Fig. 1: Novel approach for tumor antigen identification from ovarian tumor tissues. | npj Vaccines

Fig. 1: Novel approach for tumor antigen identification from ovarian tumor tissues.

From: Proteogenomic approach to immunopeptidomics of ovarian tumors identifies shared peptide vaccine candidates

Fig. 1

Samples are collected, identified by pathology, and biobanked for characterization. Tumor specimens are split to undergo RNA sequencing and HLA-I immunoaffinity purification. The assembled RNA-Seq reads generated by StringTie are utilized to construct a de novo transcriptome and to identify HLA alleles. Peptides purified through immunoaffinity are analyzed via LC-MS/MS and compared against both Uniprot proteins and the custom StringTie database. Identified peptides are then ranked based on their binding potential using MHCFlurry and differential expression in ovarian cancer. Further filtering steps eliminate rare HLA types and prioritize peptides shared by multiple patients and binding to more prevalent HLAs. Finally, candidate peptides are evaluated for immunogenicity in healthy donors and PBMCs derived from ovarian cancer patients. Infographic was created using Infographic was created using BioRender.com.

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