Integrated pan-cancer analysis and experimental verification of the roles of tropomyosin 4 in gastric cancer

Guo, Qinghua; Zhao, Ling; Ye, Nan; Li, Yan; Guo, Cheng; Dang, Shengyan; Shen, Xianliang; Han, Ji-Sheng; Luo, Ying

doi:10.3389/fimmu.2023.1148056

Cited by 11 publications

(4 citation statements)

References 54 publications

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“…This included Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and tissue enrichment analysis. Gene Set Enrichment Analyses (GSEA) of the screened overlapping genes were conducted using Xiantao academic tools( https://www.xiantaozi.com/products ) ( 17 , 18 ).…”

Section: Methodsmentioning

confidence: 99%

RETRACTED: Macrophages depletion alleviates lung injury by modulating AKT3/GXP4 following ventilator associated pneumonia

Zhu,

Chen,

Xie

et al. 2023

Front. Immunol.

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BackgroundAKT3 appears to play a role in lung cancer. However, its role in ventilator-associated pneumonia is still unclear. Therefore, this study aimed to investigate the role of AKT3 in macrophages during ventilator-associated pneumonia.MethodsThe mRNA level of AKT3, Data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), The data is analyzed using the Xiantao academic analysis tool. Additionally, the roles of AKT3 in ventilator-associated pneumonia (VAP) were investigated through in vivo experiments.ResultsAKT3 was differentially expressed in various normal and tumor tissues. Functional enrichment analysis indicated the immunomodulatory function and inflammatory response of AKT3 in lung cancer. Depletion of macrophages protected against lung epithelial cells and significantly decreased MMP9, MMP19, FTH, and FTL expression levels and increased GPX4 expression levels, while partially reversing the changes in macrophage. Mechanistically, macrophage depletion attenuates ferroptosis of lung epithelial cells by modulating AKT3 following VAP.ConclusionCollectively, this study suggests the need for further validation of the immunoregulatory function of AKT3 in lung cancer. Additionally, macrophage depletion mitigates lung injury by modulating the AKT3/GPX4 pathway in the context of VAP.

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Section: Methodsmentioning

confidence: 99%

RETRACTED: Macrophages depletion alleviates lung injury by modulating AKT3/GXP4 following ventilator associated pneumonia

Zhu,

Chen,

Xie

et al. 2023

Front. Immunol.

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“…After then, the genes closely correlated with PRIMPOL in TCGA pan-cancer were obtained from GEPIA2.0 database. At last, the Kyoto Encyclopedia of Genes and Genomes (KEGG) mediated by PRIMPOL-associated genes we predicted by Xiantao XueShu [ 22 ].…”

Section: Methodsmentioning

confidence: 99%

Multi-omics analysis of DNA replication-associated primase polymerase (PRIMPOL) in pan-cancer: a potential target for prognosis and immune response

et al. 2023

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Background It is critical to understand the mechanisms of human cancers in order to develop the effective anti-cancer therapeutic strategies. Recent studies indicated that primase polymerase (PRIMPOL) is strongly associated with the development of human cancers. Nevertheless, a systematic pan-cancer analysis of PRIMPOL remains to be further clarified. Method Comprehensive multi-omics bioinformatics algorithms, such as TIMER2.0, GEPIA2.0 and cBioPortal, were utilized to evaluate the biological roles of PRIMPOL in pan-cancer, including the expression profiles, genomic alterations, prognostic values and immune regulation. Results PRIMPOL was upregulated in glioblastoma multiforme and kidney renal clear cell carcinoma. The brain lower grade glioma patients with enhanced PRIMPOL expression displayed poor prognostic values. We also demonstrated the PRIMPOL's immunomodulating effects on pan-cancer as well as its genomic changes and methylation levels. The aberrant expression of PRIMPOL was linked to various cancer-associated pathways, including DNA damage response, DNA repair, and angiogenesis, according to single-cell sequencing and function enrichment. Conclusions This pan-cancer analysis offers a thorough review of the functional roles of PRIMPOL in human cancers, suggesting PRIMPOL as a potentially important biomarker for the progression and immunotherapy of various cancers.

