Mechanism and engineering of endoplasmic reticulum-localized membrane protein folding in Saccharomyces cerevisiae

Metabolic Engineering, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Язык: Английский

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Uncovering latent biological function associations through gene set embeddings

BMC Bioinformatics, Год журнала: 2025, Номер 26(1)

Опубликована: Март 24, 2025

Abstract Background The complexity of biological systems has increasingly been unraveled through computational methods, with network analysis now focusing on the construction and exploration well-defined interaction networks. Traditional graph-theoretical approaches have instrumental in mapping key processes using high-confidence data. However, these methods often struggle incomplete or/and heterogeneous datasets. In this study, we extend beyond conventional bipartite models by integrating attribute-driven knowledge from Molecular Signatures Database (MSigDB) node2vec algorithm. Results Our approach explores unsupervised relationships uncovers potential associations between genes terms connectivity analysis. By embedding both human mouse data into a shared vector space, validate our findings cross-species, further strengthening robustness method. Conclusions This integrative framework reveals expected novel insights, offering comprehensive perspective that complements traditional paves way for deeper understanding complex diseases.

Язык: Английский

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Pan-cancer analysis reveals immunological and prognostic significance of CCT5 in human tumors

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Апрель 24, 2025

Abstract The chaperonin containing TCP1 subunit 5 (CCT5) is believed to function as a tumor driver. However, systematic pan-cancer analysis of CCT5 still lacking. Therefore, this study aimed identify the potential role in different types tumors. This comprehensively investigated gene expression, proteomic immune infiltration, DNA methylation, genetic alterations, correlation with TMB and MSI, drug sensitivity, enrichment analysis, prognostic significance 33 tumors based on TIMER2.0, GEPIA2, UALCAN, SMART, cBioPortal, GSCA databases, TCGAplot R package. results revealed significant overexpression most was significantly associated poor OS DFS types. Reduced promoter N-shore methylation CCT5, indicating its oncogenic epigenetic roles. Amplification common type alterations. Immune infiltration strong between cells. exhibited MSI KIRC STAD. Furthermore, associations cell cycle pathway various cellular functions. These findings suggested that might serve biomarker target for immunotherapy cancers.

Язык: Английский

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Erythropoiesis and Gene Expression Analysis in Erythroid Progenitor Cells Derived from Patients with Hemoglobin H/Constant Spring Disease

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(20), С. 11246 - 11246

Опубликована: Окт. 19, 2024

Hemoglobin H/Constant Spring (Hb H/CS) disease represents a form of non-deletional Hb H characterized by chronic hemolytic anemia that ranges from moderate to severe and may lead transfusion-dependent thalassemia. To study the underlying mechanisms this disease, we conducted an analysis erythropoiesis gene expression in erythroid progenitor cells derived CD34+ hematopoietic stem/progenitor patients with H/CS normal controls. Twelve five controls were enrolled. Peripheral blood samples collected isolate for cell proliferation differentiation. Six three subsequently studied next generation sequencing analysis. Erythroid exhibited trend towards increased rates decreased viability compared those Moreover, demonstrated delayed terminal Gene profiling revealed elevated levels genes encoding molecular chaperones, including heat shock protein (HSPs) chaperonin containing TCP-1 subunit (CCTs) group. In summary, exhibit heightened proliferation, diminished viability, Additionally, chaperones was observed, providing information on potential pathophysiological mechanisms.

Язык: Английский

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Airborne fine particulate matter exposure induces transcriptomic alterations resembling asthmatic signatures: Insights from integrated omics analysis

Current Zoology, Год журнала: 2024, Номер 11(1)

Опубликована: Янв. 1, 2024

Abstract Fine particulate matter (PM2.5), an atmospheric pollutant that settles deep in the respiratory tract, is highly harmful to human health. Despite its well-known impact on lung function and ability exacerbate asthma, molecular basis of this effect not fully understood. This integrated transcriptomic epigenomic data analysis from publicly available datasets aimed determine PM2.5 exposure association with asthma airway epithelial cells. Differential gene expression binding analyses identified 349 common differentially expressed genes associated enriched H3K27ac regions both conditions. Co-expression network revealed three preserved modules (Protein Folding, Cell Migration, Hypoxia Response) significantly correlated networks. Pathways dysregulated conditions included function, hypoxia response, interleukin-17 TNF signaling, immune/inflammatory processes. Hub like TGFB2, EFNA5, PFKFB3 were implicated remodeling, cell migration, hypoxia-induced glycolysis. These findings elucidate altered patterns processes between helping understand their connection. provides guidance for future research utilize them as potential biomarkers or therapeutic targets generates evidence supporting need implementing effective air quality management strategies.

Язык: Английский

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The role of CCT5 in human tumors: a pan-cancer analysis

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Июнь 13, 2024

CCT5, a molecular chaperone protein, was analyzed in 33 different tumor types by pan-cancer analysis. This study investigated various aspects such as gene expression, proteomic immune infiltration, DNA methylation, genetic alterations, survival, enrichment analysis, and prognostic significance. The results showed that CCT5 is highly expressed most tumors, its overexpression associated with poor overall disease-free well prognosis types. Immune infiltration analysis revealed correlation between cancer-associated fibroblasts (CAFs), CD8 + T cells, NK the of patients significantly correlated expression these three tumor-infiltrating cells. suggested regulates number thereby affecting tumors. Enrichment association cell cycle RNA-binding pathways. reduced promoter N-shore indicating potential oncogenic epigenetic roles. These findings suggest may serve biomarker target for immunotherapy cancer proliferation development.

Язык: Английский

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