Angiogenesis-related genes and immune microenvironment in moyamoya disease: a transcriptomic and functional analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40722175", "kind": "science-record", "revision": 3, "content_hash": "sha256:93724c21836e18acf130cd00f8303370f53d4dabff1de669e5f903e63fc2da92", "created_at": "2026-11-01T20:30:49Z", "updated_at": "2026-11-01T22:14:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Angiogenesis-related genes and immune microenvironment in moyamoya disease: a transcriptomic and functional analysis.", "doi": "10.1186/s13023-025-03945-4", "pmid": "40722175", "authors": ["Zhenyu Zhou", "Hongchuan Niu", "Shaoqi Xu", "Junze Zhang", "Yutong Liu", "Chengxu Lei", "Shihao He", "Yuanli Zhao"], "journal": "Orphanet journal of rare diseases", "year": 2025, "abstract": "BACKGROUND: Moyamoya disease (MMD) is a chronic, progressive occlusive cerebrovascular disease. It causes recurrent cerebrovascular stroke due to vascular closure and proliferation. An unclear pathophysiological mechanism is the most significant obstacle in the diagnosis and treatment of MMD.\nMETHOD: This study prospectively included 10 MMD and 3 HC (healthy controls) participants in the discovery cohort. GSE189993 and GSE157628 were downloaded from the Gene Expression Omnibus (GEO) as validation cohorts, which included 32 patients with MMD and 20 HC. Angiogenesis-related genes were downloaded from GENECARD. Hub genes were selected by differential analysis and weighted correlation network analysis. Functional enrichment, immune infiltration, and metabolic pathway analyses and drug prediction mapping (Connectivity Map [CMap]) were performed.\nRESULT: Through differential analysis identified, 198 differentially expressed genes (DEGs), including 85 upregulated genes and 113 downregulated genes. In total, 238 angiogenesis -related genes were identified using WGCNA. Four hub genes were identified: TBC1 domain family member 9B (TBC1D9B), Phosphatidylinositol transfer protein beta (PITPNB), The ANK repeat and PH domain-containing protein 3 (ARAP3), and Ubiquitin-conjugating enzyme E2 E1 (UBE2E1). Four potential drugs were selected: calyculin A, H-9, parbendazole, and velnacrine. The results of multiple immune infiltration analyses collectively depicted the immune microenvironment characteristics of MMD.\nCONCLUSION: This study is the first to explore the mechanism by which angiogenesis related genes are involved in intimal hyperplasia in Moyamoya disease. TBC1D9B and ARAP3 may promote the pathological development of moyamoya disease through immune response, metabolism.", "claims": [{"id": "claim-method", "statement": "The diagnostic ability of hub genes was evaluated using ROC curves.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40722175", "locator": "sections[18] \"Interactions and diagnostic prediction of hub genes\" paragraph 2", "quote": "The diagnostic ability of hub genes was evaluated using ROC curves."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The databases (GSE189993 and GSE157628) are published and available in the GENE EXPRESSION OMNIBUS (https://www.ncbi.nlm.nih.gov/geo/info/datasets.html) [38]. The datasets generated and analysed during the current study are available in the GENE EXPRESSION OMNIBUS, [GSE189993, GSE157628]”.Additionally, any information presented in the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40722175", "locator": "sections[32] \"Data availability\" paragraph 2", "quote": "The databases (GSE189993 and GSE157628) are published and available in the GENE EXPRESSION OMNIBUS (https://www.ncbi.nlm.nih.gov/geo/info/datasets.html) [38]. The datasets generated and analysed during the current study are available in the GENE EXPRESSION OMNIBUS, [GSE189993, GSE157628]”.Additionally, any information presented in the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The diagnostic AUC values were 0.758 for ARAP3, 0.752 for PITPNB, 0.789 for TBC1D9B, and 0.706 for UBE2E1.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40722175", "locator": "sections[18] \"Interactions and diagnostic prediction of hub genes\" paragraph 2", "quote": "The results show the AUC values of the hub genes. ARAP3 AUC = 0.758, PITPNB AUC = 0.752, TBC1D9B AUC: 0.789, and UBE2E1 AUC: 0.706 (Fig. 5B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The diagnostic AUC values were 0.758 for ARAP3, 0.752 for PITPNB, 0.789 for TBC1D9B, and 0.706 for UBE2E1.", "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:40722175"], "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:GSE157628"], "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:GSE157628"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40722175", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13023-025-03945-4", "sha256": "sha256:3fd869bbf94664fa121393beae3fd3801e7e1288685eff66fe236790fb756cb8", "bytes": 50448, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13023-025-03945-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12306060", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE157628", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157628", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE157628", "version": null, "note": "The databases (GSE189993 and GSE157628) are published and available in the GENE EXPRESSION OMNIBUS (https://www.ncbi.nlm.nih.gov/geo/info/datasets.html) [38]. 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The datasets generated and analysed during the current study are available in the GENE EXPRESSION OMNIBUS, [GSE189993, GSE157628]”.Additionally, any information presented in the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4771802", "GSM4771803", "GSM4771804", "GSM4771805", "GSM4771806", "GSM4771807", "GSM4771808", "GSM4771809", "GSM4771810", "GSM4771811", "GSM4771812", "GSM4771813", "GSM4771814", "GSM4771815", "GSM4771816", "GSM4771817", "GSM4771818", "GSM4771819", "GSM4771820", "GSM4771821"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "16699", "taxon": "Homo sapiens", "title": "Transcriptome-wide Analysis of Intracranial Artery in Patients with Moyamoya Disease Showing Up-regulation of Immune Response, and Down-regulation of Oxidative Phosphorylation and DNA Repair", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE189993", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189993", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE189993", "version": null, "note": "The databases (GSE189993 and GSE157628) are published and available in the GENE EXPRESSION OMNIBUS (https://www.ncbi.nlm.nih.gov/geo/info/datasets.html) [38]. 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