Research and Clinical Significance of the Differentially Expressed Genes TP63 and LMO4 in Human Immunodeficiency Virus-related Penile Squamous Cell Carcinoma

2021 ◽  
Author(s):  
Wenrui Xue ◽  
Xin Zheng ◽  
Xiaopeng Hu ◽  
Yu Zhang
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Squamous Cell ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Control Group ◽  
Significant Pathway ◽  
Penile Squamous Cell Carcinoma

Abstract Background: To study the differential gene expression and clinical significance in HIVIIs (human immunodeficiency virus-infected individuals) with penile squamous cell carcinoma.Methods: At our hospital from 2019 to 2020, we selected 6 samples of HIV-related penile squamous cell carcinoma for the experimental group and 6 samples of non-HIV-related penile squamous cell carcinoma for the control group. Transcriptome sequencing of sample mRNAs was performed by high-throughput sequencing. Differential gene expression analysis, differential GO (Gene Ontology) enrichment analysis and differential KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were carried out, and the RPKM (reads per kilobase per million reads) value was used as a measure of gene expression.Results: A total of 2418 differentially expressed genes were obtained, of which 663 were upregulated and 1755 were downregulated (absolute value of logFC >1.0 and p value<0.05 FDR < 0.05). On the basis of the significance of the GO enrichment analysis, we found that the TP63 (tumor protein p63) gene was significantly upregulated and that the LMO4 (LIM domain only 4) gene was significantly downregulated in the experimental group compared with the control group. KEGG pathway analysis of the differentially expressed genes revealed that DNA replication was the most significant pathway associated with the upregulated genes and CAM (cell adhesion molecule) metabolism was the most significant pathway associated with the downregulated genes.Conclusions: The gene expression profiles of HIV-related penile squamous cell carcinoma and non-HIV-related penile squamous cell carcinoma are significantly different and involve significant GO enrichment and KEGG metabolic pathways, and this is very meaningful for the study of NADCs (non-AIDS-defining cancers). Differential expression of genes may be an important target for the prevention of penile squamous cell carcinoma in HIVIIs.

scholarly journals Research and Clinical Significance of the Differentially Expressed Genes TP63 and LMO4 in Human Immunodeficiency Virus-Related Penile Squamous Cell Carcinoma

2021 ◽  
Vol 15 (2) ◽  
pp. 155798832110113
Author(s):  
Wenrui Xue ◽  
Xin Zheng ◽  
Xiaopeng Hu ◽  
Yu Zhang
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Squamous Cell ◽  
Differentially Expressed ◽  
Control Group ◽  
Go Enrichment ◽  
Differential Gene ◽  
Penile Squamous Cell Carcinoma

To study the differential gene expression and clinical significance in human immunodeficiency virus-infected individuals (HIVIIs) with penile squamous cell carcinoma. At our hospital from 2019 to 2020, we selected six samples of HIV-related penile squamous cell carcinoma for the experimental group and six samples of non-HIV-related penile squamous cell carcinoma for the control group. Transcriptome sequencing of sample mRNAs was performed by high-throughput sequencing. Differential gene expression analysis, differential Gene Ontology (GO) enrichment analysis and differential Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out, and the reads per kilobase per million reads (RPKM) value was used as a measure of gene expression. A total of 2418 differentially expressed genes were obtained, of which 663 were upregulated and 1755 were downregulated (absolute value of logFC >1 and p value <.05). On the basis of the significance of the GO enrichment analysis, we found that the tumor protein p63 (TP63) gene was significantly upregulated and that the LIM domain only 4 (LMO4) gene was significantly downregulated in the experimental group compared with the control group. KEGG pathway analysis of the differentially expressed genes revealed that DNA replication was the most significant pathway associated with the upregulated genes and cell adhesion molecule (CAM) metabolism was the most significant pathway associated with the downregulated genes. The gene expression profiles of HIV-related penile squamous cell carcinoma and non-HIV-related penile squamous cell carcinoma are significantly different and involve significant GO enrichment and KEGG metabolic pathways, and this is very meaningful for the study of non-AIDS-defining cancers (NADCs). Differential expression of genes may be an important target for the prevention of penile squamous cell carcinoma in HIVIIs.

scholarly journals Identifying the p65-Dependent Effect of Sulforaphene on Esophageal Squamous Cell Carcinoma Progression via Bioinformatics Analysis

2020 ◽  
Vol 22 (1) ◽  
pp. 60
Author(s):  
Sichong Han ◽  
Zhe Wang ◽  
Jining Liu ◽  
Qipeng Yuan
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Squamous Cell ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Dependent Manner

