Molecular Subtype Identification and Prognosis Stratification Based on Golgi Apparatus-Related Genes in Head and Neck Squamous Cell Carcinoma DOI Creative Commons

Aichun Zhang,

He Xiao, Chen Zhang

и другие.

Research Square (Research Square), Год журнала: 2023, Номер unknown

Опубликована: Сен. 27, 2023

Abstract Background : Abnormal dynamics of the Golgi apparatus reshape tumor microenvironment and immune landscape, playing a crucial role in prognosis treatment response cancer. This study aims to investigate potential apparatus-related genes (GARGs) heterogeneity head neck squamous cell carcinoma (HNSCC). Methods The transcriptional data corresponding clinical information HNSCC were obtained from public databases. GARGs with differential expression identified, those associated identified through univariate Cox regression analysis. Consensus clustering was used classify into molecular subtypes. Lasso analysis screen construct prognostic risk features for HNSCC, receiver operating characteristic curves evaluate performance model. Differences infiltration, pathological characteristics, compared between different subtypes groups. Results: A total 321 that differentially expressed out which 69 HNSCC. Based on these genes, two showed significant differences prognosis. Additionally, feature consisting 28 constructed assessing could divide high-risk low-risk groups prognosis, ROC curve indicated excellent evaluation performance. related survival outcome, grade, T stage, chemotherapy, other features. Immune response-related pathways significantly activated group better There chemotherapy drug sensitivity therapy groups, being more suitable receiving immunotherapy. Riskscore, N radiotherapy independent factors nomogram, had good applicability. Conclusions: We have are derived GARGs. GARGs-derived risgnature also developed, can be combination assessment

Язык: Английский

GAPDH Is a Novel Ferroptosis-Related Marker and Correlates with Immune Microenvironment in Lung Adenocarcinoma DOI Creative Commons
Xiaohu Ouyang, Rui Zhu, Lan Lin

и другие.

Metabolites, Год журнала: 2023, Номер 13(2), С. 142 - 142

Опубликована: Янв. 17, 2023

Lung adenocarcinoma (LUAD) is a prevalent form of lung cancer with high morbidity and fatality rates. Ferroptosis type programmed cell death that iron-dependent. Recent findings have suggested ferroptosis inducers promising prospects for the therapy LUAD. However, ferroptosis-related gene expression in LUAD its relationship tumor prognosis immune microenvironment remain unknown. We identified total 638 genes, built risk model (FRRM) help Least Absolute Shrinkage Selection Operator (LASSO) regression analysis based on The Cancer Genome Atlas (TCGA) database, split patients into high- low-risk clusters, verified utilizing Gene Expression Omnibus (GEO) database. results FRRM’s principal component (PCA) demonstrated strong predictive power. Further, univariate multivariate Cox AUC curve analyses was independent other clinical traits served as an prognostic factor. nomogram power overall survival, according to calibration plots. also explored variations characteristics, infiltration, immune-related function, functional pathways between groups. Additionally, we used protein–protein interaction (PPI) network various genes two groups search potential target genes. GAPDH then chosen follow-up investigation. An performed survival prognosis, traits, checkpoints, immunotherapy. In vitro tests further supported probable functions marker conclusion, novel gene, GAPDH, discovered, whose connected microenvironment. combination immunotherapy targeting induce may provide therapeutical option.

Язык: Английский

Процитировано

20
The Clinicopathological and Molecular Characteristics of Endocervical Gastric-Type Adenocarcinoma and the Use of Claudin18.2 as a Potential Therapeutic Target DOI Creative Commons
Jing Yang, Peng Yang, Yan Ding

и другие.

Modern Pathology, Год журнала: 2024, Номер 37(10), С. 100569 - 100569

Опубликована: Июль 25, 2024

Язык: Английский

Процитировано

5
Integrating transcriptome and metabolomics revealed the key metabolic pathway response of Amaranthus retroflexus L. to the resistance to fomesafen DOI Creative Commons

Weifeng Song,

Qinghui Wei,

Zhenghao Shi

и другие.

