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The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression and biological processes (mRNA-seq)

ABSTRACT: The microprocessor mutation DGCR8 E518K represents one of the most prevalent and stereotypical mutations in Wilms tumor (WT). It affects the dsRNA-binding domain (dsRBD) of DGCR8, which leads to a presumably disruptive charge reversal. The E518K mutation was expressed homozygously in all cases, indicative for the mutation to act in a recessive manner. Notably, this alteration has been almost exclusively reported in WT, suggesting a specific role in WT formation. To functionally characterize the DGCR8 E518K mutation in vitro, we employed DGCR8 knockout mouse embryonic stem cell (mESC) lines with inducible overexpression of wild-type (wt) or E518K-mutant DGCR8. Absence of endogenous DGCR8 mirrors the homozygous expression of mutant DGCR8 as observed in WT. Knockout of DGCR8 is known to result in a severe miRNA processing defect with a significant downregulation of all canonical miRNAs. Wild-type DGCR8 rescued this processing defect. DGCR8-E518K, in turn, was unable to fully restore miRNA expression and showed overall reduced miRNA expression levels, confirming our previous findings in bulk tumor tissue. Differentially expressed miRNAs comprised members of the embryonic stem cell specific cell cycle-regulating (ESCC) miRNAs and the let-7 miRNA family, whose antagonism is known to play a pivotal role in the regulation of critical gene expression programs in ES cells. Along with altered miRNA expression, DGCR8-E518K exhibited changes in target gene expression affecting various biological pathways. The known proliferation deficiency and cell cycle defect of DGCR8 KO mESCs could be rescued by DGCR8-E518K, albeit not to the full extent as by wild-type DGCR8. Likewise, DGCR8-E518K failed to fully block epithelial-to-mesenchymal transition (EMT). Upon embryoid body formation, however, both DGCR8-wt and -E518K were able to restore the differentiation capacity and to silence self-renewal in the knockout. Despite impaired miRNA processing and altered target gene regulation, DGCR8-E518K mESCs were still able to restore many biological processes in a DGCR8 knockout background. These findings suggest that partial reduction in activity or altered specificity might be critical in Wilms tumorigenesis.

ORGANISM(S): Mus musculus

PROVIDER: GSE165269 | GEO | 2021/12/28

REPOSITORIES: GEO

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Project description:The microprocessor mutation DGCR8 E518K represents one of the most prevalent and stereotypical mutations in Wilms tumor (WT). It affects the dsRNA-binding domain (dsRBD) of DGCR8, which leads to a presumably disruptive charge reversal. The E518K mutation was expressed homozygously in all cases, indicative for the mutation to act in a recessive manner. Notably, this alteration has been almost exclusively reported in WT, suggesting a specific role in WT formation. To functionally characterize the DGCR8 E518K mutation in vitro, we employed DGCR8 knockout mouse embryonic stem cell (mESC) lines with inducible overexpression of wild-type (wt) or E518K-mutant DGCR8. Absence of endogenous DGCR8 mirrors the homozygous expression of mutant DGCR8 as observed in WT. Knockout of DGCR8 is known to result in a severe miRNA processing defect with a significant downregulation of all canonical miRNAs. Wild-type DGCR8 rescued this processing defect. DGCR8-E518K, in turn, was unable to fully restore miRNA expression and showed overall reduced miRNA expression levels, confirming our previous findings in bulk tumor tissue. Differentially expressed miRNAs comprised members of the embryonic stem cell specific cell cycle-regulating (ESCC) miRNAs and the let-7 miRNA family, whose antagonism is known to play a pivotal role in the regulation of critical gene expression programs in ES cells. Along with altered miRNA expression, DGCR8-E518K exhibited changes in target gene expression affecting various biological pathways. The known proliferation deficiency and cell cycle defect of DGCR8 KO mESCs could be rescued by DGCR8-E518K, albeit not to the full extent as by wild-type DGCR8. Likewise, DGCR8-E518K failed to fully block epithelial-to-mesenchymal transition (EMT). Upon embryoid body formation, however, both DGCR8-wt and -E518K were able to restore the differentiation capacity and to silence self-renewal in the knockout. Despite impaired miRNA processing and altered target gene regulation, DGCR8-E518K mESCs were still able to restore many biological processes in a DGCR8 knockout background. These findings suggest that partial reduction in activity or altered specificity might be critical in Wilms tumorigenesis.

Project description:To determine whether DGCR8 is required for maturation of all miRNAs, we performed miRNA microarray analysis. Using RNA from wild-type ES cells as our reference sample, we observed a global loss of miRNAs in DGCR8 knockout cells, but normal levels of expression in DGCR8 heterozygous cells. The similarity in expression levels between wild-type and heterozygous cells suggests that DGCR8 is not limiting in the maintenance of steady-state levels of miRNAs in ES cells. Of the eighty-nine miRNA array probes that showed significant signals with wild-type RNA, eighty-two were drastically reduced in the DGCR8 knockout cells. The remaining seven were not significantly altered in the DGCR8 knockout cells, but at least four of these seven miRNAs appear to be due to unavoidable contamination with RNA from the mouse embryonic fibroblast (MEF) feeder cells used for ES cell culture prior to the isolation of RNA. These miRNAs were highly expressed in the MEFs and decreased when the ES cells were temporarily passaged on gelatin-coated plates without feeders. The remaining three showed similar levels of expression in the heterozygous, knockout and MEF feeder cells. Therefore, these signals may be small RNAs that are not processed with the help of the microprocessor complex. Alternatively, these signals may result from unavoidable degradation products within the purified small RNA population. In either case, our results show that DGCR8 is broadly required for miRNA processing with little evidence for redundancy or bypass mechanisms. Keywords: cell type comparison, genetic modification MicroRNAs extracted from wild-type, DGCR8 heterozygous knockout and DGCR8 homozygous knockout were analyzed by microarray. In each array, wild-type samples serve as reference. Ratios were normalized based on positive control RNAs on the array. To determine if some of signals appeared in DGCR8 knockout ES cells are due to mice embryonic fibroblast (MEF) feeder cell contamination (this is unavoidable because these ES cells were grown on MEFs and passaged off MEF before RNA extraction). Two independent DGCR8 knockout ES cell lines were analyzed. For each cell line, array hybridization was done in duplicates. For DGCR8 heterozygous knockout ES cells, two independent batches of RNA samples were prepared and analyzed.

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The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression and biological processes (mRNA-seq)

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