GAPDH: A common housekeeping gene with an oncogenic role in pan-cancer

Wang, Jin; Yu, Xueting; Cao, Xiyuan; Tan, Lirong; Jia, Beibei; Chen, Rui; Li, Jianxiang

doi:10.1016/j.csbj.2023.07.034

Cited by 9 publications

(3 citation statements)

References 58 publications

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“…Based on our comprehensive analysis of GAPDH using this tool, we found that both GAPDH protein and RNA levels are significantly upregulated in various cancers, suggesting that GAPDH may act as an oncogene, consistent with our previous analyses using the TCGA database [18]. Regarding the regulatory mechanisms of GAPDH, our previous studies have identified its regulation in tumors through DNA methylation, copy number variations, and the transcription factor FOXM1 [18]. Other studies have shown that GAPDH plays crucial roles in tumor cell survival, angiogenesis, the regulation of gene expression in tumor cells, and the post-transcriptional regulation of tumor cell mRNA.…”

Section: Discussionsupporting

confidence: 89%

PCAS: An Integrated Tool for Multi-Dimensional Cancer Research Utilizing Clinical Proteomic Tumor Analysis Consortium Data

Wang,

Song,

Wei

et al. 2024

IJMS

Self Cite

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Proteomics offers a robust method for quantifying proteins and elucidating their roles in cellular functions, surpassing the insights provided by transcriptomics. The Clinical Proteomic Tumor Analysis Consortium database, enriched with comprehensive cancer proteomics data including phosphorylation and ubiquitination profiles, alongside transcriptomics data from the Genomic Data Commons, allow for integrative molecular studies of cancer. The ProteoCancer Analysis Suite (PCAS), our newly developed R package and Shinyapp, leverages these resources to facilitate in-depth analyses of proteomics, phosphoproteomics, and transcriptomics, enhancing our understanding of the tumor microenvironment through features like immune infiltration and drug sensitivity analysis. This tool aids in identifying critical signaling pathways and therapeutic targets, particularly through its detailed phosphoproteomic analysis. To demonstrate the functionality of the PCAS, we conducted an analysis of GAPDH across multiple cancer types, revealing a significant upregulation of protein levels, which is consistent with its important biological and clinical significance in tumors, as indicated in our prior research. Further experiments were used to validate the findings performed using the tool. In conclusion, the PCAS is a powerful and valuable tool for conducting comprehensive proteomic analyses, significantly enhancing our ability to uncover oncogenic mechanisms and identify potential therapeutic targets in cancer research.

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Section: Discussionsupporting

confidence: 89%

PCAS: An Integrated Tool for Multi-Dimensional Cancer Research Utilizing Clinical Proteomic Tumor Analysis Consortium Data

Wang,

Song,

Wei

et al. 2024

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…We found that GAPDH, commonly used as a reference gene, is significantly upregulated in most cancers and holds significant clinical relevance. Further mechanistic studies revealed its upregulation to be under the transcriptional regulation of FOXM1 [35]. This confirms the utility and reliability of this application and R package.…”

Section: Discussionsupporting

confidence: 69%

TFTF: An R-Based Integrative Tool for Decoding Human Transcription Factor–Target Interactions

Wang

2024

Biomolecules

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Transcription factors (TFs) are crucial in modulating gene expression and sculpting cellular and organismal phenotypes. The identification of TF–target gene interactions is pivotal for comprehending molecular pathways and disease etiologies but has been hindered by the demanding nature of traditional experimental approaches. This paper introduces a novel web application and package utilizing the R program, which predicts TF–target gene relationships and vice versa. Our application integrates the predictive power of various bioinformatic tools, leveraging their combined strengths to provide robust predictions. It merges databases for enhanced precision, incorporates gene expression correlation for accuracy, and employs pan-tissue correlation analysis for context-specific insights. The application also enables the integration of user data with established resources to analyze TF–target gene networks. Despite its current limitation to human data, it provides a platform to explore gene regulatory mechanisms comprehensively. This integrated, systematic approach offers researchers an invaluable tool for dissecting the complexities of gene regulation, with the potential for future expansions to include a broader range of species.

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“…Soybean isoflavones, rich in multiple phenolic hydroxyl groups, act as hydrogen donors to neutralize free radicals, thus inhibiting lipid peroxidation, reducing oxidative stress, and boosting antioxidant enzyme activity in the human body. These mechanisms contribute to a decreased incidence of AD (Wang et al, 2023).…”

Section: Molecular Dockingmentioning

confidence: 99%

Network pharmacology study on fermented soybeans for the prevention of Alzheimer's disease in older individuals

Shi,

2024

Biomedical Chromatography

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Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by the disruption of synaptic communication among millions of neurons. Recent research has highlighted the potential therapeutic effectiveness of natural polyphenolic compounds in addressing AD. Soybeans are abundant in polyphenols, and their polyphenolic composition undergoes significant alteration through fermentation by Eurotium cristatum. Through comprehensive database searches, we identified active components within fermented soybean polyphenols and genes associated with AD. Subsequently, we utilized Venn diagrams to analyze the overlap between AD‐related genes and these components. Furthermore, we visualized the network between intersecting targets and proteins using Cytoscape software. The anti‐AD effects of soybeans were further explored through comprehensive analysis, including protein–protein interaction analysis, pathway enrichment analysis, and molecular docking studies. Our investigation unveiled 6‐hydroxydaidzein as a major component of fermented soybean polyphenols, shedding light on its potential therapeutic significance in combating AD. The intersection between target proteins of fermented soybeans and disease‐related targets in AD comprised 34 genes. Protein–protein interaction analysis highlighted key potential targets, including glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH), glycogen synthase kinase 3 beta (GSK3B), amyloid precursor protein (APP), cyclin‐dependent kinase 5 (CDK5), and beta‐site APP cleaving enzyme 1 (BACE1). Molecular docking results demonstrated a robust binding effect between major components from fermented soybeans and the aforesaid key targets implicated in AD treatment. These findings suggest that fermented soybeans demonstrate a degree of efficacy and present promising prospects in the prevention of AD.

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GAPDH: A common housekeeping gene with an oncogenic role in pan-cancer

Cited by 9 publications

References 58 publications

PCAS: An Integrated Tool for Multi-Dimensional Cancer Research Utilizing Clinical Proteomic Tumor Analysis Consortium Data

PCAS: An Integrated Tool for Multi-Dimensional Cancer Research Utilizing Clinical Proteomic Tumor Analysis Consortium Data

TFTF: An R-Based Integrative Tool for Decoding Human Transcription Factor–Target Interactions

Network pharmacology study on fermented soybeans for the prevention of Alzheimer's disease in older individuals

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