{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T18:04:32Z","timestamp":1784570672610,"version":"3.55.0"},"reference-count":168,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T00:00:00Z","timestamp":1784505600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100022965","name":"Ministerio de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["Program 92191, Project 92268-Contract No. 800-2023"],"award-info":[{"award-number":["Program 92191, Project 92268-Contract No. 800-2023"]}],"id":[{"id":"10.13039\/100022965","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Canine mammary carcinoma (CMC) is a common tumor in unspayed dogs and poses a significant health concern for animals. This study aimed to identify differentially expressed genes (DEGs) between CMC and adjacent healthy mammary tissue through an integrated RNASeq bioinformatics analysis that combined an independently generated dataset from the present study, CPA-UN (CPA-UN), composed of RNA-seq data obtained from CMC and matched normal mammary tissue samples, with publicly available GEO datasets generated using next-generation sequencing (NGS). Candidate genes associated with diagnostic and prognostic potential were subsequently explored through integrative downstream analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods and findings<\/jats:title>\n                    <jats:p>\n                      DEGs were identified using DESeq2 and further analyzed for functional enrichment (ClusterProfiler, Pathview, and GSEA), co-expression gene networks, and tumor immune infiltrate deconvolution (CIBERSORTx). The GSE119810 dataset was used for exploratory overall survival (OS) analysis. Transcriptomic data from 88 CMC cases and adjacent healthy mammary tissue samples identified eight DEGs common across all four datasets. Among these,\n                      <jats:italic>ACAN<\/jats:italic>\n                      ,\n                      <jats:italic>COL11A1<\/jats:italic>\n                      ,\n                      <jats:italic>EDIL3<\/jats:italic>\n                      ,\n                      <jats:italic>NDUFA4L2<\/jats:italic>\n                      , and\n                      <jats:italic>IGFBP5<\/jats:italic>\n                      showed higher transcript levels in CMC tissues than in healthy mammary tissue, whereas\n                      <jats:italic>TNNC1<\/jats:italic>\n                      ,\n                      <jats:italic>PCK1<\/jats:italic>\n                      , and\n                      <jats:italic>METTL24<\/jats:italic>\n                      showed lower transcript levels in CMC tissues than in healthy mammary tissue. Functional enrichment analyses indicated that DEGs with higher transcript levels in CMC were predominantly associated with extracellular matrix remodeling, cell adhesion, tumor microenvironment interactions, immune and inflammatory responses, and signaling pathways involved in tumor progression and metastasis. In contrast, DEGs with lower transcript levels were mainly enriched for cytoskeletal organization and tissue structural integrity, suggesting a loss of normal mammary gland architecture and myoepithelial-associated functions during tumor progression. GSEA further demonstrated coordinated enrichment of hallmark gene sets related to cell-cycle dysregulation, proliferation, epithelial\u2013mesenchymal transition, metabolic adaptation, inflammatory signaling, and stromal remodeling, supporting the presence of integrated transcriptional programs that drive tumor progression and TME remodeling in CMC. Co-expression gene network analysis revealed a highly modular organization, with densely interconnected clusters of co-expressed genes that may reflect coordinated biological processes and regulatory programs. Exploratory CIBERSORTx analysis found no significant differences in the relative proportions of the 22 infiltrating immune cell types between CMCs and paired healthy controls after multiple-comparison corrections. Nevertheless, dataset-specific trends were observed in regulatory T cells, M1 macrophages, activated CD4 memory T cells, plasma cells, dendritic cells, and mast cells, though these findings should be interpreted cautiously. An exploratory survival analysis of 1,759 DEGs from the GSE119810 dataset identified 53 genes nominally associated with overall survival in CMC. However, none remained statistically significant after multiple-testing correction, underscoring the exploratory nature of these findings and the need for validation in larger cohorts.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>This study provides a preliminary transcriptomic framework for CMC, identifying candidate genes and pathways associated with tumor-related processes and supporting future functional validation to clarify their roles in tumorigenesis, progression, and tumor aggressiveness. However, these findings remain exploratory and require validation in larger cohorts to confirm their diagnostic and prognostic relevance, given the limitations of secondary data analyses and potential variability in tissue collection and processing across studies.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pone.0354033","type":"journal-article","created":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T17:38:16Z","timestamp":1784569096000},"page":"e0354033","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Diagnostic and prognostic values of differentially expressed genes in canine mammary carcinoma: An integrated bioinformatics analysis"],"prefix":"10.1371","volume":"21","author":[{"given":"Oscar Hern\u00e1n","family":"Rodr\u00edguez-Bejarano","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David Santiago","family":"Padilla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Alzate","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luc\u00eda","family":"Botero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni Vargas","family":"Hern\u00e1ndez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liliana","family":"L\u00f3pez-Kleine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4751-2500","authenticated-orcid":true,"given":"Manuel Alfonso","family":"Patarroyo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6084-8981","authenticated-orcid":true,"given":"Carlos A.","family":"Parra-Lopez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,7,20]]},"reference":[{"key":"pone.0354033.ref001","article-title":"Mammary tumours in dogs and its treatment option- a review","volume":"30","author":"H Fesseha","year":"2020","journal-title":"Biomed J Sci Tech Res"},{"key":"pone.0354033.ref002","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1002\/9781119181200.ch17","article-title":"Tumors of the mammary gland","author":"MH Goldschmidt","year":"2016","journal-title":"Tumors domest. anim. Hoboken, NJ, USA: John Wiley & Sons"},{"issue":"5","key":"pone.0354033.ref003","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0127381","article-title":"Epidemiological study of mammary tumors in female dogs diagnosed during the period 2002-2012: a growing animal health problem","volume":"10","author":"Y Salas","year":"2015","journal-title":"PLoS