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Yang S, Qin L, Wu P, Liu Y, Zhang Y, Mao B, Yan Y, Yan S, Tan F, Yue X, Liu H, Xue H. RNA sequencing revealed the multi-stage transcriptome transformations during the development of gallbladder cancer associated with chronic inflammation. PLoS One 2023; 18:e0283770. [PMID: 36996251 PMCID: PMC10062614 DOI: 10.1371/journal.pone.0283770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Gallbladder cancer (GBC) is a highly malignant tumor with extremely poor prognosis. Previous studies have suggested that the carcinogenesis and progression of GBC is a multi-stage and multi-step process, but most of them focused on the genome changes. And a few studies just compared the transcriptome differences between tumor tissues and adjacent noncancerous tissues. The transcriptome changes, relating to every stage of GBC evolution, have rarely been studied. We selected three cases of normal gallbladder, four cases of gallbladder with chronic inflammation induced by gallstones, five cases of early GBC, and five cases of advanced GBC, using next-generation RNA sequencing to reveal the changes in mRNAs and lncRNAs expression during the evolution of GBC. In-depth analysis of the sequencing data indicated that transcriptome changes from normal gallbladder to gallbladder with chronic inflammation were distinctly related to inflammation, lipid metabolism, and sex hormone metabolism; transcriptome changes from gallbladder with chronic inflammation to early GBC were distinctly related to immune activities and connection between cells; and the transcriptome changes from early GBC to advanced GBC were distinctly related to transmembrane transport of substances and migration of cells. Expression profiles of mRNAs and lncRNAs change significantly during the evolution of GBC, in which lipid-based metabolic abnormalities play an important promotive role, inflammation and immune activities play a key role, and membrane proteins are very highlighted molecular changes.
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Affiliation(s)
- Sen Yang
- Department of Hepatobiliary and Pancreatic Surgery, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Litao Qin
- Medical Genetic Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Pan Wu
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou, Henan, China
| | - Yanbing Liu
- Department of Hepatobiliary and Pancreatic Surgery, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Yanling Zhang
- Department of Pathology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Bing Mao
- Department of Clinical Research Service Center, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Yiyang Yan
- Department of Hepatobiliary and Pancreatic Surgery, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Shuai Yan
- Department of Hepatobiliary and Pancreatic Surgery, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Feilong Tan
- Department of Hepatobiliary and Pancreatic Surgery, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xueliang Yue
- Department of Hepatobiliary and Pancreatic Surgery, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hongshan Liu
- Department of Hepatobiliary and Pancreatic Surgery, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Huanzhou Xue
- Department of Hepatobiliary and Pancreatic Surgery, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
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Wang J, Li L, Jiang X, Wang B, Hu X, Liu W, Zhang Y. Silencing of long non-coding RNA TUC338 inhibits the malignant phenotype of nasopharyngeal cancer cells via modulating the miR-1226-3p/FGF2 axis. Discov Oncol 2022; 13:102. [PMID: 36224455 PMCID: PMC9556687 DOI: 10.1007/s12672-022-00544-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/08/2022] [Indexed: 11/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been suggested as essential regulators in the cancer progression. LncRNA TUC338 was found to promote the malignancy of various cancers, however, the involvement of TUC338 in nasopharyngeal cancer (NPC) has not been well characterized. Here, our results found the significant overexpression of TUC338 in NPC tissues. Higher level of TUC338 was also observed in NPC cells. Interestingly, NPC patients harboring overexpressed TUC338 have worse prognosis. Functional study indicated that down-regulated TUC338 remarkably suppressed the NPC cell proliferation and cell migration. Notably, depletion of TUC338 significantly inhibited the in vivo tumor growth. Mechanistically, TUC338 acted as molecular sponge of miR-1226-3p and attenuated the negative regulation of miR-1226-3p on the expression of fibroblast growth factor 2 (FGF2). Down-regulation of TUC338 inhibited FGF2 expression in NPC cells and tumor tissues. Overexpression of FGF2 attenuated the suppressed NPC proliferation upon the depletion of TUC338. Our results demonstrated the novel function of TUC338/miR-1226-3p/FGF2 axis in NPC progression, suggesting the potential diagnosis and therapeutics significance of TUC338 in NPC.
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Affiliation(s)
- Jian Wang
- Department of Otolaryngology, Cangzhou Central Hospital, No. 16 Xinhua West Road, Cangzhou, 061000, Hebei, China
| | - Liping Li
- Department of Otolaryngology, Cangzhou Central Hospital, No. 16 Xinhua West Road, Cangzhou, 061000, Hebei, China
| | - Xue Jiang
- Department of Otolaryngology, Cangzhou Central Hospital, No. 16 Xinhua West Road, Cangzhou, 061000, Hebei, China
| | - Bin Wang
- Department of Otolaryngology, Cangzhou Central Hospital, No. 16 Xinhua West Road, Cangzhou, 061000, Hebei, China
| | - Xiaodong Hu
- Department of Otolaryngology, Cangzhou Central Hospital, No. 16 Xinhua West Road, Cangzhou, 061000, Hebei, China
| | - Weiwei Liu
- Department of Otolaryngology, Cangzhou Central Hospital, No. 16 Xinhua West Road, Cangzhou, 061000, Hebei, China
| | - Ying Zhang
- Infection Department, Cangzhou Central Hospital, No. 16 Xinhua West Road, Cangzhou, 061000, Hebei, China.
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Liu B, Yao P, Xiao F, Guo J, Wu L, Yang Y. MYBL2-induced PITPNA-AS1 upregulates SIK2 to exert oncogenic function in triple-negative breast cancer through miR-520d-5p and DDX54. J Transl Med 2021; 19:333. [PMID: 34353336 PMCID: PMC8340450 DOI: 10.1186/s12967-021-02956-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/20/2021] [Indexed: 12/21/2022] Open
Abstract
Background In recent years, long non-coding RNAs (lncRNAs) have attracted much attention because of its regulatory role in occurrence and progression of tumors, including triple-negative breast cancer (TNBC). LncRNA PITPNA antisense RNA 1 (PITPNA-AS1) has been explored in some cancers, whereas its function and molecular mechanism in TNBC remain unclear. Methods PITPNA-AS1 expression in TNBC tissues and cells was determined by RT-qPCR. TNBC cell viability, proliferation, migration, invasion were assessed with CCK-8, colony formation, wound healing, transwell assays. Cell apoptosis was evaluated by flow cytometry. Expression of EMT-related markers was detected by western blot analyses. The molecular mechanism of PITPNA-AS1 was explored by RNA pull down, luciferase reporter, RIP and ChIP assays. Results PITPNA-AS1 showed high expression levels in TNBC tissues and cells. PITPNA-AS1 knockdown suppressed TNBC cell viability, proliferation, migration, invasion in vitro and inhibited xenograft tumor growth in mice. Mechanistically, PITPNA-AS1 upregulated SIK2 expression by sponging miR-520d-5p and recruiting DDX54 protein. Results of rescue assays suggested that the inhibitive effects of silenced PITPNA-AS1 on TNBC cellular processes were partially rescued by overexpressing SIK2 or combination of miR-520d-5p inhibition and DDX54 overexpression. More importantly, we found that the upregulation of PITPNA-AS1 in TNBC cells was attributed to transcription factor MYBL2. Conclusion PITPNA-AS1 activated by MYBL2 plays an oncogenic role in TNBC through upregulating SIK2. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02956-6.
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Affiliation(s)
- Bolong Liu
- Department of Andrology, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan, China
| | - Pingbo Yao
- Changsha Social Work College, Changsha, 421004, Hunan, China
| | - Feng Xiao
- Department of Oncology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Jianjin Guo
- Department of Endocrinology and Metabolism, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Lianghui Wu
- Department of Intensive Care Unit, Affiliated Nanhua Hospital, University of South China, No. 336, Dongfeng South Road, Zhuhui District, Hengyang, 421001, Hunan, China.
| | - Yong Yang
- Department of General Surgery, The Second Hospital, University of South China, 30 Jiefang Road, Shigu District, Hengyang, 421001, Hunan, China.
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Wang J, Liu D, Gu Y, Zhou H, Li H, Shen X, Qian X. Potential prognostic markers and significant lncRNA-mRNA co-expression pairs in laryngeal squamous cell carcinoma. Open Life Sci 2021; 16:544-557. [PMID: 34131588 PMCID: PMC8174121 DOI: 10.1515/biol-2021-0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/03/2021] [Accepted: 04/13/2021] [Indexed: 01/20/2023] Open
Abstract
lncRNA-mRNA co-expression pairs and prognostic markers related to the development of laryngeal squamous cell carcinoma (LSCC) were investigated. The lncRNA and mRNA expression data of LSCC in GSE84957 and RNA-seq data of 112 LSCC samples from TCGA database were used. Differentially expressed genes (DEGs) and lncRNAs (DE-lncRNAs) between LSCC and para-cancer tissues were identified. Co-expression analysis of DEGs and DE-lncRNA was conducted. Protein-protein interaction network for co-expressed DEGs of top 25 DE-lncRNA was constructed, followed by survival analysis for key nodes in co-expression network. Finally, expressions of several DE-lncRNAs and DEGs were verified using qRT-PCR. The lncRNA-mRNA network showed that ANKRD20A5P, C21orf15, CYP4F35P, LOC_I2_011146, XLOC_006053, XLOC_I2_003881, and LOC100506027 were highlighted in network. Some DEGs, including FUT7, PADI1, PPL, ARHGAP40, MUC21, and CEACAM1, were co-expressed with above lncRNAs. Survival analysis showed that PLOD1, GLT25D1, and KIF22 were significantly associated with prognosis. qRT-PCR results showed that the expressions of MUC21, CEACAM1, FUT7, PADI1, PPL, ARHGAP40, ANKRD20A5P, C21orf15, CYP4F35P, XLOC_I2_003881, LOC_I2_011146, and XLOC_006053 were downregulated, whereas the expression of LOC100506027 was upregulated in LSCC tissues. PLOD1, GLT25D1, and KIF22 may be potential prognostic markers in the development of LSCC. C21orf15-MUC21/CEACAM1/FUT7/PADI1/PPL/ARHGAP40 are potential lncRNA-mRNA pairs that play significant roles in the development of LSCC.
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Affiliation(s)
- Junguo Wang
- Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline (Laboratory), No. 321 Zhongshan Road, Nanjing, 210008, China
- Department of Otolaryngology, Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
| | - Dingding Liu
- Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline (Laboratory), No. 321 Zhongshan Road, Nanjing, 210008, China
- Department of Otolaryngology, Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
| | - Yajun Gu
- Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline (Laboratory), No. 321 Zhongshan Road, Nanjing, 210008, China
- Department of Otolaryngology, Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
| | - Han Zhou
- Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline (Laboratory), No. 321 Zhongshan Road, Nanjing, 210008, China
- Department of Otolaryngology, Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
| | - Hui Li
- Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline (Laboratory), No. 321 Zhongshan Road, Nanjing, 210008, China
- Department of Otolaryngology, Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
| | - Xiaohui Shen
- Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline (Laboratory), No. 321 Zhongshan Road, Nanjing, 210008, China
- Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
| | - Xiaoyun Qian
- Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline (Laboratory), No. 321 Zhongshan Road, Nanjing, 210008, China
- Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
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Ji S, Yang Z, Gozali L, Kenney T, Kocabas A, Jinsook Park C, Hynes M. Distinct expression of select and transcriptome-wide isolated 3'UTRs suggests critical roles in development and transition states. PLoS One 2021; 16:e0250669. [PMID: 33951080 PMCID: PMC8099112 DOI: 10.1371/journal.pone.0250669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 04/08/2021] [Indexed: 01/06/2023] Open
Abstract
Mature mRNA molecules are expected to be comprised of a 5’UTR, a 3’UTR and a coding region (CDS). Unexpectedly, however, there have been multiple recent reports of widespread differential expression of mRNA 3’UTRs and their cognate coding regions (CDS), reflecting the expression of isolated 3’UTRs (i3’UTRs); these i3’UTRs can be highly expressed, often in reciprocal patterns to their cognate CDS. As with other long non-coding (lncRNAs), isolated 3’UTRs are likely to play an important role in gene regulation, but little is known about the contexts in which they are deployed. To illuminate the functions of i3’UTRs, here we carry out in vitro, in vivo and in silico analyses of differential 3’UTR/CDS mRNA ratio usage across tissues, development and cell state changes both for a select list of developmentally important genes as well as by unbiased transcriptome-wide analyses. Across two developmental paradigms we find a distinct switch from high i3’UTR expression for stem cell related genes in proliferating cells to high CDS for these genes in newly differentiated cells. Unbiased transcriptome analysis across multiple gene sets shows that regardless of tissue, genes with high 3’UTR to CDS ratios belong predominantly to gene ontology categories related to cell-type specific functions. In contrast, the gene ontology categories of genes with low 3’UTR to CDS ratios are similar across tissues and relate to common cellular functions. We further show that, at least for some genes, traditional transcriptional start site genomic elements correspond to identified RNAseq 3’UTR peak regions, suggesting that some i3’UTRs may be generated by de novo transcription. Our results provide critical information from which detailed hypotheses for individual i3’UTRs can be tested, with a common theme that i3’UTRs appear poised to regulate cell-specific gene expression and state.
