Publication Spotlight: Predicting Neoantigens for Cancer Using Next-Generation IEDB & CEDAR Tools

The Journal of Advanced Technological Education (J ATE) Volume 3: Issue 2 is full of great papers, with new ideas and tools that you might be able to use in your own program!  Two particularly interesting tools for biotech programs are described in Predicting Neoantigens for Cancer Using Next-Generation IEDB & CEDAR Tools (Koudjiwan, et al). The authors describe how cancer can be caused by DNA mutations which are then translated into mutant proteins, or neoantigens. Neoantigens can be tumor-specific and therefore are candidates for immunotherapies. They concentrated on mutations within p53, a tumor suppressor gene which, when mutated, often does not block cell division when DNA damage has occurred, and thus no-longer serves as a tumor suppressor. 

The authors used an immunoformatics (bioinformatics for immunology) predictive analysis tool hosted by the Immune Epitope Database (IEDB) to predict sections (epitopes) of the mutant proteins that could be candidates for immunotherapy. They then used the Cancer Epitope Database and Analysis Resource (CEDAR) to examine experimental information about the epitopes to avoid harmful cross-reactions. The end result of this work is a list of possible targets for immunotherapy. Results such as these are particularly valuable because they could be used against solid tumors, a class of cancer that is difficult to treat for a number of reasons including delivery challenges and the tumor's Immunosuppressive microenvironment.

It is remarkable what the computational resources can do when combined in a thoughful and effective way. Even better, multiple methods and approaches can be trialed quickly so that many ideas can be examined without the need for vast resources. Community College programs can use compute-experiments to expand the possibilities for their students while staying in budget.  And IEDB has free workshops so that you can learn how to best take advantage of their offerings!  Take a look at their website to see opportunities to learn!

Manuscript Reference: DOI: 10.5281/zenodo.13345145