SnapShot: TP53 status and macrophages infiltration in TCGA-analyzed tumors

El‐Arabey, Amr Ahmed; Abdalla, Mohnad; Abd-Allah, Adel R. A.

doi:10.1016/j.intimp.2020.106758

Cited by 43 publications

(34 citation statements)

References 33 publications

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“…The TP53 gene mutation has been broadly recognized as a risk factor for the prognosis of epithelial OC. 32,33 Interestingly, in our study, we used the Timer database to analyze the relationship and found a positive correlation between ARRDC3 expression and CD8+ T cells, macrophages, neutrophils, and dendritic cells in OC, which indicates that ARRDC3 might be associated with infiltration of these immune cells. Similarly, in pyloric screw gastritis, it has been reported that ARRDC3 might be associated with immune infiltration of neutrophils and the severity of gastritis.…”

mentioning

confidence: 63%

ARRDC3 as a Diagnostic and Prognostic Biomarker for Epithelial Ovarian Cancer Based on Data Mining

Chen¹,

Tian²,

Chen³

et al. 2021

IJGM

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The dysregulation of arrestin domain containing 3 (ARRDC3) has an important effect on oncogenesis and tumor progression in many cancers, including renal cell carcinoma and breast cancer. However, the role of ARRDC3 in ovarian cancer (OC) has not been reported. Methods: The present study explored the diagnostic and prognostic roles of ARRDC3 in ovarian cancer using GEPIA, ONCOMINE, GEO, and Kaplan-Meier Plotter databases for training and validation. Then, we conducted a stratified analysis for clinicopathological factors using Kaplan-Meier Plotter and GEPIA databases. To further explore the mechanisms, we also used the MIST database to visualize the protein-protein interaction network of ARRDC3 associated with OC. The gene-gene interaction network was visualized by GeneMANIA plugin in Cytoscape 3.8.0 software, and the associated co-expression genes of ARRDC3 were analyzed by the cBioPortal database. The 100 top co-expression genes chosen for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used by the DAVID website. Results: A significant difference in ARRDC3 mRNA expression was found between OC and normal ovary tissues. ARRDC3 could potentially be implicated in the diagnosis of OC. A high ARRDC3 mRNA expression level was associated with poor overall survival and progression-free survival. However, no significance was reported in respect to post progression survival. Except for histology, which had no prognostic value for PPS in stratified analysis, stratified analysis of other factors had prognostic value for OS, PFS, and PPS. Interestingly, we found a positive correlation between ARRDC3 expression and CD8+ T cells, macrophages, neutrophils, and dendritic cells, indicating that ARRDC3 might be associated with immune infiltration of these immune cells. Coexpression genes enrichment analysis found that they were involved in the Renin-angiotensin system pathway. Conclusion: Differentially expressed ARRDC3 might be a potential prognostic and diagnostic marker in Ovarian Cancer.

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mentioning

confidence: 63%

ARRDC3 as a Diagnostic and Prognostic Biomarker for Epithelial Ovarian Cancer Based on Data Mining

Chen¹,

Tian²,

Chen³

et al. 2021

IJGM

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“…According to prognostic related genes, 1915, 1194, 822, 423 and 291 were identified good prognostic genes for the HGSCs and LGSCs. Additionally, 2075, 2274, 724, 535 and 303 genes were identified bad prognostic (21). Nakayama (22) revealed global gene upregulation by mutant p53using RNA sequencing analyses and concluded that mutant p53 inducing colorectal cancer progression was not only by a cell intrinsic mechanism, but also by the generation or activation of the microenvironment.…”

Section: Discussionmentioning

confidence: 99%

“…Yang et al (30) reported that the patients with higher CD274, CD8A, GZMA, HLA-A, HLA-B, HLA-C, IRF1, and PRF1 expression levels had significantly longer overall survival in the high-grade serous carcinoma. Ovarian Serous Cystadenocarcinoma (OV) patients with mutant TP53 had significantly higher macrophages infiltration than those with wild-type TP53 (P value <0.05) and poor prognosis associated (21).…”

Section: Discussionmentioning

confidence: 99%

The G199X and V157fs mutations in the TP53 gene promote malignancy in serous ovarian cancer: an analysis using whole-exome sequencing