One"},{"key":"pone.0354033.ref004","first-page":"477","article-title":"Breast cancer statistics 2024","volume":"74","author":"AN Giaquinto","year":"2024","journal-title":"CA Cancer J Clin"},{"issue":"5","key":"pone.0354033.ref005","doi-asserted-by":"crossref","first-page":"2891","DOI":"10.3390\/ijms25052891","article-title":"Canine mammary tumors: classification, biomarkers, traditional and personalized therapies","volume":"25","author":"N Nosalova 5","year":"2024","journal-title":"Int J Mol Sci"},{"issue":"1","key":"pone.0354033.ref006","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1177\/0300985812447830","article-title":"Prognostic value of histological grading in noninflammatory canine mammary carcinomas in a prospective study with two-year follow-up","volume":"50","author":"L Pe\u00f1a","year":"2012","journal-title":"Vet Pathol"},{"issue":"1","key":"pone.0354033.ref007","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1177\/0300985810393258","article-title":"Classification and grading of canine mammary tumors","volume":"48","author":"M Goldschmidt","year":"2011","journal-title":"Vet Pathol"},{"issue":"3","key":"pone.0354033.ref008","doi-asserted-by":"crossref","first-page":"152","DOI":"10.24070\/bjvp.1983-0246.v17i3p152-163","article-title":"Consensus on the diagnosis, prognosis, and treatment of canine and feline mammary tumors: solid arrangement \u2013 2023","volume":"17","author":"GD Cassali","year":"2024","journal-title":"Brazilian Journal of Veterinary Pathology"},{"issue":"3","key":"pone.0354033.ref009","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1007\/s10549-017-4548-2","article-title":"Canine invasive mammary carcinomas as models of human breast cancer. Part 1: natural history and prognostic factors","volume":"167","author":"F Nguyen","year":"2018","journal-title":"Breast Cancer Res Treat"},{"issue":"2","key":"pone.0354033.ref010","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1007\/s10549-017-4542-8","article-title":"Canine invasive mammary carcinomas as models of human breast cancer. Part 2: immunophenotypes and prognostic significance","volume":"167","author":"J Abadie","year":"2018","journal-title":"Breast Cancer Res Treat"},{"key":"pone.0354033.ref011","article-title":"Canine mammary tumors as a model for human disease","author":"S Abdelmegeed","year":"2018","journal-title":"Oncol Lett"},{"key":"pone.0354033.ref012","doi-asserted-by":"crossref","first-page":"106055","DOI":"10.1016\/j.tvjl.2023.106055","article-title":"Profiling canine mammary tumors: a potential model for studying human breast cancer","volume":"303","author":"L-M Gherman","year":"2024","journal-title":"Vet J"},{"key":"pone.0354033.ref013","doi-asserted-by":"crossref","first-page":"106668","DOI":"10.1016\/j.tvjl.2026.106668","article-title":"Canine mammary carcinoma: an update","volume":"317","author":"OH Rodr\u00edguez-Bejarano","year":"2026","journal-title":"Vet J"},{"issue":"1","key":"pone.0354033.ref014","doi-asserted-by":"crossref","first-page":"3616","DOI":"10.1038\/s41467-020-17458-0","article-title":"Cross-species oncogenic signatures of breast cancer in canine mammary tumors","volume":"11","author":"T-M Kim","year":"2020","journal-title":"Nat Commun"},{"issue":"2","key":"pone.0354033.ref015","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1101\/gr.256388.119","article-title":"Modeling molecular development of breast cancer in canine mammary tumors","volume":"31","author":"K Graim","year":"2020","journal-title":"Genome Res"},{"issue":"4","key":"pone.0354033.ref016","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.neo.2021.03.001","article-title":"Identification of disease-promoting stromal components by comparative proteomic and transcriptomic profiling of canine mammary tumors using laser-capture microdissected FFPE tissue","volume":"23","author":"A P\u00f6schel","year":"2021","journal-title":"Neoplasia"},{"issue":"9","key":"pone.0354033.ref017","doi-asserted-by":"crossref","first-page":"317","DOI":"10.3390\/cancers10090317","article-title":"Transcriptome signatures of canine mammary gland tumors and its comparison to human breast cancers","volume":"10","author":"K-H Lee","year":"2018","journal-title":"Cancers (Basel)"},{"key":"pone.0354033.ref018","author":"S Andrews","year":"2010"},{"issue":"1","key":"pone.0354033.ref019","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene expression omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"R Edgar","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"15","key":"pone.0354033.ref020","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"8","key":"pone.0354033.ref021","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"D Kim","year":"2019","journal-title":"Nat Biotechnol"},{"key":"pone.0354033.ref022","doi-asserted-by":"crossref","DOI":"10.1101\/002824","article-title":"HTSeq \u2013 a Python framework to work with high-throughput sequencing data","author":"S Anders","year":"2014"},{"issue":"1","key":"pone.0354033.ref023","doi-asserted-by":"crossref","first-page":"56","DOI":"10.4103\/0970-0218.106630","article-title":"R-software: a newer tool in epidemiological data analysis","volume":"38","author":"AM Khan","year":"2013","journal-title":"Indian J Community Med"},{"key":"pone.0354033.ref024","doi-asserted-by":"crossref","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":"G Yu","year":"2012","journal-title":"Omi A J Integr Biol"},{"issue":"14","key":"pone.0354033.ref025","doi-asserted-by":"crossref","first-page":"1830","DOI":"10.1093\/bioinformatics\/btt285","article-title":"Pathview: an R\/Bioconductor package for pathway-based data integration and visualization","volume":"29","author":"W Luo","year":"2013","journal-title":"Bioinformatics"},{"issue":"11","key":"pone.0354033.ref026","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0294236","article-title":"SRplot: a free online platform for data visualization and graphing","volume":"18","author":"D Tang","year":"2023","journal-title":"PLoS One"},{"issue":"43","key":"pone.0354033.ref027","doi-asserted-by":"crossref","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":"A Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"pone.0354033.ref028","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"A Liberzon","year":"2011","journal-title":"Bioinformatics"},{"issue":"6","key":"pone.0354033.ref029","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","author":"A Liberzon","year":"2015","journal-title":"Cell Syst"},{"issue":"3","key":"pone.0354033.ref030","article-title":"ComBat-seq: batch effect adjustment for RNA-seq count data","volume":"2","author":"Y Zhang","year":"2020","journal-title":"NAR Genom Bioinform"},{"key":"pone.0354033.ref031","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","author":"H Wickham","year":"2016","journal-title":"ggplot2. Cham: Springer International Publishing"},{"key":"pone.0354033.ref032","article-title":"Transcriptome analysis of the adenoma\u2013carcinoma sequences identifies novel biomarkers associated with development of canine colorectal cancer","volume":"10","author":"Z Lin","year":"2023","journal-title":"Front Vet Sci"},{"issue":"1","key":"pone.0354033.ref033","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1038\/s42003-023-05208-z","article-title":"Transcriptional