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Circ_CSPP1 Regulates the Development of Non-small Cell Lung Cancer via the miR-486-3p/BRD9 Axis. Biochem Genet 2023; 61:1-20. [PMID: 35678942 DOI: 10.1007/s10528-022-10231-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/18/2022] [Indexed: 01/24/2023]
Abstract
In this study, we explored the role of circ_CSPP1 in non-small cell lung cancer (NSCLC) using NSCLC cell lines (A549 and H1299) and human bronchial epithelioid cells (16HBE). The differential expression of circ_CSPP1, miR-486-3p and BRD9 in NSCLC by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot in A549 cells, H1299 cells, 16HBE cells, NSCLC tissues and healthy lung tissues. Dual-luciferase reporter assay was conducted to verify the interaction between circ_CSPP1 and miR-486-3p or miR-486-3p and BRD9. The effect of circ_CSPP1/miR-486-3p/BRD9 axis on NSCLC cell proliferation was evaluated using cell counting kit-8 assay, colony formation assay, and 5-ethynyl-2'-deoxyuridine assay. Additionally, transwell assays were performed to evaluate the effect of circ_CSPP1/miR-486-3p/BRD9 axis on A549 and H1299 cell migration and invasion. The effect of circ_CSPP1 on tumor tumorigenesis of A549 cells in vivo was determined by xenograft tumor model and immunohistochemistry assay. Circ_CSPP1 and BRD9 expression were upregulated, while miR-486-3p expression was downregulated in tumor tissues of NSCCL patients and A549 and H1299 cells. Circ_CSPP1 specifically bound miR-486-3p, and miR-486-3p could target BRD9. Circ_CSPP1 upregulation promoted proliferation, invasion and migration of NSCLC cells, circ_CSPP1 knockdown or miR-486-3p upregulation had the opposite effects. Circ_CSPP1 knockdown-induced effects were reverted by miR-486-3p inhibition. Similarly, the effects of miR-486-3p upregulation on NSCLC cell proliferation, invasion and migration were reversed by BRD9 overexpression. In addition, circ_CSPP1 silencing inhibited tumor growth in nude mice. Circ_CSPP1 promoted A549 and H1299 cell malignancy by competitively inhibiting BRD9 and binding to miR-486-3p.
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Sulewska A, Niklinski J, Charkiewicz R, Karabowicz P, Biecek P, Baniecki H, Kowalczuk O, Kozlowski M, Modzelewska P, Majewski P, Tryniszewska E, Reszec J, Dzieciol-Anikiej Z, Piwkowski C, Gryczka R, Ramlau R. A Signature of 14 Long Non-Coding RNAs (lncRNAs) as a Step towards Precision Diagnosis for NSCLC. Cancers (Basel) 2022; 14:cancers14020439. [PMID: 35053601 PMCID: PMC8773641 DOI: 10.3390/cancers14020439] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
LncRNAs have arisen as new players in the world of non-coding RNA. Disrupted expression of these molecules can be tightly linked to the onset, promotion and progression of cancer. The present study estimated the usefulness of 14 lncRNAs (HAGLR, ADAMTS9-AS2, LINC00261, MCM3AP-AS1, TP53TG1, C14orf132, LINC00968, LINC00312, TP73-AS1, LOC344887, LINC00673, SOX2-OT, AFAP1-AS1, LOC730101) for early detection of non-small-cell lung cancer (NSCLC). The total RNA was isolated from paired fresh-frozen cancerous and noncancerous lung tissue from 92 NSCLC patients diagnosed with either adenocarcinoma (LUAD) or lung squamous cell carcinoma (LUSC). The expression level of lncRNAs was evaluated by a quantitative real-time PCR (qPCR). Based on Ct and delta Ct values, logistic regression and gradient boosting decision tree classifiers were built. The latter is a novel, advanced machine learning algorithm with great potential in medical science. The established predictive models showed that a set of 14 lncRNAs accurately discriminates cancerous from noncancerous lung tissues (AUC value of 0.98 ± 0.01) and NSCLC subtypes (AUC value of 0.84 ± 0.09), although the expression of a few molecules was statistically insignificant (SOX2-OT, AFAP1-AS1 and LOC730101 for tumor vs. normal tissue; and TP53TG1, C14orf132, LINC00968 and LOC730101 for LUAD vs. LUSC). However for subtypes discrimination, the simplified logistic regression model based on the four variables (delta Ct AFAP1-AS1, Ct SOX2-OT, Ct LINC00261, and delta Ct LINC00673) had even stronger diagnostic potential than the original one (AUC value of 0.88 ± 0.07). Our results demonstrate that the 14 lncRNA signature can be an auxiliary tool to endorse and complement the histological diagnosis of non-small-cell lung cancer.
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Affiliation(s)
- Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (J.N.); (R.C.); (O.K.)
- Correspondence:
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (J.N.); (R.C.); (O.K.)
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (J.N.); (R.C.); (O.K.)
- Center of Experimental Medicine, Medical University of Bialystok, 15-369 Bialystok, Poland
| | - Piotr Karabowicz
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (J.R.); (Z.D.-A.)
| | - Przemyslaw Biecek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland; (P.B.); (H.B.)
| | - Hubert Baniecki
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland; (P.B.); (H.B.)
| | - Oksana Kowalczuk
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (J.N.); (R.C.); (O.K.)
| | - Miroslaw Kozlowski
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland;
| | - Patrycja Modzelewska
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (J.R.); (Z.D.-A.)
| | - Piotr Majewski
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.M.); (E.T.)
| | - Elzbieta Tryniszewska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.M.); (E.T.)
| | - Joanna Reszec
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (J.R.); (Z.D.-A.)
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Zofia Dzieciol-Anikiej
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (J.R.); (Z.D.-A.)
- Department of Rehabilitation, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Cezary Piwkowski
- Department of Thoracic Surgery, Poznan University of Medical Sciences, 60-569 Poznan, Poland;
| | - Robert Gryczka
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland; (R.G.); (R.R.)
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland; (R.G.); (R.R.)