Nie

Yue

2021

Ann Transl Med

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Background: The carcinogenic mechanisms underlying serous ovarian cancer are not fully understood.Methods: Whole-exome sequencing and targeted sequencing were performed in ovarian cancer samples to identify novel molecular markers involved in the process of cell malignancy in ovarian cancer. In vitro experiments, the oncogenic roles such as cell proliferation, migration and invasion of TP53 G199X and V157fs mutations were investigated deeply.Results: The present study identified the G199X and V157fs point mutations in the tumor protein P53 gene (TP53). The rate of TP53 mutation was 59.2% in a cohort of 76 ovarian cancer patients, compared with 9.0% in a cohort of 156 healthy women. Kaplan-Meier analysis showed that patients with a TP53 mutation had a lower 5-year overall survival (OS) rate compared with patients harboring wild type TP53. In vitro experiments in an ovarian cancer cell line demonstrated that the G199X and V157fs mutants inhibited P53 protein expression, enhanced proliferation, promoted migration and increased invasion.Conclusions: This study identified two novel markers, TP53 G199X and V157fs mutations in TP53.Functional assays indicated that these mutations enhanced the malignant phenotype in ovarian cancer cells.These novel markers will assist in the diagnosis of ovarian tumors and represent potential targets for the treatment of TP53 mutant ovarian cancers.

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“…TISIDB ( http://cis.hku.hk/TISIDB/ ) is a web portal for tumor and immune system interactions, including genomics and transcriptomics of 30 cancer types from TCGA, RNA sequencing data set of patient cohorts treated with immunotherapy [ 15 ]. The TCGA database provides a large amount of tumor public data, providing useful information for studying the complex interaction of the tumor microenvironment [ 16 ]. TISIDB has “Function,” “Literature,” “Screening,” “Immunotherapy,” “Lymphocyte,” “Immunomodulator,” “Chemokine,” “Subtype,” “Clinical,” and “Drug” modules.…”

Section: Methodsmentioning

confidence: 99%

The possible role of SRMS in colorectal cancer by bioinformatics analysis

et al. 2021

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Background Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites (SRMS) is a non-receptor tyrosine kinase that has been found to be overexpressed in various tumors. However, the role of SRMS in colorectal cancer (CRC) has not been well established. Methods We evaluated the expression levels of SRMS in CRC using GEPIA, Oncomine, and HPA datasets. Survival information and gene expression data of CRC were obtained from The Cancer Genome Atlas (TCGA). Then, the association between SRMS and clinicopathological features was analyzed using UALCAN dataset. LinkedOmics was used to determine co-expression and functional networks associated with SRMS. Besides, we used TISIDB to assess the correlation between SRMS and immune signatures, including tumor-infiltrating immune cells and immunomodulators. Lastly, protein-protein interaction network (PPI) was established and the function enrichment analysis of the SRMS-associated immunomodulators and immune cell marker genes were performed using the STRING portal. Results Compared to normal colorectal tissues, SRMS was found to be overexpressed in CRC tissues, which was correlated with a poor prognosis. In colon adenocarcinoma (COAD), the expression levels of SRMS are significantly correlated with pathological stages and nodal metastasis status. Functional network analysis suggested that SRMS regulates intermediate filament-based processes, protein autophosphorylation, translational initiation, and elongation signaling through pathways involving ribosomes, proteasomes, oxidative phosphorylation, and DNA replication. In addition, SRMS expression was correlated with infiltrating levels of CD4+ T cells, CD56dim, MEM B, Neutrophils, Th2, Th17, and Act DC. The gene ontology (GO) analysis of SRMS-associated immunomodulators and immune cell marker genes showed that they were mainly enriched in the immune microenvironment molecule-related signals. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of these genes indicated that they are involved in multiple cancer-related pathways. Conclusions SRMS is a promising prognostic biomarker and potential therapeutic target for CRC patients. In particular, SRMS regulates CRC progression by modulating cytokine-cytokine receptor interaction, chemokines, IL-17, and intestinal immune networks for IgA production signaling pathways among others. However, more studies are needed to validate these findings.

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SnapShot: TP53 status and macrophages infiltration in TCGA-analyzed tumors

Cited by 43 publications

References 33 publications

ARRDC3 as a Diagnostic and Prognostic Biomarker for Epithelial Ovarian Cancer Based on Data Mining

ARRDC3 as a Diagnostic and Prognostic Biomarker for Epithelial Ovarian Cancer Based on Data Mining

The G199X and V157fs mutations in the TP53 gene promote malignancy in serous ovarian cancer: an analysis using whole-exome sequencing

The possible role of SRMS in colorectal cancer by bioinformatics analysis

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