Cancer Biomarker Discovery: The Entropic Hallmark

Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases

Incidenza di patologie neoplastiche nei lavoratori del complesso petrolchimico di Porto Torres, 1990-2006

Cancer incidence among petrochemical workers in the Porto Torres industrial area, 1990-2006 BACKGROUND: Various epidemiological studies explored cancer mortality and incidence among petrochemical workers. We followed up cancer incidence in a cohort of 5350 male petrochemical workers in the industrial area of Porto Torres (Sardinia, Italy). MATERIAL AND METHODS: The follow-up covered the period from 01/01/1990, when completeness of the cohort was certain and reference rates by the local Cancer Registry became available, up to 31/12/2006. Cohort members were subjects employed for six months or more in one of the chemical plants of the industrial area, alive as at 01/01/1990. Overall, a total of 81,392 person-years at risk were accumulated. The standardized incidence ratio (sir), as the ratio of observed to expected events, and its 95% confidence interval (CI) were calculated for all cancers and selected cancer sites, in the total cohort and in sub-cohorts of workers in plants where exposure to chemical agents evaluated in the IARC Monographs might have occurred. RESULTS: An increase in risk for all cancers was observed in the total cohort (596 cases; sir = 1.09; 95% CI 1.00-1.18), and it was highest for non-Hodgkin lymphoma (NHL, 26 cases: sir = 1.78; 95% CI 1.22-2.62). Risk for haemolymphatic cancer was highest in the sub-cohort of workers employed for 10 years or more, with a latency period of 20 years or longer, and among those employed in the manufacture and polymerization of vinyl chloride (VCM; all cancers, 51 cases: sir = 1.43; 95% CI 1.08-1.88; NHL, 4 cases: sir=4.06; 95% CI 1.64-10.0). Risk of haemolymphatic cancer was not significantly elevated in the sub-cohort potentially exposed to benzene. An excess risk of bladder cancer (RR = 1.46; 95% CI 1.09-1.96), but not of pleural cancer, was observed in the sub-cohort potentially exposed to asbestos. No significant increase in cancer risk was observed among workers potentially exposed to acrylonitrile, butadiene, or styrene. CONCLUSIONS: Our follow-up study of petrochemical workers showed an increase in risk for all cancers, and particularly NHL, apparently concentrated among workers potentially exposed to VCM