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Wu C, Bian X, Zhang L, Hu Y, Wu Y, Pei T, Han X. Long noncoding RNA LINC00968 inhibits proliferation, migration and invasion of lung adenocarcinoma through targeting miR-22-5p/CDC14A axis. 3 Biotech 2021; 11:433. [PMID: 34603911 PMCID: PMC8440738 DOI: 10.1007/s13205-021-02981-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a high aggressive human cancer which usually diagnosed at advanced stages. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) are crucial participants in LUAD progression. In the present study, we found that lncRNA LINC00968 was significantly down-regulated in LUAD tissues and cell lines. LINC00968 level was positively correlated to survival rate, and negatively correlated to tumor node metastasis (TNM) stage, tumor size and lymph node metastasis of LUAD patients. We over-expressed LINC00968 in LUAD cells using lentivirus, inhibited proliferation and cell cycle arrest at G1 phase were detected. LINC00968 over-expression also suppressed migration, invasion and epithelial mesenchymal transition. We further validated that LINC00968 localized in cytoplasm and acted as an upstream regulator of microRNA miR-22-5p, which was up-regulated in LUAD tissues and cell lines. Besides, elevated miR-22-5p expression abolished the effect of LINC00968 over-expression on LUAD progression including in vivo tumor growth. In addition, we first validated that cell division cycle 14A (CDC14A), which was down-regulated in LUAD tissues, was a downstream target of miR-22-5p. We over-expressed CDC14A in LUAD cells and miR-22-5p induced LUAD progression was partially reversed. In conclusion, our study demonstrated that LINC00968 inhibited proliferation, migration and invasion of LUAD by sponging miR-22-5p and further restoring CDC14A. This novel regulatory axis might provide us with promising diagnostic and therapeutic target in LUAD treatment.
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Affiliation(s)
- Chao Wu
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Xuzhao Bian
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Liyuan Zhang
- Department of Respiratory Medicine of Thoracic Hospital, Xi’an International Medical Center Hospital, No.777 Xitai Road, Gaoxin District, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Yuanyuan Hu
- Medical College, Xijing University, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Yang Wu
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Tianli Pei
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - XinPeng Han
- Department of Respiratory Medicine of Thoracic Hospital, Xi’an International Medical Center Hospital, No.777 Xitai Road, Gaoxin District, Xi’an, 710100 Shaanxi People’s Republic of China
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Tong C, Wang C, Wang Y, Xiao X. TNRC6C-AS1 Promotes Thyroid Cancer Progression by Upregulating LPAR5 via miR-513c-5p. Cancer Manag Res 2021; 13:6141-6155. [PMID: 34393509 PMCID: PMC8354737 DOI: 10.2147/cmar.s312621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/19/2021] [Indexed: 12/21/2022] Open
Abstract
Background Considering the combined role of long non-coding RNA (lncRNAs)-microRNA (miRNA)-mRNA in tumorigenesis, the purpose of this study was to investigate how TNRC6C-AS1 regulates the expression of lysophosphatidic acid receptor 5 (LPAR5) by modulating miR-513c-5p, thus influencing the progression of thyroid cancer (THCA). Methods qRT-PCR and Western blotting were performed to detect the expression levels of TNRC6C-AS1, miR-513c-5p, and LPAR5 in THCA tissues and cell lines. The viability, proliferation, migration, and invasion were assessed using CCK-8, BrdU, wound healing, and transwell migration assays, respectively. Dual-luciferase reporter assay, RIP assay, and RNA pull-down assay were used to evaluate the relationship between TNRC6C-AS1, miR-513c-5p, and LPAR5. Results TNRC6C-AS1 was highly expressed in THCA tissues, and knockout of TNRC6C-AS1 reduced the viability, proliferation, migration, and invasion of THCA cells. TNRC6C-AS1 competitively adsorbed miR-513c-5p. In addition, the biological function of TNRC6C-AS1 was blocked by knocking down the thyroid cell line TNRC6C-AS1 with miR-513c-5p inhibitor transfection. LPAR5 is the target gene for miR-513c-5p, which has the ability to eliminate the influence of miR-513c-5p on THCA cells. Conclusion The TNRC6C-AS1/miR-513c-5p/LPAR5 axis is a novel signaling pathway that modulates THCA progression and may be a potential target for cancer therapy.
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Affiliation(s)
- Chuanming Tong
- Department of General Surgery, People's Hospital of Dongxihu District, Wuhan, Hubei, 430040, People's Republic of China
| | - Chuan Wang
- Department of General Surgery, People's Hospital of Dongxihu District, Wuhan, Hubei, 430040, People's Republic of China
| | - Yajie Wang
- Department of General Surgery, People's Hospital of Dongxihu District, Wuhan, Hubei, 430040, People's Republic of China
| | - Xiongsheng Xiao
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, People's Republic of China
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Xu J, Zhang Z, Shen D, Zhang T, Zhang J, De W. Long noncoding RNA LINC01296 plays an oncogenic role in colorectal cancer by suppressing p15 expression. J Int Med Res 2021; 49:3000605211004414. [PMID: 33983053 PMCID: PMC8127761 DOI: 10.1177/03000605211004414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE To examine the role of the long noncoding RNA LINC01296 in colorectal carcinoma (CRC) and to explore the underlying mechanism. METHODS We detected LINC01296 expression levels in a cohort of 51 paired CRC and normal tissues. We also assessed the effects of LINC01296 on cell proliferation and apoptosis in CRC cells in vitro, and measured its effect on tumor growth in an in vivo mouse model. We identified the potential downstream targets of LINC01296 and assessed its regulatory effects. RESULTS Expression levels of LINC01296 were elevated in 37/51 CRC tissues compared with the corresponding normal tissues and were significantly associated with tumor stage, lymph node metastasis, and distant metastasis. Knockdown of LINC01296 using antisense oligonucleotides inhibited cell proliferation and promoted apoptosis of colon cancer cells in vitro and inhibited tumor growth in vivo. Knockdown of LINC01296 also significantly increased the gene expression of p15 in colon cancer cells. LINC01296-specific suppression of p15 was validated by the interaction between enhancer of zeste homolog 2 and LINC01296. CONCLUSION Overexpression of LINC01296 suppressed the expression of p15 leading to CRC carcinogenesis. These findings may provide the basis for novel future CRC-targeted therapies.
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Affiliation(s)
- Jianing Xu
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Emergency Medicine, Jiangyin People's Hospital, Jiangyin, Jiangsu, China
| | - Zhehao Zhang
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dong Shen
- Department of Oncology, Jiangyin People's Hospital, Jiangyin, Jiangsu, China
| | - Ting Zhang
- Department of Oncology, Jiangyin People's Hospital, Jiangyin, Jiangsu, China
| | - Jinsong Zhang
- Department of Emergency Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei De
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, China
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Zhang Y, Li W, Lin Z, Hu J, Wang J, Ren Y, Wei B, Fan Y, Yang Y. The Long Noncoding RNA Linc01833 Enhances Lung Adenocarcinoma Progression via MiR-519e-3p/S100A4 Axis. Cancer Manag Res 2020; 12:11157-11167. [PMID: 33173348 PMCID: PMC7648568 DOI: 10.2147/cmar.s279623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/01/2020] [Indexed: 12/15/2022] Open
Abstract
Introduction Lung cancer (LC) is among the most prevalent malignancies worldwide, with extremely high morbidity and mortality rates. Mounting evidence has suggested that the abnormally expressed long noncoding RNA (lncRNA) in lung cancer tissues may play vital roles in tumor progression. In the present research, we aimed to examine the functions and underlying mechanism of linc01833 in lung adenocarcinoma (LUAD). Methods qRT-PCR was employed to determine transfection efficiency. CCK-8, transwell invasion assay, Western blotting analysis and qRT-PCR were used to detect proliferation as well as migration of different LUAD cell lines, and were also applied to determine the changes during epithelial–mesenchymal transformation (EMT). Afterwards, bioinformatics and dual-luciferase reporter assay were utilized to explore and to identify the potential corresponding targets of linc01833 and miR-519e-3p. Results Linc01833 OE can significantly improve proliferation as well as invasion ability of LC cells and promote the EMT process. Dual-luciferase reporter assay demonstrated that linc01833 could directly bind to miR-519e-3p, thereby inhibiting its expression. Further experiments showed that S100A4 was a direct target of miR-519e-3p. Rescue assay demonstrated that linc01833 acted on the miR-519e-3p/S100A4 axis. Conclusion We verified the mechanism of linc01833 in promoting infiltration and metastasis in LUAD. To be specific, linc01833 can function as a competitive endogenous RNA (ceRNA) to adsorb miR-519e-3p through a sponge and regulate S100A4 in lung cancer, thereby being involved in LUAD progression. Collectively, our research provides new insights towards the in-depth understanding of LC progression mechanisms.
