CD8 + T-cell marker genes reveal different immune subtypes of oral lichen planus by integrating single-cell RNA-seq and bulk RNA-sequencing.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37422617", "kind": "science-record", "revision": 3, "content_hash": "sha256:bfd553af91a4b6751012c37192400ac64c950039e035b6f362de5e3c20cbc5fd", "created_at": "2026-11-01T19:02:11Z", "updated_at": "2026-11-01T21:31:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CD8 + T-cell marker genes reveal different immune subtypes of oral lichen planus by integrating single-cell RNA-seq and bulk RNA-sequencing.", "doi": "10.1186/s12903-023-03138-0", "pmid": "37422617", "authors": ["Jinhao Zhang", "Gaoge Peng", "Hao Chi", "Jinyan Yang", "Xixi Xie", "Guobin Song", "Lisa Jia Tran", "Zhijia Xia", "Gang Tian"], "journal": "BMC oral health", "year": 2023, "abstract": "BACKGROUND: Oral lichen planus (OLP) is a local autoimmune disease induced by T-cell dysfunction that frequently affects middle-aged or elderly people, with a higher prevalence in women. CD8 + T cells, also known as killer T cells, play an important role in the progression and persistence of OLP. In order to identify different OLP subtypes associated with CD8 + T cell pathogenesis, consensus clustering was used.\nMETHODS: In this study, we preprocessed and downscaled the OLP single-cell dataset GSE211630 cohort downloaded from Gene Expression Omnibus (GEO) to finally obtain the marker genes of CD8 + T cells. Based on the expression of marker genes, we classified OLP patients into CMGs subtypes using unsupervised clustering analysis. The gene expression profiles were analyzed by WGCNA using the \"WGCNA\" R package based on the clinical disease traits and typing results, and 108 CD8 + T-cell related OLP pathogenicity-related genes were obtained from the intersection. Patients were once again classified into gene subtypes based on intersection gene expression using unsupervised clustering analysis.\nRESULTS: After obtaining the intersecting genes of CD8 + T cells related to pathogenesis, OLP patients can be precisely classified into two different subtypes based on unsupervised clustering analysis, and subtype B has better immune infiltration results, providing clinicians with a reference for personalized treatment.\nCONCLUSIONS: Classification of OLP into different subtypes improve our current understanding of the underlying pathogenesis of OLP and provides new insights for future studies.", "claims": [{"id": "claim-method", "statement": "With 11 CMGs expression profiles, we used an unsupervised clustering algorithm(“ConsensusClusterPlus” R package) [21] with 1,000 iterations to classify 14 OLP samples(Including samples GSM946260, GSM946261, GSM946262, GSM946263, GSM946264, GSM946265, GSM946266 of dataset GSE38616 and GSM260095, GSM260096, GSM260097, GSM260098, GSM260099, GSM260100, GSM260101 of dataset GSE52130)into 2 clusters.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37422617", "locator": "sections[7] \"Unsupervised clustering of OLP patients\" paragraph 2", "quote": "With 11 CMGs expression profiles, we used an unsupervised clustering algorithm(“ConsensusClusterPlus” R package) [21] with 1,000 iterations to classify 14 OLP samples(Including samples GSM946260, GSM946261, GSM946262, GSM946263, GSM946264, GSM946265, GSM946266 of dataset GSE38616 and GSM260095, GSM260096, GSM260097, GSM260098, GSM260099, GSM260100, GSM260101 of dataset GSE52130)into 2 clusters."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed in the current study are available in the GEO (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37422617", "locator": "sections[26] \"Data Availability\" paragraph 2", "quote": "The datasets analyzed in the current study are available in the GEO (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Unsupervised consensus clustering of CD8 + T-cell-related marker-gene expression classified OLP patients into two subtypes, with subtype B showing greater immune infiltration.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37422617", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "After obtaining the intersecting genes of CD8 + T cells related to pathogenesis, OLP patients can be precisely classified into two different subtypes based on unsupervised clustering analysis, and subtype B has better immune infiltration results, providing clinicians with a reference for personalized treatment."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Unsupervised consensus clustering of CD8 + T-cell-related marker-gene expression classified OLP patients into two subtypes, with subtype B showing greater immune infiltration.", "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:37422617"], "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:GSE211630"], "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:GSE211630"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37422617", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12903-023-03138-0", "sha256": "sha256:9d80152c959624d32c2b1f19e091607bec421e645e03b13733952a87180d2bb5", "bytes": 43944, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12903-023-03138-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10329325", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE211630", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211630", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE211630", "version": null, "note": "The datasets analyzed in the current study are available in the GEO (https://www.ncbi.nlm.nih.gov/geo/).", "structure": 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"resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38616", "version": null, "note": "The datasets analyzed in the current study are available in the GEO (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed in the current study are available in the GEO (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM946253", "GSM946254", "GSM946255", "GSM946256", "GSM946257", "GSM946258", "GSM946259", "GSM946260", "GSM946261", "GSM946262", "GSM946263", "GSM946264", "GSM946265", "GSM946266"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression data from primary tissue, human oral mucosa (mRNA data)", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": 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