Novel Breast Cancer Biomarkers Identified by Integrative Proteomic and Gene Expression Mapping

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• 作者：Keli Ou ; Kun Yu ; Djohan Kesuma ; Michelle Hooi ; Ning Huang ; Wei Chen ; Suet Ying Lee ; Xin Pei Goh ; Lay keng Tan ; Jia Liu ; Sou Yen Soon ; Suhaimi Bin Abdul Rashid ; Thomas C. Putti ; Hiroyuki Jikuya ; Tetsuo
• 刊名：Journal of Proteome Research
• 出版年：2008
• 出版时间：April 2008
• 年：2008
• 卷：7
• 期：4
• 页码：1518 - 1528
• 全文大小：7562K
• 年卷期：v.7,no.4(April 2008)
• ISSN：1535-3907

文摘

Proteomic and transcriptomic platforms both play important roles in cancer research, with differing strengths and limitations. Here, we describe a proteo-transcriptomic integrative strategy for discovering novel cancer biomarkers, combining the direct visualization of differentially expressed proteins with the high-throughput scale of gene expression profiling. Using breast cancer as a case example, we generated comprehensive two-dimensional electrophoresis (2DE)/mass spectrometry (MS) proteomic maps of cancer (MCF-7 and HCC-38) and control (CCD-1059Sk) cell lines, identifying 1724 expressed protein spots representing 484 different protein species. The differentially expressed cell-line proteins were then mapped to mRNA transcript databases of cancer cell lines and primary breast tumors to identify candidate biomarkers that were concordantly expressed at the gene expression level. Of the top nine selected biomarker candidates, we reidentified ANX1, a protein previously reported to be differentially expressed in breast cancers and normal tissues, and validated three other novel candidates, CRAB, 6PGL, and CAZ2, as differentially expressed proteins by immunohistochemistry on breast tissue microarrays. In total, close to half (4/9) of our protein biomarker candidates were successfully validated. Our study thus illustrates how the systematic integration of proteomic and transcriptomic data from both cell line and primary tissue samples can prove advantageous for accelerating cancer biomarker discovery.