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Affiliation(s)
- Yuan Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Wenhua Li
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Zongxiang Lin
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Jingfeng Hu
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Jingpu Wang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Yukai Ren
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - BoChong Wei
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Yuxia Fan
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Yang Yang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, People's Republic of China
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Xiao Y, Li C, Wang H, Liu Y. LINC00265 targets miR-382-5p to regulate SAT1, VAV3 and angiogenesis in osteosarcoma. Aging (Albany NY) 2020; 12:20212-20225. [PMID: 33109774 PMCID: PMC7655165 DOI: 10.18632/aging.103762] [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: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
Abstract
We explored the mechanism by which LINC00265 regulates angiogenesis of osteosarcoma cells via the miR-382-5p/spermidine/spermine N1-acetyltransferase-1 (SAT1) and miR-382-5p/vav guanine nucleotide exchange factor 3 (VAV3) axis. Cell scratch assay, Transwell assay and tube formation assay were applied to detect cell migration, invasion and tube formation abilities. The effects of LINC00265 targeting miR-382-5p in osteosarcoma in vivo were studied using a tumour-burden assay. A total of 70 genes potentially involved in osteosarcoma angiogenesis were identified, and a Gene Ontology (GO) analysis found that SAT1 and VAV3 were closely related to angiogenesis. Bioinformatics analysis and clinical experiments confirmed that LINC00265, SAT1 and VAV3 were overexpressed in osteosarcoma and related to a poor prognosis, whereas miR-382-5p was downregulated and associated with a poor prognosis. It was confirmed that LINC00265 promoted the proliferation, migration, invasion and angiogenesis of osteosarcoma cells by targeting miR-382-5p to mediate SAT1 and VAV3. Collectively, LINC00265 might promote proliferation, migration, invasion and angiogenesis by targeting miR-382-5p/SAT1 and miR-382-5p/VAV3 in osteosarcoma.
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Affiliation(s)
- Ying Xiao
- Department of Operating Center, The First Hospital of Jilin University, Changchun 130000, Jilin, China
| | - Chunling Li
- Department of Operating Center, The First Hospital of Jilin University, Changchun 130000, Jilin, China
| | - Hongyue Wang
- Department of Nephrology, The First Hospital of Jilin University, Changchun 130000, Jilin, China
| | - Yijun Liu
- Department of Orthopaedics, The First Hospital of Jilin University, Changchun 130000, Jilin, China
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Dong Z, Xu QH, Zhu YB, Wang YF, Xiong J, Dang S. Investigation of Targeting Relationship between Micro-Rna-22 and Vegfr3 in Lung Squamous Cell Carcinoma. Comb Chem High Throughput Screen 2020; 24:148-154. [PMID: 32691705 DOI: 10.2174/1386207323666200720012917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/15/2020] [Accepted: 05/24/2020] [Indexed: 11/22/2022]
Abstract
AIM The present study explored the clinical significance of microRNA-22 (miR-22) expression in lung squamous cell carcinoma and to explore the targeting relationship with vascular endothelial growth factor receptor 3 (VEGFR3). METHODS A total of 49 patients with lung squamous cell carcinoma who underwent surgical treatment were selected. The expression of miR-22 was detected by fluorescence quantitative realtime PCR (qPCR), the expression of VEGFR3 was detected by Western blotting assays, and D240 labeled microlymphatic vessels density (MLVD) was detected by immunohistochemistry (IHC). Lung squamous cell carcinoma cell line SK-MES-1 was selected and the targeting relationship between miR-22 and VEGFR3 was analyzed by double luciferase reporter gene assay. Western blotting assays were used to detect the expression of vascular endothelial growth factor-D (VEGFD) and D240 in the blank control group, empty vector transfection group, miR-22 transfection group, miR-22 and VEGFR3 co-transfection group. RESULTS The expression range of miR-22 in lung squamous cell carcinoma was 0.8-3.5. The expression of miR-22 in lung squamous cell carcinoma was significantly different by tumor maximum diameter, lymph node metastasis, vascular invasion and TNM stage. The expression of miR-22 was linked to survival time. There was a negative correlation between miR-22 and VEGFR3, miR-22 and MLVD. Double luciferase reporter gene assays showed that miR-22 reduced the luciferase activity of pGL3-VEGFR3-WT transfected cells. Compared with the control group, the expression of VEGF-D and D2-40 in the miR-22 transfection group was significantly decreased. However, VEGF-D and D240 in the miR-22 and VEGFR3 co-transfection group reversed the changes. CONCLUSION We assumed that the abnormal expression of miR-22 in lung squamous cell carcinoma may be involved in the development and progression of lung squamous cell carcinoma. MiR-22 negatively regulated the target gene VEGFR3 to mediate lymphangiogenesis. The expression of miR-22 may also be linked to the prognosis of the disease.