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Affiliation(s)
- Shaoyi Ji
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
- * E-mail: (MH); (SJ); (ZY)
| | - Ze Yang
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
- * E-mail: (MH); (SJ); (ZY)
| | - Leonardi Gozali
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
| | - Thomas Kenney
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
| | - Arif Kocabas
- Rockefeller University, New York, NY, United States of America
| | | | - Mary Hynes
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
- Rockefeller University, New York, NY, United States of America
- * E-mail: (MH); (SJ); (ZY)
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Rahimian N, Razavi ZS, Aslanbeigi F, Mirkhabbaz AM, Piroozmand H, Shahrzad MK, Hamblin MR, Mirzaei H. Non-coding RNAs related to angiogenesis in gynecological cancer. Gynecol Oncol 2021; 161:896-912. [PMID: 33781555 DOI: 10.1016/j.ygyno.2021.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Gynecological cancer affects the female reproductive system, including ovarian, uterine, endometrial, cervical, vulvar, and vaginal tumors. Non-coding RNAs (ncRNAs), and in particular microRNAs, function as regulatory molecules, which can control gene expression in a post-transcriptional manner. Normal physiological processes like cellular proliferation, differentiation, and apoptosis, and pathological processes such as oncogenesis and metastasis are regulated by microRNAs. Numerous reports have shown a direct role of microRNAs in the modulation of angiogenesis in gynecological cancer, via targeting pro-angiogenic factors and signaling pathways. Understanding the molecular mechanism involved in the regulation of angiogenesis by microRNAs may lead to new treatment options. Recently the regulatory role of some long non-coding RNAs in gynecological cancer has also been explored, but the information on this function is more limited. The aim of this article is to explore the pathways responsible for angiogenesis, and to what extent ncRNAs may be employed as biomarkers or therapeutic targets in gynecological cancer.
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Affiliation(s)
- Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | | | | | | | - Haleh Piroozmand
- Faculty of Veterinary Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Karim Shahrzad
- Department of Internal Medicine and endocrinology, Shohadae Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Ivanova E, Le Guillou S, Hue-Beauvais C, Le Provost F. Epigenetics: New Insights into Mammary Gland Biology. Genes (Basel) 2021; 12:genes12020231. [PMID: 33562534 PMCID: PMC7914701 DOI: 10.3390/genes12020231] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022] Open
Abstract
The mammary gland undergoes important anatomical and physiological changes from embryogenesis through puberty, pregnancy, lactation and involution. These steps are under the control of a complex network of molecular factors, in which epigenetic mechanisms play a role that is increasingly well described. Recently, studies investigating epigenetic modifications and their impacts on gene expression in the mammary gland have been performed at different physiological stages and in different mammary cell types. This has led to the establishment of a role for epigenetic marks in milk component biosynthesis. This review aims to summarize the available knowledge regarding the involvement of the four main molecular mechanisms in epigenetics: DNA methylation, histone modifications, polycomb protein activity and non-coding RNA functions.
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Abba MC, Canzoneri R, Gurruchaga A, Lee J, Tatineni P, Kil H, Lacunza E, Aldaz CM. LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression. Int J Mol Sci 2020; 21:ijms21197407. [PMID: 33049922 PMCID: PMC7582527 DOI: 10.3390/ijms21197407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/30/2020] [Accepted: 10/06/2020] [Indexed: 12/19/2022] Open
Abstract
Long intergenic non-protein coding RNA 885 (LINC00885) was identified as significantly upregulated in breast ductal carcinoma in situ (DCIS). The aim of this study was to characterize the phenotypic effects and signaling pathways modulated by LINC00885 in non-invasive and invasive breast cancer models. We determined that LINC00885 induces premalignant phenotypic changes by increasing cell proliferation, motility, migration and altering 3D growth in normal and DCIS breast cell lines. Transcriptomic studies (RNA-seq) identified the main signaling pathways modulated by LINC00885, which include bioprocesses related to TP53 signaling pathway and proliferative signatures such as activation of EREG, EGFR and FOXM1 pathways. LINC00885 silencing in breast cancer lines overexpressing this lncRNA leads to downregulation of proliferation related transcripts such as EREG, CMYC, CCND1 and to significant decrease in cell migration and motility. TCGA-BRCA data analyses show an association between high LINC00885 expression and worse overall survival in patients with primary invasive breast carcinomas (p = 0.024), suggesting that the pro-tumorigenic effects of LINC00885 overexpression persist post-invasion. We conclude that LINC00885 behaves as a positive regulator of cell growth both in normal and DCIS breast cells possibly operating as a ceRNA and representing a novel oncogenic lncRNA associated with early stage breast cancer progression.
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Affiliation(s)
- Martin C. Abba
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata CP1900, Argentina; (R.C.); (A.G.); (E.L.)
- Correspondence: (M.C.A.); (C.M.A.)
| | - Romina Canzoneri
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata CP1900, Argentina; (R.C.); (A.G.); (E.L.)
| | - Agustina Gurruchaga
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata CP1900, Argentina; (R.C.); (A.G.); (E.L.)
| | - Jaeho Lee
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; (J.L.); (P.T.); (H.K.)
| | - Pradeep Tatineni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; (J.L.); (P.T.); (H.K.)
| | - Hyunsuk Kil
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; (J.L.); (P.T.); (H.K.)
| | - Ezequiel Lacunza
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata CP1900, Argentina; (R.C.); (A.G.); (E.L.)
| | - C. Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; (J.L.); (P.T.); (H.K.)
- Correspondence: (M.C.A.); (C.M.A.)
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9
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Qiu J, Zhou S, Cheng W, Luo C. LINC00294 induced by GRP78 promotes cervical cancer development by promoting cell cycle transition. Oncol Lett 2020; 20:262. [PMID: 32989396 PMCID: PMC7517597 DOI: 10.3892/ol.2020.12125] [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: 05/24/2018] [Accepted: 05/27/2020] [Indexed: 12/17/2022] Open
Abstract
Cervical cancer is one of the most common gynecological malignancies, and it has become a crucial public health problem. In the present study, the expression profiles of cervical cancer and normal cervical tissues were downloaded from the Gene Expression Omnibus and The Cancer Genome Atlas databases. Subsequently, the dysregulated long non-coding RNAs (lncRNAs) in cervical cancer were identified using R software Differentially expressed lncRNAs in cervical cancer that were associated with glucose-regulated protein 78 (GRP78) were screened out and the results demonstrated that eight lncRNAs were strongly positively correlated with GRP78. In order to confirm the relationship between GRP78 and candidate lncRNAs, GRP78 small interfering RNA (siRNA) was transfected into HeLa cells. The target lncRNAs that were regulated by GRP78 were then identified by reverse transcription-quantitative PCR and it was revealed that LINC00294 was significantly downregulated following GRP78-knockdown. Subsequently, Gene Set Enrichment Analysis demonstrated that LINC00294 was mainly enriched in regulating the cell cycle and the Hedgehog pathway. Following transfection of HeLa and SiHa cells with LINC00294 siRNA, the cell cycle was arrested at the G0/G1 phase. Western blotting suggested that LINC00294-knockdown downregulated the expression of cell cycle-associated factors (cyclin D, cyclin E and cyclin Dependent kinase 4) and upregulated cell cycle inhibitory factors (p16 and p21). The Hedgehog pathway was inhibited following knockdown of LINC00294 in HeLa and SiHa cells. In summary, LINC00294 induced by GRP78 promoted the progression of cervical cancer by regulating the cell cycle via Hedgehog pathway.
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Affiliation(s)
- Jiangnan Qiu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
| | - Shulin Zhou
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
| | - Chengyan Luo
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
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Luan Y, Xie B, Wei W. REST-repressed lncRNA NPPA-AS1 regulates cervical cancer progression by modulating miR-302e/DKK1/Wnt/β-catenin signaling pathway. J Cell Biochem 2020; 122:16-28. [PMID: 32965043 DOI: 10.1002/jcb.29701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/10/2020] [Indexed: 12/15/2022]
Abstract
Long noncoding RNAs (lncRNAs), a group of transcripts, have been revealed to be critical participants in regulating multiple biological processes of malignant tumors. The knowledge of NPPA-AS1 (a new lncRNA) in cancer research is hardly known. Thus, it is of urgent need to study the underlying role of NPPA antisense RNA 1 (NPPA-AS1) in cervical cancer (CC). In this study, NPPA-AS1 was discovered to be lowly expressed and upregulation of it impaired cell proliferation and migration in CC. Besides, downregulation of it led to opposite results. Molecular mechanism assays uncovered that increased expression of NPPA-AS1 could inactivate Wnt/β-catenin signaling pathway in CC. In addition, NPPA-AS1 was found to negatively interact with miR-302e whereas positively correlate with dickkopf-1 (DKK1, an inhibitor of Wnt pathway) in CC. Besides, loss of function assay illuminated that miR-302e inhibition restrained cell proliferation and migration in CC. Subsequent rescue assays confirmed that NPPA-AS1 acted as a competing endogenous RNA in CC by sponging miR-302e to upregulate DKK1 expression. Finally, the RE-1 silencing transcription factor (REST) was testified to function as a transcription suppressor of NPPA-AS1 in CC. In brief, REST-repressed NPPA-AS1 regulates CC progression by modulating miR-302e/DKK1/Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Yanan Luan
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Bin Xie
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wenbin Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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11
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Pan Y, Jia LP, Liu Y, Han Y, Li Q, Zou Q, Zhang Z, Huang J, Deng Q. A novel signature of two long non-coding RNAs in BRCA mutant ovarian cancer to predict prognosis and efficiency of chemotherapy. J Ovarian Res 2020; 13:112. [PMID: 32950050 PMCID: PMC7502206 DOI: 10.1186/s13048-020-00712-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/04/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND In this study we aimed to identify a prognostic signature in BRCA1/2 mutations to predict disease progression and the efficiency of chemotherapy ovarian cancer (OV), the second most common cause of death from gynecologic cancer in women worldwide. METHODS Univariate Cox proportional-hazards and multivariate Cox regression analyses were used to identifying prognostic factors from data obtained from The Cancer Genome Atlas (TCGA) database. The area under the curve of the receiver operating characteristic curve was assessed, and the sensitivity and specificity of the prediction model were determined. RESULTS A signature consisting of two long noncoding RNAs(lncRNAs), Z98885.2 and AC011601.1, was selected as the basis for classifying patients into high and low-risk groups (median survival: 7.2 years vs. 2.3 years). The three-year overall survival (OS) rates for the high- and low-risk group were approximately 38 and 100%, respectively. Chemotherapy treatment survival rates indicated that the high-risk group had significantly lower OS rates with adjuvant chemotherapy than the low-risk group. The one-, three-, and five-year OS were 100, 40, and 15% respectively in the high-risk group. The survival rate of the high-risk group declined rapidly after 2 years of OV chemotherapy treatment. Multivariate Cox regression associated with other traditional clinical factors showed that the 2-lncRNA model could be used as an independent OV prognostic factor. Analyses of data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) indicated that these signatures are pivotal to cancer development. CONCLUSION In conclusion, Z98885.2 and AC011601.1 comprise a novel prognostic signature for OV patients with BRCA1/2 mutations, and can be used to predict prognosis and the efficiency of chemotherapy.
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Affiliation(s)
- Yinglian Pan
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan, China
| | - Li Ping Jia
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Yuzhu Liu
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Yiyu Han
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Qian Li
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, Wuhan, China
| | - Qin Zou
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, Wuhan, China
| | - Zhongpei Zhang
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, Wuhan, China
| | - Jin Huang
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, Wuhan, China.
| | - Qingchun Deng
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, China.
