Peroxiredoxins and Immune Infiltrations in Colon Adenocarcinoma: Their Negative Correlations and Clinical Significances, an In Silico Analysis

Zhang, Xiuzhi; Gao, Fenglan; Li, Ningning; Zhang, Jinzhong; Dai, Liping; Yang, Hongmei

doi:10.7150/jca.38057

Cited by 6 publications

(5 citation statements)

References 109 publications

(115 reference statements)

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“…msi) to batch convert probe names in the gene expression files to standard human gene names, according to the platform files. Using the “combat” function in the R package “SVA” ( 25 ), we corrected for the batch effect caused by non-biotechnological bias in these 3 datasets. Samples lacking clinical information, such as sample ID, age, sex, typing, and sampling location were deleted from the clinical information file.…”

Section: Methodsmentioning

confidence: 99%

Regulator of G-protein signaling 1 promotes choroidal neovascularization in age-related macular degeneration

Zhang¹,

Zhang²,

Guo³

et al. 2022

Ann Transl Med

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Background: Age-related macular degeneration (AMD) is the leading cause of blindness, and is associated with oxidative stress and the development of new blood vessels. At present, the main clinical treatment for AMD includes intraocular injection of vascular endothelial growth factor (VEGF). However, treatment includes repeated injections with significant side-effects. Therefore, new treatment options are required. The aim of the present study was to discover the new treatment target of AMD from the gene level. Methods: The Gene Expression Omnibus (GEO) database was used to analyze the differential gene expression in AMD, and the regulator of G-protein signaling 1 (RGS1) was obtained by bioassay. Western blotting and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were used to detect the expression levels of RGS1, VEGF, and other related molecules in human microvascular endothelial cells (HMECs) under different conditions. Cell viability, apoptosis, and proliferation of HMECs were measured by Cell Counting Kit-8 proliferation assay. Immunofluorescence and immunohistochemistry detected the interaction between RGS1, platelet endothelial cell adhesion molecule-1, and VEGF. Results: RGS1 was found to closely associated with the proliferation of vascular endothelial cells, and therefore, with angiogenesis. The expression of RGS1, VEGF, and platelet endothelial cell adhesion molecule-1 was upregulated in laser model mice and hypoxia model HMECs. Knockout of RGS1 inhibits the expression of VEGF and HMEC proliferation, thereby inhibiting AMD angiogenesis. Conclusions: Our results support the use of RGS1 as a new potential target for the future treatment of AMD.

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Section: Methodsmentioning

confidence: 99%

Regulator of G-protein signaling 1 promotes choroidal neovascularization in age-related macular degeneration

Zhang¹,

Zhang²,

Guo³

et al. 2022

Ann Transl Med

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“…Subsequently, in UCSC Xena (http://xena.ucsc), we downloaded the copy number data of LUAD ( 10 ). Using the limma package in R (The R Foundation for Statistical Computing, Vienna, Austria), the standard human gene expression matrix of each independent sample was converted from the TCGA gene expression profile, and transcripts per million (TPM) data were converted from fragments per kilobase million (FPKM) data ( 11 ). The standard human gene names were converted from two GEO files in Perl, as was the clinical information obtained from the GEO.…”

Section: Methodsmentioning

confidence: 99%

Characteristics of circadian rhythm-related genes and establishment of a prognostic scoring system for lung adenocarcinoma with experimental verification: a bioinformatics analysis

Zhang¹,

Zhang²,

Jiang³

et al. 2022

J Thorac Dis

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Background: Non-small cell lung cancer (NSCLC) is one of the most common malignant tumors worldwide. Lung adenocarcinoma (LUAD), the main subtype of NSCLC, has a poor prognosis. In recent years, circadian rhythm (CR)-related genes (CRRGs) have demonstrated associations with tumor occurrence and development, but the relationship between CRRGs and LUAD is not clear. Because of the correlation between CRRGs and tumors, we have reason to believe that CRRGs will become an important prognostic indicator for LUAD and guide the treatment of LUAD prognosis.Methods: Based on data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we explored the biological function and immune cell infiltration of LUAD in different CR clusters and quantified CR genes using principal component analysis (PCA). Then, we built a CR scoring system (CRscore) to explore the relationship between CRRGs and LUAD prognosis.Results: Patients were divided into three clusters (A, B, and C). Biological characteristics, such as survival, immune cell infiltration, and gene enrichment, were significantly different among the three clusters (P<0.001).We then established the usefulness of the CR score, which could probably predict the prognosis of LUAD.Specifically, patients with a high CR score had a better prognosis and were more sensitive to chemotherapy than those with a low CR score.Conclusions: It is possible to use CRRGs to assess the prognosis of patients with LUAD. Quantification of CR using the CRscore tool in patients with LUAD maybe help to guide personalized cancer immunotherapy strategies in the future. Thus, the CRscore may be a prognostic tool for LUAD.

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“…We took the average of the expression of the same gene. Then the FPKM (Fragments Per Kilobase Million) data were converted into the TPM (Transcripts Per Million) data [ 13 ]. The two steps were using the R package “limma”.…”

Section: Methodsmentioning

confidence: 99%

Autophagy characteristics and establishment of autophagy prognostic models in lung adenocarcinoma and lung squamous cell carcinoma

et al. 2022

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Background Non-small cell lung cancer (NSCLC), which makes up the majority of lung cancers, remains one of the deadliest malignancies in the world. It has a poor prognosis due to its late detection and lack of response to chemoradiaiton. Therefore, it is urgent to find a new prognostic marker. Methods We evaluated biological function and immune cell infiltration in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients from TCGA and GEO databases between different clusters based on autophagy related hub genes. Autophagy scores were used to assess the degree of autophagy in each individual by using component analysis. Results Three different clusters were obtained. Gene set variation analysis, single-sample gene set enrichment analysis and survive analysis showed differences among these three clusters. We demonstrated that the autophagy score of each patient could predict tumor stage and prognosis. Patients with a high autophagy score had a better prognosis, higher immune infiltration, and were more sensitive to immunotherapy and conventional chemotherapy. Conclusion It was uncovered that autophagy played an irreplaceable role in NSCLC. Quantified autophagy scores for each NSCLC patient would help guide effective treatment strategies.

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Peroxiredoxins and Immune Infiltrations in Colon Adenocarcinoma: Their Negative Correlations and Clinical Significances, an In Silico Analysis

Cited by 6 publications

References 109 publications

Regulator of G-protein signaling 1 promotes choroidal neovascularization in age-related macular degeneration

Regulator of G-protein signaling 1 promotes choroidal neovascularization in age-related macular degeneration

Characteristics of circadian rhythm-related genes and establishment of a prognostic scoring system for lung adenocarcinoma with experimental verification: a bioinformatics analysis

Autophagy characteristics and establishment of autophagy prognostic models in lung adenocarcinoma and lung squamous cell carcinoma

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