{"title":"A comprehensive bioinformatic evaluation of the NTRK family's potential as prognostic biomarkers in breast cancer.","authors":"Ramtin Mohammadi, Mohsen Ghiasi, Saber Mehdizadeh, Javad Mohammadi, Shahla Mohammad Ganji","doi":"10.1093/bioadv/vbaf030","DOIUrl":null,"url":null,"abstract":"<p><strong>Motivation: </strong>Breast cancer (BC), with its rising prevalence and mortality rate, is one of the most significant human health issues. The family of transmembrane tyrosine kinases that promote neuronal growth includes the neurotrophic tyrosine kinase receptors (NTRKs). NTRK1-3 genes encode the members of this family. Alterations of NTRK genes can induce carcinogenesis both in neurogenic and non-neurogenic cells. The prevalence of NTRK gene fusion is under 1% in solid tumours but is highly encountered in rare tumours. Since the prognostic values of NTRK families' expression in various types of cancer are becoming increasingly evident, we aimed to conduct a comprehensive bioinformatics study evaluating the prognostic significance of the NTRK family in BC. Online bioinformatic databases including TCGA, UALCAN, Kaplan-Meier plotter, bc-GenExMiner, cBioPortal, STRING, Enrichr, and TIMER were utilized for analysis.</p><p><strong>Results: </strong>High levels of NTRK2 and 3 demonstrated better associations with overall survival (OS) and recurrence-free survival (RFS) in BC patients (<i>P</i> < .05), while high levels of NTRK1 showed an applicable correlation with RFS in BC patients (<i>P</i> < .001). Our findings provide a new outlook that might aid in the field of personalized medicine and therapeutic use of NTRK as a prognostic biomarker in BC.</p><p><strong>Availability and implementation: </strong>All data generated or analysed during this study are included in this published article.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"5 1","pages":"vbaf030"},"PeriodicalIF":2.4000,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11886811/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioadv/vbaf030","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
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Abstract
Motivation: Breast cancer (BC), with its rising prevalence and mortality rate, is one of the most significant human health issues. The family of transmembrane tyrosine kinases that promote neuronal growth includes the neurotrophic tyrosine kinase receptors (NTRKs). NTRK1-3 genes encode the members of this family. Alterations of NTRK genes can induce carcinogenesis both in neurogenic and non-neurogenic cells. The prevalence of NTRK gene fusion is under 1% in solid tumours but is highly encountered in rare tumours. Since the prognostic values of NTRK families' expression in various types of cancer are becoming increasingly evident, we aimed to conduct a comprehensive bioinformatics study evaluating the prognostic significance of the NTRK family in BC. Online bioinformatic databases including TCGA, UALCAN, Kaplan-Meier plotter, bc-GenExMiner, cBioPortal, STRING, Enrichr, and TIMER were utilized for analysis.
Results: High levels of NTRK2 and 3 demonstrated better associations with overall survival (OS) and recurrence-free survival (RFS) in BC patients (P < .05), while high levels of NTRK1 showed an applicable correlation with RFS in BC patients (P < .001). Our findings provide a new outlook that might aid in the field of personalized medicine and therapeutic use of NTRK as a prognostic biomarker in BC.
Availability and implementation: All data generated or analysed during this study are included in this published article.
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