Omics
Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular ClassificationAnal squamous cell carcinoma is a rare tumor and the treatment standards have not suffered any improvement since 1970s. For this reason, a molecular characterization of the disease is still necessary. In this work, two molecular groups with a different protein and genetic profile were described. Additionally, some of these differences suggested biological processes that may be therapeutic targets.
Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine PhosphoproteomeThere are clear advantages to experimental approaches that reduce the amount of necessary cellular material for wide-scale quantitative profiling of the tyrosine phosphoproteome, particularly in biological systems where material is limited. The incorporation of boost channels in a multiplexed tandem mass tag experiment containing cells treated with the broad-spectrum tyrosine phosphatase inhibitor pervanadate enabled up to 6.3-fold deeper quantification of the tyrosine phosphoproteome while maintaining accuracy and precision.
The Challenge of Classifying Metastatic Cell Properties by Molecular Profiling Exemplified with Cutaneous Melanoma Cells and Their Cerebral Metastasis from Patient Derived Mouse XenograftsProteome profiling data of eight xenografted cutaneous and cerebellar metastasis of human melanoma cells were combined with eicosanoid and glutathione measurements as well as multiparametric morphologic analyses and immunofluorescence. The analyses revealed significant differences in the expression of molecules associated with metastatic properties, while lacking any commonalties when comparing the metastatic variants from four different donors. Apparently we lack appropriate meta-analysis strategies making use of the large number of presently identified metastasis-associated molecules for successful classification of cells.
Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and ValidationMultiple reaction monitoring with isotope dilution assays were developed for quantification of 200 proteins in dried blood spots, with median inter-day CV of 8%. Developed assays were used to measure the concentration ranges of these 200 proteins in twenty same sex, same race and age matched individuals. These, precise, sensitive, and multiplexed assays can be applied for de novo biomarker discovery and for biomarker quantification or verification experiments.
Functional Characterization and Comparison of Plasmodium falciparum Proteins as Targets of Transmission-blocking AntibodiesThe malaria agent Plasmodium falciparum continues to evade control efforts. Despite multiple datasets for the Plasmodium sexual-stage transcriptome and proteome, there have been no rational screens to identify candidate antigens for transmission-blocking vaccine (TBV) development. We demonstrate the use of rational screens and comparative functional assessments in identifying proteins of the P. falciparum transmission pathway and establishing a robust pre-clinical TBV pipeline.
Citrullinome of Porphyromonas gingivalis Outer Membrane Vesicles: Confident Identification of Citrullinated PeptidesThe citrullinome of P. gingivalis outer membrane vesicles (OMV) has been explored by a novel two-dimensional separation system combined with high resolution mass spectrometry and in-house build software. Analysis of OMVs from wild-type and two PPAD mutants resulted in confident discrimination based on citrullinated peptides. In the wild-type citrullinome 78 proteins were identified having a total of 161 validated citrullination sites. A single citrullination was identified in the C351A mutant and none in the ΔPPAD mutant.
Targeted and Interactome Proteomics Revealed the Role of PHD2 in Regulating BRD4 Proline HydroxylationTargeted quantification assays using MS-based parallel-reaction monitoring and biochemical analysis revealed PHD2 as a key regulatory enzyme of BRD4 proline hydroxylation. Quantitative MS-based interactome and biochemical analyses revealed the functional significance of the proline hydroxylation modification pathway in BRD4-mediated protein-protein interactions and transcriptional activation. Taken together, these results provided mechanistic insights into the oxygen-dependent modification of BRD4 and revealed new roles of the proline hydroxylation pathway in regulating BRD4-mediated protein-protein interaction and gene expression.
Associations of the Fecal Microbial Proteome Composition and Proneness to Diet-induced ObesityIndividuals exhibit marked heterogeneity in the degree of adiposity that results from consumption of an obesogenic diet. We hypothesized that markers of inflammation, fecal microbiome, and/or proteome composition might associate with heterogeneity in diet-induced obesity. We found the fecal proteome, which was comprised of microbial proteins that changed markedly upon exposure to the obesogenic diet associated with extent of obesity and associated dysglycemia. These results suggest the fecal microbial proteome plays a role in diet-induced obesity.
Graph Algorithms for Condensing and Consolidating Gene Set Analysis ResultsWeighted set cover and affinity propagation algorithms are used to combine results from multiple enrichment analyses. Weighted set cover first condenses enriched gene sets to use the fewest number of gene sets that cover all relevant genes. Affinity propagation then clusters the enriched pathways and selects the most representative set. Together they facilitate interpretation of multiple enrichment analysis results. A demonstration of its utility highlights both general and unique pathways associated with cancer survival across seven cancer types.