{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T05:12:05Z","timestamp":1783746725383,"version":"3.55.0"},"reference-count":53,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Neuropeptide Y [NPY; encoded by the NPY gene] is a widely expressed 36-amino-acid neuropeptide that regulates neuronal function, vascular regulation, and immune regulation; its role in glioblastoma [GBM] remains incompletely characterized. We performed an integrative in silico multi-scale transcriptomic analysis combining bulk RNA-sequencing of IDH-wildtype GBM [n = 169] and lower-grade glioma [n = 510] surgical resections from TCGA, normal cortical tissue from GTEx [n = 207], and four independent GEO validation cohorts of surgical GBM and non-tumor brain specimens [GSE4290, GSE50161, GSE131928 scRNA-seq of ~20,426 cells from 28 patients, and GSE194329 10X Visium spatial transcriptomics from five patients], along with survival modeling, pathway enrichment, single-cell RNA sequencing, spatial transcriptomics, and cell\u2013cell communication analysis. NPY and its principal receptor, NPY1R, were significantly downregulated in GBM, while genes associated with hypoxia, angiogenesis, invasion, and immune suppression were upregulated. Single-cell analysis showed that NPY-axis transcript expression was elevated in neural progenitor-like populations. In contrast, hypoxia and metabolic programs were concentrated in mesenchymal tumors and stromal compartments, indicating distinct cellular contexts. Spatial analysis revealed a weak and heterogeneous relationship between NPY and hypoxia signatures, with substantial inter-patient variability and no significant global spatial cross-correlation. These findings indicate that loss of NPY signaling is a consistent feature of GBM and is associated with hypoxia-driven tumor states, while the spatial relationship between NPY and hypoxia appears weak, heterogeneous, and patient-specific.<\/jats:p>","DOI":"10.3390\/ijms27136068","type":"journal-article","created":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T16:20:39Z","timestamp":1783354839000},"page":"6068","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Loss of Neuropeptide Y Signaling Accompanies the Neural-to-Mesenchymal Transcriptional Transition in Glioblastoma: A Multi-Scale Transcriptomic Analysis"],"prefix":"10.3390","volume":"27","author":[{"given":"Fareeha","family":"Arshad","sequence":"first","affiliation":[{"name":"College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nouran","family":"Abualsaud","sequence":"additional","affiliation":[{"name":"King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11426, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arshiya","family":"Akbar","sequence":"additional","affiliation":[{"name":"College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed Imran","family":"Khan","sequence":"additional","affiliation":[{"name":"King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bushra","family":"Rasheed","sequence":"additional","affiliation":[{"name":"College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adnan","family":"Hussain","sequence":"additional","affiliation":[{"name":"King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fahad Ali","family":"Alghamdi","sequence":"additional","affiliation":[{"name":"King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3521-217X","authenticated-orcid":false,"given":"Faisal Abdulhameed","family":"Farrash","sequence":"additional","affiliation":[{"name":"King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8355-0870","authenticated-orcid":false,"given":"Edwin N.","family":"Aroke","sequence":"additional","affiliation":[{"name":"Department of Acute, Chronic & Continuing Care, School of Nursing, University of Alabama at Birmingham, Birmingham, AL 35294, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-1795-2927","authenticated-orcid":false,"given":"Khalid Walid","family":"Freij","sequence":"additional","affiliation":[{"name":"Department of Acute, Chronic & Continuing Care, School of Nursing, University of Alabama at Birmingham, Birmingham, AL 35294, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Itika","family":"Arora","sequence":"additional","affiliation":[{"name":"College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7536-910X","authenticated-orcid":false,"given":"Ahmed","family":"Yaqinuddin","sequence":"additional","affiliation":[{"name":"College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1093\/neuonc\/noab106","article-title":"The 2021 WHO classification of tumors of the central nervous system: A summary","volume":"23","author":"Louis","year":"2021","journal-title":"Neuro-Oncol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1056\/NEJMoa043330","article-title":"Radiotherapy plus Concomitant and Adjuvant Temozolomide for Glioblastoma","volume":"352","author":"Stupp","year":"2005","journal-title":"N. Engl. J. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.ccr.2009.12.020","article-title":"Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1","volume":"17","author":"Verhaak","year":"2010","journal-title":"Cancer Cell"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.ccell.2017.06.003","article-title":"Tumor Evolution of Glioma-Intrinsic Gene Expression Subtypes Associates with Immunological Changes in the Microenvironment","volume":"32","author":"Wang","year":"2017","journal-title":"Cancer Cell"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.cell.2012.01.021","article-title":"Hypoxia-inducible factors in physiology and medicine","volume":"148","author":"Semenza","year":"2012","journal-title":"Cell"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1215\/S1152851704001115","article-title":"Hypoxia and the hypoxia-inducible-factor pathway in glioma growth and angiogenesis","volume":"7","author":"Kaur","year":"2005","journal-title":"Neuro-Oncol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/nrc3183","article-title":"HIF1\u03b1 and HIF2\u03b1: Sibling rivalry in hypoxic tumour growth and progression","volume":"12","author":"Keith","year":"2011","journal-title":"Nat. Rev. Cancer"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1084\/jem.20131916","article-title":"PD-L1 is a novel direct target of HIF-1\u03b1, and its blockade under hypoxia enhanced: MDSC-mediated T cell activation","volume":"211","author":"Noman","year":"2014","journal-title":"J. Exp. