ABPEPserver: a web application for documentation and analysis of substitutants

Area of Science:

• Oncology
• Immunology
• Bioinformatics
• Proteomics

Background:

• Cancer immunotherapy relies on identifying cell surface antigens to elicit T-cell responses.
• Neoantigens, derived from genetic alterations, are classical targets, but a new class, Substitutants, arising from aberrant protein translation, are emerging.
• Catalogues of Substitutant expression, specificity, and gene associations in human cancers are currently limited.

Purpose of the Study:

• To present ABPEPserver, an online database and analytical platform for visualizing Substitutant expression in human cancers.
• To provide tools for analyzing gene-association signatures of Substitutant peptides.
• To facilitate the comparison of Substitutant enrichment between tumor and normal tissues and identify immunotherapy candidates.

Main Methods:

• Developed ABPEPserver on an R Shiny platform.
• Integrated large-scale tumor proteomics data from the CPTAC database across eight tumor types.
• Implemented analytical functions for gene-association signatures, tissue comparisons, and candidate peptide identification.

Main Results:

• ABPEPserver provides a comprehensive catalog of Substitutant peptides across eight human cancer types.
• The platform enables analysis of Substitutant peptide-gene associations and their differential expression in tumors versus normal tissues.
• Identified candidate Substitutant peptides for potential immunotherapy design.

Conclusions:

• ABPEPserver is a valuable resource for exploring aberrant protein production in human cancer.
• The platform enhances the discovery of novel cancer antigens for immunotherapy development.
• ABPEPserver is accessible online with its code available under a GNU General Public License.