Mass Spectrometry-Based Profiling of Personalized Immunopeptidomes in Thai Renal Cell Carcinoma

ABSTRACT: This study profiles the personalized immunopeptidomes of 13 Thai Renal Cell Carcinoma (RCC) patients, addressing a critical knowledge gap for Southeast Asian populations with unique HLA allele distributions. The methodology combined whole-exome sequencing (WES) to construct a personalized proteome database with liquid chromatography-tandem mass spectrometry (LC-MS/MS), utilizing both a database search and a De Novo Sequencing approach. HLA typing revealed seven alleles (e.g., HLA-A11:29, HLA-B27:04, HLA-B15:12) absent from established databases, with HLA-A*11:01 (69%) being the most common. The database search identified only a single neoantigen (mutant JADE2) in the patient with the highest TMB, which was validated by a mutant-specific ELISPOT response. Crucially, the De Novo Sequencing strategy uncovered numerous non-canonical peptides, and subsequent PepQuery validation were present exclusively in cancer proteomes and absent from normal tissues, highlighting their potential as tumor-specific neoantigens. This integrated approach establishes a robust framework for discovering tumor-restricted peptides, creating a crucial reference for personalized immunotherapy development in Southeast Asia.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney

SUBMITTER: Poorichaya Somparn  

LAB HEAD: Poorichaya Somparn

PROVIDER: PXD072437 | Pride | 2026-10-07

REPOSITORIES: Pride