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12
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Circ_0074027 contributes to the progression of non-small cell lung cancer via microRNA-362-3p/clathrin heavy chain axis. Anticancer Drugs 2020; 32:1-10. [PMID: 32932275 DOI: 10.1097/cad.0000000000000990] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Circular RNAs are involved in the occurrence and development of different types of cancers. We aimed to illustrate the expression profile and mechanism of circ_0074027 in non-small cell lung cancer (NSCLC). Quantitative real-time PCR was employed to detect the expression of circ_0074027, paired like homeodomain 1 (PITX1) mRNA (mPITX1) and microRNA-362-3p (miR-362-3p). Western blot assay was utilized to measure the levels of clathrin heavy chain (CLTC), cyclin D1, BCL2-associated X, apoptosis regulator Bax (Bax), vimentin and matrix metallopeptidase 9. The clonogenicity, apoptosis and metastasis of NSCLC cells were examined by colony formation assay, flow cytometry and transwell migration and invasion assays. The target relationship between miR-362-3p and circ_0074027 or CLTC was predicted by starBase website and was validated by dual-luciferase reporter assay. Murine xenograft assay was applied to explore the function of circ_0074027 in vivo. We found that The enrichment of circ_0074027 and CLTC protein was elevated, and a significant reduction in the expression of miR-362-3p was observed in NSCLC tissues and cells relative to adjacent normal tissues and human bronchial epithelial cells 16HBE. Circ_0074027 possessed a stable circular structure. Circ_0074027 and CLTC could accelerate the colony formation and metastasis and suppress the apoptosis of NSCLC cells. Circ_0074027/miR-362-3p/CLTC axis was first found to regulate the malignance of NSCLC cells. The biological influence caused by circ_0074027 depletion on NSCLC cells was alleviated by the accumulation of CLTC. Circ_0074027 acted as an oncogene to promote the growth of NSCLC tumors in vivo. In conclusion, Circ_0074027 contributed to the progression of NSCLC through promoting the proliferation and motility while hampering the apoptosis of NSCLC cells via miR-362-3p/CLTC axis.
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Hu TJ, Huang HB, Shen HB, Chen W, Yang ZH. Role of long non-coding RNA MALAT1 in chronic obstructive pulmonary disease. Exp Ther Med 2020; 20:2691-2697. [PMID: 32765763 PMCID: PMC7401856 DOI: 10.3892/etm.2020.8996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a pathological inflammatory condition of the lungs that is associated with high rates of mortality. Although long non-coding RNAs (lncRNAs) serve a role in lung diseases, their functions in COPD pathogenesis are relatively unknown. The present study aimed to assess the role of differentially expressed lncRNAs in COPD. Expression profile analysis of six lncRNAs in age-matched COPD and non-COPD tissues were conducted. Among the six tested lncRNAs, metastasis-associated in lung adenocarcinoma transcript 1 (MALAT1) was the most consistently overexpressed in COPD lung tissue specimens. To model COPD in vitro, human lung fibroblasts were treated with transforming growth factor-β (TGF-β) and MALAT1 was knocked down by small interfering RNA. This promoted cell viability and concurrently inhibited the expression of mesenchymal proteins, fibronectin and α-smooth muscle actin. In COPD, cell senescence is linked to the activation of mammalian target of rapamycin complex 1 (mTORC1). Upon gene silencing of MALAT1 in non-TGF-β-treated cells, cells demonstrated constitutive activation of mTORC1, which was assessed by the protein expression levels of mTORC1 substrate S6 kinase (S6K1). By contrast, upon MALAT1 silencing in the TGF-β-treated cells, mTORC1 activation was not suppressed, despite the mesenchymal cell markers protein expression levels being downregulated. Thus, lncRNA MALAT1 may represent a potent biomarker in COPD patients and may act as a target for both diagnostic and therapeutic purposes.
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Affiliation(s)
- Tian-Jun Hu
- Department of Thoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315012, P.R. China
| | - Hong-Bo Huang
- Department of Thoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315012, P.R. China
| | - Hai-Bo Shen
- Department of Thoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315012, P.R. China
| | - Wei Chen
- Zhongyuan Union Clinical Laboratory Co. Ltd., Tianjin 300384, P.R. China
- Zhongyuan-Vcan Genetic Technology Co. Ltd., Beijing 100176, P.R. China
| | - Zhen-Hua Yang
- Department of Thoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315012, P.R. China
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Yang S, Jiang Y, Ren X, Feng D, Zhang L, He D, Hong S, Jin L, Zhang F, Lu S. FOXA1-induced circOSBPL10 potentiates cervical cancer cell proliferation and migration through miR-1179/UBE2Q1 axis. Cancer Cell Int 2020; 20:389. [PMID: 32831649 PMCID: PMC7422615 DOI: 10.1186/s12935-020-01360-2] [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: 09/29/2019] [Accepted: 06/17/2020] [Indexed: 01/30/2023] Open
Abstract
Background Recently, extensive evidence has clarified the crucial role of circular RNAs (circRNAs) as a pro-tumor or anti-cancer participant in human malignancies. A new circRNA derived from oxysterol binding protein like 10 (OSBPL10) (circOSBPL10) has not been researched in cervical cancer (CC) yet. Methods The expression of molecules was analyzed by RT-qPCR or western blot. Several functional assays were applied to explore the biological influence of circOSBPL10 on CC. The interaction between RNAs was estimated via luciferase reporter, RNA immunoprecipitation and RNA pull-down assays. Results CircOSBPL10 characterized with cyclic structure was revealed to possess elevated expression in CC cells. CircOSBPL10 downregulation elicited suppressive impacts on CC cell proliferation and migration. Interestingly, circOSBPL10 regulated CC progression by interacting with microRNA-1179 (miR-1179). Moreover, ubiquitin conjugating enzyme E2 Q1 (UBE2Q1) targeted by miR-1179 was positively regulated by circOSBPL10 in CC. Furthermore, enhanced UBE2Q1 expression or suppressed miR-1179 level countervailed the repressive effect of circOSBPL10 depletion on the malignant phenotypes of CC cells. Moreover, forkhead box A1 (FOXA1) was confirmed to induce circOSBPL10 expression in CC cells. Conclusions FOXA1-induced circOSBPL10 facilitates CC progression through miR-1179/UBE2Q1 axis, highlighting a strong potential for circOSBPL10 to serve as a promising therapeutic target in CC.
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Affiliation(s)
- Shanshan Yang
- Department of Gynecological Radiotherapy, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081 Heilongjiang China
| | - Yiwen Jiang
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Xiaoli Ren
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Dan Feng
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Liaoyun Zhang
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China.,Pharmacy Department, Sichuan Jinxin Women and Children's Hospital, No. 66 Jingxiu Road, Jinjiang District, Chengdu, 610061 Sichuan China
| | - Deying He
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Shiyao Hong
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Li Jin
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Fang Zhang
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
| | - Shun Lu
- Department of Radiotherapy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55 Renmin South Road, Chengdu, 610041 Sichuan China
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15
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Xu J, Yang B, Wang L, Zhu Y, Zhu X, Xia Z, Zhao Z, Xu L. LncRNA BBOX1-AS1 upregulates HOXC6 expression through miR-361-3p and HuR to drive cervical cancer progression. Cell Prolif 2020; 53:e12823. [PMID: 32515533 PMCID: PMC7377938 DOI: 10.1111/cpr.12823] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/20/2020] [Accepted: 03/26/2020] [Indexed: 02/07/2023] Open
Abstract
Objectives Over the past years, growing attention has been paid to deciphering the pivotal role of long non‐coding RNAs (lncRNAs) in regulating the occurrence and development of human malignancies, cervical cancer (CC) included. Nonetheless, the regulatory role of lncRNA BBOX1 antisense RNA 1 (BBOX1‐AS1) has not been explored as yet. Material and Methods The expression of BBOX1‐AS1 was detected by reverse transcription real‐time quantitative polymerase chain reaction (RT‐qPCR). Cell Counting Kit‐8 (CCK‐8), colony formation, TUNEL, Western blot, transwell and immunofluorescence assays testified the critical role of BBOX1‐AS1 in CC. The relationship between RNAs (BBOX1‐AS1, miR‐361‐3p, HOXC6 and HuR) was analysed by luciferase reporter, RNA Immunoprecipitation (RIP) and RNA pull‐down assays. Results BBOX1 antisense RNA 1 antisense RNA 1 was revealed to be highly expressed in CC. Decreased expression of BBOX1‐AS1 had suppressive effects on CC cell growth and migration. Molecular mechanism assays verified that BBOX1‐AS1 had negative interaction with miR‐361‐3p in CC. Additionally, homeobox C6 (HOXC6) was validated to be a downstream target of miR‐361‐3p in CC. Furthermore, ELAV‐like RNA‐binding protein 1, also known as HuR, was uncovered to be capable of regulating the mRNA stability of HOXC6 in CC. More importantly, rescue assays delineated that knockdown of HuR after overexpressing miR‐361‐3p could reverse BBOX1‐AS1 upregulation‐mediated effect on CC progression. Similarly, the function induced by BBOX1‐AS1 upregulation on CC progression could be countervailed by HOXC6 depletion. Conclusions BBOX1 antisense RNA 1 facilitates CC progression by upregulating HOXC6 expression via miR‐361‐3p and HuR.
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Affiliation(s)
- Jun Xu
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Baohua Yang
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Lifeng Wang
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Yunheng Zhu
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Xiuxiang Zhu
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Ziyin Xia
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Zhen Zhao
- Department of Clinical Laboratory, Minhang Hospital, Fudan University, Shanghai, China
| | - Ling Xu
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
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16
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Park SA, Kim LK, Kim YT, Heo TH, Kim HJ. Long non-coding RNA steroid receptor activator promotes the progression of endometrial cancer via Wnt/ β-catenin signaling pathway. Int J Biol Sci 2020; 16:99-115. [PMID: 31892849 PMCID: PMC6930375 DOI: 10.7150/ijbs.35643] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/20/2019] [Indexed: 01/05/2023] Open
Abstract
Rationale: Steroid receptor activator (SRA), a long non-coding RNA, serves as a critical regulator of gynecologic cancer. The objective of this study was to determine biological function and clinical significance of SRA expression in endometrial cancer. Method: We investigated whether SRA was involved in the development of endometrial cancer via binding to eukaryotic translation initiation factor 4E-binding protein 1 (EIF4E-BP1) as a transcription factor to enhance Wnt/ β-catenin signaling pathway. Results: Expression levels of SRA were upregulated in endometrial cancer tissues compared to those in adjacent control tissues. We also found high expression of SRA in EC cells. The relationship between SRA and EIF4E-BP1 was corroborated by transfection of a luciferase reporter plasmid. In addition, SRA knockdown inhibited the expression of EIF4E-BP1 known to play a critical role in the control of protein synthesis, cell growth, and cell survival, thus promoting tumourigenesis and epithelial-mesenchymal transition (EMT) important for cell motility and metastasis. Consistently, immunostaining and western blotting analysis showed that expression levels of β-catenin and 4EBP1 in the nucleus were significantly decreased by SRA knockdown but increased by SRA over-expression. Conclusions: These results suggest that SRA is involved in proliferation, migration, and invasion of endometrial cancer cells by increasing the expression of EIF4E-BP1 and activity of Wnt/ β-catenin signaling. These findings indicate that SRA might be a novel biomarker for predicting recurrence and prognosis. It might also serve as a promising therapeutic target in endometrial cancer.
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Affiliation(s)
- Sun-Ae Park
- Laboratory of Pharmacoimmunology, Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Seoul, 03722, Republic of Korea
| | - Lee Kyung Kim
- Laboratory of Pharmacoimmunology, Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Seoul, 03722, Republic of Korea
| | - Young Tae Kim
- Institute of Women's Life Medical Science, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Tae-Hwe Heo
- Laboratory of Pharmacoimmunology, Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Seoul, 03722, Republic of Korea
| | - Hee Jung Kim
- Laboratory of Pharmacoimmunology, Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Seoul, 03722, Republic of Korea
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Wang Y, Wu N, Luo X, Zhang X, Liao Q, Wang J. SOX2OT, a novel tumor-related long non-coding RNA. Biomed Pharmacother 2019; 123:109725. [PMID: 31865145 DOI: 10.1016/j.biopha.2019.109725] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 12/24/2022] Open
Abstract
SOX2OT is a long non-coding RNA that is highly expressed in embryonic stem cells. The SOX2OT gene is comprised of 10 exons and more than two transcription start sites. Dysregulation of SOX2OT is observed in various tumors, including lung cancer, gastric cancer, esophageal cancer, breast cancer, hepatocellular carcinoma, ovarian cancer, pancreatic ductal adenocarcinoma, laryngeal squamous cell carcinoma, cholangiocarcinoma, osteosarcoma, nasopharyngeal carcinoma, and glioblastoma, wherein it typically functions as an oncogene and possibly as a tumor suppressor gene. The mechanisms underlying the effects of SOX2OT are complex and involve multiple factors and signaling pathways. In this review, we describe the current evidence regarding the role and potential clinical utility of SOX2OT in human cancers.