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Affiliation(s)
- Zheng Dong
- Department of Respiration, Linyi Central Hospital, Linyi, China
| | - Qing-Hua Xu
- Department of Respiration, Linyi Central Hospital, Linyi, China
| | - Yuan-Bin Zhu
- Department of Respiration, Linyi Central Hospital, Linyi, China
| | - Yong-Feng Wang
- Department of Respiration, Linyi Central Hospital, Linyi, China
| | - Jie Xiong
- Department of Respiration, Linyi Central Hospital, Linyi, China
| | - Shuai Dang
- Teaching Department of Basic Medicine, Taishan Vocational College of Nursing, Tai'an, China
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Yao M, Xu C, Shen H, Liu T, Wang X, Shao C, Shao S. The regulatory role of miR-107 in Coxsackie B3 virus replication. Aging (Albany NY) 2020; 12:14467-14479. [PMID: 32674073 PMCID: PMC7425430 DOI: 10.18632/aging.103488] [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: 01/04/2020] [Accepted: 05/20/2020] [Indexed: 11/25/2022]
Abstract
Coxsackie B3 virus (CVB3) is a member of small RNA viruses that belongs to the genus Enterovirus of the family Picornaviridae and CVB3 is the main pathogen of acute and chronic viral myocarditis. In this study RT-qPCR was used to determine the expression of miR-107 in CVB3-infected and uninfected HeLa cells. The experimental results show that the level of miR-107 began to rise at 4 h after the infection, and significantly boosted at 6 h. Based on the results of this experiment, we consider that miR-107 expression is related to CVB3 infection. In order to further clarify the effect of miR-107 in the process of CVB3 infection, we studied the effect of miR-107 upstream and downstream target genes on CVB3 replication. Levels of the target RNAs were detected by RT-qPCR after CVB3 infection, and the expression of CVB3 capsid protein VP1 by western blot analysis. Then the virus in the supernatant was quantitated via a viral plaque assay, reflecting the release of the virus. The experimental results showed that miRNA-107 expression is associated with CVB3 replication and proliferation, while KLF4 and BACE1 as the downstream of miR-107 weakened CVB3 replication. Overexpressions of KLF4 and BACE1 negatively regulated CVB3 replication, this effect on CVB3 was completely opposite to that of miR-107. Further experiments revealed that the upstream lncRNA004787, a new lncRNA that had not been reported, was located on chromosome 5, strand - from 37073250 to 37070908 (genome assembly: hg19). We sequenced and studied lncRNA004787 and found that it partially inhibited CVB3 replication. This prompted us to speculate that lncRNA004787 probably impacted the replication by other means. In conclusion, miR-107 interfered with CVB3 replication and release.
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Affiliation(s)
- Min Yao
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Chi Xu
- Marshall International Center for Digestive Diseases, Shanghai East Hospital, Tongji University, Shanghai 200120, China
| | - Hongxing Shen
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Tingjun Liu
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiuping Wang
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Chen Shao
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Shihe Shao
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China.,Marshall International Center for Digestive Diseases, Shanghai East Hospital, Tongji University, Shanghai 200120, China
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Zhao W, Chen T, Zhao Y. Upregulated lncRNA CASC9 Contributes to Progression of Non-Small Cell Lung Cancer Through Inhibition of miR-335-3p and Activation S100A14 Expression. Onco Targets Ther 2020; 13:6027-6036. [PMID: 32606808 PMCID: PMC7321690 DOI: 10.2147/ott.s249973] [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: 02/15/2020] [Accepted: 05/14/2020] [Indexed: 12/24/2022] Open
Abstract
Introduction Non-small cell lung cancer (NSCLC) is a deadly cancer type worldwide and the main sub-type of lung cancer. Cancer susceptibility candidate-9 (CASC9) was reported to be a key player in cancer progression. However, its function and underlying mechanism in NSCLC remain unclear. Materials and Methods Expression level of CASC9 in NSCLC tissues and cells was measured with RT-qPCR. Biological roles of CASC9 in NSCLC were analyzed with a series of in vitro experiments. Potential mechanisms of CASC9 in NSCLC were analyzed by predicting and validating the possible targets of CASC9 in NSCLC. Results In this study, we found CASC9 expression was upregulated in NSCLC tissues and cell lines. High CASC9 expression was identified as a predictor for poorer overall survival of NSCLC patients. Furthermore, functional assays showed CASC9 knockdown suppressed NSCLC cell proliferation, migration, and invasion, while CASC9 overexpression caused opposite effects. We also found microRNA-335-3p (miR-335-3p) could act as a target of CASC9 in NSCLC and the inhibition effect of CASC9 knockdown on NSCLC progression required the activity of miR-335-3p. In addition, we identified S100 calcium-binding protein A14 (S100A14) acts as a target of miR-335-3p. Discussion Taken together, our study suggested CASC9 could promote NSCLC progression via miR-335-3p/S100A14 axis. The CASC9/miR-335-3p/S100A14 regulatory triplets identified in this work might provide new therapeutic strategies for NSCLC treatment.
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Affiliation(s)
- Weigang Zhao
- Department of Thoracic Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200030, People's Republic of China
| | - Tangbing Chen
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Yonghong Zhao
- Department of Thoracic Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200030, People's Republic of China
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Grillone K, Riillo C, Scionti F, Rocca R, Tradigo G, Guzzi PH, Alcaro S, Di Martino MT, Tagliaferri P, Tassone P. Non-coding RNAs in cancer: platforms and strategies for investigating the genomic "dark matter". J Exp Clin Cancer Res 2020; 39:117. [PMID: 32563270 PMCID: PMC7305591 DOI: 10.1186/s13046-020-01622-x] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/11/2020] [Indexed: 12/18/2022] Open
Abstract
The discovery of the role of non-coding RNAs (ncRNAs) in the onset and progression of malignancies is a promising frontier of cancer genetics. It is clear that ncRNAs are candidates for therapeutic intervention, since they may act as biomarkers or key regulators of cancer gene network. Recently, profiling and sequencing of ncRNAs disclosed deep deregulation in human cancers mostly due to aberrant mechanisms of ncRNAs biogenesis, such as amplification, deletion, abnormal epigenetic or transcriptional regulation. Although dysregulated ncRNAs may promote hallmarks of cancer as oncogenes or antagonize them as tumor suppressors, the mechanisms behind these events remain to be clarified. The development of new bioinformatic tools as well as novel molecular technologies is a challenging opportunity to disclose the role of the "dark matter" of the genome. In this review, we focus on currently available platforms, computational analyses and experimental strategies to investigate ncRNAs in cancer. We highlight the differences among experimental approaches aimed to dissect miRNAs and lncRNAs, which are the most studied ncRNAs. These two classes indeed need different investigation taking into account their intrinsic characteristics, such as length, structures and also the interacting molecules. Finally, we discuss the relevance of ncRNAs in clinical practice by considering promises and challenges behind the bench to bedside translation.
