Constructing a personalized prognostic risk model for colorectal cancer using machine learning and multi‐omics approach based on epithelial–mesenchymal transition‐related genes DOI

Shuze Zhang,

Wanli Fan,

He Dong

et al.

The Journal of Gene Medicine, Journal Year: 2024, Volume and Issue: 26(1)

Published: Jan. 1, 2024

Abstract The progression and the metastatic potential of colorectal cancer (CRC) are intricately linked to epithelial–mesenchymal transition (EMT) process. present study harnesses power machine learning combined with multi‐omics data develop a risk stratification model anchored on EMT‐associated genes. aim is facilitate personalized prognostic assessments in CRC. We utilized publicly accessible gene expression datasets pinpoint genes, employing CoxBoost algorithm sift through these genes for significance. resultant model, predicated levels, underwent rigorous independent validation across various datasets. Our demonstrated robust capacity segregate CRC patients into distinct high‐ low‐risk categories, each correlating markedly different survival probabilities. Notably, score emerged as an indicator High‐risk were characterized by immunosuppressive tumor milieu heightened responsiveness certain chemotherapeutic agents, underlining model's steering tailored oncological therapies. Moreover, our research unearthed putative repressive interaction between long non‐coding RNA PVT1 TIMP1 MMP1, offering new insights molecular intricacies In essence, introduces sophisticated leveraging insights, which accurately prognosticates outcomes patients, paving way more individualized effective treatment paradigms.

Language: Английский

Programmed cell death in nasopharyngeal carcinoma: Mechanisms and therapeutic targets DOI

Shen’er Qian,

Guolin Tan, Guang Lei

et al.

Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, Journal Year: 2025, Volume and Issue: 1880(1), P. 189265 - 189265

Published: Jan. 13, 2025

Language: Английский

Citations

1
Prognostic analysis of hepatocellular carcinoma based on cuproptosis -associated lncRNAs DOI Creative Commons

Mingwei Wei,

Libai Lu,

Zongjiang Luo

et al.

BMC Gastroenterology, Journal Year: 2024, Volume and Issue: 24(1)

Published: April 23, 2024

Abstract Objectives Cuproptosis represents an innovative type of cell death, distinct from apoptosis, driven by copper dependency, yet the involvement apoptosis-associated long non-coding RNAs (CRLncRNAs) in hepatocellular carcinoma (HCC) remains unclear. This study is dedicated to unveiling role and significance these apoptosis-related lncRNAs within context HCC, focusing on their impact both development disease its prognosis. Methods We conducted analysis gene transcriptomic clinical data for HCC cases sourcing information The Cancer Genome Atlas database. By incorporating cuproptosis-related genes, we established prognostic features associated with lncRNAs. Furthermore, elucidated mechanism prognosis treatment through comprehensive approaches, including Lasso Cox regression analyses, survival analyses samples, as well examinations tumor mutation burden immune function. Results developed a model featuring six lncRNAs: AC026412.3, AC125437.1, AL353572.4, MKLN1-AS, TMCC1-AS1, SLC6A1-AS1. demonstrated exceptional accuracy training validation cohorts patients tumors, showing significantly longer times those categorized low-risk group compared high-risk group. Additionally, our burden, function, Gene Ontology, Kyoto Encyclopedia Genes Genomes pathway enrichment, drug sensitivity, further potential mechanisms which cuproptosis-associated may influence outcome. Conclusions using (lncRNAs) demonstrates promising predictive capabilities immunotherapy outcomes patients. could play crucial patient management optimization immunotherapeutic strategies, offering valuable insights future research.

Language: Английский

Citations

4
Precision Prediction of Alzheimer’s Disease: Integrating Mitochondrial Energy Metabolism and Immunological Insights DOI
Wenlong Du,

Shihui Yu,

Ruiyao Liu

et al.

Journal of Molecular Neuroscience, Journal Year: 2025, Volume and Issue: 75(1)

Published: Jan. 14, 2025

Language: Английский

Citations

0
Comprehensive Analysis Reveals the Potential Diagnostic Value of Biomarkers Associated With Aging and Circadian Rhythm in Knee Osteoarthritis DOI Creative Commons
Hao Li,

Yuze Yang,

Bo Li

et al.

