{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:54:47Z","timestamp":1753890887092,"version":"3.41.2"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T00:00:00Z","timestamp":1728345600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Chronic rhinosinusitis with nasal polyps (CRSwNP) belongs to a subtype of Chronic rhinosinusitis which is a heterogeneous inflammatory condition. It has been reported that mitophagy may provide a new therapeutic option for CRSwNP.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>The GSE136825 (training dataset) and GSE179265 (validation dataset) were scoured from the Gene Expression Omnibus database. The candidate genes related to mitophagy were identified by differential expression analysis. Subsequently, the biomarkers were selected from the machine learning, Receiver Operating Characteristic curves, and expression level verification. A backpropagation (BP) neural network was generated to evaluate the diagnostic ability of biomarkers. In addition, the infiltration abundance of immune cells, potential drugs, and related ear-nose-throat (ENT) diseases were analyzed based on the biomarkers. Finally, qPCR analysis was performed to verify these biomarkers.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A total of 8 candidate genes were identified by overlapping 3,400 differentially expressed genes (DEGs) and 72 mitophagy-related genes Subsequently, TFE3 and TP53 were identified as biomarkers of CRSwNP, and the area under the curves (AUC) of the BP neural network was 0.74, which indicated that the biomarkers had excellent abilities. TFE3 and TP53 were co-enriched in the cancer pathway, cell cycle, endocytosis, etc. What\u2019s more, Macrophage and Immature dendritic cells had significant correlations with biomarkers. The drugs (Doxorubicin, Tetrachlorodibenzodioxin, etc.) and the ear-nose-throat diseases (hearing loss, sensorineural, tinnitus, etc.) related to biomarkers were predicted. Ultimately, qPCR results showed that the expression levels of TFE3 and TP53 in polyp tissue of CRSwNP were increased.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Overall, TFE3 and TP53 could be used as biomarkers or potential therapeutic targets to diagnose and treat CRSwNP.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fgene.2024.1423778","type":"journal-article","created":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T04:36:35Z","timestamp":1728362195000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["TFE3 and TP53 were novel diagnostic biomarkers related to mitochondrial autophagy in chronic rhinosinusitis with nasal polyps"],"prefix":"10.3389","volume":"15","author":[{"given":"Ning","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanjun","family":"Jia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Han","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuemin","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Fu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2024,10,8]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1431","DOI":"10.1016\/j.jaci.2015.10.010","article-title":"Current and future treatment options for adult chronic rhinosinusitis: focus on nasal polyposis","volume":"136","author":"Bachert","year":"2015","journal-title":"J. allergy Clin. Immunol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1016\/j.jaip.2018.10.014","article-title":"Clinical characteristics of patients with chronic rhinosinusitis without nasal polyps in an academic setting","volume":"7","author":"Benjamin","year":"2019","journal-title":"J. allergy Clin. Immunol. Pract."},{"key":"B3","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1177\/19458924231193526","article-title":"Genome-wide epigenetic study of chronic rhinosinusitis tissues reveals dysregulated inflammatory immunologic and remodeling pathways","volume":"37","author":"Brar","year":"2023","journal-title":"Am. J. Rhinol. Allergy"},{"key":"B4","doi-asserted-by":"publisher","first-page":"e0197355","DOI":"10.1371\/journal.pone.0197355","article-title":"Decreased expression of CCL17 in the disrupted nasal polyp epithelium and its regulation by IL-4 and IL-5","volume":"13","author":"Byoungjae","year":"2018","journal-title":"PLoS One"},{"key":"B5","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.3390\/biology11091325","article-title":"p53: from fundamental biology to clinical applications in cancer","volume":"11","author":"Capuozzo","year":"2022","journal-title":"Biology"},{"key":"B6","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1111\/pcmr.13149","article-title":"TFE3 promotes ferroptosis in melanoma","volume":"37","author":"Dias","year":"2024","journal-title":"Pigment cell and melanoma Res."