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The low‐abundance transcriptome reveals novel biomarkers, specific intracellular pathways and targetable genes associated with advanced gastric cancer
Author(s) -
Bizama Carolina,
Benavente Felipe,
Salvatierra Edgardo,
GutiérrezMoraga Ana,
Espinoza Jaime A.,
Fernández Elmer A.,
Roa Iván,
Mazzolini Guillermo,
Sagredo Eduardo A.,
Gidekel Manuel,
Podhajcer Osvaldo L.
Publication year - 2013
Publication title -
international journal of cancer
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.475
H-Index - 234
eISSN - 1097-0215
pISSN - 0020-7136
DOI - 10.1002/ijc.28405
Subject(s) - transcriptome , biology , dna microarray , suppression subtractive hybridization , cancer , microarray , gene , gene expression , gene expression profiling , computational biology , cancer research , genetics , cdna library
Studies on the low‐abundance transcriptome are of paramount importance for identifying the intimate mechanisms of tumor progression that can lead to novel therapies. The aim of the present study was to identify novel markers and targetable genes and pathways in advanced human gastric cancer through analyses of the low‐abundance transcriptome. The procedure involved an initial subtractive hybridization step, followed by global gene expression analysis using microarrays. We observed profound differences, both at the single gene and gene ontology levels, between the low‐abundance transcriptome and the whole transcriptome. Analysis of the low‐abundance transcriptome led to the identification and validation by tissue microarrays of novel biomarkers, such as LAMA3 and TTN; moreover, we identified cancer type‐specific intracellular pathways and targetable genes, such as IRS2, IL17, IFNγ, VEGF‐C, WISP1, FZD5 and CTBP1 that were not detectable by whole transcriptome analyses. We also demonstrated that knocking down the expression of CTBP1 sensitized gastric cancer cells to mainstay chemotherapeutic drugs. We conclude that the analysis of the low‐abundance transcriptome provides useful insights into the molecular basis and treatment of cancer.