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Affiliation(s)
- Ying Wang
- Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, People's Republic of China; Hunan Clinical Research Center in Gynecologic Cancer, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283, Tongzipo Road, Changsha 410013, Hunan, People's Republic of China.
| | - Nayiyuan Wu
- Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, People's Republic of China; Hunan Clinical Research Center in Gynecologic Cancer, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283, Tongzipo Road, Changsha 410013, Hunan, People's Republic of China
| | - Xia Luo
- Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, People's Republic of China
| | - Xiaoyun Zhang
- Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, People's Republic of China; Hunan Clinical Research Center in Gynecologic Cancer, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283, Tongzipo Road, Changsha 410013, Hunan, People's Republic of China
| | - Qianjin Liao
- Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, People's Republic of China.
| | - Jing Wang
- Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, People's Republic of China; Hunan Clinical Research Center in Gynecologic Cancer, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283, Tongzipo Road, Changsha 410013, Hunan, People's Republic of China.
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18
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Liu B, Cao W, Ma H. Knockdown of lncRNA LSINCT5 suppresses growth and metastasis of human glioma cells via up-regulating miR-451. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:2507-2515. [PMID: 31213092 DOI: 10.1080/21691401.2019.1626404] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background: Glioma is a main cause of brain-cancer relevant death. The present paper designed to reveal the possible role of LSINCT5 in human glioma GL15 cells. Methods: LSINCT5 and miR-451 expression in glioma tissues was examined using qRT-PCR. The impacts of LSINCT5, miR-451 and Rac1 in GL15 cells were checked by carrying out CCK-8 assay, transwell assay, and flow cytometric analysis. Further, the target gene of LSINCT5 and miR-451 was explored. Accumulation of PI3K/AKT, Wnt/β-catenin and NF-κB pathway proteins was examined using Western blot. Results: LSINCT5 was highly expressed while miR-451 low expressed in glioma tissues when compared to normal controls. Down-regulating LSINCT5 effectively declined GL15 cells viability, migration and invasion, but accelerated apoptosis. Nonetheless, the above-mentioned effects of LSINCT5 down-regulation were weakened when miR-451 was silenced. Rac1 was a target of miR-451. The tumour-suppressive effects of miR-451 on GL15 cells were weakened when Rac1 was overexpressed. Further, LSINCT5-miR-451-Rac1 axis could impact the activation of PI3K/AKT, Wnt/β-catenin and NF-κB pathways. Conclusion: Down-regulation of LSINCT5 represses glioma cells growth and metastasis in vitro likely through targeting miR-451 and thereby inhibiting Rac1-regulated PI3K/AKT, Wnt/β-catenin and NF-κB pathways.
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Affiliation(s)
- Bin Liu
- a Department of Neurosurgery, Jining No.1 People's Hospital , Jining , China
| | - Wei Cao
- a Department of Neurosurgery, Jining No.1 People's Hospital , Jining , China
| | - Hui Ma
- a Department of Neurosurgery, Jining No.1 People's Hospital , Jining , China
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Verda D, Parodi S, Ferrari E, Muselli M. Analyzing gene expression data for pediatric and adult cancer diagnosis using logic learning machine and standard supervised methods. BMC Bioinformatics 2019; 20:390. [PMID: 31757200 PMCID: PMC6873393 DOI: 10.1186/s12859-019-2953-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 06/14/2019] [Indexed: 12/27/2022] Open
Abstract
Background Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules. In this investigation the performance of LLM in classifying patients with cancer was evaluated using a set of eight publicly available gene expression databases for cancer diagnosis. LLM accuracy was assessed by summary ROC curve (sROC) analysis and estimated by the area under an sROC curve (sAUC). Its performance was compared in cross validation with that of standard supervised methods, namely: decision tree, artificial neural network, support vector machine (SVM) and k-nearest neighbor classifier. Results LLM showed an excellent accuracy (sAUC = 0.99, 95%CI: 0.98–1.0) and outperformed any other method except SVM. Conclusions LLM is a new powerful tool for the analysis of gene expression data for cancer diagnosis. Simple rules generated by LLM could contribute to a better understanding of cancer biology, potentially addressing therapeutic approaches.
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Affiliation(s)
| | - Stefano Parodi
- Epidemiology and Biostatistics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Marco Muselli
- Rulex Inc., Newton, MA, USA. .,Institute of Electronics, Computer and Telecommunication Engineering National Research Council of Italy, Via De Marini, 6, 16149, Genoa, Italy.
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Gao P, Wang Z, Hu Z, Jiao X, Yao Y. Circular RNA circ_0074027 indicates a poor prognosis for NSCLC patients and modulates cell proliferation, apoptosis, and invasion via miR-185-3p mediated BRD4/MADD activation. J Cell Biochem 2019; 121:2632-2642. [PMID: 31680319 DOI: 10.1002/jcb.29484] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/10/2019] [Indexed: 01/05/2023]
Abstract
Circular RNAs play an imperative role in cancer development and metastasis by regulating oncogenic and tumor-suppressive pathways. However, the role and mechanism of circ_0074027 in non-small-cell lung cancer (NSCLC) have not been elucidated. The expression levels of circ_0074027 were detected by qRT-PCR. The link between circ_0074027 expression and clinicopathologic parameters was analyzed by Fisher's exact test. The prognostic role of circ_0074027 was investigated by Kaplan-Meier and Cox regression analysis. Cell counting kit-8 and flow cytometric assays were utilized to evaluate NSCLC cell proliferation and apoptosis, respectively. Wound scratch and Transwell tests were applied to detect cell migratory and invasive capacities. The interaction potential of circ_0074027 and miR-185-3p was analyzed by the circBank database, and verified by dual-luciferase reporter assay. The downstream gene of miR-185-3p was also investigated. Circ_0074027 was elevated in NSCLC specimens and cell lines. Overexpressed circ_0074027 was related to more advanced TNM stages, poorer differentiation grade, and worse overall survival. Upregulated circ_0074027 increased the proliferation of H1299 cells by inhibiting cell apoptosis. Cell migration and invasion were enhanced after circ_0074027 overexpression. Silenced circ_0074027 caused the opposite effects in the A549 cell line. For mechanism investigation, circ_0074027 directly sponges miR-185-3p to enhance bromodomain-containing protein 4 (BRD4) and MAPK-activating death domain-containing protein (MADD) expression levels at the posttranscriptional level. Furthermore, we found the oncogenic function of circ_0074027 is attributed to its modulation of BRD4 and MADD. Collectively, upregulated circ_0074027 in NSCLC accelerates cell progression via miR-185-3p/BRD4/MADD pathway as a competing endogenous RNA.
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Affiliation(s)
- Ping Gao
- Department of Endocrinology and Metabolism, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhidong Wang
- Department of General Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhanliang Hu
- Department of General Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuan Jiao
- Department of Cardiovascular Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yue Yao
- Department of Endocrinology and Metabolism, Second Affiliated Hospital of Harbin Medical University, Harbin, China
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21
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Barton M, Santucci-Pereira J, Vaccaro OG, Nguyen T, Su Y, Russo J. BC200 overexpression contributes to luminal and triple negative breast cancer pathogenesis. BMC Cancer 2019; 19:994. [PMID: 31646972 PMCID: PMC6813071 DOI: 10.1186/s12885-019-6179-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 09/20/2019] [Indexed: 01/04/2023] Open
Abstract
Background Long non coding RNAs (lncRNAs) are RNA molecules longer than 200 nucleotides that are not translated into proteins, but regulate the transcription of genes involved in different cellular processes, including cancer. Epidemiological analyses have demonstrated that parous women have a decreased risk of developing breast cancer in postmenopausal years if they went through a full term pregnancy in their early twenties. We here provide evidence of the role of BC200 in breast cancer and, potentially, in pregnancy’s preventive effect in reducing the lifetime risk of developing breast cancer. Methods Transcriptome analysis of normal breast of parous and nulliparous postmenopausal women revealed that several lncRNAs are differentially expressed in the parous breast. RNA sequencing of healthy postmenopausal breast tissue biopsies from eight parous and eight nulliparous women showed that there are 42 novel lncRNAs differentially expressed between these two groups. Screening of several of these 42 lncRNAs by RT-qPCR in different breast cancer cell lines, provided evidence that one in particular, lncEPCAM (more commonly known as BC200), was a strong candidate involved in cancer progression. Proliferation, migration, invasion and xerograph studies confirmed this hypothesis. Results The poorly studied oncogenic BC200 was selected to be tested in vitro and in vivo to determine its relevance in breast cancer and also to provide us with an understanding of its role in the increased susceptibility of the nulliparous women to cancer. Our results show that BC200 is upregulated in nulliparous women, and breast cancer cells and tissue. The role of BC200 is not completely understood in any of the breast cancer subtypes. We here provide evidence that BC200 has a role in luminal breast cancer as well as in the triple negative breast cancer subtype. Conclusion When overexpressed in luminal and triple negative breast cancer cell lines, BC200 shows increased proliferation, migration, and invasion in vitro. In vivo, overexpression of BC200 increased tumor size. Although treatment for cancer using lncRNAs as targets is in its infancy, the advancement in knowledge and technology to study their relevance in disease could lead to the development of novel treatment and preventive strategies for breast cancer.
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Affiliation(s)
- Maria Barton
- Biochemistry Department, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA. .,The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA.
| | - Julia Santucci-Pereira
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Olivia G Vaccaro
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Theresa Nguyen
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Yanrong Su
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Jose Russo
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
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22
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Da J, Liu P, Wang R, Bu L. Upregulation of the long non-coding RNA FAM83H-AS1 in gastric cancer and its clinical significance. Pathol Res Pract 2019; 215:152616. [DOI: 10.1016/j.prp.2019.152616] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/14/2019] [Accepted: 08/23/2019] [Indexed: 12/25/2022]
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Saghafi T, Taheri RA, Parkkila S, Emameh RZ. Phytochemicals as Modulators of Long Non-Coding RNAs and Inhibitors of Cancer-Related Carbonic Anhydrases. Int J Mol Sci 2019; 20:ijms20122939. [PMID: 31208095 PMCID: PMC6627131 DOI: 10.3390/ijms20122939] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are classified as a group of transcripts which regulate various biological processes, such as RNA processing, epigenetic control, and signaling pathways. According to recent studies, lncRNAs are dysregulated in cancer and play an important role in cancer incidence and spreading. There is also an association between lncRNAs and the overexpression of some tumor-associated proteins, including carbonic anhydrases II, IX, and XII (CA II, CA IX, and CA XII). Therefore, not only CA inhibition, but also lncRNA modulation, could represent an attractive strategy for cancer prevention and therapy. Experimental studies have suggested that herbal compounds regulate the expression of many lncRNAs involved in cancer, such as HOTAIR (HOX transcript antisense RNA), H19, MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), PCGEM1 (Prostate cancer gene expression marker 1), PVT1, etc. These plant-derived drugs or phytochemicals include resveratrol, curcumin, genistein, quercetin, epigallocatechin-3-galate, camptothcin, and 3,3′-diindolylmethane. More comprehensive information about lncRNA modulation via phytochemicals would be helpful for the administration of new herbal derivatives in cancer therapy. In this review, we describe the state-of-the-art and potential of phytochemicals as modulators of lncRNAs in different types of cancers.
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Affiliation(s)
- Tayebeh Saghafi
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran.
| | - Ramezan Ali Taheri
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, P.O.Box 14965/161 Tehran, Iran.
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland.
- Fimlab Laboratories Ltd. and Tampere University Hospital, FI-33520 Tampere, Finland.
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran.