profiling of canine osteosarcoma identifies prognostic gene expression signatures with translational value for humans","volume":"6","author":"JD Mannheimer","year":"2023","journal-title":"Commun Biol"},{"issue":"2","key":"pone.0354033.ref034","article-title":"Comparative molecular life history of spontaneous canine and human gliomas","volume":"37","author":"SB Amin","year":"2020","journal-title":"Cancer Cell"},{"issue":"5","key":"pone.0354033.ref035","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nmeth.3337","article-title":"Robust enumeration of cell subsets from tissue expression profiles","volume":"12","author":"AM Newman","year":"2015","journal-title":"Nat Methods"},{"issue":"3","key":"pone.0354033.ref036","doi-asserted-by":"crossref","first-page":"243","DOI":"10.4314\/ovj.v8i3.3","article-title":"Comparative histopathology and immunohistochemistry of human and canine mammary tumors","volume":"8","author":"MA Al-Mansour","year":"2018","journal-title":"Open Vet J"},{"issue":"3","key":"pone.0354033.ref037","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.trsl.2011.11.005","article-title":"Canine tumors: a spontaneous animal model of human carcinogenesis","volume":"159","author":"SS Pinho","year":"2012","journal-title":"Transl Res"},{"issue":"1","key":"pone.0354033.ref038","first-page":"67","article-title":"Canine models of human cancer: bridging the gap to improve precision medicine","volume":"189","author":"RL Nance","year":"2022","journal-title":"Prog Mol Biol Transl Sci"},{"issue":"1","key":"pone.0354033.ref039","doi-asserted-by":"crossref","first-page":"8649","DOI":"10.1038\/s41598-017-08851-9","article-title":"Prognostic significance of EDIL3 Expression And Correlation With Mesenchymal Phenotype And Microvessel Density In Lung Adenocarcinoma","volume":"7","author":"D Jeong","year":"2017","journal-title":"Sci Rep"},{"key":"pone.0354033.ref040","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/1476-4598-13-226","article-title":"Elevated autocrine EDIL3 protects hepatocellular carcinoma from anoikis through RGD-mediated integrin activation","volume":"13","author":"M-X Feng","year":"2014","journal-title":"Mol Cancer"},{"key":"pone.0354033.ref041","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s12935-019-1066-9","article-title":"Over-expression of CDX2 alleviates breast cancer by up-regulating microRNA let-7b and inhibiting COL11A1 expression","volume":"20","author":"H Wang","year":"2020","journal-title":"Cancer Cell Int"},{"key":"pone.0354033.ref042","doi-asserted-by":"crossref","first-page":"2931","DOI":"10.2147\/IJGM.S321319","article-title":"Comprehensive analysis and identification of an immune-related gene signature with prognostic value for prostate cancer","volume":"14","author":"Y Zhang","year":"2021","journal-title":"Int J Gen Med"},{"issue":"2","key":"pone.0354033.ref043","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1007\/s10549-022-06537-z","article-title":"The early-stage triple-negative breast cancer landscape derives a novel prognostic signature and therapeutic target","volume":"193","author":"Y-S Yang","year":"2022","journal-title":"Breast Cancer Res Treat"},{"key":"pone.0354033.ref044","doi-asserted-by":"crossref","first-page":"983793","DOI":"10.3389\/fendo.2022.983793","article-title":"Biological effects and regulation of IGFBP5 in breast cancer","volume":"13","author":"J Dittmer","year":"2022","journal-title":"Front Endocrinol (Lausanne)"},{"issue":"1","key":"pone.0354033.ref045","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1007\/s10549-024-07397-5","article-title":"A novel role of IGFBP5 in the migration, invasion and spheroids formation induced by IGF-I and insulin in MCF-7 breast cancer cells","volume":"208","author":"K Rodr\u00edguez-Rojas","year":"2024","journal-title":"Breast Cancer Res Treat"},{"issue":"36","key":"pone.0354033.ref046","doi-asserted-by":"crossref","first-page":"4611","DOI":"10.3748\/wjg.v16.i36.4611","article-title":"High expression level of EDIL3 in HCC predicts poor prognosis of HCC patients","volume":"16","author":"J-C Sun","year":"2010","journal-title":"World J Gastroenterol"},{"issue":"10","key":"pone.0354033.ref047","doi-asserted-by":"crossref","first-page":"6313","DOI":"10.21037\/tcr-19-2967b","article-title":"EDIL3 regulates gastric cancer cell migration, invasion and epithelial-mesenchymal transition via TGF-\u03b21\/XIST\/miR-137 feedback loop","volume":"9","author":"L Zhang","year":"2020","journal-title":"Transl Cancer Res"},{"key":"pone.0354033.ref048","article-title":"EDIL3 is a potential prognostic biomarker that correlates with immune infiltrates in gastric cancer","volume":"11","author":"B Ke","year":"2023","journal-title":"PeerJ"},{"issue":"11","key":"pone.0354033.ref049","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1158\/2326-6066.CIR-23-0171","article-title":"EDIL3 as an angiogenic target of immune exclusion following checkpoint blockade","volume":"11","author":"S Tabasum","year":"2023","journal-title":"Cancer Immunol Res"},{"issue":"20","key":"pone.0354033.ref050","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.21037\/atm-21-4951","article-title":"COL11A1 promotes esophageal squamous cell carcinoma proliferation and metastasis and is inversely regulated by miR-335-5p","volume":"9","author":"Z Kang","year":"2021","journal-title":"Ann Transl Med"},{"issue":"26","key":"pone.0354033.ref051","doi-asserted-by":"crossref","first-page":"4503","DOI":"10.1038\/s41388-021-01865-8","article-title":"COL11A1 activates cancer-associated fibroblasts by modulating TGF-\u03b23 through the NF-\u03baB\/IGFBP2 axis in ovarian cancer cells","volume":"40","author":"Y-H Wu","year":"2021","journal-title":"Oncogene"},{"issue":"6","key":"pone.0354033.ref052","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1080\/1120009X.2021.1906031","article-title":"MiR-144-3p inhibits the proliferation, migration and invasion of lung adenocargen cancer cells by targeting COL11A1","volume":"33","author":"Y Sun","year":"2021","journal-title":"J Chemother"},{"key":"pone.0354033.ref053","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1186\/1471-2407-14-867","article-title":"Validation of COL11A1\/procollagen 11A1 expression in TGF-\u03b21-activated immortalised human mesenchymal cells and in stromal cells of human colon adenocarcinoma","volume":"14","author":"JA Galv\u00e1n","year":"2014","journal-title":"BMC Cancer"},{"issue":"4","key":"pone.0354033.ref054","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/s41419-021-03646-3","article-title":"NDUFA4L2 promotes glioblastoma progression, is associated with poor survival, and can be effectively targeted by apatinib","volume":"12","author":"Z Chen","year":"2021","journal-title":"Cell Death Dis"},{"issue":"44","key":"pone.0354033.ref055","article-title":"NDUFA4L2 is a novel biomarker for colorectal cancer through bioinformatics analysis","volume":"102","author":"Y Lin","year":"2023","journal-title":"Medicine (Baltimore)"},{"key":"pone.0354033.ref056","doi-asserted-by":"crossref","DOI":"10.3389\/fonc.2021.783856","article-title":"Mitochondrial Ndufa4l2 enhances deposition of lipids and expression of Ca9 in the TRACK model