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Affiliation(s)
- Katia Grillone
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Caterina Riillo
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Francesca Scionti
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Roberta Rocca
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Net4science srl, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Giuseppe Tradigo
- Laboratory of Bioinformatics, Department of Medical and Surgical Sciences, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Pietro Hiram Guzzi
- Laboratory of Bioinformatics, Department of Medical and Surgical Sciences, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Net4science srl, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Department of Health Sciences, Magna Græcia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Maria Teresa Di Martino
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Pierfrancesco Tassone
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
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12
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Cao F, Wang Z, Feng Y, Zhu H, Yang M, Zhang S, Wang X. lncRNA TPTEP1 competitively sponges miR‑328‑5p to inhibit the proliferation of non‑small cell lung cancer cells. Oncol Rep 2020; 43:1606-1618. [PMID: 32323798 PMCID: PMC7108057 DOI: 10.3892/or.2020.7522] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/31/2020] [Indexed: 12/24/2022] Open
Abstract
Accumulating evidence suggests that lncRNAs are involved in almost all normal physiological processes and that aberrant expression of lncRNAs may be involved in the development of diseases, including non‑small cell lung cancer (NSCLC). However, the roles of lncRNA‑TPTE pseudogene 1 (TPTEP1) in lung cancer and the underlying molecular mechanisms have remained elusive. In the present study, significant downregulation of TPTEP1 in tumors compared with normal tissues from patients with NSCLC was observed. Overexpression of TPTEP1 inhibited cell proliferation and induced apoptosis in NSCLC cells. A bioinformatics analysis based on miRDB predicted microRNA (miR)‑328‑5p as a potential binding miRNA for TPTEP1. Using a dual‑luciferase reporter assay and western blot analysis, it was further validated that TPTEP1 sponged miR‑328‑5p to upregulate Src kinase signaling inhibitor 1 (SRCIN1) in NSCLC cells. Through regulation of SRCIN1, TPTEP1 was indicated to inactivate the Src and STAT3 pathways in NSCLC cells. Notably, silencing of SRCIN1 reversed the TPTEP1 overexpression‑induced inhibition of cell proliferation and increase of the apoptotic rate in NSCLC cells. Pearson correlation analysis revealed a significant positive correlation between TPTEP1 and SRCIN1 mRNA levels in NSCLC tumors. The present results provided insight into the roles of TPTEP1 in NSCLC and the underlying mechanisms.
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Affiliation(s)
- Feng Cao
- Department of Radiation Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhiguo Wang
- Department of Radiation Oncology, Xinle Hospital of Traditional Chinese Medicine, Shijiazhuang, Hebei 050700, P.R. China
| | - Yong Feng
- Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Hongjun Zhu
- Department of Thoracic Surgery, Shangqiu First People's Hospital, Shangqiu, Henan 476100, P.R. China
| | - Meiju Yang
- Department of Respiratory Medicine, Shangqiu First People's Hospital, Shangqiu, Henan 476100, P.R. China
| | - Shuanglin Zhang
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Xuefeng Wang
- Department of Radiation Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
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13
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Wan Y, Yao Z, Chen W, Li D. The lncRNA NORAD/miR-520a-3p Facilitates Malignancy in Non-Small Cell Lung Cancer via PI3k/Akt/mTOR Signaling Pathway. Onco Targets Ther 2020; 13:1533-1544. [PMID: 32110050 PMCID: PMC7036992 DOI: 10.2147/ott.s230954] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND/AIMS The effects of lncRNA-NORAD/mir-520a-3p on proliferation and invasion of non-small cell lung cancer (NSCLC) were studied, and its potential molecular mechanism was discussed. METHODS qRT-PCR was used to detect the expression of lncRNA NORAD and miR-520a-3p in non-small cell lung cancer tissues and cell lines. CCK-8 method and Transwell test were used to identify the effects of lncRNA NORAD on the proliferation and invasion in NSCLC. Target gene prediction and screening and luciferase reporter assay was used to verify downstream target genes of lncRNA NORAD. The expressions of PI3K, AKT, and mTOR proteins were detected by Western blot. RESULTS Compared with normal tissues and cells, the expressions of lncRNA NORAD in cancer tissues and cells were significantly higher. Compared with normal cells, the expression of miR-520a-3p in cells was considerably lower. LncRNA NORAD could accelerate the growth and metastasis of NSCLC in vitro and in vivo. Luciferase reporter assay results indicated that miR-520a-3p was a downstream target gene of lncRNA NORAD. Further findings showed that lncRNA NORAD might bind to miR-520a-3p, thereby affecting the PI3k/Akt/mTOR signaling pathway. CONCLUSION LncRNA NORAD can regulate the proliferation of NSCLC by regulating miR-520a-3p/PI3k/Akt/mTOR signaling pathway, thus promoting the occurrence and development of NSCLC.
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Affiliation(s)
- Yunyan Wan
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong250021, People’s Republic of China
| | - Zhouhong Yao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong250021, People’s Republic of China
| | - Weijuan Chen
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong250021, People’s Republic of China
| | - Dezhi Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong250021, People’s Republic of China
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14
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Yu L, Chen D, Song J. LncRNA SNHG16 promotes non-small cell lung cancer development through regulating EphA2 expression by sponging miR-520a-3p. Thorac Cancer 2020; 11:603-611. [PMID: 31953899 PMCID: PMC7049505 DOI: 10.1111/1759-7714.13304] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Recent evidence has found that lncRNA small nucleolar RNA host gene 16 (SNHG16) was associated with cell carcinogenesis in NSCLC. Here, we further investigated the precise functions and mechanisms of SNHG16 in NSCLC progression. METHODS The expression of SNHG16, microRNA (miR)-520a-3p and EPH Receptor A2 (EphA2) was measured using quantitative real-time polymerase chain reaction and western blot, respectively. Cell proliferation was determined using 3-(4, 5)-dimethylthiahiazo (-z-y1)-3, 5-di-phenytetrazoliumromide (MTT) assay. The migrated and invaded cells were measured by Transwell assay. Flow cytometry was used to detect apoptotic cells. The interaction between miR-520a-3p and SNHG16 or EphA2 was confirmed using a dual-luciferase reporter assay. RESULTS We found that SNHG16 was upregulated in NSCLC tissues and cell lines, knockdown of SNHG16 inhibited cell proliferation, migration, invasion and induced apoptosis in vitro as well as suppressed tumor growth in vivo. MiR-520a-3p directly bound to SNHG16 and miR-520a-3p, and SNHG16 acted as a ceRNA in regulating EphA2 through competitively binding to miR-520a-3p. Additionally, rescue assay exhibited the anticancer activity mediated by SNHG16 knockdown on NSCLC could be reversed by miR-520a-3p inhibition or EphA2 overexpression. CONCLUSION SNHG16 promoted NSCLC development by regulating the miR-520a-3p/EphA2 axis, suggesting novel insights for the pathogenesis of NSCLC and new potential therapeutic targets for the treatment of NSCLC. KEY POINTS Knockdown of SNHG16 inhibited NSCLC cell proliferation, migration, invasion and induced apoptosis in vitro as well as suppressed tumor growth in vivo. SNHG16 directly interacted with miR-520a-3p. EphA2 was a target of miR-520a-3p. SNHG16 could regulate the expression of EphA2 by binding to miR-520a-3p. SNHG16 promoted NSCLC development by regulating the miR-520a-3p/EphA2 axis.
