Host: Japan Human Proteome Organisation
Advances in LC/MS technology have opened the doors for protein biomarker discovery. However, successful biomarker discovery largely depends on the ability to interpret large volumes of data. This presentation discusses the Rosetta Elucidator system, designed for managing complex proteomics data and identifying differentially expressed proteins across multiple treatment groups or disease states, and how it enables protein biomarker discovery. We will discuss the application of the system to HIV biomarker discovery.
HIV–1 infection remains a therapeutically challenge due to frequent viral gene mutations. As HIV–1 proteins have been shown to co–opt host machinery for viral replication, countering alterations in host gene expression induced by viral infection may help interfere with viral replication. We describe a characterization of time–course HIV–1 infection using microarrays and label–free LCMS, along with functional characterization of cellular pathways exhibiting various extent of accord between mRNA and protein levels.
Rosetta Elucidator System was used to align LC retention time, quantify time–aligned isotopic clusters, and identify proteins with ProteinProphets. Initial analysis yielded 116 proteins exhibiting changes in abundance upon HIV–1 infection related to uninfected cells. Data–dependent analysis has so far returned ∼400 protein ID’s from our CD4+ T cells. To isolate proteins exhibiting such differential expression in a kinetic manner, Two–way ANOVA was performed on the relative protein abundance ratios from the start and end of active virus production. Pathway analysis on the resulting list of 44 proteins revealed perturbation in proteolysis, apoptosis, and cell cycling.
Our integrative approach has shown the effects on host mRNA and protein expression and cellular functions over the course of HIV–1 replication.
