Integrated Single-Cell and Spatial Transcriptomic Analysis Identifies ISR-Related Genes Driving Immune Regulation in Parkinson's Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40687147", "kind": "science-record", "revision": 4, "content_hash": "sha256:e8ed0d86c8150cf49f942809b020cc25ec19a4475ed39861635475ade29a33e5", "created_at": "2026-11-01T20:30:47Z", "updated_at": "2026-11-01T22:56:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Single-Cell and Spatial Transcriptomic Analysis Identifies ISR-Related Genes Driving Immune Regulation in Parkinson's Disease.", "doi": "10.2147/JIR.S521744", "pmid": "40687147", "authors": ["Hua Jiang", "Xiaotian Zhang", "Shengyu Feng", "Wei Feng"], "journal": "Journal of inflammation research", "year": 2025, "abstract": "Background: Parkinson's disease (PD) is a progressive neurodegenerative disorder marked by motor dysfunction and dopaminergic neuron loss. Although its genetic and molecular underpinnings have been increasingly studied, the pathways driving PD progression remain unclear. The integrated stress response (ISR), a conserved mechanism activated by cellular stress, has been linked to several neurological diseases, but its role in PD and the key ISR-related genes involved are still poorly understood.\nMaterials and Methods: We used publicly available transcriptomic data from GEO, including single-cell RNA sequencing and spatial transcriptomics, to identify ISR-related genes involved in PD progression. ISR scores were compared across brain cell types, and differentially expressed genes in microglia were further screened using Lasso regression and random forest algorithms. Enrichment analyses (GSEA and GSVA) revealed their involvement in immune-related pathways. CIBERSORT was applied to assess immune cell infiltration, while spatial transcriptomics mapped the regional expression of key genes. Finally, DDIT4 expression was validated in PD cell and mouse models.\nResults: We identified four key ISR-related genes (DDIT4, GNA13, HSPA1B, and SLC7A5) that were differentially expressed in PD microglia. Functional enrichment analysis revealed that these genes were predominantly involved in immune-related signaling pathways, including JAK-STAT, NF-κB, and Notch, suggesting their potential role in regulating neuroinflammation. Spatial transcriptomics revealed distinct regional expression patterns of these ISR-related genes across brain tissues. In vitro and in vivo experiments confirmed the upregulation of DDIT4 in PD models, and its silencing alleviated neurotoxicity and reduced α-synuclein aggregation, highlighting its potential role in PD pathogenesis.\nConclusion: This study provides new insights into the molecular mechanisms of PD and highlights DDIT4 as a promising therapeutic target. Its regulatory role in immune signaling and cellular stress pathways may offer novel avenues for clinical intervention and personalized treatment strategies in PD.", "claims": [{"id": "claim-method", "statement": "Key diagnostic markers were selected using Lasso logistic regression and the random forest algorithm.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40687147", "locator": "sections[11] \"Feature Selection via Lasso Regression and Random Forest\" paragraph 2", "quote": "Key diagnostic markers were selected using Lasso logistic regression and the random forest algorithm."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and analyzed during the current study available from the corresponding author (Shengyu Feng) on request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40687147", "locator": "sections[36] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets used and analyzed during the current study available from the corresponding author (Shengyu Feng) on request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified four key ISR-related genes (DDIT4, GNA13, HSPA1B, and SLC7A5) that were differentially expressed in PD microglia.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40687147", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified four key ISR-related genes (DDIT4, GNA13, HSPA1B, and SLC7A5) that were differentially expressed in PD microglia."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We identified four key ISR-related genes (DDIT4, GNA13, HSPA1B, and SLC7A5) that were differentially expressed in PD microglia.", "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:40687147"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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