DNA5mC Regulator-Mediated Molecular Clusters and Tumor Microenvironment Signatures in Glioblastoma DOI Creative Commons
Xinyu Yu,

Yijun Che,

Weiyang Li

et al.

Frontiers in Cell and Developmental Biology, Journal Year: 2022, Volume and Issue: 10

Published: Nov. 8, 2022

Growing evidence links DNA methylation to tumor immunity. The impact of (5 mC) on the microenvironment surrounding tumors and immunotherapy remains be clarified. Through clustering gene expression 20 regulators, this study aimed at systematically analyzing regulator patterns characteristics TCGA-GBM patients. Various subtypes glioblastoma exhibit different microenvironments patterns. Each modification was then assigned a score (DMS). High DMS associated with good prognosis. In contrast, low group had relatively survival rate. A correlation also found between high enhanced efficacy in two immune checkpoint blocking treatment cohorts. To conclude, identifying regulation may prove critical understanding progression differentiation, as well future therapeutic targets.

Language: Английский

Prediction of facial nerve outcomes after surgery for vestibular schwannoma using machine learning-based models: a systematic review and meta-analysis DOI
Bardia Hajikarimloo,

Ibrahim Mohammadzadeh,

Mohammad Ali Nazari

et al.

Neurosurgical Review, Journal Year: 2025, Volume and Issue: 48(1)

Published: Jan. 24, 2025

Language: Английский

Citations

1
Plasma Cell-Free DNA Methylation-Based Prognosis in Metastatic Castrate-Resistant Prostate Cancer DOI

Jodie Wong,

Yijun Tian,

Manishkumar S. Patel

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 21, 2025

Molecular prognostication in metastatic castration prostate cancer (mCRPC) remains challenging due to the lack of validated biomarkers. This study developed a plasma cell-free DNA (cfDNA) methylation-based prognostic model mCRPC. Targeted cfDNA methylation sequencing 96 patients different states progression revealed 78 haplotype blocks (MHBs) differentially methylated from organ-confined mCRPC states. Among these MHBs, top 20 MHBs were associated with overall survival and most MHB levels positively correlated predicted circulating tumor (ctDNA) fraction. By integrating MHB-based risk score currently available clinical variables ctDNA fraction nomogram was which showed high predictive performance for (AUC = 0.99 6 months, AUC 0.90 1 year, 0.87 2 years). These findings demonstrate potential as molecular biology-driven biomarker prognosis.

Language: Английский

Citations

0
Deciphering the Potential Causal and Prognostic Relationships Between Gut Microbiota and Brain Tumors: Insights from Genetics Analysis and Machine Learning DOI Creative Commons
Changwu Wu, Fushu Luo, Ying Zhu

et al.

Exploration, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

ABSTRACT The concept of the microbiota‐gut‐brain axis has witnessed significant advancements, and observational studies revealed dysbiosis in gut microbiota patients with brain tumors. causal relationship between tumors potential prognostic value are still unclear. Based on multiple Mendelian randomization analyses, this study confirms effects four microbes meningioma, seven pituitary tumor, eight glioma. Sherlock framework, identifies 103 meningioma‐related microbe‐related genes (MRGs), 40 tumor‐related MRGs, 63 glioma‐related MRGs expressed tissues. Almost all associated tumor grade prognosis. Lastly, model based machine learning established study, namely signature (MRS), could robustly predict prognosis glioma provide insights for immunotherapy benefits. This presents evidence tumors, which contributes to our understanding axis. prognosis, along prediction capacity MRS its association immunotherapy, provides support use as biomarkers evaluate treatment response

Language: Английский

Citations

0
Machine learning in prediction of epidermal growth factor receptor status in non-small cell lung cancer brain metastases: a systematic review and meta-analysis DOI Creative Commons
Bardia Hajikarimloo,

Ibrahim Mohammadzadeh,

Salem M. Tos

et al.

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

Published: May 1, 2025

Language: Английский

Citations

0
Lysyl oxidase-like 1 predicts the prognosis of patients with primary glioblastoma and promotes tumor invasion via EMT pathway DOI Creative Commons

Gui-Qiang Yuan,

Guoguo Zhang,

Qian-Qian Nie

et al.

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e17579 - e17579

Published: July 5, 2024

Background Lysyl oxidase enzymes (LOXs), as extracellular matrix (ECM) protein regulators, play vital roles in tumor progression by remodeling the microenvironment. However, their glioblastoma (GBM) have not been fully elucidated. Methods The genetic alterations and prognostic value of LOXs were investigated via cBioPortal. correlations between biological functions/molecular subtypes explored Cancer Genome Atlas (TCGA) Chinese Glioma (CGGA). After Kaplan‒Meier Cox survival analyses, a Loxl1-based nomogram risk score model (PRSM) constructed evaluated time-dependent receiver operating characteristic curves, calibration decision curve analyses. Tumor enrichment pathways immune infiltrates single-cell RNA sequencing TIMER. Loxl1-related changes viability/proliferation invasion further validated CCK-8, western blot, wound healing, Transwell assays. Results GBM patients with altered had poor survival. Upregulated found IDH1-wildtype mesenchymal (not Loxl1) subtypes, promoting ECM receptor interactions GBM. PRSM showed high accuracy, reliability, net clinical benefits. Loxl1 expression was related to infiltration (B cells, neutrophils, dendritic cells). knockdown suppressed cell proliferation inhibiting EMT pathway (through downregulation N-cadherin/Vimentin/Snai1 upregulation E-cadherin). Conclusion stable individualized for assessing patient prognosis, invasive role could provide promising therapeutic strategy.

