DICER1-related tumor predisposition mutations lead to a gain of 3p-miRNA function, HERVH activity and increased metastatic potential
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE328604 | GEO | 2026/06/22
REPOSITORIES: GEO
Similar Datasets
Project description:The DICER1 gene is mutated in cancer, including Dicer1 syndrome, a rare tumour predisposition syndrome. Cancer-associated hotspots mutations have been reported in both catalytic domains of Dicer, and are predicted to disrupt miRNA processing activity. To understand these hotspot mutations in cancer development, we have generated cell lines harbouring single amino acid substitutions within either the RNAse IIIa (S1344L) and the RNAse IIIb (D1709N) domains of the endogenous Dicer1 gene. We show that both mutations result in a widespread loss of 5p miRNAs, but, unexpectedly, an increase in 3p passenger strands loading into Ago2. Similarities between both mutants can be explained as the S1344 residue is structurally also part of the RNase IIIb catalytical site. Functionally, we found that changes in the repertoire of miRNAs loaded into Ago2 result in altered gene expression, impacting critical pathways for cancer development, including metastatic potential. Our results indicate that inactivating the processing activity of Dicer does not result in genomic instability. Instead, mutations cause a specific upregulation of human endogenous retrovirus H (HERVH) and 3p miRNAs, which have the potential to be used as markers for Dicer1 syndrome tumours.
2026-06-22 | GSE313185 | GEO
Project description:The DICER1 gene is mutated in cancer, including Dicer1 syndrome, a rare tumour predisposition syndrome. Cancer-associated hotspots mutations have been reported in both catalytic domains of Dicer, and are predicted to disrupt miRNA processing activity. To understand these hotspot mutations in cancer development, we have generated cell lines harbouring single amino acid substitutions within either the RNAse IIIa (S1344L) and the RNAse IIIb (D1709N) domains of the endogenous Dicer1 gene. We show that both mutations result in a widespread loss of 5p miRNAs, but, unexpectedly, an increase in 3p passenger strands loading into Ago2. Similarities between both mutants can be explained as the S1344 residue is structurally also part of the RNase IIIb catalytical site. Functionally, we found that changes in the repertoire of miRNAs loaded into Ago2 result in altered gene expression, impacting critical pathways for cancer development, including metastatic potential. Our results indicate that inactivating the processing activity of Dicer does not result in genomic instability. Instead, mutations cause a specific upregulation of human endogenous retrovirus H (HERVH) and 3p miRNAs, which have the potential to be used as markers for Dicer1 syndrome tumours.
2026-06-22 | GSE313187 | GEO
Project description:The DICER1 gene is mutated in cancer, including Dicer1 syndrome, a rare tumour predisposition syndrome. Cancer-associated hotspots mutations have been reported in both catalytic domains of Dicer, and are predicted to disrupt miRNA processing activity. To understand these hotspot mutations in cancer development, we have generated cell lines harbouring single amino acid substitutions within either the RNAse IIIa (S1344L) and the RNAse IIIb (D1709N) domains of the endogenous Dicer1 gene. We show that both mutations result in a widespread loss of 5p miRNAs, but, unexpectedly, an increase in 3p passenger strands loading into Ago2. Similarities between both mutants can be explained as the S1344 residue is structurally also part of the RNase IIIb catalytical site. Functionally, we found that changes in the repertoire of miRNAs loaded into Ago2 result in altered gene expression, impacting critical pathways for cancer development, including metastatic potential. Our results indicate that inactivating the processing activity of Dicer does not result in genomic instability. Instead, mutations cause a specific upregulation of human endogenous retrovirus H (HERVH) and 3p miRNAs, which have the potential to be used as markers for Dicer1 syndrome tumours.
2026-06-22 | GSE313183 | GEO
Project description:The core miRNA biogenesis enzyme Dicer sustains recurrent mutations in cancer, which specifically compromise catalysis by its RNase IIIb domain. These are proposed to act as selective hypomorphs, since Dicer-RNase IIIb cleaves the 5p arms of pre-miRNA hairpins. However, the lack of knockin models has hindered a full understanding of the consequences of Dicer hotspot mutations for miRNA biogenesis. Here, we generated Dicer-KO and Dicer-S1344L (homozygous and hemizygous) hESCs; the latter is a non-catalytic mutation in RNase IIIa that impairs RNase IIIb activity. Consistent with our previous work, Dicer-KO is cell lethal in hESCs. However, in contrast to the expectation that Dicer hotspot mutations confer cell advantages, Dicer-S1344L knockin hESCs were subviable and also required a conditional genetic strategy for isolation. Small RNA sequencing using spike-in normalization reveals two broad trends: ablation of miRNA-5p species, and selective changes in miRNA-3p species. Curiously, we recognized a directional upregulation of miRNA-3p passenger strands, indicating a broad strand switch. Activity assays and Argonaute profiling of the transcriptome confirm that these confer increased repression capacity. Finally, we used in vitro assays to show 3p arm-nicked pre-miRNAs preferentially load miRNA-3p species into Argonaute, compared to corresponding miRNA/passenger duplexes. Overall, Dicer hotspot mutations have unexpected neomorphic consequences on miRNAs, including both loss- and gain-of-function.
