TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success DOI Creative Commons

Gábor Balogh,

Natasha Andressa Nogueira Jorge, Célia Dupain

et al.

Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 10, 2024

Abstract Many publicly available databases provide disease related data, that makes it possible to link genomic data medical and meta-data. The cancer genome atlas (TCGA), for example, compiles tens of thousand datasets covering a wide array types. Here we introduce an interactive highly automatized TCGA-based workflow links analyses epigenomic transcriptomic with treatment survival in order identify biomarkers indicate success. TREMSUCS-TCGA is flexible respect type provides standard methods differential expression analysis or DMR detection. Furthermore, examine several types together pan-cancer approach. Parallelisation reproducibility all steps ensured the workflowmanagement system Snakemake. produces comprehensive single report file which holds relevant results descriptive tabular form can be explored manner. As showcase application describe combination patients squamous cell carcinomas head neck, cervix lung treated cisplatin, carboplatin paclitaxel. best ranked biomarker candidates are discussed light existing literature, indicating plausible causal relationships entities.

Language: Английский

Diagnostic role of circulating long non-coding RNA LINC00312 in patients with non-small cell lung cancer: a retrospective study DOI Creative Commons

Ruoqian Zhang,

Yan Jiang, Jing Gu

et al.

BMC Cancer, Journal Year: 2025, Volume and Issue: 25(1)

Published: Jan. 9, 2025

Abstract Background LINC00312 has shown to play a suppressive role in the development and progression of non-small cell lung cancer (NSCLC). However, expression pattern diagnostic circulating NSCLC remain be confused. Methods A total 319 patients diagnosed with 180 healthy volunteers were enrolled from First Affiliated Hospital Huzhou University between January, 2022 December, 2023. The participates randomly assigned into training validation groups ratio 6:4, while remaining was named as exosomal group. Reverse transcription-quantitative PCR (RT-qPCR) employed investigate tissues, serum samples lines. Receiver operating characteristic (ROC) curve analysis carried out for distinguishing volunteers. Results Here, we revealed that lowly expressed low manifested poor prognosis. Additionally, compared volunteer group, reduction observed both groups. Further correlation indicated tightly associated lymph node metastasis, thrombus, spread through air space (STAS) status pathological type. Moreover, showed good performance distinguish higher sensitivity specificity values. Lastly, level also decreased Conclusions Taken together, these data unveil notably downregulated NSCLC, offering novel non-invasive marker diagnosis NSCLC.

Language: Английский

Citations

1
Hepatitis B Virus X Protein promotes VWF-mediated HCC progression through ST8SIA6-AS1/miR-3150b-3p/ASCL1 axis DOI
Yanqing Zhu,

Yifei Zhu,

Qinyi Deng

et al.

European Journal of Pharmacology, Journal Year: 2025, Volume and Issue: 991, P. 177315 - 177315

Published: Jan. 28, 2025

Language: Английский

Citations

0
Predictive Significance of Glycosyltransferase-Related lncRNAs in Endometrial Cancer: A Comprehensive Analysis and Experimental Validation DOI Creative Commons

Xiaoyu Shen,

Yan Liu, Jun Zhang

et al.

ACS Omega, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 24, 2025

Glycosylation is a crucial post-translational modification that regulates cellular functions and the surrounding microenvironment. The abnormal expression of glycosyltransferases, essential enzymes in this process, has been linked to tumor development. In addition, long noncoding RNAs (lncRNAs) have shown exert multifaceted regulatory influence on gene expression. Nevertheless, research glycosyltransferase-related lncRNAs (GTRLs) endometrial cancer (EC) still unclear. study, we constructed novel prognostic model based GTRLs using univariate Cox regression, Lasso, multivariate stepwise regression analysis. Our findings identified four were significantly associated with prognosis EC patients. Kaplan-Meier (KM) survival analysis revealed notable reduction overall (OS) among high-risk populations. Furthermore, independent assessments, receiver operating characteristic (ROC) curves nomograms, demonstrated risk scores derived from these outperformed other clinical variables within TCGA-UCEC data set predicting patient prognosis. And low-risk cohort exhibited increased immune infiltration decreased purity. Additionally, significant differences mutation profiles observed, burden (TMB) being higher cohort, suggesting potentially better response immunotherapy. Different subgroups also displayed varying sensitivities several chemotherapeutic agents. Finally, model's validity was confirmed through specimens vitro experiments, which AC090617.5 AP001107.9 can proliferation, migratory functions, cisplatin sensitivity EC. Therefore, features effectively predict guide therapeutic decision-making.

Language: Английский

Citations

0
TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success DOI Creative Commons

Gábor Balogh,

Natasha Andressa Nogueira Jorge, Célia Dupain

et al.

Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 10, 2024

Abstract Many publicly available databases provide disease related data, that makes it possible to link genomic data medical and meta-data. The cancer genome atlas (TCGA), for example, compiles tens of thousand datasets covering a wide array types. Here we introduce an interactive highly automatized TCGA-based workflow links analyses epigenomic transcriptomic with treatment survival in order identify biomarkers indicate success. TREMSUCS-TCGA is flexible respect type provides standard methods differential expression analysis or DMR detection. Furthermore, examine several types together pan-cancer approach. Parallelisation reproducibility all steps ensured the workflowmanagement system Snakemake. produces comprehensive single report file which holds relevant results descriptive tabular form can be explored manner. As showcase application describe combination patients squamous cell carcinomas head neck, cervix lung treated cisplatin, carboplatin paclitaxel. best ranked biomarker candidates are discussed light existing literature, indicating plausible causal relationships entities.

Language: Английский

Citations

0