Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29786170", "kind": "science-record", "revision": 6, "content_hash": "sha256:18df6c17562069a3a058f912cc0452aaff0a5f5c4682cb737b5a6077bdb60676", "created_at": "2026-11-01T15:40:33Z", "updated_at": "2026-11-01T21:21:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens.", "doi": "10.1002/pmic.201700465", "pmid": "29786170", "authors": ["Nicola Ternette", "Marloes J M Olde Nordkamp", "Julius Müller", "Amanda P Anderson", "Annalisa Nicastri", "Adrian V S Hill", "Benedikt M Kessler", "Demin Li"], "journal": "Proteomics", "year": 2018, "abstract": "The recent development in immune checkpoint inhibitors and chimeric antigen receptor (CAR) T-cells in the treatment of cancer has not only demonstrated the potency of utilizing T-cell reactivity for cancer therapy, but has also highlighted the need for developing new approaches to discover targets suitable for such novel therapeutics. Here we analyzed the immunopeptidomes of six HLA-A2-positive triple negative breast cancer (TNBC) samples by nano-ultra performance liquid chromatography tandem mass spectrometry (nUPLC-MS2 ). Immunopeptidomic profiling identified a total of 19 675 peptides from tumor and adjacent normal tissue and 130 of the peptides were found to have higher abundance in tumor than in normal tissues. To determine potential therapeutic target proteins, we calculated the average tumor-associated cohort coverage (aTaCC) that represents the percentage coverage of each protein in this cohort by peptides that had higher tumoral abundance. Cofilin-1 (CFL-1), interleukin-32 (IL-32), proliferating cell nuclear antigen (PCNA), syntenin-1 (SDCBP), and ribophorin-2 (RPN-2) were found to have the highest aTaCC scores. We propose that these antigens could be evaluated further for their potential as targets in breast cancer immunotherapy and the small cohort immunopeptidomics analysis technique could be used in a wide spectrum of target discovery. Data are available via ProteomeXchange with identifier PXD009738.", "claims": [{"id": "claim-method", "statement": "In order to prioritize the most relevant antigens, we introduced an average tumor‐associated cohort coverage (aTaCC) value for each protein that would allow us to shortlist protein antigens with the highest coverage of tumor‐associated antigen presentation across all patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29786170", "locator": "sections[10] \"Identification of Protein Antigens with Tumor‐Enrichment Presentation\" paragraph 4", "quote": "In order to prioritize the most relevant antigens, we introduced an average tumor‐associated cohort coverage (aTaCC) value for each protein that would allow us to shortlist protein antigens with the highest coverage of tumor‐associated antigen presentation across all patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE.19 partner repository with the dataset identifier PXD009738 and 10.6019/PXD009738.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29786170", "locator": "sections[6] \"Data Analysis\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE.19 partner repository with the dataset identifier PXD009738 and 10.6019/PXD009738."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29786170"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD009738"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD009738"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29786170", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/pmic.201700465", "sha256": 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the dataset identifier PXD009738 and 10.6019/PXD009738.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE.19 partner repository with the dataset identifier PXD009738 and 10.6019/PXD009738.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Immunopeptidomic profiling of HLA-A2-positive triple negative breast cancer", "resolution_checked_at": "2026-11-01T15:39:58Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29786170:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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L1 (APOL1)", "ALADGVQKV ALADGVQdKV", "0.010 0.010"]], "row_count": 9, "column_count": 4, "numeric_cells": 23, "header_rows": 1, "locator": "section[9]/table-wrap[1]#pmic12886-tbl-0002"}}, {"id": "asset:table:pmid:29786170:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a7b4720fc16993dded4cc09512dc76243b2dccf672400e2a6dfc08a373e2d5f3", "bytes": 1462, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#pmic12886-tbl-0003", "version": null, "note": "Proteins with the highest tumor‐enriched cohort coverage (aTaCC ≥ 7%)", "structure": {"pmcid": "PMC6032843", "section_index": 10, "section_title": "Identification of Protein Antigens with Tumor‐Enrichment Presentation", "row_count": 6, "column_count": 6}, "table": {"label": "Table 3", "caption": "Proteins with the highest tumor‐enriched cohort coverage (aTaCC ≥ 7%)", "rows": [["Uniprot acc.", "Protein description", "Protein length [aa]", "Peptides/patient", "aTaCC [%]", "Peptides identified"], ["P23528", "Cofilin‐1 (CFL‐1)", "166", "3.6", "16.3", "IILEEGKEILV | ILEEGKEILV | SAVISLEGKPL | DGVIKVFNDMKVRKSSTPE | GVIKVFNDMKVRKSSTPE | MIYASSKDAIK | VIKVFNDMKVRKSSTPE | A aSGVAVSD | GSAVISLEGKPL"], ["P24001", "Interleukin‐32 (IL‐32)", "234", "4.0", "11.4", "KVMRWFQAM | KVVALVHAV | DMKKLKARM o | GVLAWVKEK | SQHQAIERF | VKEKVVAL | WVKEKVVAL | AELEDDFKEGY | APRGDKEEL | LEDDFKEGY | VQ dALWKQF | VQALWKQF | YYEEQHPEL"], ["P12004", "Proliferating cell nuclear antigen (PCNA)", "261", "3.6", "10.6", "KLMDLDVEQL | SMSADVPLV | ILKKVLEAL | LMD oLDVEQL | RLVQGSILKK | VVKMPSGEF | KLM oDLDVEQL | TPLSSTVTL | SM oSADVPLV"], ["O00560", "Syntenin‐1 (SDCBP)", "298", "6.2", "8.8", "LMDHTIPEV | RPFERTITM | RPFERTITM o | SLMDHTIPEV | KVIQAQTAF | RLYPELSQY | LM oDHTIPEV | SLM oDHTIPEV | RPFERTITM s | SLMDHT hIPEV | AHKVLKQAF | KVIQAQ dTAF"], ["P04844", "Ribophorin‐2 (RPN‐2)", "631", "5.4", "7.1", 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