Cuproptosis/OXPHOS tendency prediction of prognosis and immune microenvironment of esophageal squamous cell carcinoma: Bioinformatics analysis and experimental validation

Gene, Journal Year: 2024, Volume and Issue: 902, P. 148156 - 148156

Published: Jan. 9, 2024

Language: Английский

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A bioinformatics approach to systematically analyze the molecular patterns of monkeypox virus-host cell interactions

Heliyon, Journal Year: 2024, Volume and Issue: 10(9), P. e30483 - e30483

Published: April 29, 2024

Monkeypox has been spreading worldwide since May 2022, when the World Health Organization (WHO) declared outbreak a "public health emergency of international concern." The spread monkeypox posed serious threat to people around world, but few studies have conducted, and molecular mechanism after infection remains unclear. We therefore implemented transcriptome analysis identify signaling pathways biomarkers in monkeypox-infected cells help understand monkeypox-host cell interactions. In this study, datasets GSE36854 GSE11234 were obtained from GEO. Of these, 84 significantly different genes identified dataset GSE36854, followed by KEGG, GO protein-protein interaction (PPI) construction, Hub gene extraction. also analyzed expression regulation hub screened for drugs targeting genes. results showed that activated cellular immune response. top 10 are IER3, IFIT2, IL11, ZC3H12A, EREG, IER2, NFKBIE, FST, IFIT1 AREG. AP-26113 itraconazole can be used counteract inhibitory effect on IFIT2 serve as candidate treatment virus infection. IRF1 may transcription factor IFIT. Our provide new entry point understanding how interacts with its host.

Language: Английский

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PHE-SICH-CT-IDS: A benchmark CT image dataset for evaluation semantic segmentation, object detection and radiomic feature extraction of perihematomal edema in spontaneous intracerebral hemorrhage

Computers in Biology and Medicine, Journal Year: 2024, Volume and Issue: 173, P. 108342 - 108342

Published: March 20, 2024

Language: Английский

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Systems Biology and Machine Learning Identify Genetic Overlaps Between Lung Cancer and Gastroesophageal Reflux Disease

OMICS A Journal of Integrative Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 13, 2024

One Health and planetary health place emphasis on the common molecular mechanisms that connect several complex human diseases as well ecosystem health. For example, not only lung cancer (LC) gastroesophageal reflux disease (GERD) pose a significant burden health, but also coexistence of GERD in patients with LC is often associated poor prognosis. This study reports genetic overlaps between these two conditions using systems biology-driven bioinformatics machine learning-based algorithms. A total nine hub genes including

Language: Английский

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BiPoP: Bipolar Disorder Optimized Preprocessing Framework for Stress Disorder Identification through Gene Expression Data using Deep Learning

Engineering Technology & Applied Science Research, Journal Year: 2025, Volume and Issue: 15(2), P. 22126 - 22130

Published: April 3, 2025

Gene expression data are widely used in diagnosing diseases and identifying promising genes with the advancement computational tools biology. Expression Omnibus (GEO) datasets provide gene for various disorders. For Bipolar Disorder, GSE46449 was obtained from NCBI repository. This study aimed to classify control (Normal) case (Disordered) individuals samples using Machine Learning (ML)/Deep (DL) models. The preprocessing involved removal of null values normalization R. second step focussed on selection optimal features/genes dataset. Pearson Correlation Coefficient (PCC) along Principal Component Analysis (PCA) were feature selection. then classified ML/DL A Multi-Layer Perceptron (MLP) validate set healthy disordered individuals. proposed Disorder Preprocessing Framework (BiPoP) validated its targeted use, highlighting multifunctional fine-tuned approach achieving a classification accuracy 98.9%.

Language: Английский

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AKAP12, mediated by transcription factor 21, inhibits cell proliferation, metastasis, and glycolysis in lung squamous cell carcinoma

Open Life Sciences, Journal Year: 2025, Volume and Issue: 20(1)

Published: Jan. 1, 2025

A-kinase anchor protein 12 (AKAP12) has been reported to be related lung squamous cell carcinoma (LUSC) progression. However, its role and molecular mechanisms in LUSC have not revealed. The mRNA levels of AKAP12 transcription factor 21 (TCF21) were tested by quantitative real-time PCR western blot. Cell counting kit 8 assay, EdU flow cytometry, wound healing transwell assay used evaluate proliferation, apoptosis, migration, invasion. glycolysis was measured testing glucose consumption lactate production. interaction between TCF21 assessed ChIP dual-luciferase reporter assay. A mice xenograft model constructed explore roles vivo. Our data showed that underexpressed tissues cells, overexpression inhibited growth, metastasis, glycolysis. had decreased expression LUSC, which facilitated through binding promoter region enhance transcription. Furthermore, increased repress In vivo experiments upregulation reduced tumorigenesis, knockdown reversed this effect. conclusion, might a tumor suppressor mediated could inhibit restrain malignant

Language: Английский

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Cytotoxicity and toxicoproteomics analysis of thiazolidinedione exposure in human‐derived cardiomyocytes

Journal of Applied Toxicology, Journal Year: 2024, Volume and Issue: 44(8), P. 1214 - 1235

