Transcriptome combined with Mendelian randomization to screen key genes associated with mitochondrial and programmed cell death causally associated with diabetic retinopathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39634176", "kind": "science-record", "revision": 3, "content_hash": "sha256:1866c53efa29806998088ff7ed82a88881e8ee922ffba89806c9e823a41071fa", "created_at": "2026-11-01T20:29:54Z", "updated_at": "2026-11-01T22:13:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome combined with Mendelian randomization to screen key genes associated with mitochondrial and programmed cell death causally associated with diabetic retinopathy.", "doi": "10.3389/fendo.2024.1422787", "pmid": "39634176", "authors": ["Shule Jiang", "Xuemei Han"], "journal": "Frontiers in endocrinology", "year": 2024, "abstract": "Background: Mitochondrial dysfunction in the retina can induce apoptosis of retinal capillary cells, leading to diabetic retinopathy (DR). This study aimed to explore key genes related to programmed cell death (PCD) and mitochondria in DR via bioinformatic analysis.\nMethods: A differential analysis was performed to identify differentially expressed genes (DEGs) between DR and control samples using the GSE94019 dataset from the Gene Expression Omnibus (GEO) database. Pearson correlation analysis was then utilized to select genes linked to mitochondrial function and PCD (M-PCD). Candidate genes were identified by overlapping DR-DEGs and M-PCD genes, followed by functional annotation. Mendelian randomization (MR) analysis was employed to identify genes with causal relationships to DR. Key genes were identified through protein-protein interaction (PPI) analysis using six algorithms (DEgree, DMNC, EPC, MCC, Genes are BottleNeck, and MNC) within Cytoscape software. The expression patterns of these genes were validated using GSE94019 and GSE60436 datasets, as well as RT-qPCR. Enrichment analysis provided insights into the function and pathways of these key genes in DR. Differential immune cell profiles were determined via immune infiltration analysis, followed by exploring the relationships between immune cells, cytokines, and the identified genes. Correlations between key genes and apoptosis genes were also examined. In vivo experiments using RT-PCR, immunohistochemistry (IHC), and western blot analysis confirmed that MYC and SLC7A11 expression was significantly elevated in DR rat retinal tissues.\nResults: From 658 candidate genes, 12 showed significant causal associations with DR. MYC and SLC7A11 were particularly notable, showing upregulated expression in DR samples and involvement in apoptosis and diabetes-related pathways. These genes were significantly associated with apoptotic genes and correlated positively with altered immune cell types and cytokines, suggesting a link between immune response and DR pathogenesis. In vivo findings confirmed that MYC and SLC7A11 expression was elevated in DR rat retinal tissues.\nConclusion: Key genes (MYC and SLC7A11) associated with mitochondrial function and PCD in DR were identified, offering insights into DR's pathological mechanisms and potential targets for diagnostic and therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "Subsequently, the two-sample MR analysis was executed employing five methods [Weighted median (27), MR Egger (18), Inverse variance weighted (IVW) (28), Simple median (29), and Weighted mode (29)], with the primary method being IVW (p < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39634176", "locator": "sections[5] \"MR analysis\" paragraph 2", "quote": "Subsequently, the two-sample MR analysis was executed employing five methods [Weighted median (27), MR Egger (18), Inverse variance weighted (IVW) (28), Simple median (29), and Weighted mode (29)], with the primary method being IVW (p < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39634176", "locator": "sections[27] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. 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Correlations between key genes and apoptosis genes were also examined. In vivo experiment", "expression in DR samples and involvement in apoptosis and diabetes-related pathways. These genes w", "analysis between key genes and differential apoptosis genes. Supplementary Materials Supplementary"], "order_basis": "paper_text_order:193", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["enes and apoptosis genes were also examined. In vivo experiments using RT-PCR, immunohistochemist", "between immune response and DR pathogenesis. In vivo findings confirmed that MYC and SLC7A11 expr", "expression was significantly elevated in DR rat retinal tissues. Results: From 658 candidate", "YC and SLC7A11 expression was elevated in DR rat retinal tissues. 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