
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Hao Y, Li X, Chen H, Huo H, Liu Z, Chai E. Over-expression of long noncoding RNA HOTAIRM1 promotes cell proliferation and invasion in human glioblastoma by up-regulating SP1 via sponging miR-137. Neuroreport 2020; 31:109-117. [PMID: 31876683 DOI: 10.1097/wnr.0000000000001380] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glioblastoma is the most aggressive malignant brain tumor in adults. Long noncoding RNA HOTAIRM1 (HOX antisense intergenic RNA myeloid 1) has been reported to participate in the progression of various cancers. However, the role of HOTAIRM1 in glioblastoma and its underlying mechanisms are largely unknown. The relative expression levels of HOTAIRM1, miR-137 and specificity protein 1 were detected by quantitative real-time PCR or western blot. The effects of HOTAIRM1 on cell proliferation and invasion were evaluated by Cell Counting Kit-8 assay and Transwell assay, respectively. The interactions among HOTAIRM1, miR-137 and specificity protein 1 were predicted by online softwares and confirmed by luciferase reporter assay and RNA immunoprecipitation assay. The levels of HOTAIRM1 and specificity protein 1 were significantly increased while miR-137 was significantly decreased in glioblastoma tissues and cells. Knockdown of HOTAIRM1 suppressed proliferation and invasion in glioblastoma cells. Moreover, miR-137 was bound to HOTAIRM1, and specificity protein 1 was identified as a target of miR-137. The protein level of specificity protein 1 was repressed by silencing the expression of HOTAIRM1, whereas the effect was restored by inhibiting the expression of miR-137. Downregulation of HOTAIRM1 expression suppressed the proliferation and invasion of glioblastoma cells by down-regulating specificity protein 1 expression via sponging miR-137, indicating a promising strategy for glioblastoma treatment.
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Affiliation(s)
- Yunfei Hao
- Cerebrovascular Disease Center, Gansu Provincial Hospital
| | - Xiaoli Li
- Department of Nephrology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Hecheng Chen
- Cerebrovascular Disease Center, Gansu Provincial Hospital
| | - Hongzhi Huo
- Cerebrovascular Disease Center, Gansu Provincial Hospital
| | - Zongbao Liu
- Cerebrovascular Disease Center, Gansu Provincial Hospital
| | - Erqing Chai
- Cerebrovascular Disease Center, Gansu Provincial Hospital
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24
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Li X, Chen M, Shi Q, Zhang H, Xu S. Hydrogen sulfide exposure induces apoptosis and necroptosis through lncRNA3037/miR-15a/BCL2-A20 signaling in broiler trachea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 699:134296. [PMID: 31683218 DOI: 10.1016/j.scitotenv.2019.134296] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Hydrogen sulfide (H2S) is an air pollutant, has toxic effects on respiratory tract. However, the underlying mechanisms of H2S induced respiratory toxicity and the roles of long non-coding RNAs (lncRNA) and microRNA (miRNA) in this process remain poorly understood. To clear this, we investigated the change of tracheal tissue ultrastructure and the expression profiles of lncRNAs and miRNAs of chicken trachea exposed to H2S for 42 days. Results showed that H2S exposure triggered apoptosis, necroptosis, and differential expression of 16 lncRNAs and 18 miRNAs in broiler tracheas. The results of LMH cells stimulated by NaHS in vitro also showed the occurrence of apoptosis and necroptosis. LncRNA3037 is down-regulated and miR-15a is up-regulated in tracheal tissue and LMH cells under H2S exposure. Bioinformatics analysis and dual luciferase reporter system showed lncRNA3037 bound directly to miR-15a and negatively regulates each other. A20 and BCL2 are the target genes of miR-15a and negatively regulated by it. Overexpression of miR-15a caused apoptosis and necroptosis and its inhibition partially reversed apoptosis and necroptosis of LMH cells caused by NaHS stimulation and lncRNA3037 knockdown. Taken together, we concluded that H2S exposure mediates apoptosis and necroptosis through lncRNA3037/miR-15/A20-BCL2. These results provide new insights for unveiling the biological effects of H2S in vivo and in vitro.
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Affiliation(s)
- Xiaojing Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Menghao Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Qunxiang Shi
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Shiwen Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China; Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China.
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25
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Chen F, Li Z, Deng C, Yan H. Integrated analysis identifying new lncRNA markers revealed in ceRNA network for tumor recurrence in papillary thyroid carcinoma and build of nomogram. J Cell Biochem 2019; 120:19673-19683. [PMID: 31271223 DOI: 10.1002/jcb.29273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/18/2019] [Indexed: 02/05/2023]
Abstract
OBJECT The risk of tumor recurrence is currently the focus of clinical attention in the treatment of papillary thyroid carcinoma (PTC). This study focuses on the identification of novel prognostic long noncoding RNA (lncRNA) signatures for tumor recurrence in PTC. METHOD RNA sequencing profiling of patients with PTC was obtained from the TCGA and Gene Expression Omnibus databases. Differently expressed lncRNA, microRNA (miRNA), and messenger RNA (mRNA) signatures between patients with and without tumor recurrence were selected. The lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network for tumor recurrence in PTC was constructed to identify lncRNAs associated with tumor relapse in papillary carcinoma. Functional enrichment analysis was performed. Adjusted odds ratios were estimated to identify candidate prognostic lncRNAs considering clinical covariates. Validation analysis was conducted. Nomogram was built based on the verified prognostic lncRNAs and clinical features. RESULTS The lncRNA-miRNA-mRNA ceRNA network for tumor recurrence in PTC was constructed. Functional enrichment analysis suggested that the identified lncRNAs were associated with PTC. Adjusted odds ratios indicated that 5 of the 16 selected lncRNAs were candidate biomarkers predicting tumor recurrence of thyroid carcinoma. Among which, TTTY10 was verified as novel prognostic markers in validation analysis. Nomogram was built based on the newly identified lncRNA biomarker and clinical covariates. CONCLUSION In this study, lncRNA TTTY10 was identified as potential novel prognostic markers predicting tumor recurrence in PTC. It may provide useful information for future molecular and cohort studies focusing on the prognosis of PTC.