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Affiliation(s)
- Lin Yu
- Department of Thoracic Surgery, Dalian University Affiliated Xinhua Hospital, Dalian, China
| | - Dewen Chen
- Department of Respiratory Medicine, ZaoZhuang Mining Group Central Hospital, Zaozhuang, China
| | - Jie Song
- Department of Respiratory Medicine, Yantai Yuhuangding Hospital, Yantai, China
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15
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Gao Z, Fu P, Yu Z, Zhen F, Gu Y. Comprehensive Analysis of lncRNA-miRNA- mRNA Network Ascertains Prognostic Factors in Patients with Colon Cancer. Technol Cancer Res Treat 2019; 18:1533033819853237. [PMID: 31159706 PMCID: PMC6552362 DOI: 10.1177/1533033819853237] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Non-coding RNAs are competing endogenous RNAs in the occurrence and development of tumorigenesis; numerous microRNAs are aberrantly expressed in colon cancer tissues and play significant roles in oncogenesis development and metastasis. However, large clinical and RNA data are lacking to further confirm the exact role of these RNAs in tumors. This study aimed to ascertain differential RNA expression between colon cancer and normal colon tissues. Materials and Methods: RNA sequencing and clinical data of patients with colon cancer were procured from The Cancer Genome Atlas database; differentially expressed long non-coding RNA, differentially expressed messenger RNAs, and differentially expressed microRNAs were achieved using the limma package in edgeR to generate competing endogenous RNAs networks. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were conducted with ggplot2 package, the Kaplan-Meier survival method was used to predict survival in patients with colon cancer. Results: In total, 1174 differentially expressed long non-coding RNAs, 2068 differentially expressed messenger RNAs, and 239 differentially expressed microRNAs were generated between 480 colon cancer and 41 normal colon tissue samples. Three competing endogenous RNA networks were established. Gene Ontology analysis indicated that the genes of the up-regulated microRNA network were involved in negative regulation of transcription, DNA-template, and those of down-regulated microRNA network were involved in transforming growth factor β receptor signaling pathways, response to hypoxia, cell migration, while Kyoto Encyclopedia of Genes and Genomes analyses of these networks turned out to be negative. Three long non-coding RNAs (AP004609.1, ARHGEF26-AS1, and LINC00491), 3 microRNAs (miRNA-141, miRNA-216a, and miRNA-193b) and 3 RNAs (ULBP2, PHLPP2, and TPM2) were detected to be associated with prognosis by the Kaplan-Meier survival analysis. Additionally, univariate and multivariate Cox regression analyses showed that the microRNA-216a of the competing endogenous RNA might be an independent prognostic factor in colon cancer. Conclusions: This study constructed the non-coding RNA-related competing endogenous RNA networks in colon cancer and sheds lights on underlying biomarkers for colon cancer cohorts.
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Affiliation(s)
- Zhenzhen Gao
- 1 Department of Clinical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,2 Department of Bone Oncology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Peng Fu
- 2 Department of Bone Oncology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Zhengyi Yu
- 1 Department of Clinical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fuxi Zhen
- 1 Department of Clinical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanhong Gu
- 1 Department of Clinical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Ramos PIP, Arge LWP, Lima NCB, Fukutani KF, de Queiroz ATL. Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. Front Genet 2019; 10:1120. [PMID: 31798629 PMCID: PMC6863976 DOI: 10.3389/fgene.2019.01120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022] Open
Abstract
Recent technological advances for the acquisition of multi-omics data have allowed an unprecedented understanding of the complex intricacies of biological systems. In parallel, a myriad of computational analysis techniques and bioinformatics tools have been developed, with many efforts directed towards the creation and interpretation of networks from this data. In this review, we begin by examining key network concepts and terminology. Then, computational tools that allow for their construction and analysis from high-throughput omics datasets are presented. We focus on the study of functional relationships such as co-expression, protein-protein interactions, and regulatory interactions that are particularly amenable to modeling using the framework of networks. We envisage that many potential users of these analytical strategies may not be completely literate in programming languages and code adaptation, and for this reason, emphasis is given to tools' user-friendliness, including plugins for the widely adopted Cytoscape software, an open-source, cross-platform tool for network analysis, visualization, and data integration.
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Affiliation(s)
- Pablo Ivan Pereira Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Luis Willian Pacheco Arge
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Kiyoshi F. Fukutani
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Fundação José Silveira, Salvador, Brazil
| | - Artur Trancoso L. de Queiroz
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
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Liao Z, Zheng Q, Wei T, Zhang Y, Ma J, Zhao Z, Sun H, Nan K. MicroRNA-561 Affects Proliferation and Cell Cycle Transition Through PTEN/AKT Signaling Pathway by Targeting P-REX2a in NSCLC. Oncol Res 2019; 28:147-159. [PMID: 31711559 PMCID: PMC7851535 DOI: 10.3727/096504019x15732109856009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in tumorigenesis and tumor progression. miR-561 has been reported to be downregulated in gastric cancer and affects cancer cell proliferation and metastasis. However, the role and underlying molecular mechanism of miR-561 in human non-small cell lung cancer (NSCLC) remain unknown and need to be further elucidated. In this study, we discovered that miR-561 expression was downregulated in human NSCLC tissues and cell lines. The overexpression of miR-561 inhibited NSCLC cell proliferation and cell cycle G1/S transition and induced apoptosis. The inhibition of miR-561 facilitated cell proliferation and G1/S transition and suppressed apoptosis. miR-561 expression was inversely correlated with P-REX2a expression in NSCLC tissues. P-REX2a was confirmed to be a direct target of miR-561 using a luciferase reporter assay. The overexpression of miR-561 decreased P-REX2a expression, and the suppression of miR-561 increased P-REX2a expression. Particularly, P-REX2a silencing recapitulated the cellular and molecular effects observed upon miR-561 overexpression, and P-REX2a overexpression counteracted the effects of miR-561 overexpression on NSCLC cells. Moreover, both exogenous expression of miR-561 and silencing of P-REX2a resulted in suppression of the PTEN/AKT signaling pathway. Our study demonstrates that miR-561 inhibits NSCLC cell proliferation and G1/S transition and induces apoptosis through suppression of the PTEN/AKT signaling pathway by targeting P-REX2a. These findings indicate that miR-561 plays a significant role in NSCLC progression and serves as a potential therapeutic target for NSCLC.
