Onco-proteogenomic exploration of variant peptide detection in disease models and clinical specimens

This thesis describes the efforts of integrating nucleotide sequencing results with mass spectrometry-based proteomic results to identify variants predicted from sequencing and being expressed at the proteome level within a proteogenomic framework. Specifically, the study was carried out in three levels. The first was a proof of concept study to demonstrate the feasibility of variant peptide detection in clinical specimens and reveal intrinsic strengths and weaknesses of the onco-proteogenomic pipeline. Subsequently, sequencing-predicted variants were tracked at the proteome level in cancer cell lines and breast cancer tissues. The results from both homogeneous and heterogeneous cell populations reveal the proportion of sequencing-predicted variant peptides detected at the proteome level, how different variant calling filtering criteria from sequencing raw data and alternative ways to search for variant peptides influence this number, a correlation between transcript abundance and variant peptide detection and how the translated mutant versions of the proteins may influence the observed phenotype. Overall, the results of the present dissertation provide promising evidence that the combination of the well-established sequencing technologies and the excellent capabilities of state of the art mass spectrometry instruments can effectively detect variant peptides in clinical specimens and that this approach has the potential to be optimized to harness its full potential and realize precision medicine translational applications.Ph.D