Tumor antigens are a group of proteins recognized by the cells of
immune system. Specifically, they are recognized in tumor cells where
they are present in larger than usual amounts, or are physiochemically
altered to a degree at which they no longer resemble native human
proteins. Their presence or abundance in cancer cells is often unique
and their roles and functions in tumorigenesis are, in many cases,
studied extensively. They, therefore, have the potential to be highly
specific biomarkers as well as therapeutic targets, but complex analysis
combining basic science, high-throughput methods of genomics and
proteomics, and clinical studies need to be combined. These analyses
produce large amounts of data that require advanced bioinformatics
methods for collection, management, integration and interpretation.
In this thesis, I have explored the potential of tumor antigens as
biomarkers and therapeutic agents, by developing and implementing
several computational tools and databases for immunotherapy target
discovery, and have analyzed the potential of tumor antigens as
proteogenomic biomarkers in invasive ductal carcinomas. In this
analysis I have shown that the combination of proteomics and
genomics data with a focus on tumor antigens can provide biological
insights into molecular pathways involved in tumorigenesis.