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Affiliation(s)
- ZiJun Liao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong UniversityXi'an, Shaanxi ProvinceP.R. China
| | - Qi Zheng
- First Department of Medical Oncology, Affiliated Shaanxi Provincial Cancer Hospital, College of Medicine, Xi'an Jiaotong UniversityShaanxi ProvinceP.R. China
| | - Ting Wei
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong UniversityXi'an, Shaanxi ProvinceP.R. China
| | - YanBing Zhang
- First Department of Medical Oncology, Affiliated Shaanxi Provincial Cancer Hospital, College of Medicine, Xi'an Jiaotong UniversityShaanxi ProvinceP.R. China
| | - JieQun Ma
- First Department of Medical Oncology, Affiliated Shaanxi Provincial Cancer Hospital, College of Medicine, Xi'an Jiaotong UniversityShaanxi ProvinceP.R. China
| | - Zheng Zhao
- Third Department of Medical Oncology, Affiliated Shaanxi Provincial Cancer Hospital, College of Medicine, Xi'an Jiaotong UniversityShaanxi ProvinceP.R. China
| | - HaiFeng Sun
- Third Department of Medical Oncology, Affiliated Shaanxi Provincial Cancer Hospital, College of Medicine, Xi'an Jiaotong UniversityShaanxi ProvinceP.R. China
| | - KeJun Nan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong UniversityXi'an, Shaanxi ProvinceP.R. China
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Li GH, Ma ZH, Wang X. Long non-coding RNA CCAT1 is a prognostic biomarker for the progression of oral squamous cell carcinoma via miR-181a-mediated Wnt/β-catenin signaling pathway. Cell Cycle 2019; 18:2902-2913. [PMID: 31599709 DOI: 10.1080/15384101.2019.1662257] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) ranks as the sixth most common carcinoma worldwide, and the third most common carcinoma in developing countries as well. Recently, the aberrant expression of lncRNA CCAT1 has been revealed to play an important role in the development of several cancers. However, its role in OSCC remains unknown. The expression levels of CCAT1 and miR-181a were determined in 15 paired primary OSCC tissues and their adjacent noncancerous tissues and cell lines with qPCR. shRNA against CCAT1 was employed to investigate the impact of CCAT1 on proliferation and metastasis. Then dual luciferase reporter and RIP assays were utilized to study the interaction between CCAT1 and miR-181a. Cells transfected with sh-CCAT1 or treated with miR-181a inhibitor were subjected to western blot to investigate the role of Wnt/β-catenin signaling in CCAT1-mediated proliferation and metastasis. Finally, the role of CCAT1 in OSCC was confirmed with tumor xenografts mice model. CCAT1 was upregulated in OSCC tissues and cell lines. Knockdown of CCAT1 inhibited the proliferation, migration and invasion of OSCC cells, while the cell apoptosis was enhanced. Luciferase and RIP assays revealed that miR-181a was a direct target of CCAT1. Inhibition of miR-181a partially reversed the efficacy of sh-CCAT1. Moreover, sh-CCAT1 inhibited OSCC tissues growth through inhibiting Wnt signaling in a miR-181a-dependent manner in vivo. lncRNA CCAT1 activated Wnt/β-catenin signaling via inhibiting miR-181a, resulting in the cell proliferation, migration and invasion of OSCC, suggesting that CCAT1 might serve as a potential target of OSCC treatment. Abbreviation: LncRNA: long non-coding RNA; OSCC: oral squamous cell carcinoma; 3' UTR: 3' untranslated region; ANOVA: one-way analysis of variance; CDK: cyclin-dependent kinase; ceRNA: competing endogenous RNA; FBS: fetal bovine serum; HGF: human gingival fibroblasts; MAPK: mitogen-activated protein kinase; miRNA: micro RNA; ncRNA: noncoding RNAs; PBS: phosphate-buffered saline; PI3K: phosphatidylinositol 3-kinase.
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Affiliation(s)
- Guang-Hui Li
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P. R. China
| | - Zhong-Hui Ma
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P. R. China.,The Academy of Medical Science, Zhengzhou University , Zhengzhou , Henan , P. R. China
| | - Xi Wang
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P. R. China
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19
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Xiu DH, Liu GF, Yu SN, Li LY, Zhao GQ, Liu L, Li XF. Long non-coding RNA LINC00968 attenuates drug resistance of breast cancer cells through inhibiting the Wnt2/β-catenin signaling pathway by regulating WNT2. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:94. [PMID: 30791958 PMCID: PMC6385430 DOI: 10.1186/s13046-019-1100-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/11/2019] [Indexed: 01/17/2023]
Abstract
Background Breast cancer is one the most common cancers, making it the second leading cause of cancer-related death among women. Long non-coding RNAs (lncRNAs), with tightly regulated expression patterns, also serve as tumor suppressor during tumorigenesis. The present study aimed to elucidate the role of LINC00968 in breast cancer via WNT2-mediated Wnt2/β-catenin signaling pathway. Methods Breast cancer chip GSE26910 was utilized to identify differential expression in LINC00968 and WNT2. The possible relationship among LINC00968, transcriptional repressor HEY and WNT2 was analyzed and then verified. Effects of LINC00968 on activation of the Wnt2/β-catenin signaling pathway was also tested. Drug resistance, colony formation, cell migration, invasion ability and cell apoptosis after transfection were also determined. Furthermore, tumor xenograft in nude mice was performed to test tumor growth and weight in vivo. Results WNT2 expression exhibited at a high level, whereas LINC00968 at a low expression in breast cancer which was also associated with poor prognosis in patients. LINC00968 targeted and negatively regulated WNT2 potentially via HEY1. Either overexpressed LINC00968 or silenced inhibited activation of the Wnt2/β-catenin signaling pathway, thereby reducing drug resistance, decreasing colony formation ability, as well as suppressing migration and invasion abilities of breast cancer cells in addition to inducing apoptosis. Lastly, in vivo experiment suggested that LINC00968 overexpression also suppressed transplanted tumor growth in nude mice. Conclusion Collectively, overexpressed LINC00968 contributes to reduced drug resistance in breast cancer cells by inhibiting the activation of the Wnt2/β-catenin signaling pathway through silencing WNT2. This study offers a new target for the development of breast cancer treatment.
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Affiliation(s)
- Dian-Hui Xiu
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - Gui-Feng Liu
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - Shao-Nan Yu
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - Long-Yun Li
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, No. 126, Xiantai Street, Changchun, 130033, Jilin Province, People's Republic of China
| | - Guo-Qing Zhao
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, No. 126, Xiantai Street, Changchun, 130033, Jilin Province, People's Republic of China
| | - Lin Liu
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - Xue-Feng Li
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, No. 126, Xiantai Street, Changchun, 130033, Jilin Province, People's Republic of China.
