DNA Methylation Data-Based Classification and Identification of Prognostic Signature of Children With Wilms Tumor

Tang, Fucai; Lu, Zeguang; Lei, Hanqi; Lai, Yongchang; Lu, Zechao; Li, Zhibiao; Tang, Zhicheng; Zhang, Jiahao; He, Zhaohui

doi:10.3389/fcell.2021.683242

Cited by 7 publications

(2 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition to the mutation of the gene itself can cause tumors, abnormal expression of normal genes can also cause tumors, which involves epigenetics. In recent years, epigenetic inheritance has been studied intensively in WT [9]. Epigenetics means that the DNA sequence does not change, but the gene expression has changed heritably [10].…”

Section: Introductionmentioning

confidence: 99%

Exploration of biological significance of m6A-related genes in Wilms tumor

Zhuo

Zhang

et al. 2023

Preprint

View full text Add to dashboard Cite

Background: Wilms tumor (WT) is an embryonal abdominal malignant tumor which is a common renal malignant tumor in children. N6-methyladenosine (m6A) RNA methylation can dynamically regulate the development of tumors. However, m6A-related genes in WT have not yet been identified and researched. Methods: In this study, the RNA-seq data of TARGET-WT were extracted from the UCSC Xena for bioinformatics analysis. Results: 296 candidate hub genes were obtained by intersecting 3 gene sets (8610 gene modules with significantly associated m6A RNA methylation score, 7774 differentially expressed genes (DEGs) between 121 WT patients and 6 control samples, 763 DEGs between high and low score groups of m6A RNA methylation). Survival analysis of the 296 genes yielded 4 hub genes (ADGRG2, CPD, CTHRC1, and LRTM2) associated with WT prognosis. Subsequently, a prediction model with the 4 hub genes was developed and the model had good predictive power for the WT prognosis. In addition, 7 immune gene sets were obtained by intersecting 2 gene sets (18 significant difference immune gene sets between the WT group and control group, 10 immune gene sets related to the hub genes). Among them, APC_co_stimulation, CCR, Macrophages, Parainflammation, Treg, and Type_II_IFN_Reponse were low expressed in the WT, and only Th1_cells were highly expressed in the WT. APC_co_stimulation, CCR, Macrophages, Parainflammation, Treg, and Type_II_IFN_Reponse are negatively correlated with LRTM2, Th1_cells are positively correlated with ADGRG2, CCR is negatively correlated with CPD, CCR is positively correlated with CTHRC1. Finally, qRT-PCR results showed that the expression levels of the 4 hub genes were up-regulated in different WT cell lines compared with 293T cell lines. Conclusion: In conclusion, ADGRG2, CPD, CTHRC1, and LRTM2 may be m6A-related genes in WT, which have potential prognostic value and play an immunoregulation role in WT.

show abstract

Section: Introductionmentioning

confidence: 99%

Exploration of biological significance of m6A-related genes in Wilms tumor

Zhuo

Zhang

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Wilms tumor (WT), the most common genitourinary tract cancer in the pediatric population, accounts for approximately 5% of all pediatric cancers (Tang et al 2021). Over the last 50 years, the 5-year overall survival (OS) rate of WT in developed countries can surpass 90% thanks to the concerted efforts of surgery, chemotherapy, and radiotherapy.…”

Section: Introductionmentioning

confidence: 99%

Effects of Novel Cuproptosis-related Long Noncoding RNAs on the Prognosis and Immune Microenvironment of Wilms Tumor

Xie

Wang

et al. 2023

Preprint

View full text Add to dashboard Cite

Purpose Unlike all other known types of regulated cell death, cuproptosis is a unique copper-dependent cell death pathway that is closely connected to mitochondria and metabolism. The pathogenesis of Wilms tumor (WT), a common pediatric abdominal tumor, has yet to be fully elucidated. However, studies on long noncoding RNAs related to cuproptosis in WT and the relationship between Wilms tumor, the microenvironment, and cuproptosis are still scarce. Results Our results showed that among individuals with WT, those included in the high-risk group identified using the signature were demonstrated poor survival outcomes. Moreover, we found that the high-risk group had a worse prognosis (P < 0.001) than the group of low-risk. The area under the curve value for this signature was 0.818, which was higher than that for age (0.524), sex (0.580), race (0.489), stage (0.673), and the modeling of ferroptosis-related lncRNAs (0.775). Individuals in the group of low-risk group had an elevated Tumor Immune Dysfunction and Exclusion scores and were more sensitive to 13 drugs, including BI-2536, EX-527, IspinesibMesylate, and KIN001-135. Conclusion Our model can precisely predict the prognosis of WT patients and differentiate between those at low and high risk. The current study introduces a novel approach for predicting clinical prognosis and determining the appropriate therapy for patients with WT.

show abstract

Identification of m6A-associated genes as prognostic and immune-associated biomarkers in Wilms tumor

Zhuo,

Zhang,

et al. 2023

Discov Onc

View full text Add to dashboard Cite

Objectives Wilms tumor (WT) is a common renal malignant tumor in children. We aimed to investigate the potential prognostic value of m6A-related genes and their relationship to the immune microenvironment in WT. Methods RNA-seq data and clinical information from 121 WT and 6 normal samples were obtained from the University of California Santa Cruz Xena database. We used various bioinformatics analysis tools to analyze these data and verify the expression level of m6A-related genes by experiments. Results Four m6A-related genes were successfully screened, including ADGRG2, CPD, CTHRC1, and LRTM2. Kaplan–Meier survival curves showed that the four genes were closely related to the prognosis of WT, which was also confirmed by receiver operator characteristic curves. Subsequently, in the immune microenvironment of WT, we discovered that Th1_cells were positively correlated with ADGRG2, CCR was negatively correlated with CPD, CCR was positively correlated with CTHRC1, APC_co_stimulation, CCR, Macrophages, inflammation-promoting cells, Treg, and Type_II_IFN_Reponse were negatively correlated with LRTM2. Finally, qRT-PCR showed that expression levels of the four genes were upregulated in the nephroblastoma cell lines (G-401, SK-NEP-1, and WT-CLS1) compared with the human embryonic kidney cell lines (293T). Conclusions Taken together, our study first time screened the m6A-related genes and revealed that ADGRG2, CPD, CTHRC1, and LRTM2 are the prognostic and immune-associated biomarkers in WT.

show abstract

DNA Methylation Data-Based Classification and Identification of Prognostic Signature of Children With Wilms Tumor

Cited by 7 publications

References 31 publications

Exploration of biological significance of m6A-related genes in Wilms tumor

Exploration of biological significance of m6A-related genes in Wilms tumor

Effects of Novel Cuproptosis-related Long Noncoding RNAs on the Prognosis and Immune Microenvironment of Wilms Tumor

Identification of m6A-associated genes as prognostic and immune-associated biomarkers in Wilms tumor

Contact Info

Product

Resources

About