Orthopaedic Surgery, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

ABSTRACT Objective Knee osteoarthritis (KOA) is characterized by structural changes. Aging a major risk factor for KOA. Therefore, the objective of this study was to examine role genes related aging and circadian rhythms in Methods This identified differentially expressed (DEGs) comparing gene expression levels between normal KOA samples from GEO database. Subsequently, we intersected DEGs with aging‐related rhythm obtain set aging‐associated Next, conducted Mendelian randomization (MR) analysis, using as exposure factors, their SNPs instrumental variables, outcome event, explore causal relationship these We then performed Gene Set Enrichment Analysis (GSEA) investigate pathways associated selected biomarkers, immune infiltration built competing endogenous RNA (ceRNA) network, molecular docking studies. Additionally, findings functional roles biomarkers were further validated through experiments on human cartilage tissue cell models. Results A total 75 aging‐circadian group difference primarily enriched pathway. Two (PFKFB4 DDIT4) screened MR analysis. Then, analysis showed significant differences three types cells (resting dendritic cells, resting mast M2 macrophages), groups. Drug prediction results indicated stable binding PFKFB4 estradiol bisphenol_A, while DDIT4 binds stably nortriptyline trimipramine. Finally, lines established lentiviral infection resistance screening, significantly elevated overexpressing reversed proliferation migration ability after IL‐1 β treatment. Conclusions diagnostic therapeutic identified. Functional mechanism exploration, experimental validation elucidated KOA, offering novel perspectives prevention treatment disease.

Language: Английский

Citations

0
Identification of Prognostic Genes Related to Cell Senescence and Lipid Metabolism in Glioblastoma Based on Transcriptome and Single-Cell RNA-Seq Data DOI Open Access

Qiong Li,

Hongde Liu

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(5), P. 1875 - 1875

Published: Feb. 21, 2025

Glioblastoma (GBM) is the most aggressive primary brain cancer, with poor prognosis due to its behavior and high heterogeneity. This study aimed identify cellular senescence (CS) lipid metabolism (LM)-related prognostic genes improve GBM treatment. Transcriptome scRNA-seq data, CS-associated (CSAGs), LM-related (LMRGs) were acquired from public databases. Prognostic identified by intersecting CSAGs, LMRGs, differentially expressed (DEGs), followed WGCNA univariate Cox regression. A risk model nomogram constructed. Analyses covered clinicopathological features, immune microenvironment, somatic mutations, drug sensitivity. data key cells gene expression. SOCS1 PHB2 as markers, contributing construction of a robust excellent predictive ability. High-risk group (HRG) patients had poorer survival, higher stromal scores, distinct mutation profiles. Drug sensitivity analysis revealed significant differences in IC50 values. In microglia differentiation, showed dynamic expression patterns. These findings provide new strategies for

Language: Английский

Citations

0
Unveiling the key mechanisms of FOLR2+ macrophage-mediated antitumor immunity in breast cancer using integrated single-cell RNA sequencing and bulk RNA sequencing DOI Creative Commons
Sixuan Wu,

Jiang Baohong,

Zhimin Li

et al.

Breast Cancer Research, Journal Year: 2025, Volume and Issue: 27(1)

Published: March 5, 2025

Breast cancer (BRCA) is a common malignant tumor, and its immune microenvironment plays crucial role in disease progression. In this research, we utilized single-cell RNA sequencing bulk technologies, combined with vivo vitro experiments, to thoroughly investigate the immunological functions mechanisms of FOLR2+ macrophages BRCA. Our findings demonstrate significant enhancement interaction between CD8+ T cells within tumor tissues BRCA patients. FOLR2 closely associated cell infiltration patients, particularly cells. By secreting CXCL9 engaging CXCR3, can activate functionality cells, thereby promoting apoptosis. Further animal experiments confirm that through CXCL9-CXCR3 axis, exhibiting an antitumor immunity effect play axis.

Language: Английский

Citations

0
Identification and validation of palmitoylation-related biomarkers in gestational diabetes mellitus DOI Creative Commons
Kai Zhang,

Xiaoyang Shi,

Rongrong Bian

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 7, 2025

Palmitoylation plays a crucial role in the pathophysiology of diabetes, and an increase palmitoylation may inhibit function insulin receptors, thereby affecting progression gestational diabetes mellitus (GDM). However, its involvement (GDM) remains underexplored. This study analyzed GDM-related datasets 30 palmitoylation-related genes (PRGs), identifying MNDA, FCGR3B, AQP9 as significantly upregulated biomarkers GDM samples. Consistent with dataset analysis, reverse transcription-polymerase chain reaction (RT-qPCR) confirmed elevated expression. Comprehensive analyses, including nomogram construction, enrichment immune infiltration assessment, molecular regulatory network generation, drug prediction, docking, were conducted. The biomarker-based demonstrated excellent predictive performance for risk. enriched pathways such "Myc-targets-v1" "TNFA signaling via NFkB." Additionally, eosinophil showed strong positive correlation these biomarkers. Regulatory networks involving SH3BP5-AS1-hsa-miR-182-5p-AQP9 hsa-miR-182-5p-AQP9-ELF5 identified, stable binding energies observed between corresponding drugs. These findings provide promising avenues early screening diagnosis.