of early clear cell renal cell carcinoma","volume":"11","author":"KB Laursen","year":"2021","journal-title":"Front Oncol"},{"issue":"12","key":"pone.0354033.ref057","doi-asserted-by":"crossref","first-page":"3105","DOI":"10.1158\/1078-0432.CCR-15-1987","article-title":"NDUFA4L2 fine-tunes oxidative stress in hepatocellular carcinoma","volume":"22","author":"RK-H Lai","year":"2016","journal-title":"Clin Cancer Res"},{"issue":"4","key":"pone.0354033.ref058","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1111\/1759-7714.12984","article-title":"Mitochondrial NDUFA4L2 protein promotes the vitality of lung cancer cells by repressing oxidative stress","volume":"10","author":"L Meng","year":"2019","journal-title":"Thorac Cancer"},{"issue":"1","key":"pone.0354033.ref059","article-title":"A multidimensional pan-cancer analysis of NDUFA4L2 and verification of the oncogenic value in colon cancer","volume":"39","author":"J Yi","year":"2025","journal-title":"FASEB J"},{"issue":"1","key":"pone.0354033.ref060","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1038\/s41420-024-02240-8","article-title":"PCK1 as a target for cancer therapy: from metabolic reprogramming to immune microenvironment remodeling","volume":"10","author":"N Liu","year":"2024","journal-title":"Cell Death Discov"},{"issue":"1","key":"pone.0354033.ref061","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.gendis.2022.02.010","article-title":"PCK1 dysregulation in cancer: Metabolic reprogramming, oncogenic activation, and therapeutic opportunities","volume":"10","author":"J Xiang","year":"2022","journal-title":"Genes Dis"},{"issue":"1","key":"pone.0354033.ref062","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/s41389-023-00478-y","article-title":"MLK4 promotes glucose metabolism in lung adenocarcinoma through CREB-mediated activation of phosphoenolpyruvate carboxykinase and is regulated by KLF5","volume":"12","author":"AH-K Cheung","year":"2023","journal-title":"Oncogenesis"},{"issue":"7","key":"pone.0354033.ref063","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1158\/0008-5472.CAN-14-2615","article-title":"Upregulation of cytosolic phosphoenolpyruvate carboxykinase is a critical metabolic event in melanoma cells that repopulate tumors","volume":"75","author":"Y Li","year":"2015","journal-title":"Cancer Res"},{"issue":"5","key":"pone.0354033.ref064","doi-asserted-by":"crossref","first-page":"13571","DOI":"10.1080\/21655979.2022.2080385","article-title":"Overcoming chemoresistance to b-raf inhibitor in melanoma via targeted inhibition of phosphoenolpyruvate carboxykinase1 using 3-mercaptopropionic acid","volume":"13","author":"M Ren","year":"2022","journal-title":"Bioengineered"},{"key":"pone.0354033.ref065","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.ejca.2020.09.040","article-title":"Association of phosphoenolpyruvate carboxykinase 1 protein kinase activity-dependent sterol regulatory element-binding protein 1 activation with prognosis of oesophageal carcinoma","volume":"142","author":"F Shao","year":"2021","journal-title":"Eur J Cancer"},{"issue":"10","key":"pone.0354033.ref066","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/s41419-021-04201-w","article-title":"Identification of phosphoenolpyruvate carboxykinase 1 as a potential therapeutic target for pancreatic cancer","volume":"12","author":"X-R Zhu","year":"2021","journal-title":"Cell Death Dis"},{"issue":"8","key":"pone.0354033.ref067","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1016\/j.neo.2018.03.008","article-title":"SIRT2 promotes the migration and invasion of gastric cancer through RAS\/ERK\/JNK\/MMP-9 pathway by increasing PEPCK1-related metabolism","volume":"20","author":"Y Li","year":"2018","journal-title":"Neoplasia"},{"issue":"5","key":"pone.0354033.ref068","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1016\/j.eururo.2021.12.039","article-title":"Pre-existing castration-resistant prostate cancer-like cells in primary prostate cancer promote resistance to hormonal therapy","volume":"81","author":"Q Cheng","year":"2022","journal-title":"Eur Urol"},{"issue":"5","key":"pone.0354033.ref069","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1038\/s41416-021-01631-3","article-title":"PCK1 regulates neuroendocrine differentiation in a positive feedback loop of LIF\/ZBTB46 signalling in castration-resistant prostate cancer","volume":"126","author":"Y-C Wen","year":"2022","journal-title":"Br J Cancer"},{"issue":"19","key":"pone.0354033.ref070","doi-asserted-by":"crossref","first-page":"4949","DOI":"10.1158\/0008-5472.CAN-21-0753","article-title":"Hypoxia promotes breast cancer cell growth by activating a glycogen metabolic program","volume":"81","author":"K Tang","year":"2021","journal-title":"Cancer Res"},{"issue":"11","key":"pone.0354033.ref071","doi-asserted-by":"crossref","first-page":"1900","DOI":"10.1158\/1541-7786.MCR-21-0098","article-title":"Mutant p53 attenuates oxidative phosphorylation and facilitates cancer stemness through downregulating miR-200c-PCK2 axis in basal-like breast cancer","volume":"19","author":"C-H Chao","year":"2021","journal-title":"Mol Cancer Res"},{"issue":"1","key":"pone.0354033.ref072","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1615\/CritRevEukaryotGeneExpr.2021038907","article-title":"MiR-93-5P represses the gluconeogenesis of hepatocellular carcinoma while boosting its glycolysis and malignant progression by suppressing PCK1","volume":"32","author":"X Zhou","year":"2022","journal-title":"Crit Rev Eukaryot Gene Expr"},{"issue":"23","key":"pone.0354033.ref073","doi-asserted-by":"crossref","first-page":"3984","DOI":"10.4161\/cc.8.23.10238","article-title":"The reverse Warburg effect: aerobic glycolysis in cancer associated fibroblasts and the tumor stroma","volume":"8","author":"S Pavlides","year":"2009","journal-title":"Cell Cycle"},{"key":"pone.0354033.ref074","first-page":"101528","article-title":"Emerging roles of cytosolic phosphoenolpyruvate kinase 1 (PCK1) in cancer","volume":"35","author":"E Abate","year":"2023","journal-title":"Biochem Biophys Rep"},{"key":"pone.0354033.ref075","doi-asserted-by":"crossref","first-page":"2613","DOI":"10.2147\/OTT.S241717","article-title":"PCK1 regulates glycolysis and tumor progression in clear cell renal cell carcinoma through LDHA","volume":"13","author":"L Shi","year":"2020","journal-title":"Onco Targets Ther"},{"issue":"18","key":"pone.0354033.ref076","doi-asserted-by":"crossref","first-page":"8674","DOI":"10.7150\/thno.60233","article-title":"Deficiency of the X-inactivation escaping gene KDM5C in clear cell renal cell carcinoma promotes tumorigenicity by reprogramming glycogen metabolism and inhibiting ferroptosis","volume":"11","author":"Q Zheng","year":"2021","journal-title":"Theranostics"},{"issue":"1","key":"pone.0354033.ref077","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s40246-022-00377-0","article-title":"A glycolysis-related two-gene risk model that can effectively predict the prognosis of patients with rectal cancer","volume":"16","author":"Z Liu","year":"2022","journal-title":"Hum Genomics"},{"issue":"23","key":"pone.0354033.ref078","doi-asserted-by":"crossref","first-page":"6683","DOI":"10.1111\/febs.16111","article-title":"Oncogenic