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RNA-seq consisting of FASTQ paired-end reads from cancer samples

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 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.

PROVIDER: EGAS00001003724 | EGA |

REPOSITORIES: EGA

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Project description:Abstract Background and aims. Hepatocellular carcinoma (HCC) shows limited response to checkpoint inhibitors, leaving opportunity for antigen-based immunotherapy and improved disease monitoring. This study evaluates plasma-derived soluble HLA-I (sHLA-I) peptidome as a minimally invasive source of tumor antigens by comparing them to tumor and adjacent tissue HLA ligands to assess its value for personalized treatment and diagnostics in HCC. Methods. Plasma-derived soluble HLA-I complexes and membranous HLA-I ligands from paired tumor and adjacent liver tissues of HCC and non-HCC control patients were isolated using pan-HLA-I immunoprecipitation and analyzed by LC-MS/MS. Peptide identification and patient-specific HLA binding predictions were complemented by annotation of tumor-associated antigens (TAAs) to compare ligand repertoires across HLA sources. Results The plasma soluble HLA-I (sHLA-I) peptidome from HCC and non-HCC patients was successfully characterized, with 1,553 to 9,421 unique peptides identified per sample after contaminant filtering. Peptides were enriched for canonical 8–11-mer lengths, with most predicted to bind patient-specific HLA-I alleles. Among 3,907 source proteins delivering peptides to the HCC sHLA-I peptidome, 815 were unique to HCC patients, and protein interaction analysis revealed significantly increased network connectivity centered around tumor-associated proteins. Comparison with membranous HLA-I (mHLA-I) peptidomes from tumor and adjacent tissues yielded 20 peptides from 17 tumor-associated antigens (TAAs) that were shared between sHLA-I and mHLA-I. Nine of these were only identified from HCC plasma and not from non-HCC controls, five overlapped with tumor mHLA-I. Conclusions. This pilot study demonstrates that the plasma-derived soluble HLA-I immunopeptidome in HCC patients contains peptides derived from TAAs, at least partially reflective of those presented on tumor tissue. These findings support the potential of sHLA-I profiling as a minimally invasive strategy for identifying actionable targets and tumor-specific signatures in HCC. Future improvements in analytical sensitivity and throughput, and validation in larger cohorts are now needed to establish its clinical utility.

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RNA-seq consisting of FASTQ paired-end reads from cancer samples

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