Thermal Proteome Profiling for Functional and Molecular Characterization of Variant Proteins

The increase in available genetic data has led to the knowledge of hundreds of thousands of disease associated sequence variants. Traditional molecular biology techniques to understand how pathogenic variations impact protein-protein interactions requires extensive cloning and tagging or specific antibody development. We propose the use of thermal proteome profiling (TPP) for studying the impact of these disease related sequence variants on a systems wide level. TPP is a bottom up, TMT-based, quantitative mass spectrometry technique for determining the melt curves and changes in stability of 1000s of proteins simultaneously. This seminar covers the definition and workflow of TPP. TPP is then successfully utilized to characterize the global impacts of temperature sensitive proteasome subunit mutants in yeast. We describe the use of a “boost” channel of a purified protein complex to reproducibly quantify and measure melt shifts of proteins of interest across TPP multiplexes, and a new version of our open source, freely available software for analyzing TPP data (InflectSSP). Collaborations with rare disease labs have allowed us to perform global and TPP proteomics on Diamond-Blackfan Anemia (DBA) patient derived lymphoblastic cell lines suggesting this haploinsufficient ribosomopathy stabilizes the ubiquitin translation IFN degradation pathways. We have also piloted multi-tissue TPP with Drosophila as a model for pontocerebellar hypoplasia type PCH1B, characterized by cerebellar and motor neuron degeneration arising from tissue specific impacts of variants in the RNA exosome subunit EXOSC3.