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

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.

doi:10.64898/2026.01.03.696780

bioRxiv · 10.64898/2026.01.03.696780

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

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.

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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.

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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.. 2026-01-03. Mass Spectrometry-Based Profiling of Personalized Immunopeptidomes in Thai Renal Cell Carcinoma. https://doi.org/10.64898/2026.01.03.696780

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