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Affiliation(s)
- Fangyao Chen
- Department of Epidemiology and Biostatistics, Health Science Center, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhe Li
- First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Changyu Deng
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
| | - Hong Yan
- Department of Epidemiology and Biostatistics, Health Science Center, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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26
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Walker LC, Lattimore VL, Kvist A, Kleiblova P, Zemankova P, de Jong L, Wiggins GAR, Hakkaart C, Cree SL, Behar R, Houdayer C, Investigators KC, Parsons MT, Kennedy MA, Spurdle AB, de la Hoya M. Comprehensive Assessment of BARD1 Messenger Ribonucleic Acid Splicing With Implications for Variant Classification. Front Genet 2019; 10:1139. [PMID: 31803232 PMCID: PMC6877745 DOI: 10.3389/fgene.2019.01139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022] Open
Abstract
Introduction: Case-control analyses have shown BARD1 variants to be associated with up to >2-fold increase in risk of breast cancer, and potentially greater risk of triple negative breast cancer. BARD1 is included in several gene sequencing panels currently marketed for the prediction of risk of cancer, however there are no gene-specific guidelines for the classification of BARD1 variants. We present the most comprehensive assessment of BARD1 messenger RNA splicing, and demonstrate the application of these data for the classification of truncating and splice site variants according to American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines. Methods: Nanopore sequencing, short-read RNA-seq (whole transcriptome and targeted), and capillary electrophoresis analysis were performed by four laboratories to investigate alternative BARD1 splicing in blood, breast, and fimbriae/ovary related specimens from non-cancer affected tissues. Splicing data were also collated from published studies of nine different tissues. The impact of the findings for PVS1 annotation was assessed for truncating and splice site variants. Results: We identified 62 naturally occurring alternative spliced BARD1 splicing events, including 19 novel events found by next generation sequencing and/or reverse transcription PCR analysis performed for this study. Quantitative analysis showed that naturally occurring splicing events causing loss of clinically relevant domains or nonsense mediated decay can constitute up to 11.9% of overlapping natural junctions, suggesting that aberrant splicing can be tolerated up to this level. Nanopore sequencing of whole BARD1 transcripts characterized 16 alternative isoforms from healthy controls, revealing that the most complex transcripts combined only two alternative splicing events. Bioinformatic analysis of ClinVar submitted variants at or near BARD1 splice sites suggest that all consensus splice site variants in BARD1 should be considered likely pathogenic, with the possible exception of variants at the donor site of exon 5. Conclusions: No BARD1 candidate rescue transcripts were identified in this study, indicating that all premature translation-termination codons variants can be annotated as PVS1. Furthermore, our analysis suggests that all donor and acceptor (IVS+/-1,2) variants can be considered PVS1 or PVS1_strong, with the exception of variants targeting the exon 5 donor site, that we recommend considering as PVS1_moderate.
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Affiliation(s)
- Logan C. Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Petra Kleiblova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Lucy de Jong
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - George A. R. Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Christopher Hakkaart
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simone L. Cree
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Raquel Behar
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Claude Houdayer
- Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - kConFab Investigators
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Research Department, Peter MacCallum Cancer Center, Melbourne, VIC, Australia
| | - Michael T. Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Martin A. Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Amanda B. Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
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Identification of Long Non-Coding RNA-Associated Competing Endogenous RNA Network in the Differentiation of Chicken Preadipocytes. Genes (Basel) 2019; 10:genes10100795. [PMID: 31614854 PMCID: PMC6826404 DOI: 10.3390/genes10100795] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence indicates that long noncoding RNAs (lncRNAs) play important roles in the regulation of cell differentiation by acting as competing endogenous RNA (ceRNA). However, the regulatory mechanisms of lncRNA and the lncRNA-associated ceRNA network involved in adipogenic differentiation of chicken preadipocytes remain elusive. Here, we first constructed the chicken preadipocyte in vitro induction model. Then, we identified differentially expressed lncRNAs (DELs), miRNAs (DEMis), and mRNAs (DEMs) between differentiated and undifferentiated preadipocytes. Furthermore, we constructed the lncRNA associated ceRNA network by gene expression correlation analysis and target prediction of DELs, DEMis, and DEMs. Finally, we determined twelve candidate lncRNA-miRNA-mRNA interactions from the lncRNA associated ceRNA network. Eight out of the twelve interactions were validated by RT-qPCR, indicating their potential role in the regulation of chicken preadipocytes differentiation. Among the eight interactions, TCONS_00026544-gga-miR-128-1-5p-RASD1, TCONS_00055280-gga-miR-135a-5p-JAM3, TCONS_00055280-gga-miR-135a-5p-GPR133, TCONS_00055280-gga-miR-135a-5p-CLDN1, and TCONS_00055280-gga-miR-135a-5p-TMEM123 may promote adipogenic differentiation of chicken preadipocytes while TCONS_00057272-gga-miR-146a-3p-FOXO6, TCONS_00057242-gga-miR-6615-3p-FOXO6, and TCONS_00057242-gga-miR-6615-3p-ENSGALT00000043224 have the opposite effects. Our results not only provide novel insights into ceRNA roles of lncRNAs in chicken preadipocytes differentiation and but also contribute to a better understanding of chicken fat deposition.
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28
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Wu Y, Zhang F, Li X, Hou W, Zhang S, Feng Y, Lu R, Ding Y, Sun L. Systematic analysis of lncRNA expression profiles and atherosclerosis-associated lncRNA-mRNA network revealing functional lncRNAs in carotid atherosclerotic rabbit models. Funct Integr Genomics 2019; 20:103-115. [PMID: 31392586 DOI: 10.1007/s10142-019-00705-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
Abstract
Atherosclerosis, a multifactorial and chronic immune inflammatory disorder, is the main cause of multiple cardiovascular diseases. Researchers recently reported that lncRNAs may exert important functions in the progression of atherosclerosis (AS). Some studies found that lncRNAs can act as ceRNAs to communicate with each other by the competition of common miRNA response elements. However, lncRNA-associated ceRNA network in terms of atherosclerosis is limited. In present study, we pioneered to construct and systematically analyze the lncRNA-mRNA network and reveal its potential roles in carotid atherosclerotic rabbit models. Atherosclerosis was induced in rabbits (n = 3) carotid arteries via a high-fat diet and balloon injury, while age-matched rabbits (n = 3) were treated with normal chow as controls. RNA-seq analysis was conducted on rabbits carotid arteries (n = 6) with or without plaque formation. Based on the ceRNA mechanism, a ternary interaction network including lncRNA, mRNA, and miRNA was generated and an AS-related lncRNA-mRNA network (ASLMN) was extracted. Furthermore, we analyzed the properties of ASLMN and discovered that six lncRNAs (MSTRG.10603.16, 5258.4, 12799.3, 5352.1, 12022.1, and 12250.4) were highly related to AS through topological analysis. GO and KEGG enrichment analysis indicated that lncRNA MSTRG.5258.4 may downregulate inducible co-stimulator to perform a downregulated role in AS through T cell receptor signaling pathway and downregulate THBS1 to conduct a upregulated function in AS through ECM-receptor interaction pathway. Finally, our results elucidated the important function of lncRNAs in the origination and progression of AS. We provided an ASLMN of atherosclerosis development in carotid arteries of rabbits and probable targets which may lay the foundation for future research of clinical applications.
