{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,4]],"date-time":"2026-01-04T02:45:16Z","timestamp":1767494716368,"version":"build-2065373602"},"reference-count":49,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T00:00:00Z","timestamp":1748304000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National High Level Hospital Clinical Research Funding","award":["2023-PUMCH-E-011"],"award-info":[{"award-number":["2023-PUMCH-E-011"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Bioengineering"],"abstract":"<jats:p>Moyamoya disease (MMD) is a cerebrovascular disease which can result in severe strokes. However, its etiology is still unknown. We analyzed gene expression datasets from 36 MMD patients and 24 controls to identify differentially expressed genes. Using weighted gene co-expression network analysis and databases such as KEGG, we identified hypoxia-immune-related genes. These genes were further refined through machine learning algorithms. The diagnostic value was confirmed using an external dataset, and a diagnostic nomogram was constructed. Additionally, gene set enrichment analysis was conducted, and a competitive endogenous RNA (ceRNA) network was built to predict potential therapeutic targets. Our study identified AKT1, CLDN3, ISG20, and TGFB2 as the key hypoxia-immune genes associated with MMD. These genes were implicated in epithelial\u2013mesenchymal transition, angiogenesis, and cell adhesion, suggesting a role in MMD pathogenesis. Further, our study constructed the ceRNA network and predicted potential drug targets for MMD. We obtained the top 10 drugs in the interaction of the four key genes that might serve as potential targets for the treatment of MMD. In conclusion, this study comprehensively analyzes the role of hypoxia-immune genes in MMD, which is conducive to the development of new diagnostic and therapeutic approaches and the exploration of the potential pathogenesis of MMD.<\/jats:p>","DOI":"10.3390\/bioengineering12060577","type":"journal-article","created":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T08:12:47Z","timestamp":1748419967000},"page":"577","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["A Machine Learning-Based Diagnostic Nomogram for Moyamoya Disease: The Validation of Hypoxia-Immune Gene Signatures"],"prefix":"10.3390","volume":"12","author":[{"given":"Cunxin","family":"Tan","sequence":"first","affiliation":[{"name":"Department of Neurosurgery, Peking University International Hospital, Beijing 102206, China"},{"name":"Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China"},{"name":"Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xilong","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-8848-1174","authenticated-orcid":false,"given":"Zhenyu","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yutong","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2522-8656","authenticated-orcid":false,"given":"Shihao","family":"He","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanli","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Peking University International Hospital, Beijing 102206, China"},{"name":"Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Research Committee on the Pathology and Treatment of Spontaneous Occlusion of the Circle of Willis, and Health Labour Sciences Research Grant for Research on Measures for Infractable Diseases (2012). Guidelines for diagnosis and treatment of moyamoya disease (spontaneous occlusion of the circle of Willis). Neurol. Med. Chir., 52, 245\u2013266.","DOI":"10.2176\/nmc.52.245"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1016\/S1474-4422(22)00165-X","article-title":"Moyamoya disease: Diagnosis and interventions","volume":"21","author":"Ihara","year":"2022","journal-title":"Lancet Neurol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Liu, W., Morito, D., Takashima, S., Mineharu, Y., Kobayashi, H., Hitomi, T., Hashikata, H., Matsuura, N., Yamazaki, S., and Toyoda, A. (2011). Identification of RNF213 as a susceptibility gene for moyamoya disease and its possible role in vascular development. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0022542"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"He, S., Hao, X., Liu, Z., Wang, Y., Zhang, J., Wang, X., Di, F., Wang, R., and Zhao, Y. (2023). Association between DIAPH1 variant and posterior circulation involvement with Moyamoya disease. Sci. Rep., 13.","DOI":"10.1038\/s41598-023-37665-1"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1007\/s11910-013-0423-7","article-title":"Recent advances in moyamoya disease: Pathophysiology and treatment","volume":"14","author":"Kronenburg","year":"2014","journal-title":"Curr. Neurol. Neurosci. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e1647","DOI":"10.1002\/ctm2.1647","article-title":"Circulating immune cell landscape and T-cell abnormalities in patients with moyamoya disease","volume":"14","author":"Ge","year":"2024","journal-title":"Clin. Transl. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1227\/01.NEU.0000249275.87310.FF","article-title":"Expression of hypoxia-inducing factor-1\u03b1 and endoglin in intimal hyperplasia of the middle cerebral artery of patients with Moyamoya disease","volume":"60","author":"Takagi","year":"2007","journal-title":"Neurosurgery"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.brainres.2019.05.033","article-title":"Circular RNA profiling of neutrophil transcriptome provides insights into asymptomatic Moyamoya disease","volume":"1719","author":"Ma","year":"2019","journal-title":"Brain Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e002146","DOI":"10.1161\/JAHA.115.002146","article-title":"Biochemical and Functional Characterization of RNF213 (Mysterin) R4810K, a Susceptibility Mutation of Moyamoya Disease, in Angiogenesis In Vitro and In Vivo","volume":"4","author":"Kobayashi","year":"2015","journal-title":"J. Am. Heart Assoc."