In a study published today in Cell, researchers from Baylor College of Medicine conducted a genomic and proteomic analysis of human colon cancer tissue. Their research strongly supports comprehensive characterization of tumor tissues as a means to guide further research leading to early diagnostic strategies and new treatments.
After generating genomic and proteomic data, the team used bioinformatics to analyze it. The result is the first systematic catalog of the different proteins produced by colon cancer tumors and the adjacent normal tissues.
“We were able to not only confirm previously described colon cancer molecular markers but also to uncover new differences between proteins produced by tumors and normal tissue that may be worth further study,” says senior author Bing Zhang.
The researchers also found that the combination of genomic and proteomic data greatly improved their understanding of colon cancer cells.
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“One example is SOX9,” Zhang says. “Our genomic data set indicated that SOX9 is a tumor suppressor gene because it is frequently mutated in colon cancer in ways that suggested that the function of the protein coded by the gene would be destroyed and that the protein would not be produced or produced in lesser amount. But when we looked at the proteomic data—at the actual protein in cancer tissue—we observed quite the opposite; SOX9 protein was very abundant in these tumors, more than normal. The proteomic data thus challenged the indication that SOX9 was a tumor suppressor.”
Further bioinformatics analyses suggested possible explanations for apparent contradictions between the genomic and the proteomic data such as this SOX9 example.
“Analysis of the genes tells us what might possibly go wrong. But we don’t know exactly what actually has gone wrong until we analyze the proteins,” says coauthor Tao Liu of Pacific Northwest National Laboratory.
The researchers have made all the data accessible in a web tool called LinkedOmics, which also provides computational tools for further exploration of this dataset.