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Affiliation(s)
- Yingnan Wu
- Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Feng Zhang
- Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoying Li
- Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wenying Hou
- Department of Ultrasound, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Shuang Zhang
- Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanan Feng
- Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Rui Lu
- Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Ding
- Department of Bioinformatics, Harbin Medical University, Harbin, China
| | - Litao Sun
- Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
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29
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Wang JD, Zhou HS, Tu XX, He Y, Liu QF, Liu Q, Long ZJ. Prediction of competing endogenous RNA coexpression network as prognostic markers in AML. Aging (Albany NY) 2019; 11:3333-3347. [PMID: 31164492 PMCID: PMC6555472 DOI: 10.18632/aging.101985] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/19/2019] [Indexed: 12/16/2022]
Abstract
Recently, competing endogenous RNAs (ceRNAs) hypothesis has gained a great interest in the study of molecular biological mechanisms of cancer occurrence and progression. However, studies on leukemia are limited, and there is still a lack of comprehensive analysis of lncRNA-miRNA-mRNA ceRNA regulatory network of AML based on high-throughput sequencing and large-scale sample size. We obtained RNA-Seq data and compared the expression profiles between 407 normal whole blood (GTEx) and 151 bone marrows of AML (TCGA). The similarity between two sets of genes with trait in the network was analyzed by weighted correlation network analysis (WGCNA). MiRcode, starBase, miRTarBase, miRDB and TargetScan was used to predict interactions between lncRNAs, miRNAs and target mRNAs. At last, we identified 108 lncRNAs, 10 miRNAs and 8 mRNAs to construct a lncRNA-miRNA-mRNA ceRNA network, which might act as prognostic biomarkers of AML. Among the network, a survival model with 8 target mRNAs (HOXA9+INSR+KRIT1+MYB+SPRY2+UBE2V1+WEE1+ZNF711) was set up by univariate and multivariate cox proportional hazard regression analysis, of which the AUC was 0.831, indicating its sensitivity and specificity in AML prognostic prediction. CeRNA networks could provide further insight into the study on gene regulation and AML prognosis.
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Affiliation(s)
- Jun-Dan Wang
- Department of Hematology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
- Institute of Hematology, Sun Yat-sen University, Guangzhou 510630, China
- Equal contribution
| | - Hong-Sheng Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou 510000, China
- Equal contribution
| | - Xi-Xiang Tu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yi He
- Department of Hematology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
- Institute of Hematology, Sun Yat-sen University, Guangzhou 510630, China
| | - Qi-Fa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou 510000, China
| | - Quentin Liu
- Department of Hematology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
- Institute of Hematology, Sun Yat-sen University, Guangzhou 510630, China
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116000, China
| | - Zi-Jie Long
- Department of Hematology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
- Institute of Hematology, Sun Yat-sen University, Guangzhou 510630, China
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30
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Huang C, Leng D, Lei KC, Sun S, Zhang XD. Transcriptome analysis reveals lncRNA-mediated complex regulatory network response to DNA damage in the liver tissue of Rattus norvegicus. J Cell Physiol 2019; 234:23216-23231. [PMID: 31140619 DOI: 10.1002/jcp.28889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022]
Abstract
DNA is prone to damages, which would result in genetic disorders and enhance risk of tumorigenesis. Hence, understanding the molecular mechanisms of DNA damage and repair will provide deep insights into tumorigenesis, carcinogenesis as well as the corresponding treatments. Aiming at investigating potential long noncoding RNAs (lncRNAs) response against DNA damage, we performed a comprehensive transcriptomic analysis based on RNA sequencing data of the liver tissue from Rattus norvegicus, in which DNA damage was induced using aflatoxin B1, ifosfamide and N-nitrosodimethylamine. Through our analyses, numerous novel lncRNAs are identified for the first time, and differential network analysis discloses lncRNA-mediated regulatory networks related to DNA-damage response. The result shows that these DNA-damage-inducing chemicals might disrupt many lncRNA-mediated interactions involved in diverse biological processes and pathways, for example, immune function and cell adhesion. In contrast, the host might also activate a few RNA interactions in response to DNA damage, involving response to drug and regulation of cell cycle.
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Affiliation(s)
- Chen Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Dongliang Leng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Kuan Cheok Lei
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Shixue Sun
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
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31
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Li D, Harlan-Williams LM, Kumaraswamy E, Jensen RA. BRCA1-No Matter How You Splice It. Cancer Res 2019; 79:2091-2098. [PMID: 30992324 PMCID: PMC6497576 DOI: 10.1158/0008-5472.can-18-3190] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/09/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
BRCA1 (breast cancer 1, early onset), a well-known breast cancer susceptibility gene, is a highly alternatively spliced gene. BRCA1 alternative splicing may serve as an alternative regulatory mechanism for the inactivation of the BRCA1 gene in both hereditary and sporadic breast cancers, and other BRCA1-associated cancers. The alternative transcripts of BRCA1 can mimic known functions, possess unique functions compared with the full-length BRCA1 transcript, and in some cases, appear to function in opposition to full-length BRCA1 In this review, we will summarize the functional "naturally occurring" alternative splicing transcripts of BRCA1 and then discuss the latest next-generation sequencing-based detection methods and techniques to detect alternative BRCA1 splicing patterns and their potential use in cancer diagnosis, prognosis, and therapy.
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Affiliation(s)
- Dan Li
- The University of Kansas Cancer Center, Kansas City, Kansas
| | - Lisa M Harlan-Williams
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Easwari Kumaraswamy
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Roy A Jensen
- The University of Kansas Cancer Center, Kansas City, Kansas.
