Late-breaking Poster Asia-Pacific Vaccine and Immunotherapy Congress 2024

Contribution of long non-coding RNAs to the Paediatric Diffuse Midline Glioma immunopeptidome (#157)

Tima Shamekhi 1 2 , Terry Lim 3 4 , Dongbin Jin 2 , Liesl Bramberger 1 2 , Grace Huang 1 2 , Nivedhetha Selvakumar 1 2 , Claire Sun 2 , Paul Daniel 2 , Erwin Tanuwidjaya 1 2 , Gabriel Goncalves 4 , Riccardo Dolcetti 5 , Ron Firestein 2 , Pouya Faridi 1 2 3
  1. School of Clinical Sciences, Department of Medicine, Monash University, Clayton, Victoria, Australia
  2. Centre for Cancer Research , Hudson Institute of Medical Research, Clayton, Victoria, Australia
  3. Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
  4. Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
  5. Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia

Paediatric diffuse midline glioma (pDMG) represents the most aggressive brain tumour in children, with a 9-month survival rate and no successful treatment. Peptides derived from cancer-specific antigens and presented by HLA molecules are ideal targets for precision cancer immunotherapy. Recent studies have highlighted the contribution of antigens originating from long non-coding RNA (lncRNA)s, which play pivotal roles in tumour immune recognition. In this study, we present a comprehensive immunopeptidomics analysis to identify peptide antigens derived from lncRNAs in a cohort of DMG cell lines.

 

Using transcriptomics data from 52 different DMG cell lines, we constructed an in-house database consisting of over 38,000 RNAs that are specifically overexpressed in pDMG compared to healthy tissues. We then studied the immunopeptidome of 20 DMG cell lines. In brief, 10 million cells from each cell line were subjected to immunopeptidomics using a modified SAPrlm protocol, followed by mapping against both the human proteome and our in-house pDMG-specific lncRNA database. Data were analysed by PEAKS 11, and the FDR was calculated at 1%. In total, we identified 162 peptides across all the cells presented by 14 types of HLA. Less than 1% of the identified peptides in each cell line are derived from lncRNA. We validated the authenticity of 39 lncRNA pHLA by synthetic peptides.

pDMG is a low-mutation burden tumour; therefore, there is a need to identify cancer antigens beyond classical somatic mutation-derived neoantigens. Our findings underscore the considerable contribution of lncRNA-derived tumor antigens in pDMG’s immunopeptidome, presenting a promising avenue for pDMG immunotherapy.