Cancer arises from insults to the genome. With genomic damage, the expression levels of genes are altered from their normal state. Changes in the genome, transcriptome and proteome have been found to be highly conserved among samples from adenomas to carcinomas to metastases. Because genetic changes are commonly repeated among cancer patients, a better understanding of which genes, transcripts, and proteins are affected could have broad health implications. Therefore, the best way to understand the molecular underpinnings of cancer is to dissect the deregulated pathways that are contributing to the cancer phenotype, identify the aberrantly expressed genes and their products, and decipher their effect on downstream targets. The Hummon Research Group develops high-throughput methods to evaluate both the transcriptome and the proteome in cancer cells.

We develop and adapt current mass spectrometric and sampling protocols for global molecular profiling to understand cancer systems. Cancer cells are small, complex entities, differing from normal cells in their molecular equilibria. We need analytical strategies that can do multidimensional probing of these cells to understand how and why they behave differently from normal cells. In order to accurately compare mRNA and protein levels, we need to generate high quality quantitative data.

While advancing methodologies to simultaneously probe global mRNA and protein levels, we also incorporate a loss of function approach to identify the role of individual genes contributing to the cancer phenotype. Even with the high level of annotation of the human genome, the functional role of most genes remains unknown. We use RNA interference to examine gene function in cancer.

Individual genes are perturbed, either with RNAi-based approaches or small molecule inhibitors, and then mRNA and protein profiles are generated. To profile the cancer transcriptome and proteome, we are advancing gene expression microarray and quantitative stable isotope labeling by amino acids in cell culture (SILAC) mass spectrometry protocols in cancer cell lines. Measurement and determination of the mRNA and protein profiles will expose pivotal imbalances and downstream gene targets in cancer, revealing windows for potential therapeutic manipulation.

We use a powerful approach to comprehensively and synchronously probe the gene and protein expression changes underlying the cancer phenotype while inferring gene function. This translational research assesses the contributions of mRNA and protein levels to the global molecular environment in complex biological systems like cancer, improves the understanding of the suppression mechanism of the endogenous RNAi pathways, as well as potentially having major contributions to human health in the identification of novel genetic targets for therapeutic intervention.