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
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32
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Calloni R, Bonatto D. Characteristics of the competition among RNAs for the binding of shared miRNAs. Eur J Cell Biol 2019; 98:94-102. [PMID: 31053368 DOI: 10.1016/j.ejcb.2019.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Competing endogenous RNAs (ceRNAs) are RNAs that share common miRNA binding sites and compete with each other for the miRNA association at these sites. The observation of this phenomenon in the cells altered the view of the miRNA target RNAs from molecules that are passively controlled by miRNAs to molecules that also modulate the miRNAs activity. In this review, we build a general profile of ceRNAS characteristics in order to facilitate ceRNAs identification by researchers. The information summarized here contains an actualized list of previously reported ceRNAs and classes of RNAs that can participate in this type of interaction, the expression behavior and characteristics of ceRNAs and miRNAs in the context of competition, the influence of the shared MREs/miRNAs numbers and the miRNA binding strength on the competition, reports on competition between RNAs in different subcellular localizations and the concept that ceRNAs may form a huge regulatory network in the cell.
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Affiliation(s)
- Raquel Calloni
- Departamento de Biologia Molecular e Biotecnologia, Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
| | - Diego Bonatto
- Departamento de Biologia Molecular e Biotecnologia, Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Thapar R. Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs. Molecules 2018; 23:molecules23112789. [PMID: 30373256 PMCID: PMC6278438 DOI: 10.3390/molecules23112789] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 01/12/2023] Open
Abstract
DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer. Eukaryotes have evolved two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ) to repair DSBs. Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated. This review summarizes recent discoveries on the identification of non-coding RNAs and RNA-mediated regulation of DSB repair.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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34
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Liao LM, Zhang FH, Yao GJ, Ai SF, Zheng M, Huang L. Role of Long Noncoding RNA 799 in the Metastasis of Cervical Cancer through Upregulation of TBL1XR1 Expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:580-589. [PMID: 30439646 PMCID: PMC6234527 DOI: 10.1016/j.omtn.2018.10.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 01/17/2023]
Abstract
Long noncoding RNAs (lncRNAs) are closely associated with the molecular mechanisms underlying cancer development, and it would be highly useful to study their expression and mechanisms in cervical cancer too. The current study investigated lncRNA799 expression in cervical cancer in order to determine its clinical importance in the progression of cervical cancer. lncRNA799 expression was studied in 218 cervical cancer samples. Expression of lncRNA799 was significantly higher in the cervical cancer tissue than in the adjacent normal tissue. Overexpression of lncRNA799 was found to have a significant correlation with FIGO stage, SCC-Ag level, and lymphatic metastasis, and it was also associated with poor survival. Ectopic expression of lncRNA799 promoted the metastasis of SiHa cells, whereas lncRNA799 knockdown had an inhibitory effect on metastasis. Western blot analysis demonstrated that lncRNA799 promotes the expression of transducing β-like protein 1-related protein (TBL1XR1), and that lncRNA799 and TBL1XR1 expression show strong correlation in cervical cancer. Moreover, lncRNA799 modulated the expression of TBL1XR1 by acting as a competitive endogenous RNA (ceRNA) for miR-454-3P. The results indicate that lncRNA799 could be used as a novel marker of cervical cancer prognosis. Thus, targeting the ceRNA network involving lncRNA799 could be a potential treatment strategy against cervical cancer.
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Affiliation(s)
- Ling-Min Liao
- Department of Ultrasound, The Second Affiliated Hospital of Nanchang University, Nanchang, China; JiangXi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
| | - Feng-Hao Zhang
- JiangXi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China; Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Gong-Ji Yao
- JiangXi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China; Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Su-Feng Ai
- JiangXi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China; Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Min Zheng
- Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Long Huang
- JiangXi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China; Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, China; Sun Yat-Sen University Cancer Center, Guangzhou, China.
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Li Y, Zhao W, Shi R, Jia J, Li X, Cheng J. Rs4759314 polymorphism located in HOTAIR is associated with the risk of congenital heart disease by alternating downstream signaling via reducing its expression. J Cell Biochem 2018; 119:8112-8122. [DOI: 10.1002/jcb.26736] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/29/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Yunyun Li
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Wenrong Zhao
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Ri Shi
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Jun Jia
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Xiaona Li
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Jingxin Cheng
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
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Liu AN, Qu HJ, Yu CY, Sun P. Knockdown of LINC01614 inhibits lung adenocarcinoma cell progression by up-regulating miR-217 and down-regulating FOXP1. J Cell Mol Med 2018; 22:4034-4044. [PMID: 29934982 PMCID: PMC6111824 DOI: 10.1111/jcmm.13483] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 10/31/2017] [Indexed: 02/06/2023] Open
Abstract
We tried to identify the function of LINC01614 in lung adenocarcinoma (LUAD) and reveal its underlying mechanisms. qRT‐PCR was applied to assess the expression of LINC016014 in LUAD tissues, noncancerous tissues and cells. Through colony formation assay, MTT assay and apoptosis analysis, we examined the variation of cell proliferation and apoptosis ability after silencing LINC01614. Moreover, the targeting interactions among LINC01614, miR‐217 and FOXP1 were validated via luciferase reporter assay, and then, we regulated the expression of miR‐217 and FOXP1 to ascertain their importance in cell proliferation and apoptosis. LINC01614 and FOXP1 were found to be up‐regulated in LUAD tumours and cells, whereas miR‐217 was down‐regulated. The experiment showed that target‐specific selectivity exists between LINC01614‐miR‐217 and miR‐217‐FOXP1 3′UTR. Furthermore, we disclosed that inhibition of LINC01614 could activate miR‐217, which subsequently restrained FOXP1. It was proved that LINC01614 promoted FOXP1 by inhibiting miR‐217, which ultimately stimulated the development of LUAD.
