Elsevier

Genomics

Volume 86, Issue 2, August 2005, Pages 142-158
Genomics

Synchronous global assessment of gene and protein expression in colorectal cancer progression

https://doi.org/10.1016/j.ygeno.2005.03.012Get rights and content

Abstract

Well-established models of colorectal cancer progression are based on the idea that the disease evolves through a multistep process involving sequential genetic mutations, suggesting that progression through clinically defined stages should correlate with well-defined patterns of gene expression. The majority of studies to date, however, have assessed these processes one gene and one protein at a time. We report the first comprehensive assessment of both gene and protein expression performed in parallel across progressive stages of human colorectal neoplasia. Remarkably, despite the global nature of the gene expression assessment, very few genes could be linked with certainty to specific proteins through currently available annotations. Furthermore, the correlation of expression between identified genes and proteins was poor. Nevertheless, both produced expression signatures that differentiated normal mucosa and nonmalignant adenomas from each other and from the malignant carcinomas and both produced fairly consistent subclasses of the malignancies, suggesting that a molecular staging might be more appropriate provided that these profiles can be tied to clinical outcome. This is potentially important as clinical staging is widely used as a prognostic indicator and used in the decision to pursue adjuvant therapies.

Section snippets

Results

Sixty samples, 10 from each of the six clinical stages of colorectal cancer (normal mucosa, adenoma, Duke B1, Duke C2, Duke D, and liver metastasis), were selected from those archived in the H. Lee Moffitt Cancer Center Sample Registry. Following microdissection, RNA and protein were extracted from the same frozen tissue block for cDNA microarray and proteomic analysis. RNA samples were fluorescently labeled and cohybridized with a labeled common reference RNA to a 32,488-element cDNA

Discussion

Cancer is a complex disease arising from the interplay of genetic and environmental factors. Traditionally, cancer research has been conducted using a candidate gene/factor approach, examining a single factor at a time. The success of genome sequencing projects and technological advances in functional genomics and proteomics has facilitated the transition to large-scale systemic approaches to studying disease. mRNA expression profiling by cDNA or oligonucleotide microarrays has been employed in

Sample selection

Sixty anonymous samples, 10 from each of the six clinical stages of colorectal cancer (normal mucosa, adenoma, Duke B1, Duke C2, Duke D, and liver metastasis), were selected from those archived in the H. Lee Moffitt Cancer Center Sample Registry under IRB-approved protocols. Duke’s postresectional pathologic staging segregates tumors by the depth of penetration of the cancer through the bowel wall and by the presence or absence of lymph node or distant metastases. Staging is performed according

Acknowledgments

We thank the TIGR TM4 microarray software development team for their support and advice in data analysis, Jennifer Tsai and Joseph White for bioinformatics support, and Emily Chen, Jeremy Hasseman, and Ivana Yang for technical assistance. Analyses were performed using TIGR TM4 tools developed by Dr. John Quackenbush and the TIGR microarray software development team and using BRB Arraytools developed by Dr. Richard Simon and Amy Peng, This project was supported by grants from the U.S. National

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