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Xiao S, Guo J, Zhang W, Hu X, Wang R, Chen Z, Lai C. A Six-microRNA Signature Nomogram for Preoperative Prediction of Tumor Deposits in Colorectal Cancer. Int J Gen Med 2022; 15:675-687. [PMID: 35082517 PMCID: PMC8785134 DOI: 10.2147/ijgm.s346790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Tumor deposits (TDs) are acknowledged negative prognostic factors in colorectal cancer (CRC), and their pathogenesis remains a puzzle. This study aimed to construct and validate a nomogram available for preoperative TDs prediction in CRC patients. Patients and Methods Patients from the Surveillance, Epidemiology, and End Results (SEER) and the cancer genome atlas (TCGA) databases were randomly divided into training and validation sets according to the sample size ratio of 7:3. Univariate logistic regression was performed for identifying differentially expressed microRNAs between TDs and non-TDs. Nomograms for TDs prediction were developed from the multivariate logistic regression model with least absolute shrinkage and selection operator and were validated internally in terms of accuracy, calibration, and clinical utility. Based on the target genes, pathways tightly associated with TDs were selected using enrichment analysis. Results Six clinicopathologic factors and expressions of six microRNAs (miR-614, miR-1197, miR-4770, miR-3136, miR-3173, and miR-4636) differed significantly between TDs and non-TDs CRC patients from the SEER and TCGA training sets. We compared potential prediction discrimination between two nomograms: a clinicopathologic nomogram and a six-microRNA signature nomogram. The six-microRNA signature nomogram revealed better accuracy than the clinicopathologic one for TDs prediction (AUC values of 0.96 and 0.93 in the validation cohort). The calibration plots and decision curve analysis demonstrated that the six-microRNA signature nomogram had better validity and a greater prognostic benefit versus the clinicopathologic one for TDs prediction. Calcium signaling pathways were closely associated with roles of the six microRNAs in TDs of CRC patients. Conclusion The six-microRNA signature nomogram can be used as an efficient tool for preoperative TDs prediction in CRC patients.
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Affiliation(s)
- Shihan Xiao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & Standardization, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Jianping Guo
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Wuming Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & Standardization, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Xianqin Hu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & Standardization, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Ran Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & Standardization, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Zhikang Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & Standardization, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Xiangya Hospital Central South University, Changsha, Hunan Province, People’s Republic of China
- Correspondence: Zhikang Chen; Chen Lai Department of General Surgery, Xiangya Hospital, Central South University, 87th Xiangya Road, Kaifu District, Changsha, Hunan, People’s Republic of ChinaTel +86-13875982443Tel +86-13875982443 Email ;
| | - Chen Lai
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & Standardization, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Xiangya Hospital Central South University, Changsha, Hunan Province, People’s Republic of China
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Zarei Ghobadi M, Mozhgani SH, Farzanehpour M, Behzadian F. Identifying novel biomarkers of the pediatric influenza infection by weighted co-expression network analysis. Virol J 2019; 16:124. [PMID: 31665046 PMCID: PMC6819563 DOI: 10.1186/s12985-019-1231-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/09/2019] [Indexed: 11/18/2022] Open
Abstract
Background Despite the high yearly prevalence of Influenza, the pathogenesis mechanism and involved genes have not been fully known. Finding the patterns and mapping the complex interactions between different genes help us to find the possible biomarkers and treatment targets. Methods Herein, weighted gene co-expression network analysis (WGCNA) was employed to construct a co-expression network among genes identified by microarray analysis of the pediatric influenza-infected samples. Results Three of the 38 modules were found as the most related modules to influenza infection. At a functional level, we found that the genes in these modules regulate the immune responses, protein targeting, and defense to virus. Moreover, the analysis of differentially expressed genes disclosed 719 DEGs between the normal and infected subjects. The comprehensive investigation of genes in the module involved in immune system and viral defense (yellow module) revealed that SP110, HERC5, SAMD9L, RTP4, C19orf66, HELZ2, EPSTI1, and PHF11 which were also identified as DEGs (except C19orf66) have the potential to be as the biomarkers and also drug targeting for the treatment of pediatric influenza. Conclusions The WGCN analysis revealed co-expressed genes which were involved in the innate immune system and defense to virus. The differentially expressed genes in the identified modules can be considered for designing drug targets. Moreover, modules can help to find pathogenesis routes in the future.
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Affiliation(s)
- Mohadeseh Zarei Ghobadi
- Department of Virology, School of Public Health Tehran University of Medical Sciences, Tehran, Iran.,Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.,Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahdieh Farzanehpour
- Department of Virology, School of Public Health Tehran University of Medical Sciences, Tehran, Iran
| | - Farida Behzadian
- Department of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, Iran.
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Chen ZM, Yu Q, Chen G, Tang RX, Luo DZ, Dang YW, Wei DM. MiR-193a-3p inhibits pancreatic ductal adenocarcinoma cell proliferation by targeting CCND1. Cancer Manag Res 2019; 11:4825-4837. [PMID: 31213904 PMCID: PMC6549772 DOI: 10.2147/cmar.s199257] [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: 12/22/2018] [Accepted: 03/29/2019] [Indexed: 12/31/2022] Open
Abstract
Background: MicroRNAs (miRNAs) could modulate gene expression at the posttranscriptional level by promoting mRNA degradation or blocking mRNA translation, thus affecting the occurrence and development of cancer. Methods: In this work, qRT-PCR was conducted to detect the expression of miR-193a-3p and CCND1. The ability of cell proliferation was evaluated via CCK-8 assay. Cell apoptosis and cell cycle distribution were detected by flow cytometry. Bioinformatic techniques were employed to research the regulatory relationship between miR-193a-3p and target genes. The relationship between miR-193a-3p and CCND1 was verified via dual-luciferase reporter assays. Results: MiR-193a-3p expression in pancreatic ductal adenocarcinoma (PDAC) tissue was significantly lower than in non-cancerous tissue. After overexpressing miR-193a-3p in PDAC cells, their multiplication ability was significantly inhibited, apoptosis was accelerated, and the cell cycle was blocked in the G1 and G2/M phases. CCND1 was confirmed to have a targeted relationship with miR-193a-3p. Moreover, CCND1 expression was significantly lower in PDAC cells with an overexpression of miR-193a-3p. Conclusions: MiR-193a-3p targeted CCND1 to suppress tumor growth in PDAC cells. MiR-193a-3p may function as a tumor inhibitor in PDAC development, which could offer a promising therapeutic and prognostic strategy for PDAC treatment.
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Affiliation(s)
- Zhi-Min Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Qiao Yu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Rui-Xue Tang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Dian-Zhong Luo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Dan-Ming Wei
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
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