BATF2 and PDK4 as diagnostic molecular markers of sarcoidosis and their relationship with immune infiltration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35282063", "kind": "science-record", "revision": 4, "content_hash": "sha256:8c1e8a7c3c8ae07500d03671fbeaf21cdbe2745cb36e345c22e97b9c91623602", "created_at": "2026-11-01T18:14:04Z", "updated_at": "2026-11-01T22:06:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "BATF2 and PDK4 as diagnostic molecular markers of sarcoidosis and their relationship with immune infiltration.", "doi": "10.21037/atm-22-180", "pmid": "35282063", "authors": ["Jie He", "Xiaoyan Li", "Jing Zhou", "Rong Hu"], "journal": "Annals of translational medicine", "year": 2022, "abstract": "Background: Sarcoidosis (SA) is an immune disorder disease featuring granulomas formation with a controversial etiopathogenesis. We aimed to uncover potential markers for SA diagnosis and explore how immune cell infiltration contributes to the pathogenesis of SA.\nMethods: Sarcoidosis GSE83456 samples and GSE42834 from Gene Expression Omnibus (GEO) were analyzed as the training and external validation sets, respectively. Firstly, R statistical software was employed to uncover the differentially expressed genes (DEGs) of GSE83456. Weighted gene co-expression network analysis (WGCNA) was used to reveal the key module of DEGs. Secondly, the genes of the key module were used to analyze functional correlations. Thirdly, support vector machine (SVM) algorithms and least absolute shrinkage and selection operator (LASSO) logistic regression were applied for screening and verification of the diagnostic markers for key module genes. Finally, the infiltration of immune cells in SA patients' blood samples was assessed by Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT), after which correlations of diagnostic markers immune cell and infiltration were explored. Serum samples collected from human research participants were used for confirmatory analysis of bioinformatics. A receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of BATF2 and PDK4.\nResults: In total, 580 DEGs were identified from the key module. The genes PDK4 [area under the curve (AUC) =0.942] and BATF4 (AUC =0.980) were revealed as diagnostic markers of SAs. The diagnostic power of the 2 genes was verified in GSE42834. We found that monocytes, T cells regulatory (Tregs), mast cells, macrophages, natural killer (NK) cells, and dendritic cells (DC) may contribute to SA development through immune cell infiltration study. In addition, PDK4 and BATF4 were closely associated with these immune cells. Both BATF2 and PDK4 were highly expressed in active pulmonary SA. Using non-SA patients as controls, the AUC of serum PDK4, BATF2, and their combination for the diagnosis of active pulmonary SA was 0.798 (95% CI: 0.701 to 0.876), 0.895 (95% CI: 0.813 to 0.950), and 0.910 (95% CI: 0.831 to 0.960), respectively.\nConclusions: The genes PDK4 and BATF4 could be used as diagnostic markers of active pulmonary SA. Immune cell infiltration severs an important role in SA.", "claims": [{"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://atm.amegroups.com/article/view/10.21037/atm-22-180/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35282063", "locator": "sections[27] \"Footnotes\" paragraph 2", "quote": "Data Sharing Statement: Available at https://atm.amegroups.com/article/view/10.21037/atm-22-180/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The combination of serum BATF2 and PDK4 mRNA achieved an AUC of 0.910 for diagnosing active pulmonary sarcoidosis against non-sarcoidosis controls.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Using non-SA patients as controls, the AUC of serum PDK4, BATF2, and their combination for the diagnosis of active pulmonary SA was 0.798 (95% CI: 0.701 to 0.876), 0.895 (95% CI: 0.813 to 0.950), and 0.910 (95% CI: 0.831 to 0.960), respectively."}, "evidence": [{"asset": "source:pmid:35282063", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Using non-SA patients as controls, the AUC of serum PDK4, BATF2, and their combination for the diagnosis of active pulmonary SA was 0.798 (95% CI: 0.701 to 0.876), 0.895 (95% CI: 0.813 to 0.950), and 0.910 (95% CI: 0.831 to 0.960), respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The combination of serum BATF2 and PDK4 mRNA achieved an AUC of 0.910 for diagnosing active pulmonary sarcoidosis against non-sarcoidosis controls.", "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:35282063"], "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:GSE42834"], "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:GSE42834"], "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:35282063", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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