Identification of autophagy-related genes in osteoarthritis articular cartilage and their roles in immune infiltration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38090564", "kind": "science-record", "revision": 5, "content_hash": "sha256:0b9262969e0b38d6fdd2677f33001d613fa7a25a30c63a29f474b1ec7f3e9ae8", "created_at": "2026-11-01T19:03:01Z", "updated_at": "2026-11-01T22:53:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of autophagy-related genes in osteoarthritis articular cartilage and their roles in immune infiltration.", "doi": "10.3389/fimmu.2023.1263988", "pmid": "38090564", "authors": ["Jun Qin", "Jin Zhang", "Jian-Jun Wu", "Xiao Ru", "Qiu-Ling Zhong", "Jin-Min Zhao", "Ni-Han Lan"], "journal": "Frontiers in immunology", "year": 2023, "abstract": "Background: Autophagy plays a critical role in the progression of osteoarthritis (OA), mainly by regulating inflammatory and immune responses. However, the underlying mechanisms remain unclear. This study aimed to investigate the potential relevance of autophagy-related genes (ARGs) associated with infiltrating immune cells in OA.\nMethods: GSE114007, GSE169077, and ARGs were obtained from the Gene Expression Omnibus (GEO) database and the Human Autophagy database. R software was used to identify the differentially expressed autophagy-related genes (DEARGs) in OA. Functional enrichment and protein-protein interaction (PPI) analyses were performed to explore the role of DEARGs in OA cartilage, and then Cytoscape was utilized to screen hub ARGs. Single-sample gene set enrichment analysis (ssGSEA) was used to conduct immune infiltration analysis and evaluate the potential correlation of key ARGs and immune cell infiltration. Then, the expression levels of hub ARGs in OA were further verified by the GSE169077 and qRT-PCR. Finally, Western blotting and immunohistochemistry were used to validate the final hub ARGs.\nResults: A total of 24 downregulated genes and five upregulated genes were identified, and these genes were enriched in autophagy, mitophagy, and inflammation-related pathways. The intersection results identified nine hub genes, namely, CDKN1A, DDIT3, FOS, VEGFA, RELA, MAP1LC3B, MYC, HSPA5, and HSPA8. GSE169077 and qRT-PCR validation results showed that only four genes, CDKN1A, DDT3, MAP1LC3B, and MYC, were consistent with the bioinformatics analysis results. Western blotting and immunohistochemical (IHC) showed that the expression of these four genes was significantly downregulated in the OA group, which is consistent with the qPCR results. Immune infiltration correlation analysis indicated that DDIT3 was negatively correlated with immature dendritic cells in OA, and FOS was positively correlated with eosinophils.\nConclusion: CDKN1A, DDIT3, MAP1LC3B, and MYC were identified as ARGs that were closely associated with immune infiltration in OA cartilage. Among them, DDIT3 showed a strong negative correlation with immature dendritic cells. This study found that the interaction between ARGs and immune cell infiltration may play a crucial role in the pathogenesis of OA; however, the specific interaction mechanism needs further research to be clarified. This study provides new insights to further understand the molecular mechanisms of immunity involved in the process of OA by autophagy.", "claims": [{"id": "claim-method", "statement": "The counts’ data were standardized by the transcripts per kilobase per million mapped reads (TPM), and then the DEGs between OA and normal knee cartilage tissue were screened using the R package “DESeq2” with the threshold set as |log2FoldChange| > 1 and p-value <0.05 (19).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38090564", "locator": "sections[4] \"Identification of differentially expressed autophagy-related genes\" paragraph 2", "quote": "The counts’ data were standardized by the transcripts per kilobase per million mapped reads (TPM), and then the DEGs between OA and normal knee cartilage tissue were screened using the R package “DESeq2” with the threshold set as |log2FoldChange| > 1 and p-value <0.05 (19)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material , further inquiries can be directed to the corresponding author/s.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38090564", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material , further inquiries can be directed to the corresponding author/s."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 24 downregulated and five upregulated autophagy-related genes in osteoarthritis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38090564", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 24 downregulated genes and five upregulated genes were identified, and these genes were enriched in autophagy, mitophagy, and inflammation-related pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 24 downregulated and five upregulated autophagy-related genes in osteoarthritis.", "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:38090564"], "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:GSE114007"], "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:GSE114007"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38090564", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2023.1263988", "sha256": 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Finally, Western blotting and immunohistochemistry were used to valida", "nt with the bioinformatics analysis results. Western blotting and immunohistochemical (IHC) showed that th"], "order_basis": "paper_text_order:1117", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["7 and qRT-PCR. Finally, Western blotting and immunohistochemistry were used to validate the final hub ARGs. Re", "atics analysis results. Western blotting and immunohistochemical (IHC) showed that the expression of these fo", "s. Western blotting and immunohistochemical (IHC) showed that the expression of these four ge"], "order_basis": "paper_text_order:1138", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["n the OA group, which is consistent with the qPCR results. Immune infiltration correlation ana"], "order_basis": "paper_text_order:1837", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The counts’ data were standardized by the transcripts per kilobase per million mapped reads (TPM), and then the DEGs between OA and normal knee cartilage tissue were screened using the R package “DESeq2” with the threshold set as |log2FoldChange| > 1 and p-value <0.05 (19)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}