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

Authors

Somparn, P., Sriswasdi, S., Wongkongkathep, P., Muanwien, P., Nanthawong, S., Apinan, T., Opanuraks, J., Shuangshoti, S., Hirankarn, N., Moonmuang, S., Kampoun, T., Chaiyawat, P., Pisitkun, T.

Abstract

This study profiles the personalized immunopeptidomes of 13 Thai patients with renal cell carcinoma (RCC), addressing a critical knowledge gap in Southeast Asian populations characterized by distinct HLA allele distributions. We combined whole-exome sequencing (WES)-based personalized proteome construction with liquid chromatography-tandem mass spectrometry (LC-MS/MS), using both database-driven searches and de novo peptide sequencing. HLA typing identified seven alleles not previously represented in major immunopeptidome databases, with HLA-A*11:01 being the most frequent (69%). Database - based analysis identified a single tumor-specific neoantigen derived from a mutant JADE2 peptide in the patient with the highest tumor mutational burden, which was validated by a mutant-specific ELISPOT response. In contrast, de novo sequencing revealed numerous non-canonical peptides, a subset of which were supported by proteogenomic validation using PepQuery and detected exclusively in cancer proteomes but not in normal tissue datasets, indicating their potential as tumor-associated antigens. Together, these results establish an integrated and scalable framework for identifying HLA-presented tumor-derived peptides and provide a foundational immunopeptidome resource to support personalized cancer immunotherapy development in Southeast Asia.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 05 Jan 2026.

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