Inference of cancer mechanisms through computational systems analysis

Large amounts of metabolomics data have been accumulated to study metabolic alterations in cancer that allow cancer cells to synthesize molecular materials necessary for cell growth and proliferation. Although metabolic reprogramming in cancer was discovered almost a century ago, the underlying biochemical mechanisms are still unclear. We show that metabolomics data can be used to infer likely biochemical mechanisms associated with cancer. The proposed inference method is data-driven and quite generic; its efficacy is demonstrated by the analysis of changes in purine metabolism of human renal cell carcinoma. The method and results are essentially unbiased and tolerate noise in the data well. The proposed method correctly identified and accurately quantified primary enzymatic alterations in cancer, and these account for over 80% of the metabolic alterations in the investigated carcinoma. Interestingly, the two primary action sites are not the most sensitive reaction steps in purine metabolism, which implies that sensitivity analysis is not a valid approach for identifying cancer targets. The proposed method exhibits statistically high precision and robustness even for analyses of moderately incomplete metabolomics data. By permitting analyses of individual metabolic profiles, the method may become a tool of personalized precision medicine.