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“…The RNA-sequencing data of a pan-cancer cohort ( n = 15776) incorporated in this study was downloaded from the University of California Santa Cruz (UCSC) Xena website ( https://xenabrowser.net/datapages/ ), which included different types of cancerous and normal tissues from TCGA (The Cancer Genome Atlas) and the Genotype-Tissue Expression (GTEx) [ 19 ]. The whole data was filtered to delete the missing and duplicate results and the transcripts per million (TPM) normalized expression spectrum data uniformly processed by the toil pipeline was log (TPM + 1) transformed for further analysis via using the rms function in the R package [ 20 – 23 ].…”

Section: Methodsmentioning

confidence: 99%

Integrative bioinformatics analysis of WDHD1: a potential biomarker for pan-cancer prognosis, diagnosis, and immunotherapy

Cui,

Zou,

Wang

et al. 2023

World J Surg Onc

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Background Although WD repeat and high-mobility group box DNA binding protein 1 (WDHD1) played an essential role in DNA replication, chromosome stability, and DNA damage repair, the panoramic picture of WDHD1 in human tumors remains unclear. Hence, this study aims to comprehensively characterize WDHD1 across 33 human cancers. Methods Based on publicly available databases such as TCGA, GTEx, and HPA, we used a bioinformatics approach to systematically explore the genomic features and biological functions of WDHD1 in pan-cancer. Results WDHD1 mRNA levels were significantly increased in more than 20 types of tumor tissues. Elevated WDHD1 expression was associated with significantly shorter overall survival (OS) in 10 tumors. Furthermore, in uterine corpus endometrial carcinoma (UCEC) and liver hepatocellular carcinoma (LIHC), WDHD1 expression was significantly associated with higher histological grades and pathological stages. In addition, WDHD1 had a high diagnostic value among 16 tumors (area under the ROC curve [AUC] > 0.9). Functional enrichment analyses suggested that WDHD1 probably participated in many oncogenic pathways such as E2F and MYC targets (false discovery rate [FDR] < 0.05), and it was involved in the processes of DNA replication and DNA damage repair (p.adjust < 0.05). WDHD1 expression also correlated with the half-maximal inhibitory concentrations (IC50) of rapamycin (4 out of 10 cancers) and paclitaxel (10 out of 10 cancers). Overall, WDHD1 was negatively associated with immune cell infiltration and might promote tumor immune escape. Our analysis of genomic alterations suggested that WDHD1 was altered in 1.5% of pan-cancer cohorts and the “mutation” was the predominant type of alteration. Finally, through correlation analysis, we found that WDHD1 might be closely associated with tumor heterogeneity, tumor stemness, mismatch repair (MMR), and RNA methylation modification, which were all processes associated with the tumor progression. Conclusions Our pan-cancer analysis of WDHD1 provides valuable insights into the genomic characterization and biological functions of WDHD1 in human cancers and offers some theoretical support for the future use of WDHD1-targeted therapies, immunotherapies, and chemotherapeutic combinations for the management of tumors.

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Integrated pan-cancer analysis and experimental verification of the roles of tropomyosin 4 in gastric cancer

Cited by 11 publications

References 54 publications

RETRACTED: Macrophages depletion alleviates lung injury by modulating AKT3/GXP4 following ventilator associated pneumonia

RETRACTED: Macrophages depletion alleviates lung injury by modulating AKT3/GXP4 following ventilator associated pneumonia

Multi-omics analysis of DNA replication-associated primase polymerase (PRIMPOL) in pan-cancer: a potential target for prognosis and immune response

Integrative bioinformatics analysis of WDHD1: a potential biomarker for pan-cancer prognosis, diagnosis, and immunotherapy

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