title: Genome-wide screening and co-expression network analysis identify recurrence-specific biomarkers of esophageal squamous cell carcinoma.
abstract: Tumor recurrence and metastasis after surgery are the leading causes of death in patients with esophageal squamous cell carcinoma (ESCC). Next-generation sequencing techniques have improved our understanding of the genetic alterations underlying tumor initiation and progression. To explore recurrence-specific transcriptional profiles, functional properties, and gene co-expression networks in ESCC, samples from recurrence (n = 4) and nonrecurrence (n = 4) groups were analyzed by RNA sequencing. Patients included in the nonrecurrence group had five or more years of survival without any evidence of recurrence or metastasis, while those included in the recurrence group exhibited early recurrence and metastasis and died within 2 years. We identified 533 significantly differentially expressed protein-coding and noncoding genes. Functional enrichment analysis indicated that ESCC recurrence was related to dysregulated cell-cell adherence, microenvironment homeostasis, information processing, and the immune response. Co-expression networks demonstrated differences in the patterns of gene expression and co-expression between the recurrence and nonrecurrence groups. This study provided important insights into ESCC progression and the differentially expressed genes that may represent potential targets for ESCC diagnosis and therapy.
authors.affiliation: Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai, 200032, People's Republic of China.
authors.forename: Zong-wu
authors.initials: ZW
authors.lastname: Lin
authors.forename: Jie
authors.initials: J
authors.lastname: Gu
authors.forename: Rong-hua
authors.initials: RH
authors.lastname: Liu
authors.forename: Xiao-ming
authors.initials: XM
authors.lastname: Liu
authors.forename: Feng-kai
authors.initials: FK
authors.lastname: Xu
authors.forename: Guang-yin
authors.initials: GY
authors.lastname: Zhao
authors.forename: Chun-lai
authors.initials: CL
authors.lastname: Lu
authors.forename: Di
authors.initials: D
authors.lastname: Ge
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology; D015331:Cohort Studies; D018450:Disease Progression; D004938:Esophageal Neoplasms / Q000235:genetics* / Q000473:pathology; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D015894:Genome, Human; D006801:Humans; D008297:Male; D008875:Middle Aged; D009364:Neoplasm Recurrence, Local / Q000235:genetics* / Q000473:pathology; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D014408:Biomarkers, Tumor; D012333:RNA, Messenger
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