Pancancer survival analysis of cancer hallmark genes

Nagy, Ádám; Munkácsy, Gyöngyi; Győrffy, Balázs

doi:10.1038/s41598-021-84787-5

Cited by 1,136 publications

(1,324 citation statements)

References 38 publications

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“…Then, we constructed the six preserved genes and associated gene network with the help of GeneMANIA ( http://genemania.org/ ) 18 in Fig. 1 c. We performed the KM plot in the KM plotter ( https://kmplot.com/analysis/index.php?p=service&cancer=ovar ) 19 . DNAJB6, RB1, STEAP3, BACH1, and ALOX12 were associated with prognosis (supplementary figure S1 ), while VIMP/SELENOS might be a prognosis indicator in some cases (supplementary figure S2 ).…”

Section: Resultsmentioning

confidence: 99%

A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma

Chen

et al. 2021

Sci Rep

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Ovarian cancer (OV) is a common type of carcinoma in females. Many studies have reported that ferroptosis is associated with the prognosis of OV patients. However, the mechanism by which this occurs is not well understood. We utilized Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) to identify ferroptosis-related genes in OV. In the present study, we applied Cox regression analysis to select hub genes and used the least absolute shrinkage and selection operator to construct a prognosis prediction model with mRNA expression profiles and clinical data from TCGA. A series of analyses for this signature was performed in TCGA. We then verified the identified signature using International Cancer Genome Consortium (ICGC) data. After a series of analyses, we identified six hub genes (DNAJB6, RB1, VIMP/ SELENOS, STEAP3, BACH1, and ALOX12) that were then used to construct a model using a training data set. The model was then tested using a validation data set and was found to have high sensitivity and specificity. The identified ferroptosis-related hub genes might play a critical role in the mechanism of OV development. The gene signature we identified may be useful for future clinical applications.

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Section: Resultsmentioning

confidence: 99%

A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma

Chen

et al. 2021

Sci Rep

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“…An online database Kaplan-Meier plotter ( http://kmplot.com/analysis/ ) was used to investigate the association between zinc transporters mRNA levels and survival of ovarian cancer patients (data updated July 22, 2020). The Kaplan-Meier plotter is capable to evaluate the effect of 54k genes on patient clinical outcomes in numerous cancer types including breast, ovarian, lung, and gastric cancer [ 17 ]. To analyze the prognostic value of ZIP transporters in ovarian cancer, only datasets with available raw microarray gene expression data, clinical survival information, and at least 20 patients were included.…”

Section: Methodsmentioning

confidence: 99%

Zinc transporter SLC39A13/ZIP13 facilitates the metastasis of human ovarian cancer cells via activating Src/FAK signaling pathway

Cheng

Wang

Liu

et al. 2021

J Exp Clin Cancer Res

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Background Zinc transporters have been found to be associated with the pathogenesis of numerous human diseases including cancer. As the most lethal gynecologic malignancy, ovarian cancer is characterized by rapid progression and widespread metastases. However, the function and underlying mechanism of zinc transporters in ovarian cancer metastasis remain unclear. Methods The relationship between zinc transporter gene expressions and clinical outcomes of ovarian cancer was assessed with the online database Kaplan-Meier plotter (http://kmplot.com/analysis/). Immunohistochemistry was performed to investigate the prognostic importance of ZIP13. The expression of ZIP13 in ovarian cancer cell lines was depleted to explore its effect on proliferation, adhesion, migration, and invasion both in vitro and in vivo assays. RNA-Seq, quantitative RT-PCR, and western blot analysis were performed to explore ZIP13-regulated downstream target genes. Results The expressions of several zinc transporters were highly associated the clinical outcomes of ovarian cancer patients. Among them, high ZIP13 expression was an independent prognostic factor for poor survival in patients with ovarian cancer. ZIP13 knockout suppressed the malignant phenotypes of ovarian cancer cells both in vitro and in vivo. Further investigation revealed that ZIP13 regulated intracellular zinc distribution and then affected the expressions of genes involved in extracellular matrix organization and cytokine-mediated signaling pathway. This led to the activation of Src/FAK pathway with increased expressions of pro-metastatic genes but decreased expressions of tumor suppressor genes. Conclusions ZIP13 is shown to be a novel driver of metastatic progression by modulating the Src/FAK signaling pathway, which may serve as a promising biomarker for prognostic evaluation and targeted therapy in ovarian cancer.

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“…The equality of the variances was analysed by the Levene test. To construct the Kaplan-Meier curves for disease-free survival using the data from the TCGA database, the procedure described elsewhere [59,60] was followed. When our experimentally determined isoform ratio was used, data were categorised into high and low groups according to the median values.…”

Section: Statistical Analysesmentioning

confidence: 99%

Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer

Gimeno-Valiente

Riffo‐Campos

Torres

et al. 2021

Cancers

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The ZNF518B gene, which is up-regulated in colorectal cancer, plays a role in cell dissemination and metastasis. It encodes a zinc-finger protein, which interacts with histone methyltransferases G9A and EZH2. The expression of the two major mRNA isoforms 1 (coding for the full protein) and 2 was quantified by RT-qPCR in a cohort of 66 patients. The effects of silencing ZNF518B on the transcriptome of DLD1 and HCT116 cells were analysed by Clariom-S assays and validated by RT-qPCR. The recruitment of methyltransferases and the presence of H3K27me3 were studied by chromatin immunoprecipitation (ChIP). The ratio (isoform 2)/(isoform 1) negatively correlated with the relapsing of disease. The study of the transcriptome of DLD1 and HCT116 cells revealed that many genes affected by silencing ZNF518B are related to cancer. After crossing these results with the list of genes affected by silencing the histone methyltransferases (retrieved in silico), five genes were selected. ChIP analysis revealed that the recruitment of EZH2 is ZNF518B-dependent in KAT2B, RGS4 and EFNA5; the level of H3K27me3 changes in accordance. G9A also binds RGS4 and PADI3 in a ZNF518B-dependent manner. The results highlight the importance of epigenetics in cancer and open a novel therapeutic possibility, as inhibition of histone methyltransferases may reverse the disease-linked histone marks.

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Pancancer survival analysis of cancer hallmark genes

Cited by 1,136 publications

References 38 publications

A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma

A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma

Zinc transporter SLC39A13/ZIP13 facilitates the metastasis of human ovarian cancer cells via activating Src/FAK signaling pathway

Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer

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