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Affiliation(s)
- Ai-Na Liu
- Department of Medical Oncology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong, China
| | - Hua-Jun Qu
- Department of Medical Oncology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong, China
| | - Cai-Yan Yu
- Department of Medical Oncology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong, China
| | - Ping Sun
- Department of Medical Oncology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong, China
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37
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Swain AC, Mallick B. miRNA-mediated 'tug-of-war' model reveals ceRNA propensity of genes in cancers. Mol Oncol 2018; 12:855-868. [PMID: 29603582 PMCID: PMC5983123 DOI: 10.1002/1878-0261.12198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 02/15/2018] [Accepted: 03/19/2018] [Indexed: 12/11/2022] Open
Abstract
Competing endogenous RNA (ceRNA) are transcripts that cross‐regulate each other at the post‐transcriptional level by competing for shared microRNA response elements (MREs). These have been implicated in various biological processes impacting cell‐fate decisions and diseases including cancer. There are several studies that predict possible ceRNA pairs by adopting various machine‐learning and mathematical approaches; however, there is no method that enables us to gauge as well as compare the propensity of the ceRNA of a gene and precisely envisages which among a pair exerts a stronger pull on the shared miRNA pool. In this study, we developed a method that uses the ‘tug of war of genes’ concept to predict and quantify ceRNA potential of a gene for the shared miRNA pool in cancers based on a score represented by SoCeR (score of competing endogenous RNA). The method was executed on the RNA‐Seq transcriptional profiles of genes and miRNA available at TCGA along with CLIP‐supported miRNA‐target sites to predict ceRNA in 32 cancer types which were validated with already reported cases. The proposed method can be used to determine the sequestering capability of the gene of interest as well as in ranking the probable ceRNA candidates of a gene. Finally, we developed standalone applications (SoCeR tool) to aid researchers in easier implementation of the method in analysing different data sets or diseases.
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Affiliation(s)
- Arpit Chandan Swain
- Department of Mathematics, National Institute of Technology, Rourkela, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
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38
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Li Y, Wang J, Sun L, Zhu S. RETRACTED: LncRNA myocardial infarction-associated transcript (MIAT) contributed to cardiac hypertrophy by regulating TLR4 via miR-93. Eur J Pharmacol 2018; 818:508-517. [PMID: 29157986 DOI: 10.1016/j.ejphar.2017.11.031] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 11/17/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief after concerns were raised about the article on PubPeer (https://pubpeer.com/publications/88E67BAC524E92069B2AA3474D2BB8?utm_source=Chrome&utm_medium=BrowserExtension&utm_campaign=Chrome). In addition the editor found more issues in some Western Blot figures. 1. Bands of figure 1C ANF 30min , 60min, 12h, 24h are identical to those in Fig 4C ANF control, AngII, AngII+si-NC and AngII+si-MAT 2. Beta-actin bands of Fig 1C are identical to those in Fig 4C, but blots represent different experimental conditions/samples. 3. Bands in Fig 6 D AngII and AngII+mir-NC show similarities with these of AngII+mir-93 and AngII+mir93+vector (band shapes and irregularities appear identical) After several attempts to reach out to the corresponding author, no response was provided. The manipulation of images casts doubts on all the data, and accordingly also the conclusions based on that data, in this publication. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.
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Affiliation(s)
- Yunwei Li
- Department of Cardiology, Huaihe Hospital of Henan University, Kaifeng 475000, China.
| | - Juan Wang
- Department of Cardiology, Huaihe Hospital of Henan University, Kaifeng 475000, China
| | - Lili Sun
- Department of Cardiology, Huaihe Hospital of Henan University, Kaifeng 475000, China
| | - Shengnan Zhu
- Department of Cardiology, Huaihe Hospital of Henan University, Kaifeng 475000, China
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Cimmino F, Formicola D, Capasso M. Dualistic Role of BARD1 in Cancer. Genes (Basel) 2017; 8:genes8120375. [PMID: 29292755 PMCID: PMC5748693 DOI: 10.3390/genes8120375] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 01/17/2023] Open
Abstract
BRCA1 Associated RING Domain 1 (BARD1) encodes a protein which interacts with the N-terminal region of BRCA1 in vivo and in vitro. The full length (FL) BARD1 mRNA includes 11 exons and encodes a protein comprising of six domains (N-terminal RING-finger domain, three Ankyrin repeats and two C-terminal BRCT domains) with different functions. Emerging data suggest that BARD1 can have both tumor-suppressor gene and oncogene functions in tumor initiation and progression. Indeed, whereas FL BARD1 protein acts as tumor-suppressor with and without BRCA1 interactions, aberrant splice variants of BARD1 have been detected in various cancers and have been shown to play an oncogenic role. Further evidence for a dualistic role came with the identification of BARD1 as a neuroblastoma predisposition gene in our genome wide association study which has demonstrated that single nucleotide polymorphisms in BARD1 can correlate with risk or can protect against cancer based on their association with the expression of FL and splice variants of BARD1. This review is an overview of how BARD1 functions in tumorigenesis with opposite effects in various types of cancer.
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Affiliation(s)
- Flora Cimmino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli "Federico II", 80131 Naples, Italy.
- CEINGE Biotecnologie Avanzate, 80131 Naples, Italy.
| | - Daniela Formicola
- IRCCS SDN, Istituto di Ricerca Diagnostica e Nucleare, 80143 Naples, Italy.
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli "Federico II", 80131 Naples, Italy.
- IRCCS SDN, Istituto di Ricerca Diagnostica e Nucleare, 80143 Naples, Italy.
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Song C, Zhang J, Liu Y, Pan H, Qi HP, Cao YG, Zhao JM, Li S, Guo J, Sun HL, Li CQ. Construction and analysis of cardiac hypertrophy-associated lncRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in cardiac hypertrophy. Oncotarget 2017; 7:10827-40. [PMID: 26872060 PMCID: PMC4905442 DOI: 10.18632/oncotarget.7312] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/28/2016] [Indexed: 01/08/2023] Open
Abstract
Cardiac hypertrophy (CH) could increase cardiac after-load and lead to heart failure. Recent studies have suggested that long non-coding RNA (lncRNA) played a crucial role in the process of the cardiac hypertrophy, such as Mhrt, TERMINATOR. Some studies have further found a new interacting mechanism, competitive endogenous RNA (ceRNA), of which lncRNA could interact with micro-RNAs (miRNA) and indirectly interact with mRNAs through competing interactions. However, the mechanism of ceRNA regulated by lncRNA in the CH remained unclear. In our study, we generated a global triple network containing mRNA, miRNA and lncRNA, and extracted a CH related lncRNA-mRNA network (CHLMN) through integrating the data from starbase, miRanda database and gene expression profile. Based on the ceRNA mechanism, we analyzed the characters of CHLMN and found that 3 lncRNAs (SLC26A4-AS1, RP11-344E13.3 and MAGI1-IT1) were high related to CH. We further performed cluster module analysis and random walk with restart for the CHLMN, finally 14 lncRNAs had been discovered as the potential CH related disease genes. Our results showed that lncRNA played an important role in the CH and could shed new light to the understanding underlying mechanisms of the CH.