PLoS ONE, Год журнала: 2025, Номер 20(2), С. e0312198 - e0312198

Опубликована: Фев. 13, 2025

Background Amaranthus retroflexus L . is one of the main broad-leaved weeds in soybean fields Heilongjiang Province and an important factor affecting yield. It becoming increasingly resistant to herbicides. However, studies on transcriptome level molecular mechanism secondary metabolite accumulation varieties have not been reported. Therefore, comprehensive analysis metabolome needed determine key metabolic pathways genes Results The biosynthetic pathway resistance was studied by analysis. Transcriptome showed that three comparison groups, compared with untreated (CK) group, there were 979 Differentially expressed (DEGs) (RY) group 15731 DEGs sensitive (SY) group; RY had 13822 SY group. Fluorescent quantitative PCR detection found two gene tables related Cytochrome P450 Monooxygenase (P450), Glutathione S-transferase (GST) other enzyme systems such as peroxidase (POD), polyphenol oxidase (PPO), Catalase (CAT) Superoxide dismutase (SOD) significantly reached. Using Venn for metabolomics (VIP>1 P<0.05), 239 metabolites (DEMs) selected. There are 15 common DEMs control 8 unique This study detected 76 cases 139 CK, RY, respectively. More CK groups. viewpoint provides evidence genetic differences between sensitivity L. KEGG vs mainly enriched cysteine methlonine metabololism, glycine, serine threonine aminoacyl-tRNA biosynthesis, biosynthesis variant plant metabololites, amino acids, arginine proline cofactors. may be generated acids. Conclusion In this study, identified de novo assembly metabonomic analysis, found. might produced acid pathway. discovery laid foundation further research functional characteristics

Язык: Английский

Процитировано

0
A Golgi apparatus-related signature predicts the immune microenvironment and prognosis of gastric cancer DOI

Changlei Wu,

Liang Sun, Wenjie Zhu

и другие.

Genes and Immunity, Год журнала: 2025, Номер unknown

Опубликована: Май 7, 2025

Язык: Английский

Процитировано

0
Novel application of the ferroptosis-related genes risk model associated with disulfidptosis in hepatocellular carcinoma prognosis and immune infiltration DOI Creative Commons

Jiayan Wei,

Jinsong Wang, Xinyi Chen

и другие.

PeerJ, Год журнала: 2024, Номер 12, С. e16819 - e16819

Опубликована: Фев. 2, 2024

Hepatocellular carcinoma (HCC) stands as the prevailing manifestation of primary liver cancer and continues to pose a formidable challenge human well-being longevity, owing its elevated incidence mortality rates. Nevertheless, quest for reliable predictive biomarkers HCC remains ongoing. Recent research has demonstrated close correlation between ferroptosis disulfidptosis, two cellular processes, prognosis, suggesting their potential factors HCC. In this study, we employed combination bioinformatics algorithms machine learning techniques, leveraging RNA sequencing data, mutation profiles, clinical data from samples in The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), International Consortium (ICGC) databases, develop risk prognosis model based on genes associated with disulfidptosis. We conducted an unsupervised clustering analysis, calculating score (RS) predict using these genes. Clustering analysis revealed distinct clusters, each characterized by significantly different prognostic immune features. median RS stratified TCGA, GEO, ICGC cohorts into high-and low-risk groups. Importantly, emerged independent factor all three cohorts, high-risk group demonstrating poorer more active immunosuppressive microenvironment. Additionally, exhibited higher expression levels tumor burden (TMB), checkpoints (ICs), leukocyte antigen (HLA), heightened responsiveness immunotherapy. A stem cell infiltration similarity cells group. Furthermore, drug sensitivity highlighted significant differences response antitumor drugs summary, our model, constructed ferroptosis-related effectively predicts prognosis. These findings hold implications patient stratification decision-making, offering valuable theoretical insights field.

Язык: Английский

Процитировано

2
Bioinformatics analysis of an immunotherapy responsiveness- related gene signature in predicting lung adenocarcinoma prognosis DOI Open Access
Yupeng Jiang,

Bacha Hammad,

Hong Huang

и другие.

Translational Lung Cancer Research, Год журнала: 2024, Номер 13(6), С. 1277 - 1295

Опубликована: Июнь 1, 2024

Immune therapy has become first-line treatment option for patients with lung cancer, but some respond poorly to immune therapy, especially among adenocarcinoma (LUAD). Novel tools are needed screen potential responders in LUAD patients, better predict the prognosis and guide clinical decision-making. Although many efforts have been made responsiveness of results were limited. During era immunotherapy, this study attempts construct a novel prognostic model by utilizing differentially expressed genes (DEGs) differential responses.

Язык: Английский

Процитировано

2
Molecular subtype identification and prognosis stratification based on golgi apparatus-related genes in head and neck squamous cell carcinoma DOI Creative Commons

Aichun Zhang,

He Xiao, Chen Zhang

и другие.

BMC Medical Genomics, Год журнала: 2024, Номер 17(1)

Опубликована: Фев. 16, 2024

Abstract Background Abnormal dynamics of the Golgi apparatus reshape tumor microenvironment and immune landscape, playing a crucial role in prognosis treatment response cancer. This study aims to investigate potential apparatus-related genes (GARGs) heterogeneity head neck squamous cell carcinoma (HNSCC). Methods Transcriptional data corresponding clinical information HNSCC were obtained from public databases for differential expression analysis, consensus clustering, survival infiltration therapy assessment, gene set enrichment drug sensitivity analysis. Multiple machine learning algorithms employed construct prognostic model based on GARGs. A nomogram was used integrate visualize multi-gene with pathological features. Results total 321 GARGs that differentially expressed identified, out which 69 associated HNSCC. Based these genes, two molecular subtypes showed significant differences prognosis. Additionally, risk signature consisting 28 constructed demonstrated good performance assessing divided into high-risk low-risk groups multiple clinicopathological characteristics, including outcome, grade, T stage, chemotherapy. Immune response-related pathways significantly activated group better There chemotherapy between groups, being more suitable receiving immunotherapy. Riskscore, age, radiotherapy independent factors nomogram, had applicability. Conclusions We successfully identified are derived GARGs, can be assessment responses.