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1017425","DOI":"10.3389\/fonc.2022.1017425","article-title":"Clinicopathological features and prognosis of TFE3-positive renal cell carcinoma","volume":"12","author":"Dong","year":"2022","journal-title":"Front. Oncol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"106758","DOI":"10.1016\/j.intimp.2020.106758","article-title":"SnapShot: TP53 status and macrophages infiltration in TCGA-analyzed tumors","volume":"86","author":"El-Arabey","year":"2020","journal-title":"Int. Immunopharmacol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1186\/s13148-019-0730-1","article-title":"Statistical predictions with glmnet","volume":"11","author":"Engebretsen","year":"2019","journal-title":"Clin. epigenetics"},{"key":"B10","doi-asserted-by":"publisher","first-page":"112236","DOI":"10.1016\/j.intimp.2024.112236","article-title":"Macrophages in CRSwNP: do they deserve more attention?","volume":"134","author":"Fan","year":"2024","journal-title":"Int. Immunopharmacol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4193\/Rhin20.600","article-title":"European position paper on rhinosinusitis and nasal polyps 2020","volume":"58","author":"Fokkens","year":"2020","journal-title":"Rhinology"},{"key":"B12","doi-asserted-by":"publisher","first-page":"2811","DOI":"10.1093\/bioinformatics\/btu393","article-title":"Circlize Implements and enhances circular visualization in R","volume":"30","author":"Gu","year":"2014","journal-title":"Bioinforma. Oxf. Engl."},{"key":"B13","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-seq data","volume":"14","author":"H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinforma."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1007\/s00405-022-07696-x","article-title":"Identification and validation of ferroptosis-related genes for chronic rhinosinusitis with nasal polyps","volume":"280","author":"Huang","year":"2023","journal-title":"Eur. Arch. Otorhinolaryngol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"3121","DOI":"10.1002\/1521-4141(2001010)31:10<3121::aid-immu3121>3.0.co;2-4","article-title":"CD56bright cells differ in their KIR repertoire and cytotoxic features from CD56dim NK cells","volume":"31","author":"Jacobs","year":"2001","journal-title":"Eur. J. Immunol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"323","DOI":"10.3390\/md16090323","article-title":"Fucoxanthin inhibits myofibroblast differentiation and extracellular matrix production in nasal polyp-derived fibroblasts via modulation of smad-dependent and smad-independent signaling pathways","volume":"16","author":"Jung","year":"2018","journal-title":"Mar. drugs"},{"key":"B17","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1038\/s41418-022-00989-y","article-title":"Mutant p53: it\u2019s not all one and the same","volume":"29","author":"Kennedy","year":"2022","journal-title":"Cell death Differ."},{"key":"B18","doi-asserted-by":"publisher","first-page":"343","DOI":"10.4193\/Rhin19.158","article-title":"The GALEN rhinosinusitis cohort: chronic rhinosinusitis with nasal polyps affects health-related quality of life","volume":"57","author":"Khan","year":"2019","journal-title":"Rhinology"},{"key":"B19","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1164\/rccm.201710-2112OC","article-title":"Staphylococcus aureus induces a mucosal type 2 immune response via epithelial cell-derived cytokines","volume":"198","author":"Lan","year":"2018","journal-title":"Am. J. Respir. Crit. care Med."},{"key":"B20","doi-asserted-by":"publisher","first-page":"8123281","DOI":"10.1155\/2017\/8123281","article-title":"Chemical chaperone of endoplasmic reticulum stress inhibits epithelial-mesenchymal transition induced by TGF-\u03b21 in airway epithelium via the c-Src pathway","volume":"2017","author":"Lee","year":"2017","journal-title":"Mediat. Inflamm."},{"key":"B21","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1038\/s41568-020-0262-1","article-title":"p53: 800 million years of evolution and 40 years of discovery","volume":"20","author":"Levine","year":"2020","journal-title":"Nat. Rev. Cancer"},{"key":"B22","doi-asserted-by":"publisher","first-page":"5975","DOI":"10.1038\/s41388-021-01991-3","article-title":"Spontaneous and inherited TP53 genetic alterations","volume":"40","author":"Levine","year":"2021","journal-title":"Oncogene"},{"key":"B23","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1007\/s11882-017-0690-5","article-title":"Economics of chronic rhinosinusitis","volume":"17","author":"Luke","year":"2017","journal-title":"Curr. allergy asthma Rep."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1576","DOI":"10.12688\/f1000research.16409.2","article-title":"gganatogram: an R package for modular visualisation of anatograms and tissues based on ggplot2","volume":"7","author":"Maag","year":"2018","journal-title":"F1000Research"},{"key":"B26","doi-asserted-by":"publisher","first-page":"903","DOI":"10.4161\/auto.19653","article-title":"MTORC1 functions as a transcriptional regulator of autophagy by preventing nuclear transport of TFEB","volume":"8","author":"Martina","year":"2012","journal-title":"Autophagy"},{"key":"B27","doi-asserted-by":"publisher","first-page":"ra9","DOI":"10.1126\/scisignal.2004754","article-title":"The nutrient-responsive transcription factor TFE3 promotes autophagy, lysosomal biogenesis, and clearance of cellular debris","volume":"7","author":"Martina","year":"2014","journal-title":"Sci. Signal."},{"key":"B28","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.jbior.2016.10.001","article-title":"Roles of TP53 in determining therapeutic sensitivity, growth, cellular senescence, invasion and metastasis","volume":"63","author":"McCubrey","year":"2017","journal-title":"Adv. Biol. Regul."