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24
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Chen Y, Fu Y, Song YF, Li N. Increased Expression of lncRNA UCA1 and HULC Is Required for Pro-inflammatory Response During LPS Induced Sepsis in Endothelial Cells. Front Physiol 2019; 10:608. [PMID: 31231228 PMCID: PMC6558422 DOI: 10.3389/fphys.2019.00608] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/29/2019] [Indexed: 01/15/2023] Open
Abstract
Systemic uncontrolled inflammatory response, also termed as sepsis, is responsible for many mortalities. Bacterial endotoxin, lipopolysaccharide (LPS), is a major cause of sepsis in endothelial cells. Even though a lot of research has been done to define underlying mechanisms of LPS induced sepsis, the role of long non-coding RNAs (lncRNAs), a group of >200 kb RNAs in sepsis is not well-defined. Expression of pro-inflammatory mediators IL6, ICAM1, and VCAM1 (which encodes interleukin-6, intercellular adhesion molecule-1, and vascular cell adhesion molecule-1, respectively) were determined following LPS treatment of human dermal microvascular endothelial cells (HMECs) for 24 h to confirm sepsis induction. RNA immunoprecipitation (RIP) analysis was performed using the chromatin modifying proteins (CMPs), heterogeneous nuclear ribonucleoprotein (hnRNP) K and corepressors of the RE-1 silencing transcription factor (coREST) as individual baits. Quantitative real time polymerase chain reaction (qRT-PCR) was performed on RNA isolated from immunoprecipitated pellets for six different lncRNAs. The effect of the differentially expressed lncRNAs were determined by ectopic overexpression of the lncRNAs before induction of sepsis. Expression of IL6, ICAM1, and VCAM1 were significantly upregulated following treatment of the HMECs with LPS for 24 h confirming induction of sepsis. RIP and qRT-PCR analysis revealed that the lncRNAs HULC, UCA1, and MALAT-1 were significantly enriched with the CMPs after sepsis. RNA interference using siRNAs targeting HULC and UCA1, but not MALAT-1, decreased the expression of IL6, ICAM1, and VCAM1 to endogenous levels. Our results were further validated in an in vivo model of sub-lethal LPS-induced sepsis, whereby siRNA mediated knockdown of UCA1 and HULC lncRNAs prevented induction of VCAM1, ICAM1, and IL6, as assayed by immunohistochemistry. Cumulatively, these results suggest that LPS induced in vitro sepsis in endothelial cells and induction of pre-inflammatory mediators are at least in part due to increased expression of the UCA1 and HULC lncRNAs.
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Affiliation(s)
- Ying Chen
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, China
| | - Yao Fu
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, China
| | - Yan-Fei Song
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, China
| | - Nan Li
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, China
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25
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Feng W, Su Z, Yin Q, Zong W, Shen X, Ju S. ncRNAs associated with drug resistance and the therapy of digestive system neoplasms. J Cell Physiol 2019; 234:19143-19157. [PMID: 30941775 DOI: 10.1002/jcp.28551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/25/2019] [Accepted: 03/05/2019] [Indexed: 12/19/2022]
Abstract
Digestive system cancer remains a common cancer and the main cause of cancer-related death worldwide. Drug resistance is a major challenge in the therapy of digestive system cancer, and represents a primary obstacle in the treatment of cancer by restricting the efficiency of both traditional chemotherapy and biological therapies. Existing studies indicate that noncoding RNAs play an important role in the evolution and progression of drug resistance in digestive system cancer, mainly by modulating drug transporter-related proteins, DNA damage repair, cell-cycle-related proteins, cell apoptosis-related proteins, drug target-related proteins, and the tumor microenvironment. In this review, we address the potential mechanisms of ncRNAs underlying drug resistance in digestive system tumors and discuss the possible application of ncRNAs against drug resistance in digestive system tumors.
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Affiliation(s)
- Wei Feng
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhangyao Su
- School of Medicine, Nantong University, Nantong, China
| | - Qingqing Yin
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Wei Zong
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xianjuan Shen
- Clinical Medical Research Center, Affiliated Hospital of Nantong University, Nantong, China
| | - Shaoqing Ju
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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26
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Teng M, Liu LY, Hua JT, Chen S, He HH. Orphan noncoding RNAs: novel regulators and cancer biomarkers. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S21. [PMID: 31032301 DOI: 10.21037/atm.2019.01.70] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Mona Teng
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Lydia Y Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada.,Ontario Institute for Cancer Research, Toronto, Canada
| | - Junjie Tony Hua
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada.,Ontario Institute for Cancer Research, Toronto, Canada
| | - Housheng Hansen He
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada
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27
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Zhang G, Wang Q, Lu J, Ma G, Ge Y, Chu H, Du M, Wang M, Zhang Z. Long non-coding RNA FLJ22763 is involved in the progression and prognosis of gastric cancer. Gene 2019; 693:84-91. [PMID: 30716442 DOI: 10.1016/j.gene.2019.01.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 12/27/2018] [Accepted: 01/11/2019] [Indexed: 01/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in carcinogenesis. It is necessary to uncover the detailed pattern of comprehensive lncRNA expression in the genome during the development of gastric cancer (GC). We implemented lncRNA microarray analysis in 5 paired GC tissues to detect the lncRNA expression profile. Moreover, we set out to explore the biological function, clinical application and molecular basis of the aberrant lncRNA in GC. In addition, we used the high-throughput microarray to identify the target gene of the aberrant lncRNA. We found that FLJ22763, a novel lncRNA, had significantly lower expression in GC tissues. Decreased expression of FLJ22763 was positively correlated with a lower-level histological grade and the depth of invasion. The ectopic expression of lncRNA FLJ22763 significantly suppressed the biological malignant behavior of GC cells and inhibited xenograft tumor growth (both P < 0.001). Notably, FLJ22763 displayed a considerable predictive effect in the prognosis of GC (log-rank, P = 0.003). Furthermore, we found that FLJ22763 was negatively associated with ACLY, regulating the mRNA and protein levels of ACLY. Our findings suggested that FLJ22763 may act as a suppressor gene to regulate the expression of ACLY, and its down-expression may be an independent prognostic factor in patients with GC.
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Affiliation(s)
- Gang Zhang
- Department of Neurology, Children's Hospital of Nanjing Medical University, Nanjing, China; Department of Environmental Genomics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiaoyan Wang
- Department of Environmental Genomics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jiafei Lu
- Department of Environmental Genomics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Gaoxiang Ma
- Department of Environmental Genomics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuqiu Ge
- Department of Environmental Genomics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
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28
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Liang WQ, Zeng D, Chen CF, Sun SM, Lu XF, Peng CY, Lin HY. Long noncoding RNA H19 is a critical oncogenic driver and contributes to epithelial-mesenchymal transition in papillary thyroid carcinoma. Cancer Manag Res 2019; 11:2059-2072. [PMID: 30881130 PMCID: PMC6411319 DOI: 10.2147/cmar.s195906] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Growing evidence has indicated that the long noncoding RNA H19 (lncRNA H19), frequently deregulated in almost all tumor types tested, acted as a pivotal contributor to both cancer initiation and progression. However, the role of lncRNA H19 in human papillary thyroid carcinoma (PTC) remains controversial. The aim of the study was to investigate the expression and potential function of lncRNA H19 in human PTC. PATIENTS AND METHODS The lncRNA H19 level was determined by quantitative real-time (RT)-PCR analyses in 58 PTC tissue samples and their paired paracancerous tissue samples. RNA interference, RT-PCR analysis, and Western blot assay were used to determine the impact of lncRNA H19 on epithelial-mesenchymal transition (EMT) markers in human PTC cells. The migratory and invasive capacities of PTC cells were determined by wound-healing and transwell migration and invasion assays. RESULTS lncRNA H19 expression was 2.417-fold higher in PTC tissues than their paired paracancerous tissue (95% CI: 1.898-2.935, P<0.0001). Higher level of lncRNA H19 was correlated to elevated expression of Vimentin, ZEB2, Twist, and Snail2. Inhibition of lncRNA H19 resulted in upregulation of E-cadherin and downregulation of Vimentin both at mRNA and protein levels. Conversely, enforced expression of the exogenous lncRNA H19 led to E-cadherin mRNA and protein downregulation and relative upregulation of Vimentin. Moreover, wound-healing and transwell migration and invasion assays showed that lncRNA H19 could promote the migratory and invasive abilities of PTC cells. CONCLUSION The level of lncRNA H19 was significantly higher in PTC tissues than paired paracancerous tissue or normal tissues. Overexpression of lncRNA H19 was correlated with higher tumor burden of PTC. It also contributes to EMT process, as well as promotes migration and invasion of PTC cells.
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Affiliation(s)
- Wei-Quan Liang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515000, People's Republic of China,
| | - De Zeng
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou 515031, People's Republic of China
| | - Chun-Fa Chen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515000, People's Republic of China,
| | - Shu-Ming Sun
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515000, People's Republic of China,
| | - Xiao-Feng Lu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515000, People's Republic of China,
| | - Chun-Yan Peng
- Department of Clinical Laboratory, Taihe Hospital of Hubei University of Medicine, Hubei 442008, People's Republic of China
| | - Hao-Yu Lin
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515000, People's Republic of China,
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Samson J, Cronin S, Dean K. BC200 (BCYRN1) - The shortest, long, non-coding RNA associated with cancer. Noncoding RNA Res 2018; 3:131-143. [PMID: 30175286 PMCID: PMC6114260 DOI: 10.1016/j.ncrna.2018.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022] Open
Abstract
With the discovery that the level of RNA synthesis in human cells far exceeds what is required to express protein-coding genes, there has been a concerted scientific effort to identify, catalogue and uncover the biological functions of the non-coding transcriptome. Long, non-coding RNAs (lncRNAs) are a diverse group of RNAs with equally wide-ranging biological roles in the cell. An increasing number of studies have reported alterations in the expression of lncRNAs in various cancers, although unravelling how they contribute specifically to the disease is a bigger challenge. Originally described as a brain-specific, non-coding RNA, BC200 (BCYRN1) is a 200-nucleotide, predominantly cytoplasmic lncRNA that has been linked to neurodegenerative disease and several types of cancer. Here we summarise what is known about BC200, primarily from studies in neuronal systems, before turning to a review of recent work that aims to understand how this lncRNA contributes to cancer initiation, progression and metastasis, along with its possible clinical utility as a biomarker or therapeutic target.
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Affiliation(s)
| | | | - K. Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
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30
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Corrà F, Agnoletto C, Minotti L, Baldassari F, Volinia S. The Network of Non-coding RNAs in Cancer Drug Resistance. Front Oncol 2018; 8:327. [PMID: 30211115 PMCID: PMC6123370 DOI: 10.3389/fonc.2018.00327] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/31/2018] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNAs (ncRNAs) have been implicated in most cellular functions. The disruption of their function through somatic mutations, genomic imprinting, transcriptional and post-transcriptional regulation, plays an ever-increasing role in cancer development. ncRNAs, including notorious microRNAs, have been thus proposed to function as tumor suppressors or oncogenes, often in a context-dependent fashion. In parallel, ncRNAs with altered expression in cancer have been reported to exert a key role in determining drug sensitivity or restoring drug responsiveness in resistant cells. Acquisition of resistance to anti-cancer drugs is a major hindrance to effective chemotherapy and is one of the most important causes of relapse and mortality in cancer patients. For these reasons, non-coding RNAs have become recent focuses as prognostic agents and modifiers of chemo-sensitivity. This review starts with a brief outline of the role of most studied non-coding RNAs in cancer and then highlights the modulation of cancer drug resistance via known ncRNAs based mechanisms. We identified from literature 388 ncRNA-drugs interactions and analyzed them using an unsupervised approach. Essentially, we performed a network analysis of the non-coding RNAs with direct relations with cancer drugs. Within such a machine-learning framework we detected the most representative ncRNAs-drug associations and groups. We finally discussed the higher integration of the drug-ncRNA clusters with the goal of disentangling effectors from downstream effects and further clarify the involvement of ncRNAs in the cellular mechanisms underlying resistance to cancer treatments.
