DNA Hypermethylation-Regulated CX3CL1 Reducing T Cell Infiltration Indicates Poor Prognosis in Wilms Tumour

Tao Mi; Liming Jin; Zhaoxia Zhang; Jinkui Wang; Mujie Li; Chenghao Zhanghuang; Xiaojun Tan; Zhang Wang; Xiaomao Tian; Bin Xiang; Dawei He

doi:10.3389/fonc.2022.882714

DNA Hypermethylation-Regulated CX3CL1 Reducing T Cell Infiltration Indicates Poor Prognosis in Wilms Tumour

Front Oncol. 2022 Apr 22:12:882714. doi: 10.3389/fonc.2022.882714. eCollection 2022.

Authors

Tao Mi^{1

2

3}, Liming Jin^{1

2

3}, Zhaoxia Zhang^{1

2

3}, Jinkui Wang^{1

2

3}, Mujie Li^{1

2

3}, Chenghao Zhanghuang^{1

2

3}, Xiaojun Tan^{1

2

3}, Zhang Wang^{1

2

3}, Xiaomao Tian^{1

2

3}, Bin Xiang^{1

2

3}, Dawei He^{1

2

3}

Affiliations

¹ Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China.
² Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China.
³ China International Science and Technology Cooperation Base of Child Development and Critical; National Clinical Research Center for Child Health and Disorders, Chongqing; Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, Chongqing, China.

Abstract

Objective: To investigate the role of chemokines in Wilms tumours, especially their chemotaxis to immune cells and the role of DNA methylation in regulating the expression level of chemokines.

Methods: RNAseqV2 gene expression and clinical data were downloaded from the TARGET database. DNA methylation data were downloaded from the GEO and cBioPortal database. The difference analysis and Kaplan-Meier(KM) analysis of chemokines were performed by edgeR package. Then predictive model based on chemokines was constructed by lasso regression and multivariate COX regression. ROC curve, DCA curve, Calibration curve, and Nomogram were used to evaluate the prognostic model. MCPcounter and Cibersort algorithm was used to calculate the infiltration of immune cells in Wilms tumour and para-tumour samples. Then the difference analysis of the immune cells was performed. The relationship between chemokines and immune cells were calculated by Pearson correlation. In addition, DNA methylation differences between Wilms tumour and para-tumour samples was performed. The correlation between DNA methylation and mRNA expression was calculated by Pearson correlation. Western blot(WB)and immunofluorescence were used to confirm the differential expression of CX3CL1 and T cells, and the correlation between them.

Results: A total of 16 chemokines were differentially expressed in tumour and para-tumour samples. A total of seven chemokines were associated with survival. CCL2 and CX3CL1 were positively correlated with prognosis, while high expression of CCL3, CCL8, CCL15, CCL18 and CXCL9 predicted poor prognosis. By lasso regression and multivariate COX regression, CCL3, CCL15, CXCL9 and CX3CL1 were finally included to construct a prediction model. The model shows good prediction ability. MCPcounter and Cibersort algorithm both showed that T cells were higher in para-tumour tissues than cancer tissues. Correlation analysis showed that CX3CL1 had a strong correlation with T cells. These were verified by Weston blot and immunofluorescence. DNA methylation analysis showed that various chemokines were different in para-tumours and tumours. CX3CL1 was hypermethylated in tumours, and the degree of methylation was negatively correlated with mRNA expression.

Conclusion: 1. There is low T cell infiltration in nephroblastoma. 2. Chemokines such as CX3CL1 indicate a favourable prognosis and positively correlate with the number of T cells. 3. chemokines such as CX3CL1 are negatively regulated by DNA hypermethylation.

Keywords: DNA methylation; T cells; Wilms tumour; chemokine; immune infiltration.