},{"key":"B29","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1038\/s41598-018-37522-6","article-title":"MITF has a central role in regulating starvation-induced autophagy in melanoma","volume":"9","author":"M\u00f6ller","year":"2019","journal-title":"Sci. Rep."},{"key":"B30","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1080\/1744666X.2023.2200164","article-title":"A review of current biomarkers in chronic rhinosinusitis with or without nasal polyps","volume":"19","author":"Nakayama","year":"2023","journal-title":"Expert Rev. Clin. Immunol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1111\/j.1365-2567.2008.03027.x","article-title":"CD56bright natural killer (NK) cells: an important NK cell subset","volume":"126","author":"Poli","year":"2009","journal-title":"Immunology"},{"key":"B32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.5604\/01.3001.0013.4121","article-title":"Tissue remodelling in chronic rhinosinusitis - review of literature","volume":"73","author":"Radajewski","year":"2019","journal-title":"Otolaryngologia polska = Pol. otolaryngology"},{"key":"B33","doi-asserted-by":"publisher","first-page":"667311","DOI":"10.3389\/fcell.2021.667311","article-title":"Folliculin: a regulator of transcription through AMPK and mTOR signaling pathways","volume":"9","author":"Ramirez Reyes","year":"2021","journal-title":"Front. cell Dev. Biol."},{"key":"B34","first-page":"71","article-title":"An improvement of the 2\u02c6(-delta delta CT) method for quantitative real-time polymerase chain reaction data analysis","volume":"3","author":"Rao","year":"2013","journal-title":"Biostat. Bioinforma. biomathematics"},{"key":"B35","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new features for data integration and network visualization","volume":"27","author":"Smoot","year":"2011","journal-title":"Bioinforma. Oxf. Engl."},{"key":"B36","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B37","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gky1131","article-title":"STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic acids Res."},{"key":"B38","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1073\/pnas.0911187107","article-title":"PINK1-dependent recruitment of Parkin to mitochondria in mitophagy","volume":"107","author":"Vives-Bauza","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B39","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1111\/pcmr.12922","article-title":"User guide to MiT-TFE isoforms and post-translational modifications","volume":"34","author":"Vu","year":"2021","journal-title":"Pigment cell & melanoma Res."},{"key":"B40","doi-asserted-by":"crossref","first-page":"e22944","DOI":"10.1016\/j.heliyon.2023.e22944","article-title":"Identification of the role of pyroptosis-related genes in chronic rhinosinusitis based on WGCNA","volume":"10","author":"Wan","year":"2023","journal-title":"Heliyon"},{"key":"B41","doi-asserted-by":"publisher","first-page":"2273121","DOI":"10.1155\/2022\/2273121","article-title":"The roles of autophagy, mitophagy, and the Akt\/mTOR pathway in the pathogenesis of chronic rhinosinusitis with nasal polyps","volume":"2022","author":"Wang","year":"2022","journal-title":"J. Immunol. Res."},{"key":"B42","doi-asserted-by":"publisher","first-page":"551","DOI":"10.14670\/HH-11-841","article-title":"Dynamin-related protein 1 (Drp1) mediating mitophagy contributes to the pathophysiology of nervous system diseases and brain injury","volume":"32","author":"Wu","year":"2017","journal-title":"Histology Histopathol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1097\/MOO.0b013e32835f80a0","article-title":"Nasal epithelial repair and remodeling in physical injury, infection, and inflammatory diseases","volume":"21","author":"Yan","year":"2013","journal-title":"Curr. Opin. otolaryngology & head neck Surg."},{"key":"B44","doi-asserted-by":"publisher","first-page":"653","DOI":"10.4168\/aair.2020.12.4.653","article-title":"Altered mitochondrial functions and morphologies in epithelial cells are associated with pathogenesis of chronic rhinosinusitis with nasal polyps","volume":"12","author":"Yoon","year":"2020","journal-title":"Allergy Asthma Immunol. Res."},{"key":"B45","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1007\/978-1-0716-0301-7_11","article-title":"Gene ontology semantic similarity analysis using GOSemSim","volume":"2117","author":"Yu","year":"2020","journal-title":"Methods Mol. Biol. Clift. NJ"},{"key":"B46","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"Omics a J. Integr. Biol."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2024.1423778\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T04:36:38Z","timestamp":1728362198000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2024.1423778\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,8]]},"references-count":46,"alternative-id":["10.3389\/fgene.2024.1423778"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2024.1423778","relation":{},"ISSN":["1664-8021"],"issn-type":[{"type":"electronic","value":"1664-8021"}],"subject":[],"published":{"date-parts":[[2024,10,8]]},"article-number":"1423778"}}