Plasma proteomics for detection of early stage colorectal cancer biosignatures

Colorectal cancer (CRC) is one of the top three most common cancers worldwide. In Australia, CRC alone accounted for around 13% of all new cancer cases and 10% of all cancer deaths. Early CRC detection is critical for improved survival rates and more effective treatment. Blood is an easily accessible circulating fluid that reflects the current physiological and health state of an individual. For this reason, it is thought to be one of the best sources of protein or peptide biomarkers that reflect the health or clinical status of an individual. This PhD initially addresses the possible challenges for developing a robust reproducible Tri-Tricine SDS PAGE-based technique for capturing and identifying the endogenous intact LMW protein/peptide plasma "peptidome". It compares this attempt with other conventional methods (i.e., extraction using membrane filtration with 30 KDa cut off, differential solubilization and SPE C18 chromatography) that have been practiced for the isolation of intact LMW propteins/peptides from complex biospecimens. Following that, the thesis examines the suitability of spray-dried EDTA-treated plasma samples for proteomic biomarker discovery investigations against recently developed proprietary tubes containing a cocktail of protease inhibitors (PIs). A range of proteomic analyses have been conducted on CRC plasma samples (age, sex matched with stringent exclusion/inclusion criteria) obtained from the Victoria Biobank. These investigations included immune-based multiplex assays using two different approaches: Proseek® Multiplex Oncology kit I (Proseek assay) based on novel Proximity Extension Assay (PEA) technology with real time PCR (Olink Biosciences) and Bio-Plex Pro™ human cytokine27-plex kit. The high throughput multiplex assay has identified three potential candidate biomarkers (CEA, IL-8 and prolactin) that were expressed among Dukes’ stages as well as healthy, benign and malignant groups. Finally, an extensive investigation to explore the available techniques for deep depletion of the complex plasma proteome is conducted, in the hope of allowing identification of lower abundance clinical stage specific novel diagnostic plasma biomarkers for CRC. A follow up study was designed to immunodeplete pooled CRC plasmas using commercially available Agilent MARS 14 as well as our in house patented immune based depletion methods. The depleted samples were analyzed through a data independent acquisition (DIA) method (SWATH-MS), and demonstrated that cystatin C,paraoxonase-1 and ADAM DEC1 were potential candidate biomarkers for stage specific CRC (i.e., significantly overexpressed in CRC patients). The findings reported in this thesis hold great promise for future identification of low abundance plasma proteomic biomarkers for CRC.