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Liu H, Deng H, Zhao Y, Li C, Liang Y. LncRNA XIST/miR-34a axis modulates the cell proliferation and tumor growth of thyroid cancer through MET-PI3K-AKT signaling. J Exp Clin Cancer Res 2018; 37:279. [PMID: 30463570 PMCID: PMC6249781 DOI: 10.1186/s13046-018-0950-9] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 11/06/2018] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Thyroid cancer is one of the most prevalent malignancies in endocrine system. Further understanding and revealing the molecular mechanism underlying thyroid cancer are indispensable for the development of effective diagnosis and treatments. In the present study, we attempted to provide novel basis for targeted therapy for thyroid cancer from the aspect of lncRNA-miRNA-mRNA interaction. METHODS The expression and cellular function of XIST (X-inactive specific transcript) was determined. miRNAs which may be direct targets of XIST were screened for from online GEO database and miR-34a was selected. Next, the predicted binding between XIST and miR-34a, and the dynamic effect of XIST and miR-34a on downstream MET (hepatocyte growth factor receptor)-PI3K (phosphoinositide 3-kinase)-AKT (α-serine/threonine-protein kinase) signaling was evaluated. RESULTS XIST was significantly up-regulated in thyroid cancer tissues and cell lines; XIST knockdown suppressed the cell proliferation in vivo and the tumor growth in vitro. Based on online database and online tool prediction results, miR-34a was underexpressed in thyroid cancer and might be a direct target of XIST. Herein, we confirmed the negative interaction between XIST and miR-34a; moreover, XIST knockdown could reduce the protein levels of MET, a downstream target of miR-34a, and the phosphorylation of PI3K and AKT. In thyroid cancer tissues, MET mRNA and protein levels of MET were up-regulated; MET was positively correlated with XIST while negatively correlated with miR-34a, further confirming that XIST serves as a ceRNA for miR-34a through sponging miR-34a, competing with MET for miR-34a binding, and finally modulating thyroid cancer cell proliferation and tumor growth. CONCLUSION In the present study, we provided novel experimental basis for targeted therapy for thyroid cancer from the aspect of lncRNA-miRNA-mRNA interaction.
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Affiliation(s)
- Hua Liu
- Nuclear Medicine Department, Xiangya Hospital, Central South University, Changsha, Hunan People’s Republic of China
| | - Haoyu Deng
- Nuclear Medicine Department, Xiangya Hospital, Central South University, Changsha, Hunan People’s Republic of China
| | - Yajie Zhao
- Nuclear Medicine Department, Xiangya Hospital, Central South University, Changsha, Hunan People’s Republic of China
| | - Can Li
- Nuclear Medicine Department, Xiangya Hospital, Central South University, Changsha, Hunan People’s Republic of China
| | - Yu Liang
- Oncology Department, Xiangya Hospital, Central South University, Changsha, No. 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
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Huang D, Bi C, Zhao Q, Ding X, Bian C, Wang H, Wang T, Liu H. Knockdown long non-coding RNA ANRIL inhibits proliferation, migration and invasion of HepG2 cells by down-regulation of miR-191. BMC Cancer 2018; 18:919. [PMID: 30249208 PMCID: PMC6154945 DOI: 10.1186/s12885-018-4831-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/18/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common malignant tumor with high fatality rate. Recent studies reported that up-regulation of long non-coding RNA antisense non-coding RNA in the INK4 locus (lncRNA ANRIL) was found in HCC tissues, and which could affect HCC cells biological processes. However, the potential molecular mechanism of ANRIL in HCC is still unclear. The study aimed to uncover the effect of ANRIL on HepG2 cells growth, migration and invasion. METHODS The knockdown expression vectors of ANRIL were transfected into HepG2 cells, and qRT-PCR, CCK-8, flow cytometry, Transwell and western blot assays were performed to analyze the effect of ANRIL on cell proliferation, apoptosis, migration and invasion. The relative expression of miR-191 was then examined in ANRIL knockdown vector transfected cells. These experiments were repeated again for exploring the effect of miR-191 on HepG2 cells. NF-κB and Wnt/β-catenin signaling pathways were examined by using western blot assay. RESULTS Knockdown of ANRIL inhibited proliferation, induced apoptosis, meanwhile suppressed migration and invasion of HepG2 cells. Additionally, the results showed that the expression level of miR-191 was down-regulated by ANRIL knockdown in HepG2 cells. Importantly, overexpression of miR-191 reversed the anti-tumor effect of ANRIL on cell proliferation, apoptosis, migration and invasion in HepG2 cells. Besides, we found that ANRIL knockdown inactivated NF-κB and Wnt/β-catenin pathways by regulating miR-191. CONCLUSIONS These data demonstrated that ANRIL knockdown suppressed proliferation, migration, invasion, and promoted apoptosis in HepG2 cells by down-regulating miR-191 and inactivating NF-κB and Wnt/β-catenin signaling pathways.
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Affiliation(s)
- Deyu Huang
- Department of Infectious Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003 Shandong China
| | - Chunhua Bi
- Department of Infectious Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003 Shandong China
| | - Qingxi Zhao
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Qingdao, 266003 Shandong China
| | - Xueli Ding
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Qingdao, 266003 Shandong China
| | - Cheng Bian
- Department of Infectious Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003 Shandong China
| | - Hui Wang
- Department of Infectious Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003 Shandong China
| | - Ting Wang
- Department of Infectious Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003 Shandong China
| | - Hua Liu
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, No.16, Jiangsu Road, Qingdao, 266003 Shandong China
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Xu S, Liu R, Da Y. Comparison of tumor related signaling pathways with known compounds to determine potential agents for lung adenocarcinoma. Thorac Cancer 2018; 9:974-988. [PMID: 29870138 PMCID: PMC6068465 DOI: 10.1111/1759-7714.12773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/02/2018] [Indexed: 12/14/2022] Open
Abstract
Background This study compared tumor‐related signaling pathways with known compounds to determine potential agents for lung adenocarcinoma (LUAD) treatment. Methods Kyoto Encyclopedia of Genes and Genomes signaling pathway analyses were performed based on LUAD differentially expressed genes from The Cancer Genome Atlas (TCGA) project and genotype‐tissue expression controls. These results were compared to various known compounds using the Connectivity Mapping dataset. The clinical significance of the hub genes identified by overlapping pathway enrichment analysis was further investigated using data mining from multiple sources. A drug‐pathway network for LUAD was constructed, and molecular docking was carried out. Results After the integration of 57 LUAD‐related pathways and 35 pathways affected by small molecules, five overlapping pathways were revealed. Among these five pathways, the p53 signaling pathway was the most significant, with CCNB1, CCNB2, CDK1, CDKN2A, and CHEK1 being identified as hub genes. The p53 signaling pathway is implicated as a risk factor for LUAD tumorigenesis and survival. A total of 88 molecules significantly inhibiting the five LUAD‐related oncogenic pathways were involved in the LUAD drug‐pathway network. Daunorubicin, mycophenolic acid, and pyrvinium could potentially target the hub gene CHEK1 directly. Conclusion Our study highlights the critical pathways that should be targeted in the search for potential LUAD treatments, most importantly, the p53 signaling pathway. Some compounds, such as ciclopirox and AG‐028671, may have potential roles for LUAD treatment but require further experimental verification.
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Affiliation(s)
- Song Xu
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Renwang Liu
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yurong Da
- Key Laboratory of Cellular and Molecular Immunology in Tianjin, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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