2025-08-13 | GSE274851 | GEO
Project description:The core miRNA biogenesis enzyme Dicer sustains recurrent mutations in cancer, which specifically compromise catalysis by its RNase IIIb domain. These are proposed to act as selective hypomorphs, since Dicer-RNase IIIb cleaves the 5p arms of pre-miRNA hairpins. However, the lack of knockin models has hindered a full understanding of the consequences of Dicer hotspot mutations for miRNA biogenesis. Here, we generated Dicer-KO and Dicer-S1344L (homozygous and hemizygous) hESCs; the latter is a non-catalytic mutation in RNase IIIa that impairs RNase IIIb activity. Consistent with our previous work, Dicer-KO is cell lethal in hESCs. However, in contrast to the expectation that Dicer hotspot mutations confer cell advantages, Dicer-S1344L knockin hESCs were subviable and also required a conditional genetic strategy for isolation. Small RNA sequencing using spike-in normalization reveals two broad trends: ablation of miRNA-5p species, and selective changes in miRNA-3p species. Curiously, we recognized a directional upregulation of miRNA-3p passenger strands, indicating a broad strand switch. Activity assays and Argonaute profiling of the transcriptome confirm that these confer increased repression capacity. Finally, we used in vitro assays to show 3p arm-nicked pre-miRNAs preferentially load miRNA-3p species into Argonaute, compared to corresponding miRNA/passenger duplexes. Overall, Dicer hotspot mutations have unexpected neomorphic consequences on miRNAs, including both loss- and gain-of-function.
2025-08-13 | GSE274849 | GEO
Project description:The core miRNA biogenesis enzyme Dicer sustains recurrent mutations in cancer, which specifically compromise catalysis by its RNase IIIb domain. These are proposed to act as selective hypomorphs, since Dicer-RNase IIIb cleaves the 5p arms of pre-miRNA hairpins. However, the lack of knockin models has hindered a full understanding of the consequences of Dicer hotspot mutations for miRNA biogenesis. Here, we generated Dicer-KO and Dicer-S1344L (homozygous and hemizygous) hESCs; the latter is a non-catalytic mutation in RNase IIIa that impairs RNase IIIb activity. Consistent with our previous work, Dicer-KO is cell lethal in hESCs. However, in contrast to the expectation that Dicer hotspot mutations confer cell advantages, Dicer-S1344L knockin hESCs were subviable and also required a conditional genetic strategy for isolation. Small RNA sequencing using spike-in normalization reveals two broad trends: ablation of miRNA-5p species, and selective changes in miRNA-3p species. Curiously, we recognized a directional upregulation of miRNA-3p passenger strands, indicating a broad strand switch. Activity assays and Argonaute profiling of the transcriptome confirm that these confer increased repression capacity. Finally, we used in vitro assays to show 3p arm-nicked pre-miRNAs preferentially load miRNA-3p species into Argonaute, compared to corresponding miRNA/passenger duplexes. Overall, Dicer hotspot mutations have unexpected neomorphic consequences on miRNAs, including both loss- and gain-of-function.
2025-08-13 | GSE274853 | GEO
Project description:Recurrent somatic hotspot mutations of DICER1 appear to be clustered around each of four critical metal binding residues in the RNase IIIB domain of DICER1. This domain is responsible for cleavage of the 3’ end of the 5p-miRNA strand of a pre-mRNA hairpin. To investigate the effects of these cancer-associated “hotspot” mutations we engineered mouse Dicer1-deficient ES cells to express wild-type and an allelic series of the mutant human DICER1 variants. Global miRNA and mRNA profiles from cells carrying the metal binding site mutations were compared to each other and wild-type human DICER1. The miRNA and mRNA profiles generated through the expression of the hotspot mutations were virtually identical, and the DICER1 hotspot mutation carrying cells were distinct from both wild-type and Dicer1-deficient cells. Further, miRNA profiles showed mutant DICER1 results in a dramatic loss in processing of mature 5p-miRNA strands but were still able to create 3p-strand miRNAs. Messenger-RNA profile changes were consistent with the loss of 5p-strand miRNAs and showed enriched expression for predicted targets of the lost 5p derived miRNAs. We therefore conclude that cancer-associated somatic hotspot mutations of DICER1, affecting any one of four metal binding residues in the RNase IIIB domain, are functionally equivalent with respect to miRNA-processing and are hypomorphic alleles, yielding a global loss in processing of mature 5p-strand miRNA. We further propose that this resulting 3p-strand bias in mature miRNA expression likely underpins the oncogenic potential of these hotspot mutations. A total of 28 Affymetrix Mouse Gene ST arrays were done for mRNA expression profiling of various DICER1 mutants (n=14), wildtype controls (n=6), vector only (n=3) and parental cell lines (n=5).
