Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa

Lu Feng; John R. Houck; Pawadee Lohavanichbutr; Chu Chen

doi:10.18632/oncotarget.16358

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Research Papers:

Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa

Lu Feng, John R. Houck, Pawadee Lohavanichbutr and Chu Chen _

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Oncotarget. 2017; 8:31521-31531. https://doi.org/10.18632/oncotarget.16358

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Abstract

Lu Feng1,2, John R. Houck1, Pawadee Lohavanichbutr1, Chu Chen1,3,4

1Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

2Department of Head and Neck Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China

3Department of Epidemiology, University of Washington, Seattle, Washington, USA

4Department of Otolaryngology, Head and Neck Surgery, University of Washington, Seattle, Washington, USA

Correspondence to:

Chu Chen, email: [email protected]

Keywords: oral cavity and oropharyngeal squamous cell carcinoma (OSCC), long non-coding RNA, GEO, microarray

Received: October 19, 2016 Accepted: March 09, 2017 Published: March 18, 2017

ABSTRACT

Oral cavity and oropharyngeal squamous cell carcinoma (OSCC) is a major cancer type in the head and neck region. To better understand the roles long non-coding RNA (lncRNA) play in OSCC carcinogenesis, we compared the expression levels of 3,054 probe sets for lncRNAs between 167 OSCCs and 45 healthy oral mucosa using an Affymetrix HG U133 plus 2.0 array dataset. We found 658 lncRNA transcripts (790 probe sets) to be significantly differentially expressed using a criteria of FDR < 0.01, with 36 of them (39 probe sets) showing more than a 2-fold change. We further validated the top differentially expressed lncRNAs in three independent datasets from Gene Expression Omnibus (GEO) repository: GSE42743, GSE9844, and GSE6791. Fourteen lncRNAs (15 probe sets) were validated in all three datasets using the criteria FDR < 0.01: LOC441178, C5orf66-AS1, HCG22, FLG-AS1, CCL14/CCL15-CCL14, LOC100506990, TRIP10, PCBP1-AS1, LINC01315, LINC00478, COX10-AS1/LOC100506974, MLLT4-AS1, MIR31HG, and DUXAP10/LINC01296. Three lncRNAs in the validated list which showed the highest fold change (LOC441178, HCG22 and C5orf66-AS1) were verified by quantitative RT-PCR in a subset of 20 OSCCs and 10 control samples. In silico prediction of their functional role has given us directions for further investigation.

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Research Papers:

Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa

Abstract