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Affiliation(s)
- Fabio Corrà
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Chiara Agnoletto
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Linda Minotti
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Federica Baldassari
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Stefano Volinia
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
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Expression levels of the long noncoding RNA steroid receptor activator promote cell proliferation and invasion and predict patient prognosis in human cervical cancer. Oncol Lett 2018; 16:5410-5418. [PMID: 30250612 DOI: 10.3892/ol.2018.9265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 07/26/2018] [Indexed: 01/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in developmental processes and diseases and function as critical regulators of a number of different cancer types. Previous research has revealed that lncRNAs affect cervical cancer development. Steroid receptor activator (SRA), an lncRNA, serves as a critical regulator of gynecologic cancer. However, the association between SRA expression and cervical cancer remains unclear. In the present study, the SRA expression levels in patients with cervical cancer were examined and the association between SRA expression and clinicopathological factors was determined. SRA expression was observed in cervical cancer tissues (n=100) and corresponding normal tissues (n=22) using reverse transcription-quantitative polymerase chain reaction, and its associations with clinical parameters and prognosis were analyzed. SRA expression was significantly greater in tissues from patients with cervical cancer compared with in control patients (P<0.001). Multivariate analysis revealed that high SRA expression was an independent prognostic factor of overall survival (hazard ratio=3.714, P=0.031). The present study additionally investigated the biofunctional consequences of SRA overexpression in vitro using Cell Counting kit-8, wound healing migration and Matrigel invasion assays. The results demonstrated that SRA overexpression enhanced cell proliferation, migration and invasion in vitro. Furthermore, SRA overexpression induced the epithelial-mesenchymal transition (EMT). Therefore, SRA may promote tumor aggressiveness through the upregulation of EMT-associated genes. These results indicated that SRA may represent a novel biomarker for predicting recurrence and prognosis and serve as a promising therapeutic target in cervical cancer.
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Wu Y, Wei J, Ming Y, Chen Z, Yu J, Mao R, Chen H, Zhou G, Fan Y. Orchestrating a biomarker panel with lncRNAs and mRNAs for predicting survival in pancreatic ductal adenocarcinoma. J Cell Biochem 2018; 119:7696-7706. [PMID: 29923223 DOI: 10.1002/jcb.27119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/04/2018] [Indexed: 12/15/2022]
Abstract
The low survival of patients with pancreatic ductal adenocarcinoma (PDAC) makes the treatment of this disease one of the most challenging task in modern medicine. Here, by mining a large-scale cancer genome atlas data set of pancreatic cancer tissues, we identified 21 long noncoding RNAs (lncRNAs) that significantly associated with overall survival in patients with PDAC (P < .01). Further analysis revealed that 8 lncRNAs turned out to be independently correlated with patients' overall survival, and the risk score could be calculated based on their expression. To obtain a better predicting power, we integrated lncRNA data with a total of 410 differently expressed messenger RNAs (mRNAs) screened from PDAC and normal tissues in gene expression omnibus (GEO) database. The integration resulted in a much better panel including 8 lncRNAs (RP3.470B24.5, CTA.941F9.9, RP11.557H15.3, LINC00960, AP000479.1, LINC00635, LINC00636, and AC073133.1) and 8 mRNAs (DHRS9, ONECUT1, OR8D4, MT1M, TCN1, MMP9, DPYSL3, and TTN) to predict prognosis. A functional evaluation showed that these lncRNAs might play roles in pancreatic secretion, cell adhesion, and proteolysis. Using normal and pancreatic cancer cell lines, we confirmed that a majority of identified lncRNAs and mRNAs showed altered expressions in pancreatic cancer cells. Especially, LINC01589, LINC00960, TCN1, and MT1M showed a profoundly increased expression in pancreatic cancer cells, which suggests their potentially important role in pancreatic cancer. The results of our work indicate that lncRNAs have vital roles in PADC and provide new insights to integrate multiple kinds of markers in clinical practices.
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Affiliation(s)
- Yingcheng Wu
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, China
| | - Jinhuan Wei
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, China
| | - Yue Ming
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Zhanghao Chen
- Department of Computer Science, New York University, New York, USA.,Department of Computer Science, New York University Shanghai, Shanghai, China
| | - Jinzhong Yu
- Department of Computer Science, New York University, New York, USA.,Department of Computer Science, New York University Shanghai, Shanghai, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, China
| | - Hao Chen
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, China
| | - Guoxiong Zhou
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yihui Fan
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, China.,Department of Immunology, School of Medicine, Nantong University, Nantong, China
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Richard JLC, Eichhorn PJA. Deciphering the roles of lncRNAs in breast development and disease. Oncotarget 2018; 9:20179-20212. [PMID: 29732012 PMCID: PMC5929455 DOI: 10.18632/oncotarget.24591] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 02/21/2018] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second leading cause of cancer related deaths in women. It is therefore important to understand the mechanisms underlying breast cancer development as well as raises the need for enhanced, non-invasive strategies for novel prognostic and diagnostic methods. The emergence of long non-coding RNAs (lncRNAs) as potential key players in neoplastic disease has received considerable attention over the past few years. This relatively new class of molecular regulators has been shown from ongoing research to act as critical players for key biological processes. Deregulated expression levels of lncRNAs have been observed in a number of cancers including breast cancer. Furthermore, lncRNAs have been linked to breast cancer initiation, progression, metastases and to limit sensitivity to certain targeted therapeutics. In this review we provide an update on the lncRNAs associated with breast cancer and mammary gland development and illustrate the versatility of such lncRNAs in gene control, differentiation and development both in normal physiological conditions and in diseased states. We also highlight the therapeutic and diagnostic potential of lncRNAs in cancer.
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Affiliation(s)
- John Lalith Charles Richard
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- Current Address: Genome Institute of Singapore, Agency for Science Technology and Research, 138672, Singapore
| | - Pieter Johan Adam Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- School of Pharmacy, Curtin University, Perth, 6845, Australia
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ncRNA-disease association prediction based on sequence information and tripartite network. BMC SYSTEMS BIOLOGY 2018; 12:37. [PMID: 29671405 PMCID: PMC5907179 DOI: 10.1186/s12918-018-0527-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Background Current technology has demonstrated that mutation and deregulation of non-coding RNAs (ncRNAs) are associated with diverse human diseases and important biological processes. Therefore, developing a novel computational method for predicting potential ncRNA-disease associations could benefit pathologists in understanding the correlation between ncRNAs and disease diagnosis, treatment, and prevention. However, only a few studies have investigated these associations in pathogenesis. Results This study utilizes a disease-target-ncRNA tripartite network, and computes prediction scores between each disease-ncRNA pair by integrating biological information derived from pairwise similarity based upon sequence expressions with weights obtained from a multi-layer resource allocation technique. Our proposed algorithm was evaluated based on a 5-fold-cross-validation with optimal kernel parameter tuning. In addition, we achieved an average AUC that varies from 0.75 without link cut to 0.57 with link cut methods, which outperforms a previous method using the same evaluation methodology. Furthermore, the algorithm predicted 23 ncRNA-disease associations supported by other independent biological experimental studies. Conclusions Taken together, these results demonstrate the capability and accuracy of predicting further biological significant associations between ncRNAs and diseases and highlight the importance of adding biological sequence information to enhance predictions.
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Landskron L, Steinmann V, Bonnay F, Burkard TR, Steinmann J, Reichardt I, Harzer H, Laurenson AS, Reichert H, Knoblich JA. The asymmetrically segregating lncRNA cherub is required for transforming stem cells into malignant cells. eLife 2018; 7:31347. [PMID: 29580384 PMCID: PMC5871330 DOI: 10.7554/elife.31347] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/06/2018] [Indexed: 12/20/2022] Open
Abstract
Tumor cells display features that are not found in healthy cells. How they become immortal and how their specific features can be exploited to combat tumorigenesis are key questions in tumor biology. Here we describe the long non-coding RNA cherub that is critically required for the development of brain tumors in Drosophila but is dispensable for normal development. In mitotic Drosophila neural stem cells, cherub localizes to the cell periphery and segregates into the differentiating daughter cell. During tumorigenesis, de-differentiation of cherub-high cells leads to the formation of tumorigenic stem cells that accumulate abnormally high cherub levels. We show that cherub establishes a molecular link between the RNA-binding proteins Staufen and Syncrip. As Syncrip is part of the molecular machinery specifying temporal identity in neural stem cells, we propose that tumor cells proliferate indefinitely, because cherub accumulation no longer allows them to complete their temporal neurogenesis program. Many biological signals control how cells grow and divide. However, cancer cells do not obey these growth-restricting signals, and as a result large tumors may develop. Recent experiments have suggested that stem cells – the precursors to the different types of specialized cells found in the body – are particularly important for generating tumors. A stem cell normally divides unequally to form a self-renewing cell and a more specialized cell (often a progenitor cell that will give rise to increasingly specialized cell types). The timing of when the specialization occurs can be key to guiding the ultimately produced cell progenies to their final identity. However, in a tumor cells can retain the ability to self-renew. Ultimately, the resulting ‘tumor stem cells’ become immortal and proliferate indefinitely. It is not fully understood why this uncontrolled proliferation occurs. Just like mammals (including humans), fruit flies can develop tumors. Some of the DNA mutations responsible for tumor development were already identified in flies as early as in the 1970s. This has made fruit flies a well-studied model system for uncovering the principle defects that cause tumors to form. Landskron et al. have now studied the neural stem cells found in brain tumors in fruit flies. Additional DNA mutations were not responsible for these cells becoming immortal. Instead, certain RNA molecules – products that are ‘transcribed’ from the DNA – were present in different amounts in tumor cells. The RNA that showed the greatest increase in tumor cells is a so-called long non-coding RNA named cherub. This RNA molecule has no important role in normal fruit flies, but is critical for tumor formation. Landskron et al. found that during cell division cherub segregates from the neural stem cells to the newly formed progenitor cells, where it breaks down over time. Progenitor cells that contain high levels of cherub give rise to tumor-generating neural stem cells. At the molecular level, cherubhelps two proteins to interact with each other: one called Syncrip that makes the neural stem cells take on a older identity, and another one (Staufen) that tethers it to the cell membrane. By restricting Syncrip to a particular location in the cell, cherub alters the timing of stem cell specialization, which contributes to tumor formation. Overall, the results presented by Landskron et al. reveal a new role for long non-coding RNAs: controlling the localization of the proteins that determine the fate of the cell. They also highlight a critical link between the timing of stem cell development and the proliferation of the cells. Further work is now needed to test whether the same control mechanism works in species other than fruit flies.
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Affiliation(s)
- Lisa Landskron
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Steinmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Francois Bonnay
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas R Burkard
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Jonas Steinmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Ilka Reichardt
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Heike Harzer
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Jürgen A Knoblich
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
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Kim HJ, Eoh KJ, Kim LK, Nam EJ, Yoon SO, Kim KH, Lee JK, Kim SW, Kim YT. The long noncoding RNA HOXA11 antisense induces tumor progression and stemness maintenance in cervical cancer. Oncotarget 2018; 7:83001-83016. [PMID: 27792998 PMCID: PMC5347748 DOI: 10.18632/oncotarget.12863] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/14/2016] [Indexed: 01/08/2023] Open
Abstract
Recent research has focused on the impact of long noncoding RNA (lncRNA) in cervical carcinogenesis. However, whether HOXA11 antisense (HOXA11-AS) is involved in cervical cancer remains to be elucidated. In the present study, we examined HOXA11-AS expression levels in cervical cancer patients and determined the relationships between HOXA11-AS expression and clinicopathological factors. We also investigated the bio-functional consequences of HOXA11-AS overexpression both in vitro and in vivo. HOXA11-AS expression was significantly greater in tissues from patients with cervical cancer than in control patients (P<0.001). Multivariate analysis showed that high HOXA11-AS was an independent prognosticator of overall survival (Hazard ratio=2.450, P=0.032). HOXA11-AS overexpression enhanced cell proliferation, migration, and tumor invasion in vitro, whereas HOXA11-AS knockdown inhibited these biologic aggressive features. These adverse changes were accompanied by characteristics of epithelial-mesenchymal transition (EMT). In vivo xenograft experiments using the siHOXA11-AS-transfected HeLa cells revealed that HOXA11-AS strongly induced tumor growth. Furthermore, we found that HOXA11-AS knockdown decreased cancer stemness and triggered the EMT program. In conclusion, HOXA11-AS overexpression correlated with poor survival in patients with cervical cancer. Thus, HOXA11-AS may be a pivotal target for exploring novel cervical cancer therapeutics.