2012-10-01 | E-GEOD-40965 | biostudies-arrayexpress
Project description:Recurrent somatic hotspot mutations of DICER1 appear to be clustered around each of four critical metal binding residues in the RNase IIIB domain of DICER1. This domain is responsible for cleavage of the 3’ end of the 5p-miRNA strand of a pre-mRNA hairpin. To investigate the effects of these cancer-associated “hotspot” mutations we engineered mouse Dicer1-deficient ES cells to express wild-type and an allelic series of the mutant human DICER1 variants. Global miRNA and mRNA profiles from cells carrying the metal binding site mutations were compared to each other and wild-type human DICER1. The miRNA and mRNA profiles generated through the expression of the hotspot mutations were virtually identical, and the DICER1 hotspot mutation carrying cells were distinct from both wild-type and Dicer1-deficient cells. Further, miRNA profiles showed mutant DICER1 results in a dramatic loss in processing of mature 5p-miRNA strands but were still able to create 3p-strand miRNAs. Messenger-RNA profile changes were consistent with the loss of 5p-strand miRNAs and showed enriched expression for predicted targets of the lost 5p derived miRNAs. We therefore conclude that cancer-associated somatic hotspot mutations of DICER1, affecting any one of four metal binding residues in the RNase IIIB domain, are functionally equivalent with respect to miRNA-processing and are hypomorphic alleles, yielding a global loss in processing of mature 5p-strand miRNA. We further propose that this resulting 3p-strand bias in mature miRNA expression likely underpins the oncogenic potential of these hotspot mutations.
2012-10-01 | GSE40965 | GEO
Project description:Background: Germline truncating mutations in DICER1, an RNase III-type endoribonuclease essential for processing of microRNAs, are seen in families with the pleuropulmonary blastoma-family tumor and dysplasia syndrome; these individuals have a propensity to develop non-epithelial ovarian tumors (i.e. sex-cord stromal and germ cell tumors). Methods: We sequenced the whole transcriptomes or exomes of 14 non-epithelial ovarian tumors and noted closely clustered mutations in the RNase IIIb domain of DICER1 in four cases. Using Sanger sequencing, we then analyzed additional ovarian tumors for mutations in this region. The impact of the mutations on the enzymatic activity of Dicer1 was determined using in vitro RNA cleavage assays. Results: RNase IIIb domain DICER1 mutations were found in 30/102 non-epithelial ovarian tumors (29%), predominantly Sertoli-Leydig cell tumors (26/43, 60%), including 4/4 from individuals with germline DICER1 mutations. The mutations were restricted to metal binding sites within the RNase IIIb catalytic centres critical for miRNA interaction and cleavage, and were somatic in all 14 cases where germline DNA was available for testing. Of 266 epithelial ovarian and endometrial cancers tested, one case, an ovarian carcinosarcoma, had a hotspot mutation. In vitro, the mutant DICER proteins showed reduced RNase IIIb activity but retained RNase IIIa activity. Conclusions: Somatic missense mutations of the RNase IIIb domain of DICER1 are common in non-epithelial ovarian tumors. Genetic, pathologic, and functional evidence suggest that these mutations do not obliterate DICER1 function, rather, they alter it in specific cell types, a novel mechanism through which perturbed microRNA expression is oncogenic.
| EGAS00001000135 | EGA
Project description:DICER1 plays a critical role in microRNA (miRNA) biogenesis. Recurrent somatic “hotspot” mutations at four mental binding sites within the RNase IIIb domain of DICER1, were identified in ovarian sex cord-stromal tumors and have since been described in other pediatric tumors. In this study, we identified and characterized DICER1 hotspot mutations in endometrial cancers derived from The Cancer Genome Atlas (TCGA) and our local tumor bank. DICER1 hotspot mutations are found in ~2% of endometrial tumors. Using Illumina and Sanger targeted resequencing we observed biallelic DICER1 mutations in more than 50% of cases with hotspot mutations and identified an additional recurrent mutation G1809R in 2 cases. Through small RNA deep sequencing and real-time PCR, we demonstrated mutations that add a positively charged side chain to residue 1809 have similar detrimental effects on 5p miRNA production as mutations at metal binding sites. In one case G1809R was compound heterozygous with a germline S839F mutation, which contributes to loss of DICER1 expression by promoting protein degradation. As expected, 5p miRNAs are globally reduced in tumors and cell lines with hotspot mutations. Pathway analysis of gene expression profiles indicated that genes derepressed due to loss of 5p miRNAs are strongly associated with cell cycle related pathways. Using a Dicer null cell line model, we demonstrated that DICER1 hotspot mutants abolished the inhibitory effects of wildtype DICER1 on cell proliferation upon re-expression. Furthermore, targets of let-7 family miRNAs are enriched among the upregulated genes, suggesting loss of let-7 may be impacting downstream pathways.
2015-03-16 | GSE65092 | GEO