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40","author":"McCarthy","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1093\/bioinformatics\/bts034","article-title":"The sva package for removing batch effects and other unwanted variation in high-throughput experiments","volume":"28","author":"Leek","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_12","first-page":"e62528","article-title":"Three Differential Expression Analysis Methods for RNA Sequencing: Limma, EdgeR, DESeq2","volume":"175","author":"Liu","year":"2021","journal-title":"J. Vis. Exp. (JoVE)"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.cancergen.2021.10.008","article-title":"Integrative analysis of DNA methylation and gene expression profiles to identify biomarkers of glioblastoma","volume":"258\u2013259","author":"Alivand","year":"2021","journal-title":"Cancer Genet."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Xiao, B., Liu, L., Li, A., Xiang, C., Wang, P., Li, H., and Xiao, T. (2020). Identification and Verification of Immune-Related Gene Prognostic Signature Based on ssGSEA for Osteosarcoma. Front. Oncol., 10.","DOI":"10.3389\/fonc.2020.607622"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Langfelder, P., and Horvath, S. (2008). WGCNA: An R package for weighted correlation network analysis. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-559"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Yu, H., Gu, L., Du, L., Dong, Z., Li, Z., Yu, M., Yin, Y., Wang, Y., Yu, L., and Ma, H. (2023). Identification and analysis of key hypoxia- and immune-related genes in hyper-trophic cardiomyopathy. Biol. Res., 56.","DOI":"10.1186\/s40659-023-00451-4"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Xie, K., Chen, Z., Feng, J., Pan, L., Wang, N., Luo, J., Yao, Y., Ma, H., Feng, Y., and Jiang, W. (2024). Identification and validation of prognostic and immunotherapeutic responses in esophageal squamous carcinoma based on hypoxia phenotype-related genes. Front. Pharmacol., 15.","DOI":"10.3389\/fphar.2024.1344317"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"McEligot, A.J., Poynor, V., Sharma, R., and Panangadan, A. (2020). Logistic LASSO Regression for Dietary Intakes and Breast Cancer. Nutrients, 12.","DOI":"10.3390\/nu12092652"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.neunet.2022.07.029","article-title":"Attention-based random forest and contamination model","volume":"154","author":"Utkin","year":"2022","journal-title":"Neural Netw."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Sanz, H., Valim, C., Vegas, E., Oller, J.M., and Reverter, F. (2018). SVM-RFE: Selection and visualization of the most relevant features through non-linear kernels. BMC Bioinform., 19.","DOI":"10.1186\/s12859-018-2451-4"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Robin, X., Turck, N., Hainard, A., Tiberti, N., Lisacek, F., Sanchez, J.-C., and M\u00fcller, M. (2011). pROC: An open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-77"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1002\/cac2.12067","article-title":"A nomogram for predicting overall survival in patients with low-grade endometrial stromal sarcoma: A population-based analysis","volume":"40","author":"Wu","year":"2020","journal-title":"Cancer Commun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1038\/s41596-018-0103-9","article-title":"Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap","volume":"14","author":"Reimand","year":"2019","journal-title":"Nat. Protoc."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software environment for integrated models of Biomolecular Interaction Networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Han, Z., Zhang, J., Su, Y., Zhou, Z., Wang, Y., Xu, S., Zhao, Y., He, S., and Wang, R. (2024). Identification of oxidative phosphorylation-related genes in moyamoya disease by combining bulk RNA-sequencing analysis and machine learning. Front. Genet., 15.","DOI":"10.3389\/fgene.2024.1417329"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e70461","DOI":"10.1096\/fj.202401445R","article-title":"Identification of the potential role of S1PR1 in adult moyamoya disease based on multiple bioinformatics analysis and experimental verification","volume":"39","author":"Zhou","year":"2025","journal-title":"FASEB J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"E5","DOI":"10.3171\/2021.6.FOCUS21284","article-title":"Experimental animal models for moyamoya disease and treatment: A pathogenesis-oriented scoping review","volume":"51","author":"Rallo","year":"2021","journal-title":"Neurosurg. Focus"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1002\/2211-5463.13382","article-title":"ISG20: An enigmatic antiviral RNase targeting multiple viruses","volume":"12","author":"Deymier","year":"2022","journal-title":"FEBS Open Bio"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.neo.2017.10.007","article-title":"Stimulation of Interferon-Stimulated Gene 20 by Thyroid Hormone Enhances Angiogenesis in Liver Cancer","volume":"20","author":"Lin","year":"2018","journal-title":"Neoplasia"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1089\/jir.2008.0030","article-title":"Identification of Interferon-\u03b2-Stimulated Genes that Inhibit Angiogenesis In