Mining and Predicting Prostate Cancer Progression for Better Patient Care

A detailed understanding of the molecular changes related to cancer progression from the primary tumor to early metastatic and late-stage drug-resistant disease is key for the development of biomarkers or drug targets. We have recently overcome important biases in cross-study analyses of RNA sequencing data and generated a harmonized Prostate Cancer Gene Expression Atlas that describes the roadmap to tumor progression in an unprecedented qualitative and quantitative manner.

For this project, we will further enlarge the current Atlas to develop new biomarkers for prostate cancer patients and a marketable web tool to mine molecular changes related to prostate cancer progression and patient outcomes. For this purpose, we will update and complement in work package (WP) 1 the Atlas with newly released DNA and RNA sequencing and curated clinical follow-up data. A corresponding professional tool will be generated to mine molecular changes related to prostate cancer progression and therapy resistance in a customized and multidimensional manner. Customers in industry and academia may use the resource to identify and validate novel drug targets, while clinicians may consult the tool to search for specific therapeutic opportunities for their patients. In WP2, we will take advantage of the resource to develop combinatorial biomarkers of patient outcomes and therapy responses using an innovative k-mer representation algorithm that enables unprecedented multitype feature extraction. Biomarkers will be protected and subsequently further developed with established industrial partners to maximize patient outcomes and reduce over-treatment. Commercialization will be pursued with an existing company in Switzerland (e.g., BigOmics SA (web tool), Proteomedix AG (biomarkers)) based on a licensing agreement. Perspectives for further growth may include additional molecular features and branching out to other tumor types, such as breast cancer.