Язык: Английский

Процитировано

1
Identification of a novel prognostic signature based on vitamin metabolism clustering-related genes in lung adenocarcinoma DOI Open Access
Yu Chen, Yupeng Jiang, Xionghui Li

и другие.

Translational Lung Cancer Research, Год журнала: 2024, Номер 13(5), С. 1084 - 1100

Опубликована: Май 1, 2024

Background: Vitamins, and their metabolic processes play essential regulatory roles in controlling proliferation, differentiation, growth carcinogenesis. However, the role of vitamin metabolism lung adenocarcinoma (LUAD) has rarely been reported. Here, we established a novel prognostic model based on metabolism-related genes LUAD. Methods: In this research, aimed to identify associated with differentially expressed (DEGs) LUAD utilizing The Cancer Genome Atlas (TCGA)-LUAD, GSE68465 GSE72094 data. Unsupervised clustering classified patients into distinct subgroups. By least absolute shrinkage selection operator (LASSO)-Cox regression analysis, could be used construct model. Then gene-related risk score (VRS) was calculated best cut-off splitting. Kaplan-Meier time-dependent receiver operating characteristic (ROC) univariate multivariate Cox analyses, chemotherapeutic drugs sensitivity immune infiltration analysis nomogram were conducted verify our models' accuracy. Finally, CPS1 identified as relevant diagnostic marker using Random Forests algorithms, single-cell RNA sequencing data confirm its expression. Results: We investigated relationship between patterns, overall survival (OS), levels A signature consisting 11 developed, which able classify high low VRS groups. Through gene enrichment cell cycle mainly enriched. Compared group, group exhibited poorer OS, demonstrated by analysis. Furthermore, an independent predictor poor prognosis indicated both analyses. Additionally, constructed improve accuracy predictions patients. also found that two groups might respond differently targets anti-tumor drugs. expression confirmed Conclusions: Overall, findings suggest can influence patients, represents potentially helpful resource for predicting patient outcomes informing clinical decision-making.

Язык: Английский

Процитировано

1
Prognostic Significance of Ribosome-related Genes Signature in Diffuse Large B Cell Lymphoma DOI Creative Commons
Wenqi Wu, Jinhuan Wang,

Yanan Jiang

и другие.

Journal of Cancer, Год журнала: 2023, Номер 14(3), С. 403 - 416

Опубликована: Янв. 1, 2023

Background: The diffuse large B-cell lymphoma (DLBCL) is a heterogeneous with dismal outcome, due to approximately 40% patients will be relapsed or refractory the standard therapy of rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP). Therefore, we need urgently explore approach classify risk DLBCL accurately targeting therapy. ribosome vital cellular organelle that mainly responsible for translation mRNA into protein, moreover, more reports revealed was associated proliferation tumorigenesis. our study aimed construct prognostic model using ribosome-related genes (RibGs). Method: We screened differentially expressed RibGs between healthy donors' B cells patients' malignant in GSE56315 dataset. Next, performed analyses univariate Cox regression, least absolute shrinkage selection operator (LASSO) regression multivariate establish consisting 15 GSE10846 training set. Then, validated by range including Kaplan-Meier survival, ROC curve, nomogram validation cohorts. Results: showed reliably predictive capability. found upregulated pathways high-risk group most innate immune reaction such as interferon response, complement inflammatory responses. In addition, age, gender, IPI score constructed help explain model. also discovered were sensitive some certain drugs. Finally, knocking out NLE1 could inhibit cell lines. Conclusion: As far know, it first time predict prognosis give new sight treatment. Importantly, acted supplementary classifying patients.

Язык: Английский

Процитировано

3
Prognostic value of GARS in bladder cancer and its role in the tumor microenvironment DOI Open Access

Kaifei Chen,

Shuaiqi Chen,

Shangrong Wu

и другие.

Translational Cancer Research, Год журнала: 2024, Номер 13(6), С. 2825 - 2846

Опубликована: Июнь 1, 2024

Background: Bladder cancer (BC), as a common type of cancer, has poor prognosis, also some invasive prognostic or therapeutic markers are difficult to obtain, which makes further treatment BC difficult. Glycyl-tRNA synthetase (GARS), one the aminoacyl-tRNA synthetases that charge tRNAs with their cognate amino acids, been identified target in many diseases, including tumors.

Язык: Английский

Процитировано

0