Development and application of the protein biomarker discovery platform GPS (Global Proteome Survey)

This project aims to develop and apply a unique protein biomarker discovery platform to identify human disease fingerprints for use as novel biomarker panels solving urgent clinical problems.

Early diagnosis of cancer disease remains to be one of the most determining factors for a positive outcome for a patient. As an example, epithelial ovarian cancers diagnosed at an advanced stage have a 5-year survival rate of 30%. Early stage tumors are on the contrary to a large extent curable (90% 5-year survival). Quantitative measurements of specific protein biomarkers is a cornerstone in clinical diagnostics, prognostics and disease progression monitoring. The best biomarkers known to date are tumor-derived proteins and there is a continued need for additional ones. To increase both the diagnostic sensitivity and specificity when testing patients, a panel of biomarkers that together forms the “diagnostic signature” will in the majority of cases be required. In addition to the advances in developing early diagnostic biomarkers, cancer treatment is also currently being revolutionized through novel, targeted therapies based on molecular understanding of the tumor subtypes. With this comes also the need to identify the specific disease subtypes that will benefit from targeted treatments and to follow disease progression. Such companion diagnostics also require biomarkers.

Global Proteome Survey (GPS) To develop novel biomarker panels, we do proteomic analysis of large fractions of the total protein contents in clinical samples. Due to the complexity of a proteome and inherent limitations of current methodologies, proteomic analyses often result in incomplete coverage and inconsistent measurements. We have therefore developed a novel proteomic technology platform titled Global Proteome Survey (GPS) that combines the sensitivity of antibodies and the specificity of mass spectrometry. Special for purpose recombinant single-chain variable antibody fragments (scFv) termed Context Independent Motif Specific (CIMS) antibodies are designed to recognize short peptide motifs shared by many proteins. These are used for specific enrichment of subsets of peptides which are analyzed through mass spectrometry (MS) to generate a high-quality protein signature1. This project proposal aims at further advancing the GPS technology and apply it for the discovery of novel biomarker panels solving clinical problems.

The proposed doctoral project has the following overall goals

1. Develop the next generation GPS platform to allow state-of-the-art sensitivity and specificity for multi-biomarker discovery. The student will develop and evaluate a wider range of CIMS antibodies to target more peptide motifs. Also, the antibody immobilization strategy will be advanced to allow for more efficient peptide captures.
2. Demonstrate and validate the next generation GPS platform as a tool to identify treatment-response biomarker signatures in oncology patients. GPS has until now been demonstrated on tumor tissue samples. For clinical purposes, biomarkers should preferably be detected in blood (serum or plasma) because of its minimally invasive format and the student will be developing protocols to allow GPS analysis of both tissue- and blood.
3. Apply the novel GPS platform to specific clinical samples and questions for biomarker discovery. Ongoing research is assessing early differential diagnosis in ovarian cancer and stratification of breast cancer for improved classification and prognostication.