Identification of shared immune infiltration characteristic molecules in dermatomyositis and nasopharyngeal carcinoma using bioinformatics: Traits in dermatomyositis and nasopharyngeal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39081134", "kind": "science-record", "revision": 3, "content_hash": "sha256:0fefed2a5946c7f67219b83cc5f1b1b0aae21909be11e1c40c83559abe8027fe", "created_at": "2026-11-01T20:29:09Z", "updated_at": "2026-11-01T22:12:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of shared immune infiltration characteristic molecules in dermatomyositis and nasopharyngeal carcinoma using bioinformatics: Traits in dermatomyositis and nasopharyngeal cancer.", "doi": "10.1111/srt.13871", "pmid": "39081134", "authors": ["Jinyan Kai", "Haitao Huang", "Jiaqi Su", "Qiong Chen"], "journal": "Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)", "year": 2024, "abstract": "BACKGROUND: Dermatomyositis (DM) is a kind of dermatologically associated autoimmune disease that is notably associated with an increased risk of concurrent malignancies, although the underlying mechanisms remain to be fully elucidated. The purpose of this investigation was to examine the immunological parallels between DM and nasopharyngeal carcinoma (NPC), with the aim of identifying pivotal biomarkers that could facilitate a deeper understanding and enhance the predictive capabilities of NPC in DM patients.\nMETHOD: Data for DM and NPC were sourced from the Gene Expression Omnibus (GEO) database. Immune infiltration was analyzed using the \"cibersort\" R package, differentially expressed genes (DEGs) were identified with the \"limma\" package, and functional pathways were investigated through Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses. Characteristic genes were determined by Utilizing Protein-Protein Interaction (PPI) and Least Absolute Shrinkage and Selection Operator (LASSO), and their features were validated using the GSE53819 dataset.\nRESULTS: In comparison to normal samples, significant infiltration of macrophage M1 was observed in both DM and NPC. The analysis revealed 77 DEGs in DM and 1051 DEGs in NPC, with 22 genes found to be co-DEGs. Following PPI and LASSO analysis, six distinctive genes were retained. Notably, CCL8, IFIH1, CXCL10, and CXCL11 exhibited optimal diagnostic efficacy for NPC and displayed significant correlation with macrophage M1 infiltration within the carcinoma.\nCONCLUSION: Four characteristic genes, CCL8, IFIH1, CXCL10, and CXCL11 are risk factors for both DM and NPC. They exhibit a robust correlation with the incidence of NPC and offer a commendable diagnostic efficacy. Furthermore, they may serve as prospective predictive biomarkers for the emergence of NPC in DM.", "claims": [{"id": "claim-data-access", "statement": "The data that support the findings of this study are available in the GEO database at https://www.ncbi.nlm.nih.gov/gds/?term = . These data were derived from the following resources available in the public domain:—GSE1551, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE1551 ‐ GSE128470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE128470 ‐ GSE12452, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE12452 ‐ GSE53819, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE53819", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39081134", "locator": "sections[21] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data that support the findings of this study are available in the GEO database at https://www.ncbi.nlm.nih.gov/gds/?term = . These data were derived from the following resources available in the public domain:—GSE1551, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE1551 ‐ GSE128470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE128470 ‐ GSE12452, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE12452 ‐ GSE53819, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE53819"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis revealed 77 DEGs in DM and 1051 DEGs in NPC, with 22 genes found to be co‐DEGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39081134", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The analysis revealed 77 DEGs in DM and 1051 DEGs in NPC, with 22 genes found to be co‐DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis revealed 77 DEGs in DM and 1051 DEGs in NPC, with 22 genes found to be co‐DEGs.", "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:39081134"], "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:GSE12452"], "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:GSE12452"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39081134", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/srt.13871", "sha256": "sha256:542a76a120e1a6ecc8e0262d2dc8eb2d8c6c6dba8a9d6b09115aa93008414a7d", "bytes": 23621, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/srt.13871", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11289422", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12452", "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=GSE12452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12452", "version": null, "note": "The data that support the findings of this study are available in the GEO database at https://www.ncbi.nlm.nih.gov/gds/?term = . These data were derived from the following resources available in the public domain:—GSE1551, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE1551 ‐ GSE128470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE128470 ‐ GSE12452, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE12452 ‐ GSE53819, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE53819", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available in the GEO database at https://www.ncbi.nlm.nih.gov/gds/?term = . These data were derived from the following resources available in the public domain:—GSE1551, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE1551 ‐ GSE128470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE128470 ‐ GSE12452, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE12452 ‐ GSE53819, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE53819", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM312896", "GSM312897", "GSM312898", "GSM312899", "GSM312900", "GSM312901", "GSM312902", "GSM312903", "GSM312904", "GSM312905", "GSM312906", "GSM312907", "GSM312908", "GSM312909", "GSM312910", "GSM312911", "GSM312912", "GSM312913", "GSM312914", "GSM312915", "GSM312916", "GSM312917", "GSM312918", "GSM312919", "GSM312920", "GSM312921", "GSM312922", "GSM312923", "GSM312924", "GSM312925", "GSM312926", "GSM312927", "GSM312928", "GSM312929", "GSM312930", "GSM312931", "GSM312932", "GSM312933", "GSM312934", "GSM312935", "GSM312936"], "sample_count": 41, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "mRNA expression profiling of nasopharyngeal carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE128470", "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=GSE128470", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE128470", "version": null, "note": "The data that support the findings of this study are available in the GEO database at https://www.ncbi.nlm.nih.gov/gds/?term = . These data were derived from the following resources available in the public domain:—GSE1551, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE1551 ‐ GSE128470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE128470 ‐ GSE12452, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE12452 ‐ GSE53819, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE53819", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available in the GEO database at https://www.ncbi.nlm.nih.gov/gds/?term = . These data were derived from the following resources available in the public domain:—GSE1551, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE1551 ‐ GSE128470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE128470 ‐ GSE12452, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE12452 ‐ GSE53819, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE53819", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3676247", "GSM3676248", "GSM3676249", "GSM3676250", "GSM3676251", "GSM3676252", "GSM3676253", "GSM3676254", "GSM3676255", "GSM3676256", "GSM3676257", "GSM3676258", "GSM3676259", "GSM3676260", "GSM3676261", "GSM3676262", "GSM3676263", "GSM3676264", "GSM3676265", "GSM3676266", "GSM3676267", "GSM3676268", "GSM3676269", "GSM3676270", "GSM3676271", "GSM3676272", "GSM3676273", "GSM3676274", "GSM3676275", "GSM3676276", "GSM3676277", "GSM3676278", "GSM3676279", "GSM3676280", "GSM3676281", "GSM3676282", "GSM3676283", "GSM3676284", "GSM3676285", "GSM3676286", "GSM3676287", "GSM3676288", "GSM3676289", "GSM3676290", "GSM3676291", "GSM3676292", "GSM3676293", "GSM3676294", "GSM3676295", "GSM3676296", "GSM3676297", "GSM3676298", "GSM3676299", "GSM3676300", "GSM3676301", "GSM3676302", "GSM3676303", "GSM3676304", "GSM3676305", "GSM3676306", "GSM3676307", "GSM3676308", "GSM3676309", "GSM3676310", "GSM3676311", "GSM3676312", "GSM3676313", "GSM3676314", "GSM3676315", "GSM3676316", "GSM3676317", "GSM3676318", "GSM3676319", "GSM3676320", "GSM3676321", "GSM3676322", "GSM3676323"], "sample_count": 77, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Myositis muscle", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE1551", "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=GSE1551", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1551", "version": null, "note": "The data that support the findings of this study are available in the GEO database at https://www.ncbi.nlm.nih.gov/gds/?term = . These data were derived from the following resources available in the public domain:—GSE1551, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE1551 ‐ GSE128470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE128470 ‐ GSE12452, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE12452 ‐ GSE53819, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE53819", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available in the GEO database at https://www.ncbi.nlm.nih.gov/gds/?term = . These data were derived from the following resources available in the public domain:—GSE1551, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE1551 ‐ GSE128470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE128470 ‐ GSE12452, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE12452 ‐ GSE53819, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE53819", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM26512", "GSM26513", "GSM26514", "GSM26515", "GSM26516", "GSM26517", "GSM26518", "GSM26519", "GSM26520", "GSM26521", "GSM26522", "GSM26523", "GSM26524", "GSM26525", "GSM26526", "GSM26527", "GSM26528", "GSM26529", "GSM26530", "GSM26531", "GSM26532", "GSM26533", "GSM26534"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "dermatomyositis", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE53819", "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=GSE53819", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53819", "version": null, "note": "The data that support the findings of this study are available in the GEO database at https://www.ncbi.nlm.nih.gov/gds/?term = . 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These data were derived from the following resources available in the public domain:—GSE1551, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE1551 ‐ GSE128470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE128470 ‐ GSE12452, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE12452 ‐ GSE53819, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE53819", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1301444", "GSM1301445", "GSM1301446", "GSM1301447", "GSM1301448", "GSM1301449", "GSM1301450", "GSM1301451", "GSM1301452", "GSM1301453", "GSM1301454", "GSM1301455", "GSM1301456", "GSM1301457", "GSM1301458", "GSM1301459", "GSM1301460", "GSM1301461", "GSM1301462", "GSM1301463", "GSM1301464", "GSM1301465", "GSM1301466", "GSM1301467", "GSM1301468", "GSM1301469", "GSM1301470", "GSM1301471", "GSM1301472", "GSM1301473", "GSM1301474", "GSM1301475", "GSM1301476", "GSM1301477", "GSM1301478", "GSM1301479"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Genome-wide expressing profiling of nasopharyngeal carcinoma primary tumors versus non-cancerous nasopharyngeal tissues.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE12452 not downloaded", "asset:data:geo:GSE12452 licence not read", "asset:data:geo:GSE128470 not downloaded", "asset:data:geo:GSE128470 licence not read", "asset:data:geo:GSE1551 not downloaded", "asset:data:geo:GSE1551 licence not read", "asset:data:geo:GSE53819 not downloaded", "asset:data:geo:GSE53819 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Protein-Protein Interaction"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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