Language: Английский

Citations

3
Development and validation of a predictive model in diagnosis and prognosis of primary glioblastoma patients based on Homeobox A family DOI Creative Commons
Zong-Qing Zheng,

Gui-Qiang Yuan,

Guo-Guo Zhang

et al.

Discover Oncology, Journal Year: 2023, Volume and Issue: 14(1)

Published: June 23, 2023

Homeobox A (HOXA) family is involved in the development of malignancies as either tumor suppressors or oncogenes. However, their roles glioblastoma (GBM) and clinical significance have not been fully elucidated.HOXA mutation expressions pan-cancers were investigated using GSCA Oncomine, which GBM validated by cBioPortal, Chinese Glioma Genome Atlas (CGGA), The Cancer (TCGA) datasets. Kaplan-Meier analyses conducted to determine prognostic values HOXAs at genetic mRNA levels. Diagnostic classification explored GlioVis R software. Independent identified Cox survival analyses, least absolute shrinkage selection operator (LASSO) regression, quantitative real-time PCR, immunohistochemical staining. HOXAs-based nomogram prediction model was developed evaluated analysis, time-dependent Area Under Curve, calibration plots, Decision Curve Analysis training validation cohorts.HOXAs highly mutated overexpressed pan-cancers, especially CGGA TCGA Genetic alteration expression both found be prognostic. Specific could distinguish IDH (HOXA1-7, HOXA9, HOXA13) molecular subtypes (HOXA1-2, HOXA9-11, HOXA13). HOXA1/2/3/10 confirmed independent members, with high tissues. exhibited good performance net benefits for patients cohorts.HOXA has diagnostic values, effective prediction, providing a novel approach support treatment patients.

Language: Английский

Citations

3
Development and Validation of CXCR4 Nomogram-Based Immune Infiltration/Tumor Inflammation in Primary Glioblastoma DOI Creative Commons
Guannan Jiang, Zong-Qing Zheng, Jie Zhang

et al.

Brain Sciences, Journal Year: 2023, Volume and Issue: 13(8), P. 1152 - 1152

Published: Aug. 1, 2023

Glioblastoma (GBM) is a highly malignant and aggressive tumor with poor prognosis. Therefore, the discovery of new prognostic molecular markers great significance for clinical The CXC chemokine receptor (CXCR) members play key regulatory role in many cancers. In this study, we explore value application CXCR primary glioblastoma. Two GBM datasets from Cancer Genome Atlas (TCGA) China Glioma (CGGA) databases were used to relationship between differential expression CXCRs subtypes as well immune infiltration. C-X-C motif 4 (CXCR4) was screened an independent factor, nomogram risk prediction model developed tested CGGA database using TCGA database. Receiver operating curve (ROC) decision analysis (DCA) found good accuracy net benefit models. correlation CXCR4 infiltration analyzed CancerSEA TIMER. vitro experiments, that significantly overexpressed glioblastoma closely related inflammatory response U251/U87 cells. excellent factor positively correlates inflammation.

Language: Английский

Citations

1
Alternative Splicing Factor Heterogeneous Nuclear Ribonucleoprotein U as a Promising Biomarker for Gastric Cancer Risk and Prognosis with Tumor-Promoting Properties DOI Creative Commons

Yingying Dong,

Mengya Wang,

Jingjing Jing

et al.

American Journal Of Pathology, Journal Year: 2023, Volume and Issue: 194(1), P. 13 - 29

Published: Nov. 2, 2023

Language: Английский

Citations

1
DNA5mC Regulator-Mediated Molecular Clusters and Tumor Microenvironment Signatures in Glioblastoma DOI Creative Commons
Xinyu Yu,

Yijun Che,

Weiyang Li

et al.

Frontiers in Cell and Developmental Biology, Journal Year: 2022, Volume and Issue: 10

Published: Nov. 8, 2022

Growing evidence links DNA methylation to tumor immunity. The impact of (5 mC) on the microenvironment surrounding tumors and immunotherapy remains be clarified. Through clustering gene expression 20 regulators, this study aimed at systematically analyzing regulator patterns characteristics TCGA-GBM patients. Various subtypes glioblastoma exhibit different microenvironments patterns. Each modification was then assigned a score (DMS). High DMS associated with good prognosis. In contrast, low group had relatively survival rate. A correlation also found between high enhanced efficacy in two immune checkpoint blocking treatment cohorts. To conclude, identifying regulation may prove critical understanding progression differentiation, as well future therapeutic targets.

Language: Английский

Citations

0