KRAS creates an aspartate metabolism signature in colorectal cancer cells","volume":"288","author":"PF Doubleday","year":"2021","journal-title":"FEBS J"},{"key":"pone.0354033.ref079","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.52135","article-title":"PCK1 and DHODH drive colorectal cancer liver metastatic colonization and hypoxic growth by promoting nucleotide synthesis","volume":"8","author":"N Yamaguchi","year":"2019","journal-title":"Elife"},{"issue":"1","key":"pone.0354033.ref080","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1186\/s12935-023-02894-x","article-title":"PCK1 activates oncogenic autophagy via down-regulation Serine phosphorylation of UBAP2L and antagonizes colorectal cancer growth","volume":"23","author":"X Zhang","year":"2023","journal-title":"Cancer Cell Int"},{"key":"pone.0354033.ref081","doi-asserted-by":"crossref","DOI":"10.3389\/fonc.2021.561247","article-title":"Prognostic impact of PCK1 protein kinase activity-dependent nuclear SREBP1 activation in non-small-cell lung carcinoma","volume":"11","author":"F Shao","year":"2021","journal-title":"Frontiers in Oncology"},{"issue":"7","key":"pone.0354033.ref082","first-page":"619","article-title":"Characterization of TNNC1 as a novel tumor suppressor of lung adenocarcinoma","volume":"43","author":"S Kim","year":"2020","journal-title":"Mol Cells"},{"key":"pone.0354033.ref083","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.bbrc.2021.02.021","article-title":"TNNC1 knockout reverses metastatic potential of ovarian cancer cells by inactivating epithelial-mesenchymal transition and suppressing F-actin polymerization","volume":"547","author":"JH Yin","year":"2021","journal-title":"Biochem Biophys Res Commun"},{"key":"pone.0354033.ref084","doi-asserted-by":"crossref","first-page":"5092","DOI":"10.1038\/ncomms6092","article-title":"Calcium-dependent FAK\/CREB\/TNNC1 signalling mediates the effect of stromal MFAP5 on ovarian cancer metastatic potential","volume":"5","author":"CS Leung","year":"2014","journal-title":"Nat Commun"},{"key":"pone.0354033.ref085","article-title":"TNNC1 reduced gemcitabine sensitivity of nonsmall-cell lung cancer by increasing autophagy","volume":"26","author":"X Ye","year":"2020","journal-title":"Med Sci Monit"},{"key":"pone.0354033.ref086","doi-asserted-by":"crossref","first-page":"1509222","DOI":"10.3389\/fimmu.2025.1509222","article-title":"Prognostic significance of calcium-related genes in lung adenocarcinoma and the role of TNNC1 in macrophage polarization and erlotinib resistance","volume":"16","author":"J Feng","year":"2025","journal-title":"Front Immunol"},{"issue":"5","key":"pone.0354033.ref087","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/s41556-019-0319-0","article-title":"RNA modifications regulating cell fate in cancer","volume":"21","author":"S Delaunay","year":"2019","journal-title":"Nat Cell Biol"},{"issue":"1","key":"pone.0354033.ref088","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1186\/s40364-024-00652-3","article-title":"METTL protein family: focusing on the occurrence, progression and treatment of cancer","volume":"12","author":"H Zhang","year":"2024","journal-title":"Biomark Res"},{"key":"pone.0354033.ref089","doi-asserted-by":"crossref","first-page":"926461","DOI":"10.3389\/fimmu.2022.926461","article-title":"A comprehensive investigation discovered the novel methyltransferase METTL24 as one presumably prognostic gene for kidney renal clear cell carcinoma potentially modulating tumor immune microenvironment","volume":"13","author":"Z Jiang","year":"2022","journal-title":"Front Immunol"},{"issue":"2","key":"pone.0354033.ref090","doi-asserted-by":"crossref","first-page":"683","DOI":"10.31557\/APJCP.2022.23.2.683","article-title":"ACAN, MDFI, and CHST1 as candidate genes in gastric cancer: a comprehensive insilco analysis","volume":"23","author":"F Vafaeie","year":"2022","journal-title":"Asian Pac J Cancer Prev"},{"issue":"1","key":"pone.0354033.ref091","doi-asserted-by":"crossref","first-page":"7590","DOI":"10.1038\/s41598-021-87037-w","article-title":"Mining the plasma-proteome associated genes in patients with gastro-esophageal cancers for biomarker discovery","volume":"11","author":"FS Vizeacoumar","year":"2021","journal-title":"Sci Rep"},{"key":"pone.0354033.ref092","doi-asserted-by":"crossref","first-page":"17588359211027836","DOI":"10.1177\/17588359211027836","article-title":"NDUFA4L2 promotes trastuzumab resistance in HER2-positive breast cancer","volume":"13","author":"Y Yuan","year":"2021","journal-title":"Ther Adv Med Oncol"},{"issue":"1","key":"pone.0354033.ref093","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1186\/s12935-024-03415-0","article-title":"Key genes and molecular mechanisms related to paclitaxel resistance","volume":"24","author":"AI Alalawy","year":"2024","journal-title":"Cancer Cell Int"},{"key":"pone.0354033.ref094","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/s41420-020-00322-x","article-title":"EDIL3 promotes epithelial-mesenchymal transition and paclitaxel resistance through its interaction with integrin \u03b1V\u03b23 in cancer cells","volume":"6","author":"J Gasca","year":"2020","journal-title":"Cell Death Discov"},{"issue":"1","key":"pone.0354033.ref095","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1007\/s11033-024-09776-z","article-title":"Nischarin inhibits the epithelial-mesenchymal transition process and angiogenesis in breast cancer cells by inactivating FAK\/ERK signaling pathway via EGF like repeats and discoidin domains 3","volume":"51","author":"R Zheng","year":"2024","journal-title":"Mol Biol Rep"},{"issue":"42","key":"pone.0354033.ref096","article-title":"Highly sensitive fluorescent detection of EDIL3 overexpressed exosomes for the diagnosis of triple-negative breast cancer","volume":"33","author":"Y-X Wei","year":"2022","journal-title":"Nanotechnology"},{"key":"pone.0354033.ref097","doi-asserted-by":"crossref","first-page":"110432","DOI":"10.1016\/j.vetimm.2022.110432","article-title":"Identification of EDIL3 biomarkers as a biomarker and potential therapeutic target of canine mammary carcinomas based on integrated bioinformatics analysis","volume":"249","author":"Z Lin","year":"2022","journal-title":"Vet Immunol Immunopathol"},{"key":"pone.0354033.ref098","doi-asserted-by":"crossref","first-page":"935860","DOI":"10.3389\/fgene.2022.935860","article-title":"COL11A1 serves as a biomarker for poor prognosis and correlates with immune infiltration in breast cancer","volume":"13","author":"Q Luo","year":"2022","journal-title":"Front Genet"},{"key":"pone.0354033.ref099","doi-asserted-by":"crossref","first-page":"937125","DOI":"10.3389\/fimmu.2022.937125","article-title":"COL11A1 as an novel biomarker for breast cancer with machine learning and immunohistochemistry validation","volume":"13","author":"W Shi","year":"2022","journal-title":"Front Immunol"},{"issue":"21","key":"pone.0354033.ref100","doi-asserted-by":"crossref","first-page":"31137","DOI":"10.18632\/oncotarget.9082","article-title":"A comprehensive expression analysis of the MIA gene family in malignancies: MIA gene family members are novel, useful markers of esophageal, lung, and cervical