Construction and validation of a diagnostic model for rheumatoid arthritis based on mitochondrial autophagy-related genes.

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Consequently, there is a pressing need to investigate additional biomarkers and therapeutic targets relevant to RA diagnosis. Mitochondrial autophagy, a biological process that regulates the quantity of mitochondria, is intricately linked to the development of tumor diseases. However, the role of autophagy in RA remains unclear. To address this, transcriptome data from the GEO database were collected for RA and its controls and subjected to differential expression analysis. The differentially expressed genes obtained were then intersected with mitochondrial autophagy-related genes. Subsequently, the overlapping genes were further intersected with genes from critical modules obtained through the weighted co-expression network algorithm. Diagnostic genes were identified, and diagnostic models were constructed for the resulting genes using the random forest and LASSO algorithms. The model achieved an AUC of 0.916 in the GSE93272 dataset and 0.951 in the GSE17755 dataset. Additionally, qPCR experiments were conducted on the diagnostic genes. Finally, we explored the correlation between the abundance of immune cell infiltration and diagnostic genes, constructing a drug-gene interaction network. The diagnostic genes identified in this study can serve as a reference for early diagnosis and the discovery of therapeutic targets in RA.", "claims": [{"id": "claim-method", "statement": "We constructed a diagnostic model for RA based on eight diagnostic genes and used the logistic regression algorithm.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38327427", "locator": "sections[17] \"Screening and diagnostic model construction of critical mitochondrial autophagy genes\" paragraph 4", "quote": "We constructed a diagnostic model for RA based on eight diagnostic genes and used the logistic regression algorithm."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data in this paper come from GEO database (https://www.ncbi.nlm.nih.gov/geo/) GSE93272 and GSE17755.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38327427", "locator": "sections[21] \"Data availability\" paragraph 2", "quote": "The data in this paper come from GEO database (https://www.ncbi.nlm.nih.gov/geo/) GSE93272 and GSE17755."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Ultimately, eight diagnostic genes (ATG5, GSK3A, MFN1, NRAS, RELA, RRAS2, SLC25A46 and TSCA) were retained.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38327427", "locator": "sections[17] \"Screening and diagnostic model construction of critical mitochondrial autophagy genes\" paragraph 3", "quote": "Ultimately, eight diagnostic genes (ATG5, GSK3A, MFN1, NRAS, RELA, RRAS2, SLC25A46 and TSCA) were retained."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Ultimately, eight diagnostic genes (ATG5, GSK3A, MFN1, NRAS, RELA, RRAS2, SLC25A46 and TSCA) were retained.", "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:38327427"], "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. 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Additionally, qPCR experiments were conducted on the diagnostic", "pate in this study. Experimental consumables qPCR: enzyme-free pipette tip, 1.5 ml enzyme-free", "g); 0.2 ml PCR single tube (Aisigen); 0.1 ml qPCR eight-strip tube (BIO-RAD); fluorescence qua", "d cDNA Synthesis Kit, Taq Pro Universal SYBR qPCR Master Mix (Vazyme, China). Statistical anal"], "order_basis": "paper_text_order:1307", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We constructed a diagnostic model for RA based on eight diagnostic genes and used the logistic regression algorithm."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}