title: Integrated transcriptome analysis reveals miRNA-mRNA crosstalk in laryngeal squamous cell carcinoma.
abstract: Next generation sequencing (NGS) has proven to be a powerful tool in delineating myriads of molecular subtypes of cancer, as well as in revealing accumulation of genomic mutations throughout cancer progression. Whole genome microRNA (miRNA) and mRNA expression profiles were obtained from patients with laryngeal squamous cell carcinoma (LSCC) using deep sequencing technology, and were analyzed by utilizing integrative computational approaches. A large number of protein-coding and non-coding genes were detected to be differentially expressed, indicating a functional switch in LSCC cells. A total of 127 mutated genes were detected to be significantly associated with ectoderm and epidermis development. Eleven miRNAs were found to be differentially expressed, including a potential cancer suppressor miRNA, mir-34c, which was dramatically down-regulated. Integrated analysis of mRNA and miRNA transcriptomes further revealed correlated dynamics among 11 miRNAs and 138 targeted genes, forming a highly dynamical co-regulation network response to LSCC development.
authors: Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Key Laboratory of Otolaryngology Head and Neck Surgery, Beijing 100005, China.
authors: Yang
authors: Y
authors: Zhang
authors: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors: Yong
authors: Y
authors: Chen
authors: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors: Jinhai
authors: J
authors: Yu
authors: Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: liugm@big.ac.cn.
authors: Guiming
authors: G
authors: Liu
authors: Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Key Laboratory of Otolaryngology Head and Neck Surgery, Beijing 100005, China. Electronic address: huangzhigangent@163.com.
authors: Zhigang
authors: Z
authors: Huang
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D015536:Down-Regulation; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007822:Laryngeal Neoplasms / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D059645:Mutation Rate; D012333:RNA, Messenger / Q000235:genetics*; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D004272:DNA, Mitochondrial; D035683:MicroRNAs; D012333:RNA, Messenger
keywords: Data integration; Gene expression; Laryngeal squamous cell carcinoma; Small RNAs