Proteomic and inducible transgenic approaches to study disease processes.
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Animals↗
Biomedical subjects
Frank A Witzmann
Publications and source records attributed to Frank A Witzmann.
Proteomic evaluation of cell preparation methods in primary hepatocyte cell culture.
In vitro liver preparations are being used increasingly to study various aspects of chemical hepatotoxicity and thus have become powerful alternatives to in vivo toxicologic models. Primary hepatocyte culture systems are especially useful in screening cytotoxic and genotoxic compounds and assessing biochemical lesions associated with chemical exposure. We have begun to use this approach in combination with proteomic analysis to construct a molecular "toxicoproteomic" test system for a broad range of relevant and potentially toxic chemicals. Using a highly parallel two-dimensional electrophoretic (2-DE) protein separation system to analyze cells from culture systems, we previously observed significant variations in protein expression that were unrelated to chemical exposure. We hypothesized these artifactual protein alterations were the result of the variations in the culture conditions or cell manipulations, or both. Therefore, we conducted a study to assess the expression of hepatocyte proteins cultured on 6-well plates and recovered for analysis either by scraping/pelleting or direct in-well solubilization. Following incubation of 1.2 x 10(6) hepatocytes in six-well plate, recovery and solubilization of the cells and 2-DE of the solubilized lysates of 100 000 cells, we detected 1388 proteins in the in-well solubilized samples compared to 899 proteins in the washed/scraped/pelleted cell samples, a loss of 35%. Based on protein identification by peptide mass fingerprinting, the subcellular location of nearly all of the proteins whose abundance decreased were cytosolic and those few that increased were either microsomal, mitochondrial, or cytoskeletal proteins. These results emphasize the variation introduced by cell-handling during recovery of hepatocytes from culture plates and may explain at least some of the artifactual differences observed in earlier in vitro experiments.
Animals↗
Proteomics: technologies and applications.
Enabling technologies for proteomics (studies examining the protein complement of the genome) have been in development for over 20 years. However, more recently, the field has become formalized by combining the techniques for large-scale protein separation (two-dimensional electrophoresis) with very precise, high fidelity approaches to the analysis and characterisation of the separated proteins (mass spectrometry). These approaches bring to reality the powerful scope of proteomics, enabling the interpretation of cell physiology through profiling the molecular biodescriptors of gene expression, the proteins. Applications of proteomics are wide ranging and can be found within many disciplines, although one of the more developed fields that is examined here covers the arena of toxicological and pharmacological profiling. In this paper, the current technologies that make proteomics possible will be looked at. Some areas where proteomics has delivered valuable biological insight will also be considered, and there will be a look towards future areas of development.
Electrophoresis, Gel, Two-Dimensional↗
Cutting-edge technology. II. Proteomics: core technologies and applications in physiology.
Technologies for proteomics, e.g., studies examining the protein complement of the genome, have been in development for over 20 years. More recently, proteomics has become formalized by combining techniques for large-scale protein separation with very precise, high-fidelity approaches that analyze, identify, and characterize the separated proteins. These methods bring to reality the powerful scope of proteomics, enabling researchers to investigate cellular function at the protein level and thus representing one of proteomics' most fitting applications. In this review, we take a brief and concise look at some of the current, physiologically relevant technologies that comprise proteomics and report specific applications in which proteomics has provided valuable biological insight.
Animals↗
Impaired collateral development in mature rats.
The effect of maturation on collateral development of resistance arteries was investigated. Three to four sequential mesenteric arteries were ligated to create collateral pathways in anesthetized young (approximately 200 g) and mature (approximately 600 g) rats. Blood flow was similarly elevated in collaterals of young and mature animals. In vivo inner arterial diameter was increased only within young collaterals (33 +/- 7%, P < 0.001). Increases in number of intimal nuclei (57 +/- 10% vs. 52 +/- 14%) and cross-sectional medial area (33 +/- 13% vs. 38 +/- 5%) were similar between young and mature collaterals. Relative to the same animal controls, collateral endothelial nitric oxide synthase mRNA was increased as much in mature as in young rats. Proteomic analysis revealed significant differences in protein expression with maturation between control arteries as well as flow-loaded collateral vessels. The results indicate that, whereas intimal and medial remodeling events were similar in collaterals of young and mature rats, luminal expansion occurred only in young rats. Alteration in arterial protein expression with maturation and altered responses to stimuli for collateral development may contribute to this impairment.
Aging↗
On the dependence of a characterization of proteomics maps on the number of protein spots considered.
We have reexamined the numerical characterization of proteomics maps based on the construction of novel distance matrices associated with the nearest neighbor graph for the protein spots. In particular we consider dependence of a characterization of proteomics map on the number of proteins considered in the analysis. We examined a collection of proteomics maps in which we approximately doubled the number of spots to be used for quantitative analysis, considering cases of maps having 30, 50, 100, 250, 500, and 1054 protein spots. For each case we have compared the similarity-dissimilarity results for five proteomics maps of rat liver cells associated with the control group and four proliferators administrated by intraperitoneal injection. We found that proteins maps based on a set of about the 250 most abundant proteins spots suffice for a satisfactory numerical characterization of such maps.
Animals↗
Combining chemodescriptors and biodescriptors in quantitative structure-activity relationship modeling.
In view of the wide distribution of halocarbons in our world, their toxicity is a public health concern. Previous work has shown that various measures of toxicity can be predicted with standard molecular descriptors. In our work, biodescriptors of the effect of halocarbons on the liver were obtained by exposing hepatocytes to 14 halocarbons and a control and by producing two-dimensional electrophoresis gels to assess the expressed proteome. The resulting spot abundances provide additional biological information that might be used in toxicity prediction. QSAR models were fitted via ridge regression to predict eight dependent toxicity measures: d37, arr, EC50MTT, EC50LDH, EC20SH, LECLP, LECROS, and LECCAT. Three predictor sets were used for each-the chemodescriptors alone, the biodescriptors alone, and the combined set of both chemo- and biodescriptors. The results differed somewhat from one dependent to another, but overall it was shown that better results could be obtained by using both chemo- and biodescriptors in the model than by using either chemo- or biodescriptors alone. The library of compounds used was small and quite homogeneous, so our immediate conclusions are correspondingly limited in scope, but we believe the underlying methodologies have broad applicability at the interface of chemical and biological descriptors.
Animals↗