squamous cell carcinoma","volume":"7","author":"T Sasahira","year":"2016","journal-title":"Oncotarget"},{"key":"pone.0354033.ref101","doi-asserted-by":"crossref","first-page":"109429","DOI":"10.1016\/j.identj.2026.109429","article-title":"COL11A2 methylation as a biomarker for radiosensitivity and microenvironment remodelling in oral squamous cell carcinoma","volume":"76","author":"M Liu","year":"2026","journal-title":"Int Dent J"},{"issue":"2","key":"pone.0354033.ref102","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1007\/s10120-021-01259-5","article-title":"Cancer-associated fibroblasts-derived HAPLN1 promotes tumour invasion through extracellular matrix remodeling in gastric cancer","volume":"25","author":"T Zhang","year":"2022","journal-title":"Gastric Cancer"},{"issue":"1","key":"pone.0354033.ref103","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1186\/s13058-025-02176-6","article-title":"Secreted frizzled-related protein 2 monoclonal antibody-mediated IFN-\u03d2 reprograms tumor-associated macrophages to suppress triple negative breast cancer","volume":"27","author":"L Hsu","year":"2025","journal-title":"Breast Cancer Res"},{"key":"pone.0354033.ref104","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s12935-019-0870-6","article-title":"The role of fibromodulin in cancer pathogenesis: implications for diagnosis and therapy","volume":"19","author":"MH Pourhanifeh","year":"2019","journal-title":"Cancer Cell Int"},{"key":"pone.0354033.ref105","doi-asserted-by":"crossref","first-page":"1191980","DOI":"10.3389\/fonc.2023.1191980","article-title":"Biglycan and reduced glycolysis are associated with breast cancer cell dormancy in the brain","volume":"13","author":"A Sunderland","year":"2023","journal-title":"Front Oncol"},{"issue":"2","key":"pone.0354033.ref106","doi-asserted-by":"crossref","first-page":"11567","DOI":"10.1080\/21655979.2021.1971028","article-title":"Inhibin subunit beta A promotes cell proliferation and metastasis of breast cancer through Wnt\/\u03b2-catenin signaling pathway","volume":"12","author":"T Xueqin","year":"2021","journal-title":"Bioengineered"},{"key":"pone.0354033.ref107","first-page":"689","article-title":"Intermediate filaments in breast cancer progression, and potential biomarker for cancer therapy: a narrative review","volume":"16","author":"WA Shalannandia","year":"2024","journal-title":"Breast Cancer (Dove Med Press)"},{"key":"pone.0354033.ref108","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.lfs.2018.07.034","article-title":"TNNT1 facilitates proliferation of breast cancer cells by promoting G1\/S phase transition","volume":"208","author":"Y Shi","year":"2018","journal-title":"Life Sci"},{"issue":"6","key":"pone.0354033.ref109","doi-asserted-by":"crossref","first-page":"9513","DOI":"10.18632\/oncotarget.13434","article-title":"LMO2 promotes tumor cell invasion and metastasis in basal-type breast cancer by altering actin cytoskeleton remodeling","volume":"8","author":"Y Liu","year":"2017","journal-title":"Oncotarget"},{"key":"pone.0354033.ref110","doi-asserted-by":"crossref","first-page":"21644","DOI":"10.1038\/s41598-025-05351-z","article-title":"Surface keratin 1, a tumor-selective peptide target in human triple-negative breast cancer","volume":"15","author":"SJ Yao","year":"2025","journal-title":"Scientific Reports"},{"issue":"18","key":"pone.0354033.ref111","doi-asserted-by":"crossref","first-page":"2161","DOI":"10.1038\/onc.2010.591","article-title":"Kruppel-like factor 4 (KLF4) is required for maintenance of breast cancer stem cells and for cell migration and invasion","volume":"30","author":"F Yu","year":"2011","journal-title":"Oncogene"},{"key":"pone.0354033.ref112","doi-asserted-by":"crossref","first-page":"1079076","DOI":"10.3389\/fcell.2022.1079076","article-title":"Role of CD36 in cancer progression, stemness, and targeting","volume":"10","author":"SL Guerrero-Rodr\u00edguez","year":"2022","journal-title":"Front Cell Dev Biol"},{"issue":"8","key":"pone.0354033.ref113","doi-asserted-by":"crossref","first-page":"680","DOI":"10.3390\/cells13080680","article-title":"Decorin (DCN) downregulation activates breast stromal fibroblasts and promotes their pro-carcinogenic effects through the IL-6\/STAT3\/AUF1 signaling","volume":"13","author":"WA Aljagthmi","year":"2024","journal-title":"Cells"},{"issue":"5","key":"pone.0354033.ref114","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.3390\/cancers12051173","article-title":"Breast fibroblasts and ECM components modulate breast cancer cell migration through the secretion of MMPs in a 3D microfluidic co-culture model","volume":"12","author":"KM Lugo-Cintr\u00f3n","year":"2020","journal-title":"Cancers (Basel)"},{"issue":"8","key":"pone.0354033.ref115","doi-asserted-by":"crossref","first-page":"2995","DOI":"10.3390\/ijms21082995","article-title":"Extracellular matrix derived from high metastatic human breast cancer triggers epithelial-mesenchymal transition in epithelial breast cancer cells through \u03b1v\u03b23 integrin","volume":"21","author":"R M Brand\u00e3o-Costa","year":"2020","journal-title":"Int J Mol Sci"},{"issue":"3","key":"pone.0354033.ref116","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1021\/acs.molpharmaceut.6b00652","article-title":"Breast Cancer Targeting Peptide Binds Keratin 1: A New Molecular Marker For Targeted Drug Delivery To Breast Cancer","volume":"14","author":"R Soudy","year":"2017","journal-title":"Mol Pharm"},{"issue":"1","key":"pone.0354033.ref117","doi-asserted-by":"crossref","first-page":"9735","DOI":"10.1038\/s41598-020-66847-4","article-title":"Identification of candidate aberrantly methylated and differentially expressed genes in Esophageal squamous cell carcinoma","volume":"10","author":"B-A Han","year":"2020","journal-title":"Sci Rep"},{"issue":"6","key":"pone.0354033.ref118","first-page":"7443","article-title":"Downregulation of klotho \u03b2 is associated with invasive ductal carcinoma progression","volume":"14","author":"P Li","year":"2017","journal-title":"Oncol Lett"},{"key":"pone.0354033.ref119","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1186\/s12957-015-0642-2","article-title":"Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes","volume":"13","author":"F Liang","year":"2015","journal-title":"World J Surg Oncol"},{"issue":"5","key":"pone.0354033.ref120","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1093\/annonc\/mdy082","article-title":"MSR1 repeats modulate gene expression and affect risk of breast and prostate cancer","volume":"29","author":"AM Rose","year":"2018","journal-title":"Ann Oncol"},{"issue":"5","key":"pone.0354033.ref121","article-title":"Human tumor-associated macrophage and monocyte transcriptional landscapes reveal cancer-specific reprogramming, biomarkers, and therapeutic targets","volume":"35","author":"L Cassetta","year":"2019","journal-title":"Cancer Cell"},{"issue":"1","key":"pone.0354033.ref122","doi-asserted-by":"crossref","first-page":"2360768","DOI":"10.1080\/15384047.2024.2360768","article-title":"Circ_RPPH1 facilitates progression of breast cancer via miR-1296-5p\/TRIM14 axis","volume":"25","author":"J Jiang","year":"2024","journal-title":"Cancer Biol