Transcriptome analysis reveals tumor antigen and immune subtypes of melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37305390", "kind": "science-record", "revision": 3, "content_hash": "sha256:49d7e603f067d506ca02cf23e03ff479a3985907003d06a8b7d1fdae590a6b99", "created_at": "2026-11-01T19:02:02Z", "updated_at": "2026-11-01T22:09:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome analysis reveals tumor antigen and immune subtypes of melanoma.", "doi": "10.32604/or.2023.029274", "pmid": "37305390", "authors": ["Jiaheng Xie", "Mengmeng Ou", "Pan Yu", "Dan Wu", "Qikai Tang", "Yuan Cao", "Jing Hang", "L U Yin", "Tinghong Xiang", "Ming Wang", "Jingping Shi"], "journal": "Oncology research", "year": 2023, "abstract": "Purpose: To screen potential tumor antigens for melanoma vaccine development and identify different immune subtypes.\nMethods: Transcriptional data (HTSEQ-FPKM) and clinical information of a 472 Melanoma cohort GDC TCGA Melanoma (SKCM) were downloaded from the UCSC XENA website (http://xena.ucsc.edu/). Subsequently, transcriptome data and clinical information of 210 melanoma cohort GSE65904 were downloaded from Gene Expression Omnibus (GEO), a large global public database. All the transcriptome expression data matrices were log2 transformed for subsequent analysis. GEPIA, TIMER, and IMMPORT databases are also used for analysis. Cell function experiments were performed to validate the role of the IDO1 gene in melanoma cell line A375.\nResults: Our study provides potential tumor antigens for vaccine development in melanoma patients: GZMB, GBP4, CD79A, APOBEC3F, IDO1, JCHAIN, LAG3, PLA2G2D, XCL2. In addition, we divide melanoma patients into two immune subtypes that have significant differences in tumor immunity and may have different responses to vaccination. In view of the unclear role of IDO1 in melanoma, we selected IDO1 for cell assay validation. Cell function assay showed that IDO1 was significantly overexpressed in the melanoma A375 cell line. After IDO1 knockdown, the activity, invasion, migration and healing ability of A375 cell lines were significantly decreased.\nConclusion: Our study could provide a reference for the development of vaccines for melanoma patients.", "claims": [{"id": "claim-method", "statement": "We first identified immune-related genes with prognostic value in melanoma by univariate COX analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37305390", "locator": "sections[8] \"Unsupervised cluster analysis\" paragraph 2", "quote": "We first identified immune-related genes with prognostic value in melanoma by univariate COX analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data can be found in the manuscript.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37305390", "locator": "sections[36] \"Availability of Data and Materials\" paragraph 2", "quote": "All the data can be found in the manuscript."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified nine potential melanoma tumor antigens—GZMB, GBP4, CD79A, APOBEC3F, IDO1, JCHAIN, LAG3, PLA2G2D, and XCL2—and divided melanoma patients into two immune subtypes with significant differences in prognosis and immunity.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37305390", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Our study provides potential tumor antigens for vaccine development in melanoma patients: GZMB, GBP4, CD79A, APOBEC3F, IDO1, JCHAIN, LAG3, PLA2G2D, XCL2."}, {"asset": "source:pmid:37305390", "locator": "sections[30] \"Conclusion\" paragraph 2", "quote": "We identified potential tumor antigens for cutaneous melanoma using a combination of multiple assayed methods."}, {"asset": "source:pmid:37305390", "locator": "sections[30] \"Conclusion\" paragraph 2", "quote": "In addition, we divided melanoma patients into two immune subtypes, which have significant differences in prognosis and immunity, which may provide reference for the appropriate population for vaccination."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified nine potential melanoma tumor antigens—GZMB, GBP4, CD79A, APOBEC3F, IDO1, JCHAIN, LAG3, PLA2G2D, and XCL2—and divided melanoma patients into two immune subtypes with significant differences in prognosis and immunity.", "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:37305390"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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