title: Gene microarray analysis of lncRNA and mRNA expression profiles in patients with hypopharyngeal squamous cell carcinoma.
abstract: BACKGROUND
  Studies have shown that long noncoding RNAs (lncRNAs) are involved in the development and progression of many types of cancer. However, the mechanisms by which lncRNAs influence development and progression of hypopharyngeal squamous cell carcinoma (HSCC) are unclear.
  
  
  METHODS
  We investigated differences in lncRNA and mRNA expression profiles between 3 pairs of HSCC tissues and adjacent nontumor tissues by microarray analysis.
  
  
  RESULTS
  In HSCC tissues, 1299 lncRNAs were significantly upregulated (n=669) or downregulated (n=630) compared to levels in adjacent nontumor tissues. Moreover, 1432 mRNAs were significantly upregulated (n=684) or downregulated (n=748) in HSCC tissues. We randomly selected 2 differentially expressed lncRNAs (AB209630, AB019562) and 2 differentially expressed mRNAs (SPP1, TJP2) for confirmation of microarray results using qRT-PCR. The qRT-PCR results matched well with the microarray data. The differentially expressed lncRNAs and mRNAs were distributed on each of the chromosomes, including the X and Y chromosomes. Pathway analysis indicated that the biological functions of differentially expressed mRNAs were related to 48 cellular pathways that may be associated with HSCC development. GO analysis revealed that 593 mRNAs involved in biological processes, 50 mRNAs involved in cellular components, and 46 mRNAs involved in molecular functions were upregulated in the carcinomas; 280 mRNAs involved in biological processes, 58 mRNAs involved in cellular components, and 71 mRNAs involved in molecular functions were downregulated in the carcinomas. In addition, 8 enhancer-like lncRNAs and 21 intergenic lncRNAs with their adjacent mRNA pairs were identified as coregulated transcripts.
  
  
  CONCLUSIONS
  These findings provide insight into the mechanisms underlying HSCC tumorigenesis and will facilitate identification of new therapeutic targets and diagnostic biomarkers for this disease.
authors.affiliation: Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, Ministry of Health Jinan, Shandong 250012, P. R. China.
authors.forename: Jieyu
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, Ministry of Health Jinan, Shandong 250012, P. R. China.
authors.forename: Wenming
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, Ministry of Health Jinan, Shandong 250012, P. R. China.
authors.forename: Tong
authors.initials: T
authors.lastname: Jin
authors.affiliation: Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, Ministry of Health Jinan, Shandong 250012, P. R. China.
authors.forename: Xuan
authors.initials: X
authors.lastname: Xiang
authors.affiliation: Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, Ministry of Health Jinan, Shandong 250012, P. R. China.
authors.forename: Maocai
authors.initials: M
authors.lastname: Li
authors.affiliation: Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, Ministry of Health Jinan, Shandong 250012, P. R. China.
authors.forename: Juan
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center Houston, TX 77030, USA.
authors.forename: Guojun
authors.initials: G
authors.lastname: Li
authors.affiliation: Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, Ministry of Health Jinan, Shandong 250012, P. R. China.
authors.forename: Xinliang
authors.initials: X
authors.lastname: Pan
authors.affiliation: Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, Ministry of Health Jinan, Shandong 250012, P. R. China.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Lei
keywords: Hypopharyngeal squamous cell carcinoma; expression profile; lncRNA; mRNA; microarray