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Affiliation(s)
- Chao Song
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Jian Zhang
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Yan Liu
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Hao Pan
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Han-Ping Qi
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Yong-Gang Cao
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Jian-Mei Zhao
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Shang Li
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Jing Guo
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Hong-Li Sun
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Chun-Quan Li
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
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41
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Baicalein inhibits cervical cancer progression via downregulating long noncoding RNA BDLNR and its downstream PI3K/Akt pathway. Int J Biochem Cell Biol 2017; 94:107-118. [PMID: 29175387 DOI: 10.1016/j.biocel.2017.11.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 12/29/2022]
Abstract
Baicalein, an active flavonoid extracted from the root of Scutellaria baicalensis Georgi, has fascinating anti-cancer effects on many cancers. Our previous study also found that baicalein inhibited cervical cancer cell proliferation and migration, and induced cervical cancer cell apoptosis and cell cycle arrest. However, the molecular mechanisms underlying the anti-cancer effects of baicalein are largely unknown. In this study, we identified a novel long noncoding RNA (lncRNA), which is downregulated by baicalein in a dose- and time-dependent manner in cervical cancer. We named this lncRNA as baicalein down-regulated long noncoding RNA (BDLNR). Gain-of- and loss-of-function assays showed that BDLNR was required for baicalein-induced cell proliferation inhibition, cell death induction, migration inhibition, and in vivo tumor growth inhibition of cervical cancer. Mechanistically, BDLNR physically bound to YBX1, recruited YBX1 to PIK3CA promoter, activated PIK3CA expression and PI3K/Akt pathway. Furthermore, BDLNR was upregulated in cervical cancer and associated with poor prognosis of cervical cancer patients. Collectively, our data demonstrated that BDLNR mediated the anti-cancer effects of baicalein in cervical cancer via activating PI3K/Akt pathway, and implied that BDLNR would be potential therapeutic target for enhancing the anti-cancer effects of baicalein in cervical cancer.
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An J, Lv W, Zhang Y. LncRNA NEAT1 contributes to paclitaxel resistance of ovarian cancer cells by regulating ZEB1 expression via miR-194. Onco Targets Ther 2017; 10:5377-5390. [PMID: 29180871 PMCID: PMC5691924 DOI: 10.2147/ott.s147586] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Chemoresistance is one of the major obstacles for cancer therapy in the clinic. Nuclear paraspeckle assembly transcript 1 (NEAT1) has been reported as an oncogene in most malignancies such as lung cancer, esophageal cancer, and gastric cancer. This study is designed to investigate the function of NEAT1 in paclitaxel (PTX) resistance of ovarian cancer and its potential molecular mechanism. Patients and methods The expressions of NEAT1 and miR-194 in ovarian cancer tissues and cells were estimated by quantitative real-time polymerase chain reaction (qRT-PCR). MTT, flow cytometry, and Western blot assays were used to assess the effect of NEAT1 on PTX resistance in PTX-resistant ovarian cancer cells. Luciferase reporter assay was applied to examine the association between NEAT1, zinc finger E-box-binding homeobox 1 (ZEB1) and miR-194. Xenograft tumor model was established to confirm the biological role of NEAT1 in PTX resistance of ovarian cancer in vivo. Results NEAT1 was upregulated, and miR-194 was downregulated in PTX-resistant ovarian cancer tissues and cells. Functionally, NEAT1 knockdown enhanced cell sensitivity to PTX via promoting PTX-induced apoptosis in vitro. NEAT1 was identified as a molecular sponge of miR-194 to upregulate ZEB1 expression. Mechanistically, NEAT1-knockdown-induced PTX sensitivity was mediated by miR-194/ZEB1 axis. Moreover, NEAT1 knockdown improved PTX sensitivity of ovarian cancer in vivo. Conclusion NEAT1 contributed to PTX resistance of ovarian cancer cells at least partly through upregulating ZEB1 expression by sponging miR-194, elucidating a novel regulatory pathway of chemoresistance in PTX-resistant ovarian cancer cells and providing a possible long noncoding RNA (lncRNA)-targeted therapy for ovarian cancer.
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Affiliation(s)
- Jihong An
- Department of Clinical Pharmacy, Huaihe Hospital of Henan University, Kaifeng, People's Republic of China
| | - Weiling Lv
- Department of Clinical Pharmacy, Huaihe Hospital of Henan University, Kaifeng, People's Republic of China
| | - Yongzhou Zhang
- Department of Clinical Pharmacy, Huaihe Hospital of Henan University, Kaifeng, People's Republic of China
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43
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Luo H, Yang H, Lin Y, Zhang Y, Pan C, Feng P, Yu Y, Chen X. LncRNA and mRNA profiling during activation of tilapia macrophages by HSP70 and Streptococcus agalactiae antigen. Oncotarget 2017; 8:98455-98470. [PMID: 29228702 PMCID: PMC5716742 DOI: 10.18632/oncotarget.21427] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022] Open
Abstract
Objectives To investigate the lncRNA profiling during tilapia peritoneal macrophages (TPMs) activation and discuss the relationship between lncRNA and mRNA. Materials and Methods RNA sequencing was used to investigate the lncRNA and mRNA profiles of TPMs activation following stimulation with Streptococcus agalactiae (Sa) antigen, heat shock protein 70 (HSP70) and HSP70+Sa. The expressions of lncRNA and mRNA were confirmed by qPCR. 356 lncRNA, 10173 mRNA and 1782 transcripts of uncertain coding potential (TUCP) were differentially expressed by pairwise comparison. These lncRNAs were shorter in length, fewer in exon number and higher in expression levels as compared with mRNAs. 683 lncRNAs and 4320 mRNAs were co-located, while 316 lncRNAs and 9997 mRNAs were in co-expression networks. Seven mRNAs (ANKRD34A, FMODA, GJA3, CNTN5, BMP10, BAI2 and HS3ST6) were involved in both networks of LNC_00035 and LNC_000466. Differentially expressed genes were involved in signaling pathways, such as "phosphorylation", "cytokine-cytokine receptor interaction", "endocytosis" and "MHC protein complex". LNC_000792, LNC_000215, LNC_000035 and LNC_000310, with cis and/or trans relationships with mRNAs, were also involved in ceRNA network. Conclusions These results might represent the first identified expression profile of lncRNAs and mRNAs in tilapia macrophages activated by HSP70 and Sa.
