title: An integrative framework to identify cell death-related microRNAs in esophageal squamous cell carcinoma.
abstract: Cell death is a critical biological process involved in many important functions, and defects in this system are usually linked with numerous human diseases including cancers. Esophageal squamous cell carcinoma is one of the most chemo- and biological therapy resistant cancers. Based on knowledge repository and four miRNAs profiling data, we proposed a general framework to hunt for cell death miRNAs in a context dependent manner. We predicted 12 candidate miRNAs from hundreds of others. Follow-up experimental verification of 7 miRNAs indicated at least 3 miRNAs (MIR20b, MIR498 and MIR196) were involved in both apoptosis and autophagy processes. These results indicated miRNAs intimately connected the two cell death modules in esophageal squamous cell carcinoma. This integrative framework can also be easily extended to identify miRNAs in other key cellular signaling pathways or may find conditional specific miRNAs in other cancer types.
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China.|Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
authors.forename: Bing-Li
authors.initials: BL
authors.lastname: Wu
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China.|College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Wang
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China.|Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
authors.forename: Wen-Jing
authors.initials: WJ
authors.lastname: Bai
authors.affiliation: Department of Bioinformatics, Shantou University Medical College, Shantou 515041, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Department of Bioinformatics, Shantou University Medical College, Shantou 515041, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Zhao
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Yi
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Department of Bioinformatics, Shantou University Medical College, Shantou 515041, China.
authors.forename: Wen-Jun
authors.initials: WJ
authors.lastname: Shen
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China.|Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
authors.forename: En-Min
authors.initials: EM
authors.lastname: Li
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China.|Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, China.
authors.forename: Li-Yan
authors.initials: LY
authors.lastname: Xu
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China.|Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.|Department of Bioinformatics, Shantou University Medical College, Shantou 515041, China.
authors.forename: Jian-Zhen
authors.initials: JZ
authors.lastname: Xu
mesh_terms: D017209:Apoptosis; D001343:Autophagy; D002294:Carcinoma, Squamous Cell / Q000175:diagnosis* / Q000235:genetics*; D016923:Cell Death; D045744:Cell Line, Tumor; D019295:Computational Biology; D004938:Esophageal Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D000077277:Esophageal Squamous Cell Carcinoma; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D015398:Signal Transduction; D012984:Software
chemical_list: C542543:MIRN196 microRNA, human; C534451:MIRN20a microRNA, human; C578093:MIRN498 microRNA, human; D035683:MicroRNAs
keywords: apoptosis; autophagy; cell death; esophageal squamous cell carcinoma; miRNA