Co-expression analysis of pancreatic cancer proteome reveals biology and prognostic biomarkers.

PURPOSE: Despite extensive biological and clinical studies, including comprehensive genomic and transcriptomic profiling efforts, pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease, with a poor survival and limited therapeutic options. The goal of this study was to assess co-expressed PDAC proteins and their associations with biological pathways and clinical parameters. METHODS: Correlation network analysis is emerging as a powerful approach to infer tumor biology from omics data and to prioritize candidate genes as biomarkers or drug targets. In this study, we applied a weighted gene co-expression network analysis (WGCNA) to the proteome of 20 surgically resected PDAC specimens (PXD015744) and confirmed its clinical value in 82 independent primary cases. RESULTS: Using WGCNA, we obtained twelve co-expressed clusters with a distinct biology. Notably, we found that one module enriched for metabolic processes and epithelial-mesenchymal-transition (EMT) was significantly associated with overall survival (p = 0.01) and disease-free survival (p = 0.03). The prognostic value of three proteins (SPTBN1, KHSRP and PYGL) belonging to this module was confirmed using immunohistochemistry in a cohort of 82 independent resected patients. Risk score evaluation of the prognostic signature confirmed its association with overall survival in multivariate analyses. Finally, immunofluorescence analysis confirmed co-expression of SPTBN1 and KHSRP in Hs766t PDAC cells. CONCLUSIONS: Our WGCNA analysis revealed a PDAC module enriched for metabolic and EMT-associated processes. In addition, we found that three of the proteins involved were associated with PDAC survival.

Reproductive output, costs of reproduction, and ecology of the smooth snake, Coronella austriaca, in the eastern Italian Alps.

A 5-year mark-recapture study of smooth snakes (Coronella austriaca) in the Carnic Alps (1100 m above sea level) of north-eastern Italy provided extensive information on the biology and life-history of these small viviparous snakes. Offspring were relatively large (mean=15 cm total length, 2.9 g) when they were born in late summer, and females grew to maturity (44 cm, 50 g) in approximately 4 years. Larger neonates retained their size advantage for at least 12 months, but did not have a higher probability of survival. Although sexual size dimorphism (at birth and at mean adult body sizes) was minor, the sexes differed significantly in several respects. Females grew faster than males during juvenile life, and adult females diverged in dietary habits from the rest of the population. Whereas juveniles (of both sexes) and adult males fed primarily on lizards, larger females shifted to feeding less frequently, but taking larger prey (mammals and snakes). Reproductive output increased strongly with maternal body size: larger females reproduced more frequently, produced larger litters of larger neonates, had higher relative clutch masses (RCMs), and had a lower proportion of stillborn off-spring. Most females produced a litter every 2nd or 3rd year. We did not detect significant year-to-year variation in reproductive traits over the 5 years of our study. Females were consistent from one litter to the next in several traits (e.g., litter sizes, offspring sizes and shapes, proportions of stillborn neonates, RCMs), but this consistency was due to differences in body size among females rather than to size-independent maternal effects. Overall litter sex ratios averaged 50/50, but sex ratios tended to be more male-biased in litters that were unusually large relative to maternal body size, and in litters containing a high proportion of stillborn offspring. "Costs" of reproduction appear to be high in this population, in terms of both energy allocation and risk. Reproduction reduced growth rates, and females that recovered condition more quickly in the year after reproduction were able to reproduce again after a briefer delay. Mortality was highest in reproducing females with high RCMs, and in females that were very emaciated after parturition. The marked increase in reproductive output with increasing maternal body size in C. austriaca may reflect a reduction in "costs" as females grow larger, and the dietary shift to larger prey may enhance the rate that females can accumulate energy for reproduction.