Immune-Related Genes Associated with Interstitial Lung Disease in Dermatomyositis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39563787", "kind": "science-record", "revision": 4, "content_hash": "sha256:5e6f159ee21c296b9ecec1f2000a50d7bc82bdd804ccb0ed65a35cca4afcc405", "created_at": "2026-11-01T20:29:49Z", "updated_at": "2026-11-01T22:55:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immune-Related Genes Associated with Interstitial Lung Disease in Dermatomyositis.", "doi": "10.2147/IJGM.S490294", "pmid": "39563787", "authors": ["Changjian Liu", "Yongpeng Ge"], "journal": "International journal of general medicine", "year": 2024, "abstract": "Background: Interstitial lung disease (ILD) is one of the significant complications of dermatomyositis (DM), but the mechanisms by which it occurs remain incompletely elucidated. This study aimed to explore further the possible genetic mechanisms by which this complication occurs.\nMethods: Gene expression profiles for DM (GSE39454, GSE46239, GSE143323) and ILD (GSE32537, GSE110147, GSE150910) were downloaded from the Gene Expression Omnibus (GEO) database. After identifying common differentially expressed genes (DEGs) to DM and ILD using the \"limma\" R package and the \"VennDiagram\" R package, functional annotation, relationship to immune cell infiltration, identification of transcription factors (TFs), we also collected clinical cases of DM-associated ILD (DM-ILD), including 3 cases of rapidly progressive ILD (RP-ILD) and 3 cases of none-RP-ILD, and explored whether there were differences in serum lymphocyte subpopulations.\nResults: A total of 4 common DEGs (SLAMF7, SPP1, TDO2, and VCAM1) were screened and Gene Ontology (GO) enrichment analysis showed that these genes were mainly enriched in T cell activation, regulation of lymphocyte activation, lymphocyte differentiation, leukocyte proliferation and regulation of T cell activation. In terms of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, the three significantly enriched pathways were the PI3K-Akt signaling pathway, MAPK signaling pathway, and Cytokine-cytokine receptor interaction. In lung and muscle tissues, 21 and 3 TFs may regulate the expression of these genes, respectively. Finally, by analysing the serum lymphocyte subpopulations, we also found a decrease in the absolute number of CD8+ T cells and an increase in the CD4+ /CD8+ T cell ratio in DM combined with RP-ILD.\nConclusion: These common pathways and key genes may provide new ideas for further research into DM-ILD.", "claims": [{"id": "claim-method", "statement": "The “limma” R package was used to analyze the DEGs between disease and normal tissues, including two datasets of DM (GSE39454, GSE46239) and two datasets of ILD (GSE32537, GSE110147). DEGs were identified when P-value < 0.05 and |LogFC| ≥ 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39563787", "locator": "sections[4] \"Obtaining the Common Differentially Expressed Genes (DEGs)\" paragraph 2", "quote": "The “limma” R package was used to analyze the DEGs between disease and normal tissues, including two datasets of DM (GSE39454, GSE46239) and two datasets of ILD (GSE32537, GSE110147). DEGs were identified when P-value < 0.05 and |LogFC| ≥ 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets of DM (GSE39454, GSE46239, GSE143323) and ILD (GSE32537, GSE110147, GSE150910) generated and/or analysed during the current study are available in the GEO database (http://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39563787", "locator": "sections[3] \"Data Sources\" paragraph 2", "quote": "The datasets of DM (GSE39454, GSE46239, GSE143323) and ILD (GSE32537, GSE110147, GSE150910) generated and/or analysed during the current study are available in the GEO database (http://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 4 common DEGs (SLAMF7, SPP1, TDO2, and VCAM1) were screened and Gene Ontology (GO) enrichment analysis showed that these genes were mainly enriched in T cell activation, regulation of lymphocyte activation, lymphocyte differentiation, leukocyte proliferation and regulation of T cell activation.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39563787", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 4 common DEGs (SLAMF7, SPP1, TDO2, and VCAM1) were screened and Gene Ontology (GO) enrichment analysis showed that these genes were mainly enriched in T cell activation, regulation of lymphocyte activation, lymphocyte differentiation, leukocyte proliferation and regulation of T cell activation."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 4 common DEGs (SLAMF7, SPP1, TDO2, and VCAM1) were screened and Gene Ontology (GO) enrichment analysis showed that these genes were mainly enriched in T cell activation, regulation of lymphocyte activation, lymphocyte differentiation, leukocyte proliferation and regulation of T cell activation.", "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:39563787"], "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:GSE110147"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE110147"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39563787", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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