Poster Presentation AUS-oMicS 2025

Characterization of the immunopeptidome from tumor, PBMC and plasma in glioma patients. (121528)

Erwin Tanuwidjaya 1 2 , Terry Lim 1 2 , Joel R Steele 1 , Ralf B Schittenhelm 1 , Pouya Faridi 1 2
  1. Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
  2. Monash University, Clayton, VIC, Australia

Introduction:

The human leukocyte antigen (HLA) complexes are pivotal in guiding human adaptive immune responses through their presentation of peptide ligands. Characterizing this peptide repertoire, collectively known as the immunopeptidome, is critical in understanding the biology of adaptive immune defence and is central to the development of personalized cancer immunotherapies. Recent developments in mass spectrometry (MS)-based immunopeptidomics workflow have enabled studies on smaller input amounts of cells and tissues, and more importantly from biofluids. To determine whether plasma HLA peptidome could represent tumor-derived HLA peptidome repertoire, here we introduce the our SAPrIm 2.0 workflow to dissect the similarities and differences in the immunopeptidome of tumor, plasma, and peripheral blood mononuclear cells (PBMC) derived from three glioma patient donors under the Brain on Monash Live Bio-Banking (MoLBi) initiative. 

 

Method:

Immunopeptidomics profiling was performed on tumor, plasma and PBMC derived from three glioma patient donors (1 glioma and 2 glioblastoma patients). These samples were subjected to the SAPrIm2.0 workflow, leveraging the KingFisher instrument for automation. Liquid chromatography/Mass spectrometry (LC/MS) analyses on the enriched immunopeptides were performed using Orbitrap Exploris 480 mass spectrometer operating on data-independent acquisition (DIA). RAW files were analyzed using PEAKS Studio 12.5 DeepNovo library-free workflow. Peptide identification and bioinformatics analysis was conducted using R, and peptide binding prediction analysis was done on NetMHCpan-4.1.

 

Preliminary result:

Here, we highlight our SAPrIm 2.0 immunopeptidomics workflow, as well as the findings of the Brain on MoLBi initiative on 3 glioma patients. More than 17,000 unique HLA-I immunopeptides were identified from the 3 donors after filtering and NetMHCpan-4.1 binding prediction analysis. Clear overlap  was observed when comparing the peptidome repertoire from the matched tumor, plasma and PBMC samples. Additionally, moderate correlation was observed across tissue compartments, suggesting that plasma soluble HLA peptidome provides a good representation of tumor HLA repertoire.