Search for Key Genes and Functional Pathways of Ulcerative Colitis to Colon Cancer Based on Bioinformatics

Wang, Shengbao; Zhen, Lingling; Li, Xiaoli; Fu, Xu; Li, Peiwu; Zhang, Dekui

doi:10.3389/fonc.2022.857148

Cited by 4 publications

(3 citation statements)

References 31 publications

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“…The NF-κB pathway has long been recognized as a classic proinflammatory signaling pathway. Increased NF-B activity indirectly encourages the development of neutrophil extracellular traps (NET), one of neutrophils' antimicrobial defense mechanisms [49]. It has been demonstrated that Sirtuin 1 (SIRT1) binds to HSF1 and controls the acetylation status of HSF1 to act as a regulator of HSF1 DNA-binding activity [50].…”

Section: Resultsmentioning

confidence: 99%

Food Toxicity of Mycotoxin Citrinin and Molecular Mechanisms of Its Potential Toxicity Effects through the Implicated Targets Predicted by Computer-Aided Multidimensional Data Analysis

Zargar

Wani

2023

Life

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The mycotoxin citrinin, which can contaminate food, is a major global concern. Citrinin is regarded as an inevitable pollutant in foods and feed since fungi are widely present in the environment. To identify contentious toxicity and lessen its severity by understanding the targets of citrinin in the human body and the impacted biosynthetic pathways, we analyzed the production of citrinin from Aspergillus flavus and Penicillium notatum and used a thorough bioinformatics analysis to characterize the toxicity and predict genes and protein targets for it. The predicted median fatal dosage (LD50) for citrinin was 105 mg/kg weight, and it belonged to toxicity class 3 (toxic if swallowed). Citrinin was found to be well absorbed by human intestinal epithelium and was a Pgp nonsubstrate (permeability glycoprotein), which means that once it is absorbed, it cannot be pumped out, hence leading to bioconcentration or biomagnification in the human body. The main targets of toxicity were casp3, TNF, IL10, IL1B, BAG3, CCNB1, CCNE1, and CDC25A, and the biological pathways implicated were signal transduction involved in DNA damage checkpoints, cellular and chemical responses to oxidative stress, DNA damage response signal transduction by P53, stress-activated protein kinase signaling cascade, netrin–UNC5B signaling, PTEN gene regulation, and immune response. Citrinin was linked to neutrophilia, squamous cell carcinoma, Fanconi anemia, leukemia, hepatoblastoma, and fatty liver diseases. The transcription factors E2F1, HSF1, SIRT1, RELA, NFKB, JUN, and MYC were found to be responsible. When data mining was performed on citrinin targets, the top five functional descriptions were a cell’s response to an organic cyclic compound, the netrin–UNC5B signaling pathway, lipids and atherosclerosis, thyroid cancer, and controlling the transcription of the PTEN gene.

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Section: Resultsmentioning

confidence: 99%

Food Toxicity of Mycotoxin Citrinin and Molecular Mechanisms of Its Potential Toxicity Effects through the Implicated Targets Predicted by Computer-Aided Multidimensional Data Analysis

Zargar

Wani

2023

Life

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“…WGCNA is a powerful tool that identifies highly collaborative gene sets and helps to discover candidate biomarkers and therapeutic targets for cancer. Besides, it helps to discover biologically significant co-expressed gene modules by analyzing the interconnectivity of gene sets and their association with phenotypes, and to study the relationship between gene networks and disease [ 14 ]. In this investigation, CAH-B-, LC- and HCC-related gene modules were analyzed using WGCNA.…”

Section: Methodsmentioning

confidence: 99%

Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis, cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques