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Affiliation(s)
- Honglin Luo
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fishery Sciences, Nanning, P.R. China.,Guangxi Medical University, Nanning, P.R. China
| | - Huizan Yang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fishery Sciences, Nanning, P.R. China.,College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Yong Lin
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fishery Sciences, Nanning, P.R. China
| | - Yongde Zhang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fishery Sciences, Nanning, P.R. China
| | - Chuanyan Pan
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fishery Sciences, Nanning, P.R. China
| | - Pengfei Feng
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fishery Sciences, Nanning, P.R. China
| | - Yanling Yu
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fishery Sciences, Nanning, P.R. China
| | - Xiaohan Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fishery Sciences, Nanning, P.R. China
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Zhang Y, Li Y, Wang Q, Zhang X, Wang D, Tang HC, Meng X, Ding X. Identification of an lncRNA‑miRNA‑mRNA interaction mechanism in breast cancer based on bioinformatic analysis. Mol Med Rep 2017; 16:5113-5120. [PMID: 28849135 PMCID: PMC5647044 DOI: 10.3892/mmr.2017.7304] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 04/06/2017] [Indexed: 12/14/2022] Open
Abstract
Non-coding RNAs serve important roles in regulating the expression of certain genes and are involved in the principal biological processes of breast cancer. The majority of studies have focused on defining the regulatory functions of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs/miRs), and few studies have investigated how lncRNAs and miRNAs are transcriptionally regulated. In the present study, based on the breast invasive carcinoma dataset from The Cancer Genome Atlas at cBioPortal, and using a bioinformatics computational approach, an lncRNA-miRNA-mRNA network was constructed. The network consisted of 601 nodes and 706 edges, which represented the complex web of regulatory effects between lncRNAs, miRNAs and target genes. The results of the present study demonstrated that miR-510 was the most potent miRNA controller and regulator of numerous target genes. In addition, it was observed that the lncRNAs PVT1, CCAT1 and linc00861 exhibited possible interactions with clinical biomarkers, including receptor tyrosine-protein kinase erbB-2, estrogen receptor and progesterone receptor, demonstrated using RNA-protein interaction prediction software. The network of lncRNA-miRNA-mRNA interactions will facilitate further experimental studies and may be used to refine biomarker predictions for developing novel therapeutic approaches in breast cancer.
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Affiliation(s)
- Yuhan Zhang
- College of Life Science, Zhejiang Sci‑Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Yongfeng Li
- Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Qing Wang
- College of Life Science, Zhejiang Sci‑Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Xiping Zhang
- Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Dajin Wang
- College of Life Science, Zhejiang Sci‑Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Hong Chao Tang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Xuli Meng
- Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Xianfeng Ding
- College of Life Science, Zhejiang Sci‑Tech University, Hangzhou, Zhejiang 310018, P.R. China
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Wang Y, Yang T, Zhang Z, Lu M, Zhao W, Zeng X, Zhang W. Long non-coding RNA TUG1 promotes migration and invasion by acting as a ceRNA of miR-335-5p in osteosarcoma cells. Cancer Sci 2017; 108:859-867. [PMID: 28205334 PMCID: PMC5448616 DOI: 10.1111/cas.13201] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/07/2017] [Accepted: 02/11/2017] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNA (lncRNA) have been the focus of increasing attention due to the role they play in many diseases, including osteosarcoma. The function of taurine upregulated gene 1 (TUG1) and its mechanism in osteosarcoma remain unclear. In our research, we found that TUG1 was elevated and correlated with a poor prognosis in osteosarcoma patients. In addition, the following functional experiment showed that decreased TUG1 could remarkably inhibit osteosarcoma cell migration and invasion, indicating that TUG1 functioned as an oncogene in osteosarcoma. Moreover, we revealed that TUG1 and Rho-associated coiled-coil-containing protein kinase 1 (ROCK1), a metastasis-related gene targeted by microRNA-335-5p (miR-335-5p), had the same miR-335-5p combining site. The subsequent luciferase assay verified TUG1 was a target of miR-335-5p. Furthermore, the results of a real-time quantitative PCR showed that TUG1 and miR-335-5p could affect each other's expression. respectively. Finally, we affirmed that TUG1 affected ROCK1 expression and ROCK1-mediated migration/invasion by working as a competitive endogenous RNA (ceRNA) via miR-335-5p. In summary, the findings of this study, based on ceRNA theory, combining the research foundation of miR-335-5p and ROCK1, and taking TUG1 as a new study point, provide new insight into molecular-level reversing migration and invasion of osteosarcoma.
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Affiliation(s)
- Yong Wang
- The 4th Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China.,Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Tao Yang
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhen Zhang
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ming Lu
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wei Zhao
- The 4th Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Xiandong Zeng
- Department of Surgery Oncology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Weiguo Zhang
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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46
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MicroR-545 mediates colorectal cancer cells proliferation through up-regulating epidermal growth factor receptor expression in HOTAIR long non-coding RNA dependent. Mol Cell Biochem 2017; 431:45-54. [PMID: 28364379 DOI: 10.1007/s11010-017-2974-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/07/2017] [Indexed: 01/01/2023]
Abstract
The functional impact of recently discovered miRNAs in human cancer remains to be clarified. One miRNA in colorectal cancer which has attracted attention is miR-545. In this study, we examined the function of miR-545 in proliferation of colorectal cancer cells. Expressions of HOTAIR, miRNA-545, and epidermal growth factor receptor (EGFR) mRNA were measured in 100 paired cancerous and non-cancerous tissues as well as in SW480 and LOVO colorectal cancer cell (CRC) lines by quantitative RT-PCR. The relative protein level of EGFR was measured using western blotting. Effects of miRNA-545 and HOTAIR on gastric cancer cells were studied by overexpression and RNA interference approaches. Insight of mechanism of promotion cancer by miR-545 was gained from luciferase reporter assay and gene expression analysis. CRC proliferation was evaluated using clone formation and MTT assay. Differential expressions of HOTAIR, miR-545, and EGFR were observed in cancerous tissues in comparison to non-cancerous tissues. By expressional management of miR-545, we observed that miR-545 negatively regulated cell proliferation. Also luciferase reporter assay revealed that miR-545 inhibited regulated EGFR expression by affecting its 3'-UTR activity. In addition, miR-545 expression was suppressed by HOTAIR overexpression whereas enhanced by HOTAIR silence. Suppression of EGFR expression by miR-545 mimic was abrogated by HOTAIR overexpression. Monitoring of tumor growth in mice showed that miR-545 overexpression suppressed LOVO tumor growth. Our data suggested that HOTAIR long non-coding RNA mediates microR-545 regulating colorectal cancer cells proliferation.
