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Liu S, Zeng F, Fan G, Dong Q. Identification of Hub Genes and Construction of a Transcriptional Regulatory Network Associated With Tumor Recurrence in Colorectal Cancer by Weighted Gene Co-expression Network Analysis. Front Genet 2021; 12:649752. [PMID: 33897765 PMCID: PMC8058478 DOI: 10.3389/fgene.2021.649752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/15/2021] [Indexed: 12/26/2022] Open
Abstract
Tumor recurrence is one of the most important risk factors that can negatively affect the survival rate of colorectal cancer (CRC) patients. However, the key regulators dictating this process and their exact mechanisms are understudied. This study aimed to construct a gene co-expression network to predict the hub genes affecting CRC recurrence and to inspect the regulatory network of hub genes and transcription factors (TFs). A total of 177 cases from the GSE17536 dataset were analyzed via weighted gene co-expression network analysis to explore the modules related to CRC recurrence. Functional annotation of the key module genes was assessed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. The protein and protein interaction network was then built to screen hub genes. Samples from the Cancer Genome Atlas (TCGA) were further used to validate the hub genes. Construction of a TFs-miRNAs–hub genes network was also conducted using StarBase and Cytoscape approaches. After identification and validation, a total of five genes (TIMP1, SPARCL1, MYL9, TPM2, and CNN1) were selected as hub genes. A regulatory network of TFs-miRNAs-targets with 29 TFs, 58 miRNAs, and five hub genes was instituted, including model GATA6-MIR106A-CNN1, SP4-MIR424-TPM2, SP4-MIR326-MYL9, ETS1-MIR22-TIMP1, and ETS1-MIR22-SPARCL1. In conclusion, the identification of these hub genes and the prediction of the Regulatory relationship of TFs-miRNAs-hub genes may provide a novel insight for understanding the underlying mechanism for CRC recurrence.
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Affiliation(s)
- Shengwei Liu
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Fanping Zeng
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Guangwen Fan
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Qiyong Dong
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
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Klingler A, Regensburger D, Tenkerian C, Britzen-Laurent N, Hartmann A, Stürzl M, Naschberger E. Species-, organ- and cell-type-dependent expression of SPARCL1 in human and mouse tissues. PLoS One 2020; 15:e0233422. [PMID: 32437418 PMCID: PMC7241726 DOI: 10.1371/journal.pone.0233422] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/05/2020] [Indexed: 12/30/2022] Open
Abstract
SPARCL1 is a matricellular protein with anti-adhesive, anti-proliferative and anti-tumorigenic functions and is frequently downregulated in tumors such as colorectal carcinoma or non-small cell lung cancer. Studies have identified SPARCL1 as an angiocrine tumor suppressor secreted by tumor vessel endothelial cells, thereby exerting inhibitory activity on angiogenesis and tumor growth, in colorectal carcinoma. It is unknown whether SPARCL1 may exert these homeostatic functions in all organs and in other species. Therefore, SPARCL1 expression was comparatively analysed between humans and mice in a systematic manner. Murine Sparcl1 (mSparcl1) is most strongly expressed in the lung; expressed at an intermediate level in most organs, including the large intestine; and absent in the liver. In human tissues, SPARCL1 (hSPARCL1) was detected in all organs, with the strongest expression in the stomach, large intestine and lung, mostly consistent with the murine expression pattern. A striking difference between human and murine tissues was the absence of mSparcl1 expression in murine livers, while human livers showed moderate expression. Furthermore, mSparcl1 was predominantly associated with mural cells, whereas hSPARCL1 was detected in both mural and endothelial cells. Human SPARCL1 expression was downregulated in different carcinomas, including lung and colon cancers. In conclusion, this study revealed species-, organ- and cell-type-dependent expression of SPARCL1, suggesting that its function may not be similar between humans and mice.
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Affiliation(s)
- Anika Klingler
- Division of Molecular and Experimental Surgery, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Translational Research Center, Erlangen, Germany
| | - Daniela Regensburger
- Division of Molecular and Experimental Surgery, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Translational Research Center, Erlangen, Germany
| | - Clara Tenkerian
- Division of Molecular and Experimental Surgery, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Translational Research Center, Erlangen, Germany
| | - Nathalie Britzen-Laurent
- Division of Molecular and Experimental Surgery, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Translational Research Center, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Translational Research Center, Erlangen, Germany
| | - Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Translational Research Center, Erlangen, Germany
- * E-mail:
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Wang J, Yu XF, OUYang N, Luo QL, Zhao SY, Guan XF, Chen T, Li JX. Multi-platform analysis of methylation-regulated genes in human lung adenocarcinoma. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2019; 82:37-45. [PMID: 30626254 DOI: 10.1080/15287394.2018.1551645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lung adenocarcinoma (LUAD) is the most frequent pathological type of lung cancer that has a poor prognosis and high mortality rate. DNA methylation plays a critical role in various biological processes during development, while dysregulation results in pathological consequences. Thus, this study aimed to identify DNA methylation-regulated genes involved in LUAD occurrence. Initially, 300 downregulated and 168 upregulated mRNA expression levels were identified in two databases: Gene Expression Omnibus (GEO) and The Cancer Genome Atlas. In addition, GEO was utilized to detect 243 DNA hyper-methylated sites. Based on our observations, it was possible to correlate downregulation of mRNA expression and DNA hyper-methylation of six genes (ABCA3, COX7A1, HOXA5, SLIT3, SOX17, and SPARCL1). Functional analysis of the six genes indicated that these genes are predominantly enriched in cancer-related pathways and may promote carcinogenesis by regulating epithelialmesenchymal transition processes. In conclusion, our study identified a panel of DNA methylation-regulated genes involved in LUAD and may serve as potential epigenetic markers for this type of carcinoma.
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Affiliation(s)
- Jin Wang
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases , Suzhou , Jiangsu , China
| | - Xiao-Fan Yu
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases , Suzhou , Jiangsu , China
| | - Nan OUYang
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
| | - Qiu-Lin Luo
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
| | - Shi-Yu Zhao
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
| | - Xi-Fei Guan
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
| | - Tao Chen
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases , Suzhou , Jiangsu , China
| | - Jian-Xiang Li
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases , Suzhou , Jiangsu , China
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