Ther"},{"issue":"5","key":"pone.0354033.ref123","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.tranon.2018.07.006","article-title":"Prognostic significance of CSN2, CD8, and MMR status-associated nomograms in patients with colorectal cancer","volume":"11","author":"B Zhu","year":"2018","journal-title":"Transl Oncol"},{"key":"pone.0354033.ref124","article-title":"Nrf2\u2010ARE signaling partially attenuates lipopolysaccharide\u2010induced mammary lesions via regulation of oxidative and organelle stresses but not inflammatory response in mice","author":"Y Li","year":"2021","journal-title":"Oxid Med Cell Longev"},{"issue":"6","key":"pone.0354033.ref125","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1002\/jso.24705","article-title":"Caspase14 expression is associated with triple negative phenotypes and cancer stem cell marker expression in breast cancer patients","volume":"116","author":"T Handa","year":"2017","journal-title":"J Surg Oncol"},{"issue":"1","key":"pone.0354033.ref126","doi-asserted-by":"crossref","first-page":"316","DOI":"10.18632\/aging.203795","article-title":"Deglycosylated EpCAM regulates proliferation by enhancing autophagy of breast cancer cells via PI3K\/Akt\/mTOR pathway","volume":"14","author":"L Yang","year":"2022","journal-title":"Aging (Albany NY)"},{"issue":"1","key":"pone.0354033.ref127","doi-asserted-by":"crossref","first-page":"5412","DOI":"10.3390\/ijms26115412","article-title":"Knockdown of Claudin-8 (CLDN8) indicates a link between breast cancer cell sensitivity to chemotherapeutics and reveals a potential use of CLDN8 as a molecular diagnostic and target for therapy","volume":"26","author":"W Ji","year":"2025","journal-title":"Int J Mol Sci"},{"issue":"6","key":"pone.0354033.ref128","doi-asserted-by":"crossref","first-page":"2807","DOI":"10.62347\/OXPE5390","article-title":"ESRP1 drives subtype-specific breast cancer progression through ER-regulated transcriptional programs and EMT-related splicing switch","volume":"15","author":"X Wang","year":"2025","journal-title":"Am J Cancer Res"},{"issue":"6","key":"pone.0354033.ref129","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/ncb2756","article-title":"Mechanotransduction and YAP-dependent matrix remodelling is required for the generation and maintenance of cancer-associated fibroblasts","volume":"15","author":"F Calvo","year":"2013","journal-title":"Nat Cell Biol"},{"key":"pone.0354033.ref130","article-title":"Comprehensive bioinformatics and machine learning analyses for breast cancer staging using TCGA dataset","volume":"26","author":"SC Das","year":"2024","journal-title":"Brief Bioinform"},{"key":"pone.0354033.ref131","doi-asserted-by":"crossref","first-page":"1836170","DOI":"10.3389\/fcell.2026.1836170","article-title":"TNNT3 as a candidate node in breast cancer mechanobiology: current evidence, mechanistic models, and key knowledge gaps","volume":"14","author":"L Wei","year":"2026","journal-title":"Front Cell Dev Biol"},{"issue":"1","key":"pone.0354033.ref132","doi-asserted-by":"crossref","first-page":"28","DOI":"10.3390\/metabo11010028","article-title":"Metabolic reprogramming of cancer cells during tumor progression and metastasis","volume":"11","author":"K Ohshima","year":"2021","journal-title":"Metabolites"},{"key":"pone.0354033.ref133","doi-asserted-by":"crossref","first-page":"104389","DOI":"10.1016\/j.critrevonc.2024.104389","article-title":"A review concerning the breast cancer-related tumour microenvironment","volume":"199","author":"OH Rodr\u00edguez-Bejarano","year":"2024","journal-title":"Crit Rev Oncol Hematol"},{"issue":"11","key":"pone.0354033.ref134","doi-asserted-by":"crossref","first-page":"20036","DOI":"10.1002\/jcp.28600","article-title":"A lymph node metastasis-related protein-coding genes combining with long noncoding RNA signature for breast cancer survival prediction","volume":"234","author":"Y Sui","year":"2019","journal-title":"J Cell Physiol"},{"key":"pone.0354033.ref135","article-title":"Loss of Stoml1 promotes apoptosis in gemcitabine-resistant breast cancer cells by restricting Parl-induced Pink1 degradation","author":"Q Wang","year":"2025"},{"issue":"1","key":"pone.0354033.ref136","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1007\/s11060-023-04390-8","article-title":"Signal-transducing adaptor protein 1 (STAP1) in microglia promotes the malignant progression of glioma","volume":"164","author":"X Yang","year":"2023","journal-title":"J Neurooncol"},{"key":"pone.0354033.ref137","article-title":"Relationship between STAP1 methylation in peripheral blood T cells and the clinicopathological characteristics and prognosis of patients within 5-cm diameter HCC","volume":"70","author":"L Sun","year":"2024","journal-title":"Minerva Gastroenterol"},{"key":"pone.0354033.ref138","doi-asserted-by":"crossref","DOI":"10.1177\/1533033820977547","article-title":"The lung adenocarcinoma microenvironment mining and its prognostic merit","volume":"19","author":"R Zhao","year":"2020","journal-title":"Technol Cancer Res Treat"},{"issue":"10","key":"pone.0354033.ref139","doi-asserted-by":"crossref","first-page":"3572","DOI":"10.21037\/tcr-22-1377","article-title":"Expression of NMU, PPBP and GNG4 in colon cancer and their influences on prognosis","volume":"11","author":"D Chen","year":"2022","journal-title":"Transl Cancer Res"},{"issue":"3","key":"pone.0354033.ref140","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1111\/cas.12603","article-title":"Overexpression of chemokine receptor CXCR2 and ligand CXCL7 in liver metastases from colon cancer is correlated to shorter disease-free and overall survival","volume":"106","author":"T Desurmont","year":"2015","journal-title":"Cancer Sci"},{"issue":"12","key":"pone.0354033.ref141","doi-asserted-by":"crossref","first-page":"1090","DOI":"10.1038\/s41419-021-04231-4","article-title":"Monocytes secrete CXCL7 to promote breast cancer progression","volume":"12","author":"Y-H Wang","year":"2021","journal-title":"Cell Death Dis"},{"key":"pone.0354033.ref142","doi-asserted-by":"crossref","first-page":"803","DOI":"10.2147\/IJGM.S347171","article-title":"Correlation of SIDT1 with poor prognosis and immune infiltration in patients with non-small cell lung cancer","volume":"15","author":"Y Tian","year":"2022","journal-title":"Int J Gen Med"},{"key":"pone.0354033.ref143","doi-asserted-by":"crossref","first-page":"8401","DOI":"10.2147\/OTT.S215898","article-title":"Integrated bioinformatics data analysis reveals prognostic significance of SIDT1 in triple-negative breast cancer","volume":"12","author":"Y Wang","year":"2019","journal-title":"Onco Targets Ther"},{"issue":"3","key":"pone.0354033.ref144","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1007\/s12029-022-00881-5","article-title":"Integrated analysis identifies novel fusion transcripts in laterally spreading tumors suggestive of distinct etiology than colorectal cancers","volume":"54","author":"S Rai","year":"2023","journal-title":"J Gastrointest Cancer"},{"key":"pone.0354033.ref145","doi-asserted-by":"crossref","first-page":"677111","DOI":"10.3389\/fonc.2021.677111","article-title":"The RNA-binding protein NELFE promotes gastric cancer growth and metastasis through E2F2","volume":"11","author":"C