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

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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.

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Acknowledgments

This work was supported by grants from the Polish Ministry of Science and Higher Education: PBZ-MNiI-2/1/2005 and R13 010 03 (MS software development). We thank for technical assistance to Magdalena Skrzypczak.

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Authors and Affiliations

  1. Department of Oncological Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland

    Michal Mikula, Jakub Karczmarski & Jerzy Ostrowski

  2. Laboratory of Bioinformatics and Systems Biology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland

    Tymon Rubel

  3. Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education Warsaw, Warsaw, Poland

    Krzysztof Goryca & Jerzy Ostrowski

  4. Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland

    Michal Dadlez

  5. Institute of Radioelectronics, Warsaw University of Technology, Warsaw, Poland

    Tymon Rubel

  6. Cancer Center-Institute, Roentgena 5, 02-781, Warsaw, Poland

    Jerzy Ostrowski

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  1. Michal Mikula
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Correspondence to Jerzy Ostrowski.

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Mikula, M., Rubel, T., Karczmarski, J. et al. Integrating proteomic and transcriptomic high-throughput surveys for search of new biomarkers of colon tumors. Funct Integr Genomics 11, 215–224 (2011). https://doi.org/10.1007/s10142-010-0200-5

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  • DOI: https://doi.org/10.1007/s10142-010-0200-5

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