Integrative omics provide new insights on association of RNA splicing with the tumorigenesis of Wilms’ Tumor

Abstract Background The tumorigenesis of Wilms’ tumor (WT) or nephroblastoma is still unclear. The alteration of RNA splicing and EMT is the manifestation of tumorigenesis. Therefore, this study aims to study the association between RNA splicing and epithelial-mesenchymal transition (EMT), for better understanding on the tumorigenesis of WT. Methods Using the high-resolution mass spectrometry to collect the peptide information in WT and control kidney (CK) after the pre-treatment (extraction, purification and digestion) of protein, intending to find out the protein profiles of WT via database alignment. Then a label-free quantification method based on the SWATH-MSALL proteomic technology was performed to identify differentially expressed proteins (DEPs) between WT and CK. The bioinformatics analysis employs the GO (Gene Ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, and PPI (protein-protein interaction) analysis. Integrated with the data from single cell RNA-sequencing (scRNA-seq) and bulk RNA-seq transcriptomicss, aiming to further annotation of DEGs enrichment in WT tumorigenesis via GO, KEGG and Gene Set Enrichment Analysis (GSEA). Results In our study, 2005 proteins were identified from Wilms’ tumor with a global false discovery rate (FDR) of 1% (FDR threshold, 84%), followed by 330 DEPs between WT and CK (P＜0.05, |log2fold-change (FC)| ≥ 1). Integrated with the data of scRNA-seq and bulk RNA-seq transcriptomicss, the function enrichment of DEGs represented RNA splicing and epigenetic modification. The validation assays also revealed the over-expression of the transcription factors heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and poly(ADP-ribose) polymerase 1 (PARP1) in WT, compared with CK tissue. Further investigation revealed the aberrant accumulation of hnRNP A1 and PARP1 in the mesenchymal compartment of WT, indicative of the critical roles in the dysregulation of EMT. Conclusions There were amounts of DEPs between WT/CK engaging in RNA splicing, indicative of the complicated transcription regulatory in tumorigenesis of nephroblastoma. Integrated with data from multi-omics and validation assay, hnRNP A1 and PARP1 could play role of the tumor-enriched biomarkers. However, the possibility of hnRNP A1 and PARP1 in targeted therapy for WT remained to consideration. It’s necessary to further investigate the role of hnRNP A1 and PARP1 on the alternative splicing (AS) and EMT for tumorigenesis of WT.