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Shi YM, Niu YC, Lu ML, Huang H, Chang J, He HY. Progress in research of competing endogenous RNAs related to gastrointestinal cancers. Shijie Huaren Xiaohua Zazhi 2017; 25:596-601. [DOI: 10.11569/wcjd.v25.i7.596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Competing endogenous RNAs (ceRNAs) are RNA transcripts which can communicate with each other by sponging and decreasing target microRNAs (miRNAs) and thus de-repressing messenger RNAs (mRNAs). ceRNAs have crucial roles in oncogenic pathways involved in many types of gastrointestinal cancers by sponging miRNAs. Here, we review oncocer-related findings found up to now and analyze the cross-talk between ceRNAs and miRNAs, with an aim to give a novel perspective to the understanding of oncocer-mediated mechanisms in gastrointestinal cancers.
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48
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Identifying survival-associated modules from the dysregulated triplet network in glioblastoma multiforme. J Cancer Res Clin Oncol 2017; 143:661-671. [DOI: 10.1007/s00432-016-2332-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/23/2016] [Indexed: 12/25/2022]
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49
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Nan A, Zhou X, Chen L, Liu M, Zhang N, Zhang L, Luo Y, Liu Z, Dai L, Jiang Y. A transcribed ultraconserved noncoding RNA, Uc.173, is a key molecule for the inhibition of lead-induced neuronal apoptosis. Oncotarget 2016; 7:112-24. [PMID: 26683706 PMCID: PMC4807986 DOI: 10.18632/oncotarget.6590] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/26/2015] [Indexed: 01/05/2023] Open
Abstract
As a common toxic metal, lead has significant neurotoxicity to brain development. Long non-coding RNAs (lncRNAs) function in multiple biological processes. However, whether lncRNAs are involved in lead-induced neurotoxicity remains unclear. Uc.173 is a lncRNA from a transcribed ultra-conservative region (T-UCR) of human, mouse and rat genomes. We established a lead-induced nerve injury mouse model. It showed the levels of Uc.173 decreased significantly in hippocampus tissue and serum of the model. We further tested the expression of Uc.173 in serum of lead-exposed children, which also showed a tendency to decrease. To explore the effects of Uc.173 on lead-induced nerve injury, we overexpressed Uc.173 in an N2a mouse nerve cell line and found Uc.173 had an inhibitory effect on lead-induced apoptosis of N2a. To investigate the molecular mechanisms of Uc.173 in apoptosis associated with lead-induced nerve injury, we predicted the target microRNAs of Uc.173 by using miRanda, TargetScan and RegRNA. After performing quantitative real-time PCR and bioinformatics analysis, we showed Uc.173 might inter-regulate with miR-291a-3p in lead-induced apoptosis and regulate apoptosis-associated genes. Our study suggests Uc.173 significantly inhibits the apoptosis of nerve cells, which may be mediated by inter-regulation with miRNAs in lead-induced nerve injury.
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Affiliation(s)
- Aruo Nan
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Xinke Zhou
- Institute for Chemical Carcinogenesis, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, PR China
| | - Lijian Chen
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Meiling Liu
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Nan Zhang
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Li Zhang
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Yuanwei Luo
- Institute for Chemical Carcinogenesis, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, PR China
| | - Zhenzhong Liu
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Lijun Dai
- Laboratory Animal Center, Guangzhou Medical University, Guangzhou, PR China
| | - Yiguo Jiang
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
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50
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Sui J, Li YH, Zhang YQ, Li CY, Shen X, Yao WZ, Peng H, Hong WW, Yin LH, Pu YP, Liang GY. Integrated analysis of long non-coding RNA‑associated ceRNA network reveals potential lncRNA biomarkers in human lung adenocarcinoma. Int J Oncol 2016; 49:2023-2036. [PMID: 27826625 DOI: 10.3892/ijo.2016.3716] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/27/2016] [Indexed: 11/06/2022] Open
Abstract
Accumulating evidence has highlighted the important roles of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in tumor biology. However, the roles of cancer specific lncRNAs in lncRNA-related ceRNA network of lung adenocarcinoma (LUAD) are still unclear. In the present study, the 465 RNA sequencing profiles in LUAD patients were obtained from the cancer genome atlas (TCGA) database, which provides large sample RNA sequencing data free of charge, and 41 cancer specific lncRNAs, 25 miRNAs and 1053 mRNAs (fold change >2, p<0.05) were identified. Then, the lncRNA-miRNA-mRNA ceRNA network of LUAD was constructed with 29 key lncRNAs, 24 miRNAs and 72 mRNAs. Subsequently, we selected these 29 key lncRNAs to analyze their correlation with clinical features, and 21 of them were aberrantly expressed with tumor pathological stage, TNM staging system, lymph node metastasis and patient outcome assessment, respectively. Furthermore, there were 5 lncRNAs (BCRP3, LINC00472, CHIAP2, BMS1P20 and UNQ6494) positively correlated with overall survival (OS, log-rank p<0.05). Finally, 7 cancer specific lncRNAs were randomly selected to verify the expression in 53 newly diagnosed LUAD patients using qRT-PCR. The expression results between TCGA and qRT-PCR were 100% in agreement. The correlation between AFAP1-AS1 and LINC00472 and clinical features were also confirmed. Thus, our results showed the lncRNA expression profiles and we constructed an lncRNA-miRNA-mRNA ceRNA network in LUAD. The present study provides novel insight for better understanding of lncRNA-related ceRNA network in LUAD and facilitates the identification of potential biomarkers for diagnosis and prognosis.
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Affiliation(s)
- Jing Sui
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yun-Hui Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yan-Qiu Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Cheng-Yun Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Xian Shen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Wen-Zhuo Yao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Hui Peng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Wei-Wei Hong
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Li-Hong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yue-Pu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Ge-Yu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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