Zhang,

Yu,

Zhou

et al. 2024

BMC Gastroenterol

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Background Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Hepatitis B virus (HBV) is one of the major causes of liver cirrhosis (LC) and HCC. Therefore, the discovery of common markers for hepatitis B or LC and HCC is crucial for the prevention of HCC. Methods Expressed genes for to chronic active hepaititis B (CAH-B), LC and HCC were obtained from the GEO and TCGA databases, and co-expressed genes were screened using Protein-protein interaction (PPI) networks, least absolute shrinkage and selection operator (LASSO), random forest (RF) and support vector machine - recursive feature elimination (SVM-RFE). The prognostic value of genes was assessed using Kaplan-Meier (KM) survival curves. Columnar line plots, calibration curves and receiver operating characteristic (ROC) curves of individual genes were used for evaluation. Validation was performed using GEO datasets. The association of these key genes with HCC clinical features was explored using the UALCAN database (https://ualcan.path.uab.edu/index.html). Results Based on WGCNA analysis and TCGA database, the co-expressed genes (565) were screened. Moreover, the five algorithms of MCODE (ClusteringCoefficient, MCC, Degree, MNC, and DMNC) was used to select one of the most important and most closely linked clusters (the top 50 genes ranked). Using, LASSO regression model, RF model and SVM-RFE model, four key genes (UBE2T, KIF4A, CDCA3, and CDCA5) were identified for subsequent research analysis. These 4 genes were highly expressed and associated with poor prognosis and clinical features in HCC patients. Conclusion These four key genes (UBE2T, KIF4A, CDCA3, and CDCA5) may be common biomarkers for CAH-B and HCC or LC and HCC, promising to advance our understanding of the molecular basis of CAH-B/LC/HCC progression.

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“…In gallbladder cancer, positive CCT2 expression was negatively correlated with low postoperative patient survival and positively correlated with high mortality ( 10 ). In our previous study, we found that CCT2 expression showed an increasing trend in normal, ulcerative colitis, and colon cancer tissues by analyzing data from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database and predicted the possibility that CCT2 may be closely associated with the development of colon inflammation or cancer and that CCT2 is a prognostic factor for colon cancer ( 11 ). Therefore, a combination of previous studies and our previous study started from CCT2 and cited the clinical data of various human cancers, genomic variants, mRNA expression, miRNA expression, methylation, and other data included in TCGA database as well as protein expression in different human tissues and organs included in the Human Protein Atlas (HPA) database in order to explore the function of the role CCT2 plays in various cancers.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive prognostic and immunological analysis of CCT2 in pan-cancer

Shi²,

Pan³

et al. 2022

Front. Oncol.

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CCT2 acts as a molecular chaperone protein that assists in the proper folding of proteins, thus ensuring a dynamic balance of cellular homeostasis. Despite increasing evidence supporting the important role of CCT2 in the tumorigenesis of certain cancers, few articles that provide a systematic pan-cancer analysis of CCT2 have been published. Hence, to evaluate the expression status and prognostic significance of CCT2 in pan-cancers, an analysis of the relationship between CCT2 and different tumor immune cell infiltrations was conducted using datasets from the Cancer Genome Atlas, Cancer Cell Lineage Encyclopedia, and so on. In most cancers, CCT2 expression was high and was associated with poor prognosis. Moreover, CCT2 gene expression was negatively correlated with infiltration of most immune cells in 10 cancer types, and CCT2 expression was related to tumor mutation burden and microsatellite instability. The role that CCT2 plays in tumorigenesis and tumor immunity suggests that it can serve as a prognostic marker in many cancers.

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Search for Key Genes and Functional Pathways of Ulcerative Colitis to Colon Cancer Based on Bioinformatics

Cited by 4 publications

References 31 publications

Food Toxicity of Mycotoxin Citrinin and Molecular Mechanisms of Its Potential Toxicity Effects through the Implicated Targets Predicted by Computer-Aided Multidimensional Data Analysis

Food Toxicity of Mycotoxin Citrinin and Molecular Mechanisms of Its Potential Toxicity Effects through the Implicated Targets Predicted by Computer-Aided Multidimensional Data Analysis

Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis, cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques

Comprehensive prognostic and immunological analysis of CCT2 in pan-cancer

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