NDLI: Integrating proteomic and transcriptomic high-throughput surveys for search of new biomarkers of colon tumors

Content Provider	Springer Nature Link
Author	Mikula, Michal Rubel, Tymon Karczmarski, Jakub Goryca, Krzysztof Dadlez, Michal Ostrowski, Jerzy
Copyright Year	2010
Abstract	To the search of new colon tumor biomarkers in the transition from normal colon (NC) mucosa to adenoma (AD) and adenocarcinoma (AC), we integrated microarray data with the results of a high-throughput proteomic workflow. In proteomic study, we used a modified isoelectric focusing protocol on strips with an immobilized pH gradient to separate peptides labeled with iTRAQ (isobaric tags for relative and absolute quantitation) tags followed by liquid chromatography–tandem mass spectrometry analysis. Gene expression measurements were done using Affymetrix GeneChip HG-U133plus2 microarrays and quantitative reverse transcriptase PCR (q-RT-PCR). We identified 3,886 proteins with at least two peptides. Of them, 1,061 proteins were differentially expressed [FC ≥ 1.5; FDR ≤ 0.01] in two pair-wise comparisons: AD vs. NC and AC vs. AD while 15 and 23 proteins were progressively up-regulated and down-regulated in the NC/AD/AC sequence, respectively. The quantitative proteomic information was subsequently correlated with microarray data. For a collection of genes with the same direction of changes of both mRNA and protein levels, we obtained 785/853/795 genes in AD vs. NC/AC vs. NC/AC vs. AD comparison, respectively. Further evaluation of sequentially altered gene expression by q-RT-PCR on individual samples of 24 NCs, 42 ADs, and 26 ACs confirmed progressive expression of six genes: biglycan, calumenin, collagen type XII, alpha 1 (COL12A1), monoamine oxidase A (MAOA), ectonucleoside triphosphate diphosphohydrolase 5 (ENTPD5), and MOCO sulphurase C-terminal domain-containing 2 (MOSC2). Among them, three continuously down-regulated (MAOA, ENTPD5, and MOSC2) and one continuously overexpressed (COL12A1) are reported, to our best knowledge, for the first time in a connection to colon cancer onset.
Starting Page	215
Ending Page	224
Page Count	10
File Format	PDF
ISSN	1438793X
Journal	Functional & Integrative Genomics
Volume Number	11
Issue Number	2
e-ISSN	14387948
Language	English
Publisher	Springer-Verlag
Publisher Date	2010-11-09
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Gene expression Colorectal cancer Microarrays Mass spectrometry Data integration Animal Genetics and Genomics Bioinformatics Plant Genetics & Genomics Microbial Genetics and Genomics Cell Biology Biochemistry
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine

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