Vitro","volume":"28","author":"Taylor","year":"2008","journal-title":"J. Interf. Cytokine Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1006\/exmp.2002.2418","article-title":"Parasitic Adaptive Mechanisms in Infection by Leishmania","volume":"72","author":"Cunningham","year":"2002","journal-title":"Exp. Mol. Pathol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1053\/j.seminhematol.2005.09.001","article-title":"Pathophysiology of graft-versus-host disease","volume":"43","author":"Ferrara","year":"2006","journal-title":"Semin. Hematol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1146\/annurev.immunol.22.012703.104538","article-title":"Cell biology of antigen processing in vitro and in vivo","volume":"23","author":"Trombetta","year":"2005","journal-title":"Annu. Rev. Immunol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"6214","DOI":"10.1038\/s41467-023-41999-9","article-title":"Claudin-23 reshapes epithelial tight junction architecture to regulate barrier function","volume":"14","author":"Rajagopal","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Hashimoto, I., and Oshima, T. (2022). Claudins and Gastric Cancer: An Overview. Cancers, 14.","DOI":"10.3390\/cancers14020290"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s43046-022-00125-4","article-title":"Potential roles of claudin-3 and claudin-4 in ovarian cancer management","volume":"34","author":"Uthayanan","year":"2022","journal-title":"J. Egypt. Natl. Cancer Inst."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1016\/S1474-4422(08)70240-0","article-title":"Moyamoya disease: Current concepts and future perspectives","volume":"7","author":"Kuroda","year":"2008","journal-title":"Lancet Neurol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1111\/j.1440-1789.2004.00550.x","article-title":"Pathological and immunohistochemical findings of an au-topsy case of adult moyamoya disease","volume":"24","author":"Takekawa","year":"2004","journal-title":"Neuropathology"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Pepe, G., Fioriniello, S., Marracino, F., Capocci, L., Maglione, V., D\u2019esposito, M., Di Pardo, A., and Della Ragione, F. (2023). Blood\u2013Brain Barrier Integrity Is Perturbed in a Mecp2-Null Mouse Model of Rett Syndrome. Biomolecules, 13.","DOI":"10.3390\/biom13040606"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Kawasaki, T., and Kawai, T. (2014). Toll-like receptor signaling pathways. Front. Immunol., 5.","DOI":"10.3389\/fimmu.2014.00461"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1996","DOI":"10.1016\/j.ymthe.2018.05.002","article-title":"MicroRNA-148b Targets the TGF-\u03b2 Pathway to Regulate Angiogenesis and Endothelial-to-Mesenchymal Transition during Skin Wound Healing","volume":"26","author":"Miscianinov","year":"2018","journal-title":"Mol. Ther."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1002\/humu.23407","article-title":"A mutation update on the LDS-associated genes TGFB2\/3 and SMAD2\/3","volume":"39","author":"Schepers","year":"2018","journal-title":"Hum. Mutat."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1016\/j.devcel.2023.03.009","article-title":"Prerequisite endocardial-mesenchymal transition for murine cardiac trabecular angiogenesis","volume":"58","author":"Lu","year":"2023","journal-title":"Dev. Cell"},{"key":"ref_44","first-page":"95","article-title":"The alloimmune response and effector mechanisms of allograft rejection","volume":"20","author":"Arakelov","year":"2000","journal-title":"Semin. Nephrol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1186\/s12964-019-0450-3","article-title":"Distinct functions of AKT isoforms in breast cancer: A comprehensive review","volume":"17","author":"Hinz","year":"2019","journal-title":"Cell Commun. Signal."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s12943-018-0935-5","article-title":"Circular RNA circNRIP1 acts as a microRNA-149-5p sponge to promote gastric cancer progression via the AKT1\/mTOR pathway","volume":"18","author":"Zhang","year":"2019","journal-title":"Mol. Cancer"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"8207","DOI":"10.1158\/0008-5472.CAN-07-0755","article-title":"Cutaneous human papillomaviruses down-regulate AKT1, whereas AKT2 up-regulation and activation associates with tumors","volume":"67","author":"Akgul","year":"2007","journal-title":"Cancer Res."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2515","DOI":"10.1007\/s12035-024-04423-x","article-title":"Comprehensive Analysis and In Vitro Verification of Endothelial-Mesenchymal Transition-Related Genes in Moyamoya Disease","volume":"62","author":"Li","year":"2025","journal-title":"Mol. Neurobiol."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Cao, L., Ai, Y., Dong, Y., Li, D., Wang, H., Sun, K., Wang, C., Zhang, M., Yan, D., and Li, H. (2023). Bioinformatics analysis reveals the landscape of immune cell infiltration and novel immune-related biomarkers in moyamoya disease. Front. Genet., 14.","DOI":"10.3389\/fgene.2023.1101612"}],"container-title":["Bioengineering"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5354\/12\/6\/577\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:41:39Z","timestamp":1760031699000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5354\/12\/6\/577"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,27]]},"references-count":49,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2025,6]]}},"alternative-id":["bioengineering12060577"],"URL":"https:\/\/doi.org\/10.3390\/bioengineering12060577","relation":{},"ISSN":["2306-5354"],"issn-type":[{"type":"electronic","value":"2306-5354"}],"subject":[],"published":{"date-parts":[[2025,5,27]]}}}