Bioinformatics analysis identifies candidate biomarkers associated with sarcoidosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41396114", "kind": "science-record", "revision": 4, "content_hash": "sha256:879ce16cc397bf7d4056c040f3e99cb7a650a6a1a4ba0dded5488c7d65ba9515", "created_at": "2026-11-01T20:31:24Z", "updated_at": "2026-11-01T22:57:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis identifies candidate biomarkers associated with sarcoidosis.", "doi": "10.36141/svdld.v42i4.17074", "pmid": "41396114", "authors": ["Linling Jin", "Chunfeng Pan", "Yujie Sun", "Jiayi Zhang", "Weiping Xie", "Mengyu He"], "journal": "Sarcoidosis, vasculitis, and diffuse lung diseases : official journal of WASOG", "year": 2025, "abstract": "BACKGROUND AND AIM: Sarcoidosis is a complex inflammatory disorder characterized by the formation of non-caseating granulomas, which can affect multiple systems, with a predominant impact on the lungs and thoracic lymph nodes. The aim of the study is to identify potential biomarkers and explore the infiltration of immune cells associated with sarcoidosis. Methods: The datasets of GSE19314, GSE83456, and GSE37912 were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened by comparing sarcoidosis samples to healthy controls in GSE19314 and GSE83456. Functional enrichment analyses and protein-protein interactions (PPIs) network construction were performed to elucidate the functional roles of the DEGs. Hub genes were identified through PPI network analysis. The GSE37912 dataset was used as a validation set. Immune cell infiltration in sarcoidosis patients was investigated. Furthermore, the trehalose 6,6'-dimycolate-granuloma (TDM)-induced granuloma experimental model was employed to resemble human sarcoid granulomas, and the expression of hub genes in lung tissues was detected by qRT-PCR.\nRESULTS: A total of 71 common DEGs, including 53 upregulated DEGs and 18 downregulated DEGs, were identified between sarcoidosis patients and controls. The signal transducer and activator of transcription 1 (STAT1), C-X-C motif chemokine ligand 10 (CXCL10) and basic leucine zipper ATF-like transcription factor 2 (BATF2) were considered as hub genes, showing promising diagnostic potential for sarcoidosis. Immune infiltration analysis indicated that compared with the controls, sarcoidosis samples exhibited increased infiltration of activated NK cells, monocytes, macrophage, activated dendritic cells and resting mast cells. In the TDM-induced lung granuloma model, STAT1, CXCL10 and BATF2 expression was upregulated in sarcoidosis lung tissue.\nCONCLUSIONS: Bioinformatics analysis indicated that STAT1, CXCL10 and BATF2 may as candidate biomarkers associated with sarcoidosis.", "claims": [{"id": "claim-method", "statement": "To screen the disparities between the sarcoidosis group and the control group, we utilized the R package “limma” to standardize datasets and uncover the DEGs in GSE19314 and GSE83456 (13). Genes with fold change (|logFC|) >0.5 and adjusted P value <0.05 using the false discovery rate (FDR) were identified as common DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41396114", "locator": "sections[4] \"2.2 Identification of DEGs\" paragraph 2", "quote": "To screen the disparities between the sarcoidosis group and the control group, we utilized the R package “limma” to standardize datasets and uncover the DEGs in GSE19314 and GSE83456 (13). Genes with fold change (|logFC|) >0.5 and adjusted P value <0.05 using the false discovery rate (FDR) were identified as common DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and analyzed in the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41396114", "locator": "sections[21] \"Data Availability:\" paragraph 2", "quote": "The datasets used and analyzed in the current study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "STAT1, CXCL10 and BATF2 were identified as potential biomarkers associated with sarcoidosis pathogenesis, underscoring the central role of immune dysregulation in its development and progression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41396114", "locator": "sections[19] \"Discussion\" paragraph 2", "quote": "In conclusion, STAT1, CXCL10, and BATF2 were identified as potential biomarkers associated with sarcoidosis pathogenesis, underscoring the central role of immune dysregulation in its development and progression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "STAT1, CXCL10 and BATF2 were identified as potential biomarkers associated with sarcoidosis pathogenesis, underscoring the central role of immune dysregulation in its development and progression.", "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:41396114"], "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:GSE19314"], "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": {"fdr_threshold": "limma with false discovery rate adjustment, ROC/AUC ana"}, "inputs": ["data:geo:GSE19314"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41396114", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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