RETRACTED: Identification of Early Diagnostic and Prognostic Biomarkers via WGCNA in Stomach Adenocarcinoma

Ruoyue Tan; Ruoyue Tan; Ruoyue Tan; Guanghui Zhang; Guanghui Zhang; Ruochen Liu; Ruochen Liu; Jianbing Hou; Jianbing Hou; Zhen Dong; Zhen Dong; Chaowei Deng; Chaowei Deng; Sicheng Wan; Sicheng Wan; Xiaodong Lai; Hongjuan Cui; Hongjuan Cui; Hongjuan Cui

doi:10.3389/fonc.2021.636461

Frontiers in Oncology (Jun 2021)

RETRACTED: Identification of Early Diagnostic and Prognostic Biomarkers via WGCNA in Stomach Adenocarcinoma

Ruoyue Tan,
Ruoyue Tan,
Ruoyue Tan,
Guanghui Zhang,
Guanghui Zhang,
Ruochen Liu,
Ruochen Liu,
Jianbing Hou,
Jianbing Hou,
Zhen Dong,
Zhen Dong,
Chaowei Deng,
Chaowei Deng,
Sicheng Wan,
Sicheng Wan,
Xiaodong Lai,
Hongjuan Cui,
Hongjuan Cui,
Hongjuan Cui

Affiliations

Ruoyue Tan: State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
Ruoyue Tan: Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
Ruoyue Tan: NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
Guanghui Zhang: State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
Guanghui Zhang: Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
Ruochen Liu: State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
Ruochen Liu: Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
Jianbing Hou: State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
Jianbing Hou: Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
Zhen Dong: State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
Zhen Dong: Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
Chaowei Deng: State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
Chaowei Deng: Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
Sicheng Wan: State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
Sicheng Wan: Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
Xiaodong Lai: Department of Critical Care Medicine, The Thirteenth People’s Hospital of Chongqing, Chongqing, China
Hongjuan Cui: State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
Hongjuan Cui: Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
Hongjuan Cui: NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China

DOI: https://doi.org/10.3389/fonc.2021.636461
Journal volume & issue: Vol. 11

Abstract

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Stomach adenocarcinoma (STAD) is a leading cause of cancer deaths, and the outcome of the patients remains dismal for the lack of effective biomarkers of early detection. Recent studies have elucidated the landscape of genomic alterations of gastric cancer and reveal some biomarkers of advanced-stage gastric cancer, however, information about early-stage biomarkers is limited. Here, we adopt Weighted Gene Co-expression Network Analysis (WGCNA) to screen potential biomarkers for early-stage STAD using RNA-Seq and clinical data from TCGA database. We find six gene clusters (or modules) are significantly correlated with the stage-I STADs. Among these, five hub genes, i.e., MS4A1, THBS2, VCAN, PDGFRB, and KCNA3 are identified and significantly de-regulated in the stage-I STADs compared with the normal stomach gland tissues, which suggests they can serve as potential early diagnostic biomarkers. Moreover, we show that high expression of VCAN and PDGFRB is associated with poor prognosis of STAD. VCAN encodes a large chondroitin sulfate proteoglycan that is the main component of the extracellular matrix, and PDGFRB encodes a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor (PDGF) family. Consistently, Gene Ontology (GO) analysis of differentially expressed genes in the STADs indicates terms associated with extracellular matrix and receptor ligand activity are significantly enriched. Protein-protein network interaction analysis (PPI) and Gene Set Enrichment Analysis (GSEA) further support the core role of VCAN and PDGFRB in the tumorigenesis. Collectively, our study identifies the potential biomarkers for early detection and prognosis of STAD.

Published in Frontiers in Oncology

ISSN: 2234-943X (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Medicine: Internal medicine: Neoplasms. Tumors. Oncology. Including cancer and carcinogens
Website: https://www.frontiersin.org/journals/oncology/

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