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Affiliation(s)
- Hee Jung Kim
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung Jin Eoh
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea.,Department of Obstetrics and Gynecology, Yonsei University Graduate School, Seoul, Korea
| | - Lee Kyung Kim
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Ji Nam
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Sun Och Yoon
- Department of Pathology, Gangnam Severance Cancer Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kun-Hong Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Kwan Lee
- Department of Obstetrics and Gynecology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Sang Wun Kim
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Young Tae Kim
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
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Wang JY, Feng Y, Fu YH, Liu GL. Effect of Sevoflurane Anesthesia on Brain Is Mediated by lncRNA HOTAIR. J Mol Neurosci 2018; 64:346-351. [PMID: 29352445 DOI: 10.1007/s12031-018-1029-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/10/2018] [Indexed: 01/19/2023]
Abstract
Postoperative cognitive dysfunction in elderly patients has been related to neurodegenerative disorders and mortality. Sevoflurane anesthesia has been implicated in both postoperative cognitive dysfunction and neurotoxicity. Given the advantages of using inhaled anesthetics like sevoflurane, it is important to understand how their usage results in neurotoxicity and subsequently devise ways to circumvent or attenuate the anesthetic-mediated induction in neurotoxicity. Long noncoding RNAs (LncRNAs) are a group of > 200 bp long RNAs and show specific spatiotemporal expression profiles. Several recent reports suggest that lncRNAs are involved in responses of the central nervous system (CNS) following acute injuries. However, their role in sevoflurane anesthesia-mediated cognitive dysfunction has not been studied. RNA immunoprecipitation (RIP) combined with qRT-PCR detection of six different lncRNAs showed that the HOTAIR lncRNAs were significantly more bound to both Sin3A and coREST, both corepressors of the RE-1 silencing transcription factor, within rat hippocampus following sevoflurane anesthesia compared with sham. Sevoflurane inhalation resulted in significant inhibition of brain-derived neurotrophic factor (BDNF) and cognitive impairment. Treatment with a combination of siRNAs targeting HOTAIR rescued BDNF expression and improved cognitive responses. Taken together, our results suggest that sevoflurane-mediated brain function impairment is at least in part mediated by the HOTAIR lncRNA.
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Affiliation(s)
- Jian-Yue Wang
- Department of Anesthesiology, Binzhou People's Hospital, No.515, Huangheqi Road, Binzhou, Shandong, 256610, China.
| | - Yong Feng
- Department of Anesthesiology, Binzhou People's Hospital, No.515, Huangheqi Road, Binzhou, Shandong, 256610, China
| | - Yan-Hong Fu
- Department of Anesthesiology, Binzhou People's Hospital, No.515, Huangheqi Road, Binzhou, Shandong, 256610, China
| | - Guang-Li Liu
- Department of Anesthesiology, Binzhou People's Hospital, No.515, Huangheqi Road, Binzhou, Shandong, 256610, China
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Hao S, Yao L, Huang J, He H, Yang F, Di Y, Jin C, Fu D. Genome-Wide Analysis Identified a Number of Dysregulated Long Noncoding RNA (lncRNA) in Human Pancreatic Ductal Adenocarcinoma. Technol Cancer Res Treat 2018; 17:1533034617748429. [PMID: 29343207 PMCID: PMC5784569 DOI: 10.1177/1533034617748429] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/25/2017] [Accepted: 11/14/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Long noncoding RNAs have been shown to play crucial roles in cancer biology, while the long noncoding RNA landscapes of pancreatic ductal adenocarcinoma have not been completely characterized. We aimed to determine whether long noncoding RNA could serve as early diagnostic biomarkers for pancreatic ductal adenocarcinoma. METHOD We conducted a genome-wide microarray analysis on pancreatic ductal adenocarcinoma and their adjacent noncancerous tissues from 8 Chinese patients. RESULTS A total of 3352 significantly differentially expressed long noncoding RNAs were detected. Of total, 1249 long noncoding RNAs were upregulated and 2103 were downregulated (fold change ≥2, P < 0.05, FDR <0.05). These differentially expressed long noncoding RNAs were not evenly distributed among chromosomes in human genome. Hierarchical clustering of these differentially expressed long noncoding RNAs revealed large variabilities in long noncoding RNA expression among individual patient, indicating that certain long noncoding RNAs could play a unique role or be used as a biomarker for specific subtype of pancreatic ductal adenocarcinoma. Gene Ontology enrichment and pathway analysis identified several remarkably dysregulated pathways in pancreatic ductal adenocarcinoma tissue, such as interferon-γ-mediated signaling pathway, mitotic cell cycle and proliferation, extracellular matrix receptor interaction, focal adhesion, and regulation of actin cytoskeleton. The co-expression network analysis detected 393 potential interactions between 80 differentially expressed long noncoding RNAs and 105 messenger RNAs. We experimentally verified 7 most markedly dysregulated long noncoding RNAs from the network. CONCLUSION Our study provided a genome-wide survey of dysregulated long noncoding RNAs and long noncoding RNA/messenger RNA co-regulation networks in pancreatic ductal adenocarcinoma tissue. These dysregulated long noncoding RNA/messenger RNA networks could be used as biomarkers to provide early diagnosis of pancreatic ductal adenocarcinoma or its subtype, predict prognosis, and evaluate treatment efficacy.
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Affiliation(s)
- Sijie Hao
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Lie Yao
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiaxin Huang
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Hang He
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Feng Yang
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yang Di
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Chen Jin
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Deliang Fu
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, China
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Eoh KJ, Paek J, Kim SW, Kim HJ, Lee HY, Lee SK, Kim YT. Long non-coding RNA, steroid receptor RNA activator (SRA), induces tumor proliferation and invasion through the NOTCH pathway in cervical cancer cell lines. Oncol Rep 2017; 38:3481-3488. [PMID: 29039612 PMCID: PMC5783589 DOI: 10.3892/or.2017.6023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/02/2017] [Indexed: 12/24/2022] Open
Abstract
Contemporary research has focused on the function of long non-coding RNAs (lncRNAs) in carcinogenesis. However, the involvement of the lncRNA, steroid receptor RNA activator (SRA), in cervical carcinogenesis remains to be elucidated. In the present study, we investigated the bio-functional consequences of lncRNA SRA knockdown in vitro. To verify the role of lncRNA SRA in cell proliferation, migration, and invasion, lncRNA RNA interference was utilized to knock down lncRNA SRA expression in cervical cancer cell lines, resulting in our discovery that lncRNA SRA knockdown inhibited cell proliferation, cell migration and tumor invasion in the cervical cancer cell lines. Additionally, in vitro experiments using the lncRNA SRA-knockdown cervical cancer cell lines revealed that lncRNA SRA is a strong inducer and modulator of the expression of genes related to epithelial-mesenchymal transition and the NOTCH signaling pathway. In conclusion, our findings demonstrated that lncRNA SRA is highly correlated with cancer progression and cervical cancer cell proliferation and migration. Furthermore, these results indicate that lncRNA SRA may be a potential therapeutic target and prognostic marker for cervical malignancy.
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Affiliation(s)
- Kyung Jin Eoh
- Institute of Women's Life Medical Science, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jiheum Paek
- Departments of Obstetrics and Gynecology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sang Wun Kim
- Institute of Women's Life Medical Science, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hee Jung Kim
- Institute of Women's Life Medical Science, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hye Yeon Lee
- Department of Anatomy, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sang Kil Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Young Tae Kim
- Institute of Women's Life Medical Science, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
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Liu J, Liu L, Wan JX, Song Y. Long noncoding RNA SNHG20 promotes gastric cancer progression by inhibiting p21 expression and regulating the GSK-3β/ β-catenin signaling pathway. Oncotarget 2017; 8:80700-80708. [PMID: 29113337 PMCID: PMC5655232 DOI: 10.18632/oncotarget.20959] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 08/24/2017] [Indexed: 12/27/2022] Open
Abstract
Recent studies have indicated that long non-coding RNAs (lncRNAs) play important regulatory roles in tumor development and progression. However, the contribution of small nucleolar RNA host gene 20 (SNHG20) to gastric cancer development remains largely unknown. The aim of the study is to investigate the functional significance of SNHG20 involved in gastric cancer (GC) progression. In the study, our results demonstrated that the expression levels of SNHG20 were remarkably up-regulated in GC cells. Functionally, SNHG20 promoted the GC MKN45 and BGC-823 cells proliferation and invasion. Furthermore, knockdown of SNHG20 significantly inhibited the epithelial-mesenchymal transition (EMT) in MKN45 and BGC-823 cells, whereas, the overexpression of SNHG20 had the promoting effects. Moreover, we found that overexpression of SNHG20 in MKN45 and BGC-823 cells significantly inhibited the expression of E-cadherin and p21 via binding to EZH2 and regulated the GSK-3β/β-catenin signaling pathway. Thus, the results showed that SNHG20 acted as an oncogene in GC and targeting SNHG20 may serve as a therapeutic target for GC.
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Affiliation(s)
- Jie Liu
- Department of Intensive Care Unit, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Lanyu Liu
- Department of Gynecology and Obstetrics, Weifang Hospital of Maternal and Child Health, Weifang, Shandong Province, China
| | - Jin-Xiang Wan
- Department of Medical Ultrasonics, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Ying Song
- Department of Outpatient, People's Hospital of Zoucheng, Zoucheng, China
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41
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Imai-Sumida M, Chiyomaru T, Majid S, Saini S, Nip H, Dahiya R, Tanaka Y, Yamamura S. Silibinin suppresses bladder cancer through down-regulation of actin cytoskeleton and PI3K/Akt signaling pathways. Oncotarget 2017; 8:92032-92042. [PMID: 29190895 PMCID: PMC5696161 DOI: 10.18632/oncotarget.20734] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 08/07/2017] [Indexed: 01/17/2023] Open
Abstract
Silibinin is the major active constituent of silymarin, an extract of milk thistle seeds. Silibinin has been shown to have significant anti-cancer effects in a variety of malignancies. However, the molecular mechanisms of silibinin action in bladder cancer have not been studied extensively. In the present study, we found that silibinin (10 μM) significantly suppressed proliferation, migration, invasion and induced apoptosis of T24 and UM-UC-3 human bladder cancer cells. Silibinin down-regulated the actin cytoskeleton and phosphatidylinositide 3-kinase (PI3K)/Akt signaling pathways in these cancer cell lines. These pathways were found to crosstalk through RAS cascades. We found that silibinin suppressed levels of trimethylated histone H3 lysine 4 and acetylated H3 at the KRAS promoter. Furthermore, silibinin targets long non-coding RNA: HOTAIR and ZFAS1, which are known to play roles as oncogenic factors in various cancers. This study shows that silibinin exerts anti-cancer effects through down-regulation of actin cytoskeleton and PI3K/Akt pathways and thus suppresses bladder cancer growth and progression.
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Affiliation(s)
- Mitsuho Imai-Sumida
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
| | - Takeshi Chiyomaru
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA.,Current address: Department of Urology, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan
| | - Shahana Majid
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
| | - Sharanjot Saini
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
| | - Hannah Nip
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
| | - Rajvir Dahiya
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
| | - Yuichiro Tanaka
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
| | - Soichiro Yamamura
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
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Zheng Y, Liu L, Shukla GC. A comprehensive review of web-based non-coding RNA resources for cancer research. Cancer Lett 2017; 407:1-8. [PMID: 28823961 DOI: 10.1016/j.canlet.2017.08.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/02/2017] [Accepted: 08/08/2017] [Indexed: 12/13/2022]
Abstract
Non-coding RNAs include many kinds of RNAs that did not encode proteins. Recent evidences reveal that ncRNAs play critical roles in initiation and progression of cancers. But it is not easy for cancer biologists and medical doctors to easily know the potential roles of ncRNAs in cancer and retrieve the information of ncRNAs under their investigations. To make the available web-based resources more accessible and understandable, we made a comprehensive review for 49 web-based resources of three types of ncRNAs, i.e., microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). We also listed some preferred resources for 6 different types of analyses related to ncRNAs.
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Affiliation(s)
- Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Girish C Shukla
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, 44115, USA
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Moschovis D, Gazouli M, Tzouvala M, Vezakis A, Karamanolis G. Long non-coding RNA in pancreatic adenocarcinoma and pancreatic neuroendocrine tumors. Ann Gastroenterol 2017; 30:622-628. [PMID: 29118556 PMCID: PMC5670281 DOI: 10.20524/aog.2017.0185] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 07/05/2017] [Indexed: 12/21/2022] Open
Abstract
Interest in non-coding regions of DNA has been increasing since the mapping of the human genome revealed that human DNA contains far fewer genes encoding proteins than previously expected. However, analysis of the derivatives of DNA transcription (transcriptomics) revealed that the majority of the genetic material is transcribed into non-coding RNA (ncRNA), indicating that these molecules probably provide the functional diversity and complexity of the physiology of the human body that cannot be attributed to the proteins. Of these ncRNA, long ncRNA (lncRNA) have a length greater than 200 nucleotides and share many common components with the coding messenger RNA (mRNA): They are transcribed by RNA polymerase II, comprised of multiple exons and subjected to normal RNA splicing giving RNA products of several kilobases. Scientific data reveal the regulatory role of lncRNA in the control of gene expression during cell development and homeostasis. However, to date, very few lncRNAs have been characterized in depth, and lncRNAs are thought to have a wide range of functions in cellular and developmental processes. These molecules will have the possibility to be used as biomarkers and contribute to the development of targeted therapies. Concerning pancreatic cancer, there are limited data in the literature that correlate the growth of these tumors with deregulation of various lncRNA. We herein review the literature regarding the role of lncRNA as a diagnostic and prognostic biomarker and possible therapeutic target in the neoplasms of the pancreas, particularly pancreatic adenocarcinoma and pancreatic neuroendocrine tumors.
