Dataset Information

Non-canonical HLA peptides in cancer

ABSTRACT: Efforts to precisely identify tumor human leukocyte antigen presented peptides (HLAp) capable of mediating T cell based tumor rejection still face important challenges. Recent reports suggest that non-canonical cancer HLAp could be immunogenic but their identification requires highly sensitive and accurate mass-spectrometry (MS)-based proteogenomics approaches. Here, we present a novel MS-based analytical pipeline that can precisely characterize the non-canonical HLAp repertoire, incorporating whole exome sequencing, bulk and single cell transcriptomics, ribosome profiling, and a combination of two MS/MS search tools. This approach results in the accurate identification of hundreds of shared and tumor-specific non-canonical HLAp. Albeit often at low levels and in distinct subpopulations of cells, numerous non-canonical HLAp are shared across tumors. This analytical platform holds great promise for the discovery of novel cancer antigens for cancer immunotherapy.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

DISEASE(S): Lung Cancer,Melanoma

SUBMITTER: Michal Bassani-Sternberg

LAB HEAD: Michal Bassani-Sternberg

PROVIDER: PXD013649 | Pride | 2020-03-27

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20170831_QEh1_LC1_ChC_SA_HLAIp_ONVC_DAC_1_R1.raw	Raw
	20170831_QEh1_LC1_ChC_SA_HLAIp_ONVC_DAC_1_R2.raw	Raw
	20170831_QEh1_LC1_ChC_SA_HLAIp_ONVC_DAC_2_R1.raw	Raw
	20170831_QEh1_LC1_ChC_SA_HLAIp_ONVC_DAC_2_R2.raw	Raw
	20170831_QEh1_LC1_ChC_SA_HLAIp_ONVC_DAC_3_R1.raw	Raw

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Publications

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.

Chong Chloe C Müller Markus M Pak HuiSong H Harnett Dermot D Huber Florian F Grun Delphine D Leleu Marion M Auger Aymeric A Arnaud Marion M Stevenson Brian J BJ Michaux Justine J Bilic Ilija I Hirsekorn Antje A Calviello Lorenzo L Simó-Riudalbas Laia L Planet Evarist E Lubiński Jan J Bryśkiewicz Marta M Wiznerowicz Maciej M Xenarios Ioannis I Zhang Lin L Trono Didier D Harari Alexandre A Ohler Uwe U Coukos George G Bassani-Sternberg Michal M

Nature communications 20200310 1

Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides derived from annotated non-coding regions could elicit anti-tumor immune responses. However, sensitive and accurate mass spectrometry (MS)-based proteogenomics approaches are required to robustly identify these non-canonical peptides. We present an MS-based analytic ...[more]

PMID: 32157095

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Project description:Background: Patient derived organoids (PDOs) can be established from colorectal cancers as in vitro models to interrogate cancer biology and its clinical relevance. We applied mass spectrometry (MS) immunopeptidomics to investigate neoantigen presentation and whether this can be augmented through interferon gamma (IFN) or MEK-inhibitors. Methods: Four PDOs from chemotherapy refractory and one from a treatment naïve CRC were expanded to replicates with 100 million cells each, and HLA class I and class II peptide ligands were analysed by MS. Results: We identified an average of 9,936 unique peptides per PDO which compares favourably against published immunopeptidomics studies, suggesting high sensitivity. Loss of heterozygosity of the HLA locus was associated with low peptide diversity in one PDO. Peptides from genes without detectable expression by RNA-sequencing were rarely identified by MS. Only 3 out of 612 non-silent mutations encoded for neoantigens that were detected by MS. Treatment of four PDOs with IFN upregulated HLA class I expression and qualitatively changed the immunopeptidome, with increased presentation of IFN-inducible genes. HLA class II presented peptides increased on average 16-fold with IFN treatment. MEK-inhibitor treatment showed no consistent effect on class I or II HLA expression or the peptidome. Importantly, no additional HLA class I or II presented neoantigens became detectable with any treatment. Conclusions: Only 3 out of 612 non-synonymous mutations encoded for neoantigens that were detectable by MS. Although MS has sensitivity limits and biases, and likely underestimated the true neoantigen burden, this established a lower bound of the percentage of non-silent mutations that encode for presented neoantigens, which may be as low as 0.5%. This could be a reason for the poor responses of non-hypermutated CRCs to immune checkpoint inhibitors. MEK-inhibitors recently failed to improve checkpoint-inhibitor efficacy in CRC and the observed lack of HLA upregulation or improved peptide presentation may explain this.