A proteogenomic approach to target neoantigens in solid tumors

Area of Science:

• Oncology
• Immunology
• Proteogenomics

Background:

• Neoantigens are tumor-specific peptides derived from mutations, recognized by T cells to elicit an antitumor response.
• Their selective expression on cancer cells makes them promising targets for cancer immunotherapy.

Purpose of the Study:

• To review proteogenomic strategies for identifying cancer neoantigens.
• To present a pipeline for neoantigen discovery using multi-omics data.
• To discuss recent advancements and tools in neoantigen identification.

Main Methods:

• Utilizing whole-exome sequencing (WES) data.
• Employing RNA sequencing (RNA-seq) data.
• Leveraging MHC peptidomics data.

Main Results:

• Proteogenomic approaches enable the identification of novel cancer-specific neoantigens.
• A comprehensive pipeline integrating WES, RNA-seq, and MHC peptidomics facilitates neoantigen discovery.
• Recent bioinformatics tools and technological improvements enhance neoantigen identification efficiency.

Conclusions:

• Despite limitations in current technology, advancements in sequencing and mass spectrometry offer promising avenues for neoantigen identification.
• The development of reliable epitope prediction algorithms is crucial.
• Translating these workflows to patient samples could revolutionize personalized neoantigen cancer vaccines.