Chen","year":"2021","journal-title":"Front Oncol"},{"issue":"1","key":"pone.0354033.ref146","doi-asserted-by":"crossref","first-page":"277","DOI":"10.3892\/ol.2015.3882","article-title":"GADD45A expression is correlated with patient prognosis in esophageal cancer","volume":"11","author":"H Ishiguro","year":"2016","journal-title":"Oncol Lett"},{"issue":"34","key":"pone.0354033.ref147","article-title":"Blockade of nuclear \u03b2-catenin signaling via direct targeting of RanBP3 with NU2058 induces cell senescence to suppress colorectal tumorigenesis","volume":"9","author":"C-C Zheng","year":"2022","journal-title":"Adv Sci (Weinh)"},{"issue":"8","key":"pone.0354033.ref148","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1038\/sj.onc.1209899","article-title":"A novel amplification target, DUSP26, promotes anaplastic thyroid cancer cell growth by inhibiting p38 MAPK activity","volume":"26","author":"W Yu","year":"2007","journal-title":"Oncogene"},{"key":"pone.0354033.ref149","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2022\/6951885","article-title":"Identification of specific cervical cancer subtypes and prognostic gene sets in tumor and nontumor tissues based on GSVA analysis","author":"Z Zhong","year":"2022","journal-title":"J Oncol"},{"issue":"1","key":"pone.0354033.ref150","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1186\/s12885-022-09854-0","article-title":"The importin beta superfamily member RanBP17 exhibits a role in cell proliferation and is associated with improved survival of patients with HPV+\u2009HNSCC","volume":"22","author":"R Mandic","year":"2022","journal-title":"BMC Cancer"},{"key":"pone.0354033.ref151","doi-asserted-by":"crossref","first-page":"1817492","DOI":"10.3389\/fimmu.2026.1817492","article-title":"Comprehensive analysis of fatty acid desaturase 3 in clear cell renal cell carcinoma: insights into tumor progression, immune microenvironment, and clinical outcomes","volume":"17","author":"S-T Chen","year":"2026","journal-title":"Front Immunol"},{"key":"pone.0354033.ref152","doi-asserted-by":"crossref","first-page":"111437","DOI":"10.1016\/j.cellsig.2024.111437","article-title":"Integrative analysis of FADS3 as a marker for prognosis and immunity in head and neck squamous cell carcinoma","volume":"124","author":"H Tang","year":"2024","journal-title":"Cell Signal"},{"issue":"6","key":"pone.0354033.ref153","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.3390\/diagnostics13061169","article-title":"Identifying ITGB2 as a Potential Prognostic Biomarker in Ovarian Cancer","volume":"13","author":"C Li","year":"2023","journal-title":"Diagnostics (Basel)"},{"issue":"21","key":"pone.0354033.ref154","doi-asserted-by":"crossref","first-page":"6421","DOI":"10.3390\/jcm11216421","article-title":"The profile and clinical significance of ITGB2 expression in non-small-cell lung cancer","volume":"11","author":"L Zu","year":"2022","journal-title":"J Clin Med"},{"key":"pone.0354033.ref155","article-title":"ZCCHC17 served as a predictive biomarker for prognosis and immunotherapy in hepatocellular carcinoma","volume":"11","author":"F Liu","year":"2022","journal-title":"Frontiers in Oncology"},{"issue":"5","key":"pone.0354033.ref156","article-title":"Expression profile and prognostic value of SFN in human ovarian cancer","volume":"39","author":"Y Hu","year":"2019","journal-title":"Biosci Rep"},{"key":"pone.0354033.ref157","article-title":"The expression and clinical significance of GADD45A in breast cancer patients","volume":"6","author":"J Wang","year":"2018","journal-title":"PeerJ"},{"issue":"21","key":"pone.0354033.ref158","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.1038\/s41388-023-02686-7","article-title":"UBXN2A suppresses the Rictor-mTORC2 signaling pathway, an established tumorigenic pathway in human colorectal cancer","volume":"42","author":"S Sane","year":"2023","journal-title":"Oncogene"},{"issue":"14","key":"pone.0354033.ref159","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.2217\/fon-2018-0516","article-title":"WASF3 expression correlates with poor prognosis in gastric cancer patients","volume":"15","author":"Y Nie","year":"2019","journal-title":"Future Oncol"},{"issue":"3","key":"pone.0354033.ref160","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.3892\/ol.2014.2276","article-title":"Expression of WASF3 in patients with non-small cell lung cancer: Correlation with clinicopathological features and prognosis","volume":"8","author":"J Wu","year":"2014","journal-title":"Oncol Lett"},{"issue":"9","key":"pone.0354033.ref161","doi-asserted-by":"crossref","first-page":"2139","DOI":"10.3390\/diagnostics12092139","article-title":"Mir-29b in breast cancer: a promising target for therapeutic approaches","volume":"12","author":"S Grassilli","year":"2022","journal-title":"Diagnostics (Basel)"},{"key":"pone.0354033.ref162","doi-asserted-by":"crossref","first-page":"1424197","DOI":"10.3389\/fimmu.2024.1424197","article-title":"FAM20A: a potential diagnostic biomarker for lung squamous cell carcinoma","volume":"15","author":"Y Zhang","year":"2024","journal-title":"Front Immunol"},{"key":"pone.0354033.ref163","first-page":"14161","article-title":"Expression and functional role of miR-29b in renal cell carcinoma","volume":"8","author":"Y Xu","year":"2015","journal-title":"Int J Clin Exp Pathol"},{"issue":"4","key":"pone.0354033.ref164","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1177\/03936155241299429","article-title":"The predictive value of miR-29b-2-5p on the prognosis of cervical cancer and its inhibitory effect on cervical cancer progression","volume":"39","author":"Q Liu","year":"2024","journal-title":"Int J Biol Markers"},{"issue":"9","key":"pone.0354033.ref165","doi-asserted-by":"crossref","first-page":"2623","DOI":"10.1007\/s10620-013-2690-1","article-title":"A high level of TM4SF5 is associated with human esophageal cancer progression and poor patient survival","volume":"58","author":"Y Wu","year":"2013","journal-title":"Dig Dis Sci"},{"key":"pone.0354033.ref166","article-title":"Clinicopathological and prognostic significance of TM4SF5 in colorectal cancer","author":"Z Yu","year":"2021"},{"key":"pone.0354033.ref167","first-page":"3560340","article-title":"Bioinformatics analysis identifies ASCL1 as the key transcription factor in hepatocellular carcinoma progression","volume":"2023","author":"H-Y Zhang","year":"2023","journal-title":"Dis Markers"},{"key":"pone.0354033.ref168","doi-asserted-by":"crossref","first-page":"612393","DOI":"10.3389\/fmed.2020.612393","article-title":"Long non-coding RNAs in cancer: implications for diagnosis, prognosis, and therapy","volume":"7","author":"Y Qian","year":"2020","journal-title":"Front Med (Lausanne)"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0354033","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T17:38:38Z","timestamp":1784569118000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0354033"}},"subtitle":[],"editor":[{"given":"Alexis G. Murillo","family":"Carrasco","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,7,20]]},"references-count":168,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0354033","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,20]]}}}