Understanding the mechanism by which sulforaphene (SFE) affects esophageal squamous cell carcinoma (ESCC) contributes to the application of this isothiocyanate as a chemotherapeutic agent. Thus, we attempted to investigate SFE regulation of ESCC characteristics more deeply. We performed gene set enrichment analysis (GSEA) on microarray data of SFE-treated ESCC cells and found that differentially expressed genes are enriched in TNFα_Signaling_via_the_NFκB_Pathway. Coupled with the expression profile data from the GSE20347 and GSE75241 datasets, we narrowed the set to 8 genes, 4 of which (C-X-C motif chemokine ligand 10 (CXCL10), TNF alpha induced protein 3 (TNFAIP3), inhibin subunit beta A (INHBA), and plasminogen activator, urokinase (PLAU)) were verified as the targets of SFE. RNA-sequence (RNA-seq) data of 182 ESCC samples from The Cancer Genome Atlas (TCGA) were grouped into two phenotypes for GSEA according to the expression of CXCL10, TNFAIP3, INHBA, and PLAU. The enrichment results proved that they were all involved in the NFκB pathway. ChIP-seq analyses obtained from the Cistrome database indicated that NFκB-p65 is likely to control the transcription of CXCL10, TNFAIP3, INHBA, and PLAU, and considering TNFAIP3 and PLAU are the most significantly differentially expressed genes, we used chromatin immunoprecipitation-polymerase chain reaction (ChIP-PCR) to verify the regulation of p65 on their expression. The results demonstrated that SFE suppresses ESCC progression by down-regulating TNFAIP3 and PLAU expression in a p65-dependent manner.

scholarly journals Identification of Differentially Expressed Genes and miRNAs Associated with Esophageal Squamous Cell Carcinoma by Integrated Analysis of Microarray Data

2020 ◽  
Vol 2020 ◽  
pp. 1-16
Author(s):  
Lemeng Zhang ◽  
Jianhua Chen ◽  
Tianli Cheng ◽  
Hua Yang ◽  
Changqie Pan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Survival Analysis ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Microarray Data ◽  
Regulatory Network ◽  
Differentially Expressed ◽  
Pathway Enrichment

To identify candidate key genes and miRNAs associated with esophageal squamous cell carcinoma (ESCC) development and prognosis, the gene expression profiles and miRNA microarray data including GSE20347, GSE38129, GSE23400, and GSE55856 were downloaded from the Gene Expression Omnibus (GEO) database. Clinical and survival data were retrieved from The Cancer Genome Atlas (TCGA). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs) was analyzed via DAVID, while the DEG-associated protein-protein interaction network (PPI) was constructed using the STRING database. Additionally, the miRNA target gene regulatory network and miRNA coregulatory network were constructed, using the Cytoscape software. Survival analysis and prognostic model construction were performed via the survival (version 2.42-6) and rbsurv R packages, respectively. The results showed a total of 2575, 2111, and 1205 DEGs, and 226 differentially expressed miRNAs (DEMs) were identified. Pathway enrichment analyses revealed that DEGs were mainly enriched in 36 pathways, such as the proteasome, p53, and beta-alanine metabolism pathways. Furthermore, 448 nodes and 1144 interactions were identified in the PPI network, with MYC having the highest random walk score. In addition, 7 DEMs in the microarray data, including miR-196a, miR-21, miR-205, miR-194, miR-103, miR-223, and miR-375, were found in the regulatory network. Moreover, several reported disease-related miRNAs, including miR-198a, miR-103, miR-223, miR-21, miR-194, and miR-375, were found to have common target genes with other DEMs. Survival analysis revealed that 85 DEMs were related to prognosis, among which hsa-miR-1248, hsa-miR-1291, hsa-miR-421, and hsa-miR-7-5p were used for a prognostic survival model. Taken together, this study revealed the important roles of DEGs and DEMs in ESCC development, as well as DEMs in the prognosis of ESCC. This will provide potential therapeutic targets and prognostic predictors for ESCC.

scholarly journals Differentially expressed genes and lincRNAs throughout oral squamous cell carcinoma development

2012 ◽  
Vol 26 (S1) ◽  
Author(s):  
João Paulo Oliveira-Costa ◽  
Alex Fiorini Carvalho ◽  
Silvia Vanessa Lourenco ◽  
Luiz Paulo Kowalski ◽  
Dirce Maria Carraro ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Squamous Cell ◽  
Differentially Expressed
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