Published: April 23, 2024

Abstract Thiazolidinediones (TZDs) (e.g. pioglitazone and rosiglitazone), known insulin sensitiser agents for type II diabetes mellitus, exhibit controversial effects on cardiac tissue. Despite consensus their association with increased heart failure risk, limiting TZD use in management, the underlying mechanisms remain uncharacterised. Herein, we report a comprehensive vitro investigation utilising novel toxicoproteomics pipeline coupled cytotoxicity assays human adult cardiomyocytes to elucidate mechanistic insights into cardiotoxicity. The assay findings showed significant loss of mitochondrial adenosine triphosphate production upon exposure either agents, which may underpin Our analysis revealed that dysfunction primarily stems from oxidative phosphorylation impairment, distinct signalling observed both agents. cell death differed strikingly between two rosiglitazone exhibiting features caspase‐dependent apoptosis implicating mitochondrial‐mediated necroptosis, as evidenced by protein upregulation phosphoglycerate mutase family 5–dynamin‐related 1 axis. Furthermore, our additional aspects cardiotoxicity, showcasing drug specificity. downregulation various proteins involved machinery processing endoplasmic reticulum was rosiglitazone‐treated cells, proteostasis Regarding pioglitazone, suggested potential activation interplay complement coagulation systems disruption cytoskeletal architecture, mediated through integrin‐signalling pathways responsible pioglitazone‐induced myocardial contractile failure. Collectively, this study unlocks substantial insight providing rationale future optimisation antidiabetic therapies.

Language: Английский

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Integrative analysis reveals a four-gene signature for predicting survival and immunotherapy response in colon cancer patients using bulk and single-cell RNA-seq data

Frontiers in Oncology, Journal Year: 2023, Volume and Issue: 13

Published: Oct. 31, 2023

Colon cancer (CC) ranks as one of the leading causes cancer-related mortality globally. Single-cell transcriptome sequencing (scRNA-seq) offers precise gene expression data for distinct cell types. This study aimed to utilize scRNA-seq and bulk (bulk RNA-seq) from CC samples develop a novel prognostic model.scRNA-seq was downloaded GSE161277 database. R packages including "Seurat", "Harmony", "singleR" were employed categorize eight major types within normal tumor tissues. By comparing samples, differentially expressed genes (DEGs) across these identified. Gene Ontology (GO) enrichment analyses DEGs each type conducted using "Metascape". DEGs-based signature construction involved Cox regression least absolute shrinkage operator (LASSO) analyses, performed on The Cancer Genome Atlas (TCGA) training cohort. Validation occurred in GSE39582 GSE33382 datasets. pattern verified spatial (ST-seq) data. Ultimately, an established nomogram based age calibrated. Sensitivity chemotherapeutic drugs predicted with "oncoPredict" package.Using scRNA-Seq data, we examined 33,213 cells, categorizing them into samples. GO analysis revealed various pathways Among 55 identified via univariate regression, four independent emerged: PTPN6, CXCL13, SPINK4, NPDC1. Expression validation through ST-seq confirmed PTPN6 CXCL13 predominance immune while SPINK4 NPDC1 relatively epithelial cell-specific. Creating four-gene signature, Kaplan-Meier survival emphasized higher risk scores correlating unfavorable prognoses, cohorts. score emerged factor, supported by reliable nomogram. Intriguingly, drug sensitivity unveiled contrasting anti-cancer responses two groups, suggesting significant clinical implications.We developed model, may act potential therapeutic targets CC.

Language: Английский

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Cytotoxicity and Toxicoproteomic Analysis of Pioglitazone Exposure in Human-derived Cardiomyocytes

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 16, 2023

Abstract Pioglitazone (PGZ) is a peroxisome proliferator-activated receptor gamma agonist widely used as an insulin sensitiser agent for type II diabetes mellitus. The heterogeneity of PGZ effects on cardiac tissue has remained controversial, contradictory data exist in the literature. Nevertheless, consensus reported associated increased risk heart failure (HF) following chronic systemic exposure to PGZ, which hampered its clinical use management. mechanism PGZ-induced HF remains largely uncharacterised. Here, we report comprehensive vitro study combining novel toxico-proteomic pipeline with cytotoxicity assays human adult cardiomyocytes elucidate mechanistic insights into cardiotoxicity and identify driver proteins such effects. Cytotoxicity assay findings showed significant loss mitochondrial adenosine triphosphate production exposure, suggesting that this decline underpins cardiotoxicity. Interestingly, proteomics analysis revealed dysfunction was attributed mediating uncoupling ultimately cardiomyocyte death. cell death also found be related mitochondria—protein upregulation phosphoglycerate mutase family 5–dynamin-related protein 1 axis, mitochondrial-mediated necroptosis. Furthermore, our suggested potential activation interplay between complement coagulation systems disruption cytoskeletal architecture, primarily mediated through integrin-signalling pathways, responsible myocardial contractile failure. Collectively, provide substantial insight adverse may eventually rationale future optimisation antidiabetic therapies. (239 words)

Language: Английский

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A robust primary liver cancer subtype related to prognosis and drug response based on a multiple combined classifying strategy

Heliyon, Journal Year: 2024, Volume and Issue: 10(3), P. e25570 - e25570

Published: Feb. 1, 2024

The recurrence or resistance to treatment of primary liver cancer (PLL) is significantly related the heterogeneity present within tumor. In this study, we integrated prognosis risk score, mRNAsi index, and immune characteristics clustering classify patients. four subtypes obtained from combined classification are associated with PLC's drug response. these subtypes, observed mRNAsiH_ICCA subtype, intersection between high A, had worst prognosis. Specifically, B (ICC_B) sensitivity in most drugs regardless value mRNAsi. On other hand, patients low responded better ten including KU-55933 NU7441, while might benefit like Leflunomide. By matching specific each subtype drug-induced cell line expression profile, identified a group potential therapeutic that regulate disease signature genes. We developed feasible multiple typing strategy, hoping guide selection promote development precision medicine.

Language: Английский

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