Experimental reproducibility limits the correlation between mRNA and protein abundances in tumour proteomic profiles

Large-scale studies of human proteomes have revealed only a moderate correlation between mRNA and protein abundances. It is unclear to what extent this moderate correlation reflects post-transcriptional regulation and to what extent it reflects measurement error. Here, by analysing replicate proteomic profiles of tumour samples, we show that there is considerable variation in the reproducibility of measurements of individual proteins. We show that proteins with more reproducible measurements tend to have higher mRNA-protein correlation, suggesting that a substantial fraction of the unexplained variation between mRNA and protein abundances may be attributed to limitations in the reproducibility of proteomic quantification. We find that proteins that have high reproducibility in one study tend to have high reproducibility in others and exploit this to develop an 'aggregate protein reproducibility' score. This score can explain a substantial amount of the variation in mRNA-protein correlation across multiple studies of both healthy and tumour samples.

P.061 Multi-modal synchrotron imaging techniques to quantify elemental and molecular changes after stroke in an animal model

Background: Effects of stroke at the cellular and sub-cellular level remain poorly understood by conventional techniques. We use synchrotron-based imaging techniques to study elemental and biochemical changes in the infarct and penumbra after stroke in an experimental model. Methods: Ischemic stroke is induced in mice using the previously validated photothrombotic model. Animals are sacrificed at various time-points after stroke. Fourier transform infrared spectroscopic imaging (FTIRI) is used to gather sub-cellular (<1 µm spatial resolution) imaging data of lipid oxidation and protein aggregation in the areas of interest. X-ray fluorescence (XRF) imaging is used to image the distribution of bio-important elements at the cellular and sub-cellular spatial resolutions. Routine histology and immunohistochemistry are used to co-localize cell-types to areas of interest. Results: Preliminary XRF results indicate significant reduction in the concentration of multiple elements in the infarct, compared to the penumbra, at day 1 post-stroke. Some elements begin to return to normal concentration in the penumbra at day 3. FTIRI data shows that lipid and total protein levels decrease, while aggregate protein levels increase in the penumbra. Conclusions: Multi-modality synchrotron imaging can be used to map elements as well as bio-molecules in a stroke model. A better understanding of these changes can guide therapeutic interventions after stroke.

Protein Aggregates: an Aging Factor Involved in Cell Death

ABSTRACT In a previous study, we demonstrated the presence of protein aggregates in an exponentially grown Escherichia coli culture. In light of these observations, protein aggregates could be considered damage to cells that is able to pass from one generation to the next. Based on the assumption that the amount of aggregate protein could represent an aging factor, we monitored this amount in a bacterial culture during senescence. In doing so, we observed (i) a significant increase in the amount of aggregate protein over time, (ii) a proportional relationship between the amount of aggregate protein and the level of dead cells, (iii) a larger amount in dead cells than in culturable cells, (iv) a heterogeneous distribution of different amounts within a homogenous population of culturable cells entering stasis, and (v) that the initial amount of aggregate protein within a culturable population conditioned the death rate of the culture. Together, the results presented in this study suggest that protein aggregates indeed represent one aging factor leading to bacterial cell death.