標題: Triple-layer dissection of the lung adenocarcinoma transcriptome - regulation at the gene, transcript, and exon levels
作者: Hsu, Min-Kung
Wu, I-Ching
Cheng, Ching-Chia
Su, Jen-Liang
Hsieh, Chang-Huain
Lin, Yeong-Shin
Chen, Feng-Chi
生物科技學系
Department of Biological Science and Technology
關鍵字: lung adenocarcinoma;transcriptome analysis;alternative splicing;differential expression;transcript-specific regulation
公開日期: 6-十月-2015
摘要: Lung adenocarcinoma is one of the most deadly human diseases. However, the molecular mechanisms underlying this disease, particularly RNA splicing, have remained underexplored. Here, we report a triple-level (gene-, transcript-, and exon-level) analysis of lung adenocarcinoma transcriptomes from 77 paired tumor and normal tissues, as well as an analysis pipeline to overcome genetic variability for accurate differentiation between tumor and normal tissues. We report three major results. First, more than 5,000 differentially expressed transcripts/exonic regions occur repeatedly in lung adenocarcinoma patients. These transcripts/exonic regions are enriched in nicotine metabolism and ribosomal functions in addition to the pathways enriched for differentially expressed genes (cell cycle, extracellular matrix receptor interaction, and axon guidance). Second, classification models based on rationally selected transcripts or exonic regions can reach accuracies of 0.93 to 1.00 in differentiating tumor from normal tissues. Of the 28 selected exonic regions, 26 regions correspond to alternative exons located in such regulators as tumor suppressor (GDF10), signal receptor (LYVE1), vascular-specific regulator (RASIP1), ubiquitination mediator (RNF5), and transcriptional repressor (TRIM27). Third, classification systems based on 13 to 14 differentially expressed genes yield accuracies near 100%. Genes selected by both detection methods include C16orf59, DAP3, ETV4, GABARAPL1, PPAR, RADIL, RSPO1, SERTM1, SRPK1, ST6GALNAC6, and TNXB. Our findings imply a multilayered lung adenocarcinoma regulome in which transcript-/exon-level regulation may be dissociated from gene-level regulation. Our described method may be used to identify potentially important genes/transcripts/exonic regions for the tumorigenesis of lung adenocarcinoma and to construct accurate tumor vs. normal classification systems for this disease.
URI: http://dx.doi.org/10.18632/oncotarget.4810
http://hdl.handle.net/11536/128419
ISSN: 1949-2553
DOI: 10.18632/oncotarget.4810
期刊: ONCOTARGET
Issue: 30
起始頁: 28755
結束頁: 28773
顯示於類別:期刊論文