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/nn.4185","article-title":"The role of microglia and macrophages in glioma maintenance and progression","volume":"19","author":"Hambardzumyan","year":"2015","journal-title":"Nat. Neurosci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1016\/j.ccell.2017.02.009","article-title":"The Microenvironmental Landscape of Brain Tumors","volume":"31","author":"Quail","year":"2017","journal-title":"Cancer Cell"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Grundwald, N.J., Ben\u00edtez, D.P., and Brunton, P.J. (2016). Sex-Dependent Effects of Prenatal Stress on Social Memory in Rats: A Role for Differential Expression of Central Vasopressin-1a Receptors. J. Neuroendocr., 28.","DOI":"10.1111\/jne.12343"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.npep.2015.09.008","article-title":"Neuropeptide Y: A stressful review","volume":"55","author":"Reichmann","year":"2016","journal-title":"Neuropeptides"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/S0166-2236(96)01057-0","article-title":"Y-receptor subtypes\u2014How many more?","volume":"20","author":"Blomqvist","year":"1997","journal-title":"Trends Neurosci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/S0031-6997(24)01352-8","article-title":"XVI. International union of pharmacology recommendations for the nomenclature of neuropeptide Y, peptide YY, and pancreatic polypeptide receptors","volume":"50","author":"Michel","year":"1998","journal-title":"Pharmacol. Rev."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.npep.2004.05.004","article-title":"Overexpression of NPY and Y2 receptors in epileptic brain tissue: An endogenous neuroprotective mechanism in temporal lobe epilepsy?","volume":"38","author":"Vezzani","year":"2004","journal-title":"Neuropeptides"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0165-5728(02)00424-1","article-title":"Relevance of neuropeptide Y for the neuroimmune crosstalk","volume":"134","author":"Bedoui","year":"2003","journal-title":"J. Neuroimmunol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1016\/j.bbi.2007.03.008","article-title":"Autonomic innervation and regulation of the immune system [1987\u20132007]","volume":"21","author":"Nance","year":"2007","journal-title":"Brain Behav. Immun."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/j.peptides.2006.08.038","article-title":"Neuropeptide Y [NPY] in neuroblastoma: Effect on growth and vascularization","volume":"28","author":"Kitlinska","year":"2007","journal-title":"Peptides"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Chen, W.C., Liu, Y.B., Liu, W.F., Zhou, Y.Y., He, H.F., and Lin, S. (2020). Neuropeptide Y Is an Immunomodulatory Factor: Direct and Indirect. Front. Immunol., 11.","DOI":"10.3389\/fimmu.2020.580378"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1097\/NEN.0b013e318180e618","article-title":"Neuropeptide Y Receptors in Primary Human Brain Tumors: Overexpression in High-Grade Tumors","volume":"67","author":"Reubi","year":"2008","journal-title":"J. Neuropathol. Exp. Neurol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1093\/neuonc\/noq034","article-title":"Elevated blood markers 1 year before manifestation of malignant glioma","volume":"12","author":"Gartner","year":"2010","journal-title":"Neuro-Oncology"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/S0196-9781(01)00344-8","article-title":"Neuropeptide Y Y2 receptor signalling mechanisms in the human glioblastoma cell line LN319","volume":"22","author":"Grouzmann","year":"2001","journal-title":"Peptides"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"4392","DOI":"10.1158\/1538-7445.AM2024-4392","article-title":"Abstract 4392: Neuropeptide Y system in glioblastoma","volume":"84","author":"Abualsaud","year":"2024","journal-title":"Cancer Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"10931","DOI":"10.1073\/pnas.88.23.10931","article-title":"Neuropeptide Y secretion increases in the paraventricular nucleus in association with increased appetite for food","volume":"88","author":"Kalra","year":"1991","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/35007534","article-title":"Central nervous system control of food intake","volume":"404","author":"Schwartz","year":"2000","journal-title":"Nature"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"9727","DOI":"10.1523\/JNEUROSCI.0879-12.2012","article-title":"Endothelial cell-derived nitric oxide enhances aerobic glycolysis in astrocytes via HIF-1\u03b1-mediated target gene activation","volume":"32","author":"Brix","year":"2012","journal-title":"J. Neurosci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1152\/physiol.00022.2015","article-title":"Oxygen sensing and homeostasis","volume":"30","author":"Prabhakar","year":"2015","journal-title":"Physiology"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1161\/01.RES.83.2.187","article-title":"Neuropeptide Y a novel angiogenic factor from the sympathetic nerves and endothelium","volume":"83","author":"Rose","year":"1998","journal-title":"Circ. Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1016\/j.cell.2020.05.007","article-title":"Interrogation of the Microenvironmental Landscape in Brain Tumors Reveals Disease-Specific Alterations of Immune Cells","volume":"181","author":"Klemm","year":"2020","journal-title":"Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e71","DOI":"10.1093\/nar\/gkv1507","article-title":"TCGAbiolinks: An R\/Bioconductor package for integrative analysis of TCGA data","volume":"44","author":"Colaprico","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"Limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v033.i01","article-title":"Regularization paths for generalized linear models via coordinate descent","volume":"33","author":"Friedman","year":"2010","journal-title":"J. Stat. Softw."},{"key":"ref_33","unstructured":"Korotkevich, G., Sukhov, V., Budin, N., Atryomov, M.N., and Sergushichev, A. (2021). Fast gene set enrichment analysis. bioRxiv."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"vbaf178","DOI":"10.1093\/bioadv\/vbaf178","article-title":"Gene-set enrichment analysis and visualization on the web using EnrichmentMap:RNASeq","volume":"5","author":"Franz","year":"2025","journal-title":"Bioinform. Adv."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v036.i03","article-title":"Conducting meta-analyses in R with the metafor package","volume":"36","author":"Viechtbauer","year":"2010","journal-title":"J. Stat. Softw."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1016\/j.cell.2019.06.024","article-title":"An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma","volume":"178","author":"Neftel","year":"2019","journal-title":"Cell"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e50","DOI":"10.1093\/nar\/gkab043","article-title":"SPOTlight: Seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes","volume":"49","author":"Nieto","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1016\/j.ccell.2022.05.009","article-title":"Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma","volume":"40","author":"Ravi","year":"2022","journal-title":"Cancer Cell"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1101\/gr.240663.118","article-title":"Benchmark and integration of resources for the estimation of human transcription factor activities","volume":"29","author":"Holland","year":"2019","journal-title":"Genome Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2019","DOI":"10.4155\/fmc.13.166","article-title":"A pharmacophore-based virtual screening approach for the discovery of Trypanosoma cruzi GAPDH inhibitors","volume":"5","author":"Maluf","year":"2013","journal-title":"Future Med. Chem."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1007\/s00401-018-1913-0","article-title":"cIMPACT-NOW update 3: Recommended diagnostic criteria for \u201cDiffuse astrocytic glioma, IDH-wildtype, with molecular features of glioblastoma, WHO grade IV.\u201d","volume":"136","author":"Brat","year":"2018","journal-title":"Acta Neuropathol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1981","DOI":"10.1093\/bioinformatics\/btw052","article-title":"MetaCCA: Summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis","volume":"32","author":"Cichonska","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1158\/2326-6066.CIR-23-0211","article-title":"Single-Cell Transcriptomics Reveals the Heterogeneity of the Immune Landscape of IDH\u2013Wild-Type High-Grade Gliomas","volume":"12","author":"Ran","year":"2024","journal-title":"Cancer Immunol. Res."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Moussa, M., and M\u0103ndoiu, I.I. (2021). Computational Cell Cycle Analysis of Single Cell RNA-Seq Data. Lecture Notes in Computer Science [Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics], Springer.","DOI":"10.1101\/2020.11.21.392613"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1038\/nature06905","article-title":"NF-kappaB links innate immunity to the hypoxic response through transcriptional regulation of HIF-1alpha","volume":"453","author":"Rius","year":"2008","journal-title":"Nature"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"2393","DOI":"10.1002\/stem.188","article-title":"Targeting interleukin 6 signaling suppresses glioma stem cell survival and tumor growth","volume":"27","author":"Wang","year":"2009","journal-title":"Stem Cells"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41571-020-00447-z","article-title":"EANO guidelines on the diagnosis and treatment of diffuse gliomas of adulthood","volume":"18","author":"Weller","year":"2021","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.cell.2015.12.028","article-title":"Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma","volume":"164","author":"Ceccarelli","year":"2016","journal-title":"Cell"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1847","DOI":"10.1158\/1078-0432.CCR-24-2618","article-title":"A Phase I Dose-Escalation Study of the HIF-2 Alpha Inhibitor DFF332 in Patients with Advanced Clear-Cell Renal Cell Carcinoma","volume":"31","author":"Pal","year":"2025","journal-title":"Clin. Cancer Res."},{"key":"ref_51","first-page":"100141","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1038\/ng.3593","article-title":"Functional characterization of somatic mutations in cancer using network-based inference of protein activity","volume":"48","author":"Alvarez","year":"2016","journal-title":"Nat. Genet."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/13\/6068\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T04:18:19Z","timestamp":1783743499000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/13\/6068"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,6]]},"references-count":53,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["ijms27136068"],"URL":"https:\/\/doi.org\/10.3390\/ijms27136068","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,6]]}}}