Language: Английский

Citations

0
METTL7B-induced histone lactylation prevents heart failure by ameliorating cardiac remodelling DOI Creative Commons
Zhong‐Hua Chen,

Meijun Zhong,

Yu‐Hui Lin

et al.

Journal of Molecular and Cellular Cardiology, Journal Year: 2025, Volume and Issue: 202, P. 64 - 80

Published: March 9, 2025

Language: Английский

Citations

0
Identification biomarkers and therapeutic targets of disulfidptosis-related in rheumatoid arthritis via bioinformatics, molecular dynamics simulation, and experimental validation DOI Creative Commons
Bin Xu, Hui Zhang, Bo Shen

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 13, 2025

The relationship between disulfidptosis and rheumatoid arthritis (RA) remains unclear. We aimed to identified biomarkers disulfidptosis-related in RA revealed potential targeted drugs. Two microarray datasets (GSE93272, GSE45291) related were downloaded from the Gene Expression Omnibus (GEO) database. Disulfidptosis-related genes(DRGs) extracted FerrDb GSE93272 was used identify DRGs, GSE45291 verify results. Multivariate Cox regression analysis candidate disulfidptosis-associated hub genes. differentiated values of DRGs determined by receiver operator characteristic (ROC) monofactor judge their quality as biomarkers. RT-qPCR validate expression Additionally, we analyzed connection genes filtration immune cells RA. made predictions about miRNAs, TFs possible drugs that regulate Subsequently, molecular docking carried out predict combination with targets. Finally, dynamics simulation conducted further findings. Oxoacyl-ACP Synthase Mitochondrial(OXSM) a biomarker high diagnostic value, an model based on OXSM for single gene constructed. showed accuracy distinguishing healthy controls (AUC = 0.802) validated external datasets, showing excellent power 0.982). Twelve against recognized comparative toxicogenomics database (CTD). Molecular results ICG 001 had highest binding affinity OXSM, simulations confirmed stability this complexes. Furthermore, CIBERSORT significant correlation cell infiltration regulatory network TFs-gene-miRNAs comprising 8 miRNAs 34 identified. significantly increased peripheral blood patients compared controls, consistent bioinformatics analysis. These studies suggest may be therapeutic target diagnosing RA, drug findings provide new avenues effective diagnosis treatment

Language: Английский

Citations

0
Identification and characterization of mitochondrial autophagy-related genes in osteosarcoma and predicting clinical prognosis DOI Creative Commons
Hongliang Zhang, Jingyu Zhang, Kai Zhu

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 24, 2025

Abstract Osteosarcoma (OS), the most prevalent primary malignant bone tumor, is characterized by a poor prognosis and high metastatic potential. Mitochondrial autophagy has been implicated in cancer suppression. This study aimed to identify prognostic genes associated with mitochondrial OS. Public datasets, including TARGET-OS, GSE99671, GSE21257, were retrieved for analysis. Differentially expressed (DEGs1) between OS normal samples identified from GSE99671. Single-sample Gene Set Enrichment Analysis (ssGSEA) was applied quantify enrichment scores of 29 autophagy-related (MARGs) categorizing them into high- low-score groups extract DEGs2. The intersection DEGs1 DEGs2 yielded autophagy-associated differentially (MDGs). Prognostic subsequently screened through multi-step regression analysis, risk score computed. TARGET-OS stratified low-risk based on optimal cutoff value score. GSEA conducted two groups. Additionally, associations immune microenvironment explored. A total 31 MDGs overlap 3,207 622 Five genes—KLK2, NRXN1, HES5, OR2W3, HS3ST4—were further selected. Kaplan-Meier survival analysis indicated significantly reduced high-risk group. revealed ABC transporter activity glycolysis/gluconeogenesis pathways. Immunoanalysis demonstrated significant differences 11 cell populations three functions groups, notably myeloid-derived suppressor cells (MDSCs) Type 1 T helper cells. HS3ST4 exhibited strongest positive correlation macrophages, whereas NRXN1 showed pronounced negative memory B Expressions HAVCR2 PDCD1LG2 elevated Functional dysfunction patterns five constructed model, offering novel insights diagnosis therapeutic strategies.

Language: Английский

Citations

0