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Affiliation(s)
- Dimitrios Moschovis
- Department of Gastroenterology, Agios Panteleimon General Hospital, Nikea (Dimitrios Moschovis, Maria Tzouvala), Greece
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens (Maria Gazouli), Greece
| | - Maria Tzouvala
- Department of Gastroenterology, Agios Panteleimon General Hospital, Nikea (Dimitrios Moschovis, Maria Tzouvala), Greece
| | - Antonios Vezakis
- 2 Department of Surgery, Aretaieion University Hospital, National and Kapodistrian University of Athens (Antonios Vezakis), Greece
| | - George Karamanolis
- Gastroenterology Unit, 2 Department of Surgery, Aretaieio University Hospital, National and Kapodistrian University of Athens (George Karamanolis), Greece
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Zhao TF, Jia HZ, Zhang ZZ, Zhao XS, Zou YF, Zhang W, Wan J, Chen XF. LncRNA H19 regulates ID2 expression through competitive binding to hsa-miR-19a/b in acute myelocytic leukemia. Mol Med Rep 2017; 16:3687-3693. [PMID: 28765931 DOI: 10.3892/mmr.2017.7029] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/06/2017] [Indexed: 11/06/2022] Open
Abstract
Acute myelocytic leukemia (AML) is the most common type of acute leukemia. Long non‑coding RNAs (lncRNAs) serve an important role in regulating gene expression through chromatin modification, transcription and post‑transcriptional processing. LncRNA H19 was considered as an independent prognostic marker for patients with tumors. The expression of lncRNA H19 was identified to be significantly upregulated in bone marrow samples from patients with AML‑M2. Furthermore, it was demonstrated that the knockdown of lncRNA H19 resulted in increased expression of hsa‑microRNA (miR)‑19a/b and decreased expression of inhibitor of DNA binding 2 (ID2) in AML cells. The knockdown of lncRNA H19 inhibited the proliferation of AML cells in vitro, which could be partially reversed by ID2 overexpression. Furthermore, the results of the bioinformatic analysis revealed potential hsa‑miR‑19a/b‑3p binding sites in lncRNA H19 and ID2. Altogether, the results of the present study suggest that lncRNA H19 regulates the expression of ID2 through competitive binding to hsa‑miR‑19a and hsa‑miR‑19b, which may serve a role in AML cell proliferation.
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Affiliation(s)
- Tong-Feng Zhao
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University‑The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, P.R. China
| | - Hui-Zhen Jia
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University‑The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, P.R. China
| | - Zhen-Zhen Zhang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University‑The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, P.R. China
| | - Xiao-Su Zhao
- Department of Hematology, Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, P.R. China
| | - Yan-Fen Zou
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Wei Zhang
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Biomedical Research Institute, Shenzhen Peking University‑The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, P.R. China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University‑The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, P.R. China
| | - Xiao-Fan Chen
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Biomedical Research Institute, Shenzhen Peking University‑The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, P.R. China
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Abstract
The accuracy and efficiency of tumor treatment depends mainly on early and precise diagnosis. Although histopathology is always the gold standard for cancer diagnosis, noninvasive biomarkers represent an opportunity for early detection and molecular staging of cancer. Besides the classical tumor markers, noncoding RNAs (ncRNAs) emerge to be a novel category of biomarker for cancer diagnosis since the dysregulation of ncRNAs is closely associated with the development and progression of human cancers such as liver, lung, breast, gastric, and other kinds of cancers. In this chapter, we will summarize the different types of ncRNAs in the diagnosis of major human cancers. In addition, we will introduce the recent advances in the detection and applications of circulating serum or plasma ncRNAs and non-blood fluid ncRNAs because the noninvasive body fluid-based assays are easy to examine for cancer diagnosis and monitoring.
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Lv Y, Li H, Li F, Liu P, Zhao X. Long Noncoding RNA MNX1-AS1 Knockdown Inhibits Cell Proliferation and Migration in Ovarian Cancer. Cancer Biother Radiopharm 2017; 32:91-99. [PMID: 28414551 DOI: 10.1089/cbr.2017.2178] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Yan Lv
- Department of Obstetrics and Gynaecology, Qilu Hospital of Shandong University, Jinan, China
- Department of Obstetrics and Gynaecology, Zhongxin Hospital of Huizhou, Huizhou, China
| | - Huan Li
- Department of Obstetrics and Gynaecology, Beijing University Shenzhen Hospital, Shenzhen, China
| | - Fengling Li
- Department of Obstetrics and Gynaecology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Peishu Liu
- Department of Obstetrics and Gynaecology, Qilu Hospital of Shandong University, Jinan, China
| | - Xinrui Zhao
- Department of Obstetrics and Gynaecology, Qilu Hospital of Shandong University, Jinan, China
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Hu Q, Li S, Chen C, Zhu M, Chen Y, Zhao Z. 17β-Estradiol treatment drives Sp1 to upregulate MALAT-1 expression and epigenetically affects physiological processes in U2OS cells. Mol Med Rep 2017; 15:1335-1342. [DOI: 10.3892/mmr.2017.6115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/16/2016] [Indexed: 11/05/2022] Open
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Reid BM, Permuth JB, Chen YA, Teer JK, Monteiro AN, Chen Z, Tyrer J, Berchuck A, Chenevix-Trench G, Doherty JA, Goode EL, Iverson ES, Lawrenson K, Pearce CL, Pharoah PD, Phelan CM, Ramus SJ, Rossing MA, Schildkraut JM, Cheng JQ, Gayther SA, Sellers TA. Integration of Population-Level Genotype Data with Functional Annotation Reveals Over-Representation of Long Noncoding RNAs at Ovarian Cancer Susceptibility Loci. Cancer Epidemiol Biomarkers Prev 2017; 26:116-125. [PMID: 28035019 PMCID: PMC5312656 DOI: 10.1158/1055-9965.epi-16-0341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/19/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified multiple loci associated with epithelial ovarian cancer (EOC) susceptibility, but further progress requires integration of epidemiology and biology to illuminate true risk loci below genome-wide significance levels (P < 5 × 10-8). Most risk SNPs lie within non-protein-encoding regions, and we hypothesize that long noncoding RNA (lncRNA) genes are enriched at EOC risk regions and represent biologically relevant functional targets. METHODS Using imputed GWAS data from about 18,000 invasive EOC cases and 34,000 controls of European ancestry, the GENCODE (v19) lncRNA database was used to annotate SNPs from 13,442 lncRNAs for permutation-based enrichment analysis. Tumor expression quantitative trait locus (eQTL) analysis was performed for sub-genome-wide regions (1 × 10-5 > P > 5 × 10-8) overlapping lncRNAs. RESULTS Of 5,294 EOC-associated SNPs (P < 1.0 × 10-5), 1,464 (28%) mapped within 53 unique lncRNAs and an additional 3,484 (66%) SNPs were correlated (r2 > 0.2) with SNPs within 115 lncRNAs. EOC-associated SNPs comprised 130 independent regions, of which 72 (55%) overlapped with lncRNAs, representing a significant enrichment (P = 5.0 × 10-4) that was more pronounced among a subset of 5,401 lncRNAs with active epigenetic regulation in normal ovarian tissue. EOC-associated lncRNAs and their putative promoters and transcription factors were enriched for biologically relevant pathways and eQTL analysis identified five novel putative risk regions with allele-specific effects on lncRNA gene expression. CONCLUSIONS lncRNAs are significantly enriched at EOC risk regions, suggesting a mechanistic role for lncRNAs in driving predisposition to EOC. IMPACT lncRNAs represent key candidates for integrative epidemiologic and functional studies. Further research on their biologic role in ovarian cancer is indicated. Cancer Epidemiol Biomarkers Prev; 26(1); 116-25. ©2016 AACR.
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Affiliation(s)
- Brett M. Reid
- Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | - Y. Ann Chen
- Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Jamie K. Teer
- Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | - Zhihua Chen
- Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | | | | | | | | | | | | | | | | | | | | | - Susan J. Ramus
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | | | - Jin Q. Cheng
- Moffitt Cancer Center & Research Institute, Tampa, FL
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Liu G, Xiang T, Wu QF, Wang WX. Long Noncoding RNA H19-Derived miR-675 Enhances Proliferation and Invasion via RUNX1 in Gastric Cancer Cells. Oncol Res 2016; 23:99-107. [PMID: 26931432 PMCID: PMC7838630 DOI: 10.3727/096504015x14496932933575] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The lncRNA H19 and its mature product miR-675 have recently been shown to be upregulated and promote the progression of gastric cancer. However, the detailed function and underlying molecular mechanism of H19/miR-675 in the carcinogenesis of gastric cancer remains unclear. In this study, we found that H19 depended on miR-675 to enhance the proliferation and invasion of gastric cancer AGS cells, and the expression of miR-675 was positively correlated with H19 in patients with gastric cancer. Subsequently, the tumor-suppressor runt domain transcription factor 1 (RUNX1) was confirmed to be a downstream molecule of H19/miR-675 axis, since overexpression of H19 or miR-675 significantly decreased RUNX1 expression in AGS cells, and knockdown of H19 or miR-675 enhanced RUNX1 expression. More importantly, a series of assays further demonstrated that introduction of RUNX1 abrogated H19/miR-675-induced Akt/mTOR pathway activation and the following cellular proliferation and invasion of AGS cells. To our knowledge, this is the time to demonstrate that RUNX1 serves as a link between H19/miR-675 axis and Akt/mTOR signaling and is a pivotal mediator in gastric cancer progression induced by H19/miR-675. Thus, our study provides important clues for understanding the key roles of lncRNA-miRNA functional network and identifying new therapeutic targets for gastric cancer.
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Affiliation(s)
- Gao Liu
- Department of Hepatobiliary and Laparoscopic Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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Liu W, Ma J, Cheng Y, Zhang H, Luo W, Zhang H. HMMR antisense RNA 1, a novel long noncoding RNA, regulates the progression of basal-like breast cancer cells. BREAST CANCER-TARGETS AND THERAPY 2016; 8:223-229. [PMID: 27920576 PMCID: PMC5125767 DOI: 10.2147/bctt.s119997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recently, accumulating evidence has suggested that long noncoding RNAs (lncRNAs) play crucial roles in carcinogenesis and cancer progression. Hyaluronan-mediated motility receptor (HMMR) is an essential cancer-related gene in basal-like breast cancer (BLBC). In our study, HMMR antisense RNA 1 (HMMR-AS1) was analyzed in BLBC patients through polymerase chain reaction analysis. Here, we found that the expression of HMMR was positively correlated with HMMR-AS1 (RP11-80G.1). When HMMR-AS1 (RP11-80G.1) was knocked down, the expression of HMMR markedly reduced. Furthermore, in MDA-MB-231 and MDA-MB-468 breast cancer cells, the proliferation and migration abilities were remarkably suppressed via knocking down HMMR-AS1 (RP11-80G.1) in vitro. The results showed that lncRNA HMMR-AS1 (RP11-80G.1) influenced the progression of BLBCs through regulating HMMR, suggesting that HMMR-AS1 (RP11-80G.1) could be regarded as a novel biomarker and therapeutic target in the treatment of BLBCs in future.
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Affiliation(s)
- Wei Liu
- Department of Radiation Oncology, Anhui Provincial Hospital, Hefei, People's Republic of China
| | - Jun Ma
- Department of Radiation Oncology, Anhui Provincial Hospital, Hefei, People's Republic of China
| | - Yong Cheng
- Department of Radiation Oncology, Anhui Provincial Hospital, Hefei, People's Republic of China
| | - Hongbo Zhang
- Department of Radiation Oncology, Anhui Provincial Hospital, Hefei, People's Republic of China
| | - Wengguang Luo
- Department of Radiation Oncology, Anhui Provincial Hospital, Hefei, People's Republic of China
| | - Hongyan Zhang
- Department of Radiation Oncology, Anhui Provincial Hospital, Hefei, People's Republic of China
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