Effect of extracellular spliceosomal snRNAs on the transcriptome of ovarian cancer cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE241912 | GEO | 2024/04/24
REPOSITORIES: GEO
Similar Datasets
Project description:A Drosophila line (l(2)k01105) with a P-element insertion in U6atac snRNA, an essential component of the U12-type spliceosome, was used to investigate the impact of disrupted U12-dependent splicing during larval development. A custom-designed exon array was used to study the expression of genes containing U12-type introns and genes involved in downstream pathways affected by deficient U12-dependent splicing. Flies homozygous for the U6atac mutation (U6atac/U6atac) were compared to heterozygotes (U6atac/CyO-GFP) which have a normal phenotype.
2010-10-11 | GSE24148 | GEO
Project description:A Drosophila line (l(2)k01105) with a P-element insertion in U6atac snRNA, an essential component of the U12-type spliceosome, was used to investigate the impact of disrupted U12-dependent splicing during larval development. A custom-designed exon array was used to study the expression of genes containing U12-type introns and genes involved in downstream pathways affected by deficient U12-dependent splicing. Flies homozygous for the U6atac mutation (U6atac/U6atac) were compared to heterozygotes (U6atac/CyO-GFP) which have a normal phenotype. Samples from homozygous and heterozygous U6atac mutant larvae at 1st, 2nd and 3rd larval instar were labelled with three colours and hybridized three samples per array. Three independently harvested biological replicates were made, with dye swap, except only two replicates for 3rd stage heterozygous control. This study presents exon-level data. Supplementary files: Raw data (.gpr) files. Series variables and repeats information.
2010-10-11 | E-GEOD-24148 | biostudies-arrayexpress
Project description:We identify RBM41 as a novel unique protein component of the minor spliceosome. RBM41 has no previously recognized cellular function but has been identified as a paralog of the U11/U12-65K protein, a known unique component of the minor spliceosome that functions during the early steps of minor intron recognition as a component of the U11/U12 di-snRNP. We show that both proteins use their highly similar C-terminal RRMs to bind to 3'-terminal stem-loops in U12 and U6atac snRNAs with comparable affinity. Our BioID data indicate that the unique N-terminal domain of RBM41 is necessary for its association with complexes containing DHX8, an RNA helicase, which in the major spliceosome drives the release of mature mRNA from the spliceosome. Consistently, we show that RBM41 associates with excised U12-type intron lariats, is present in the U12 mono-snRNP, and is enriched in Cajal bodies, together suggesting that RBM41 functions in the post-splicing steps of the minor spliceosome assembly/disassembly cycle. This contrasts with the U11/U12-65K protein, which uses the N-terminal region to interact with U11 snRNP during the intron recognition step. Finally, we show that while RBM41 knockout cells are viable, they show alterations in the splicing of U12-type introns, particularly differential U12-type 3' splice site usage. Together, our results highlight the role 3’-terminal stem-loop of U12 snRNA as a dynamic binding platform for the paralogous U11/U12-65K and RBM41 proteins, which function at distinct stages of minor spliceosome assembly/disassembly cycle.
2024-02-04 | GSE246283 | GEO
Project description:Spliceosomal small nuclear RNAs (snRNAs) are modified by small Cajal body (CB) specific ribonucleoproteins (scaRNPs) to ensure snRNP biogenesis and pre-mRNA splicing. However, the function and subcellular site of snRNA modification are largely unknown. We show that CB localization of the protein Nopp140 is essential for concentration of scaRNPs in that nuclear condensate; and that phosphorylation by casein kinase 2 (CK2) at some 80 serines targets Nopp140 to CBs. Transiting through CBs, snRNAs are apparently modified by scaRNPs. Indeed, Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2’-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Additionally, alternative splicing patterns change indicating that these modifications in U1, U2, U5, and U12 snRNAs safeguard splicing fidelity. Given the importance of CK2 in this pathway, compromised splicing could underlie the mode of action of small molecule CK2 inhibitors currently considered for therapy in cholangiocarcinoma, hematological malignancies, and COVID-19.
2021-07-01 | GSE173171 | GEO
Project description:Mpn1 proteins are evolutionarily conserved exonucleases that modify spliceosomal U6 small nuclear RNAs (snRNAs) post-transcriptionally. Mutations in the human MPN1 gene are associated to the genodermatosis Clericuzio-type poikiloderma with neutropenia (PN). Mpn1 deficiency leads to aberrant U6 3M-bM-^@M-^Y end processing and accelerated U6 decay through unknown molecular mechanisms. Here we show that in mpn1M-NM-^T fission yeast cells U6 is barely bound by the protective Lsm2-8 complex, undergoes extensive oligoadenylation and is degraded by the nuclear RNA exonuclease Rrp6 independently of the poly(A) polymerase Cid14/Trf4. Mpn1 processes U6 in a spliceosome-dependent manner, as mutant U6 molecules that fail to join the spliceosome are not substrates for Mpn1. Moreover, human U6atac, the U6-like snRNA of the minor spliceosome, is a novel substrate for hMpn1. We unveil mechanistic details of a new U6 degradation pathway and further corroborate the notion that inefficient canonical and minor pre-mRNA splicing promotes PN. the 3' termini of human U6, U6atac and vtRNA1-1 transcripts from PN patient derived cells and from PN patient cells, compensated with hMPN1 were sequenced.
2014-08-08 | E-GEOD-60196 | biostudies-arrayexpress
Project description:CD47 is a transmembrane glycoprotein that is ubiquitously expressed in different organs and tissues (Barclay and Van den Berg 2014; Liu, et al. 2017). In the human immune system, CD47 interacts with some integrins, two counter-receptor signal regulator protein (SIRP) family members, and the secreted thrombospondin-1 (TSP1) (Barclay and Van den Berg 2014; Gao, et al. 2016; Kaur, et al. 2013; Oldenborg, et al. 2000). CD47 has two established roles in the immune system. The CD47-SIRPα interaction was identified as a critical innate immune checkpoint, which delivers an antiphagocytic signal to macrophages and inhibits neutrophil cytotoxicity (Martínez- Sanz, et al. 2021). Its interaction with inhibitory SIRPα is a physiological anti-phagocytic “don’t eat me” signal on circulating red blood cells that is co-opted by cancer cells (Matlung, et al. 2017). Many malignant cells overexpress CD47 (Betancur, et al. 2017; Chao, et al. 2011; Jaiswal, et al. 2009; Majeti, et al. 2009; Oronsky, et al. 2020; Petrova, et al. 2017). CD47/SIRPα-targeted therapeutics have been developed to overcome this immune checkpoint for cancer treatment (Kaur, et al. 2020; Matlung, et al. 2017). Secondly, engagement of CD47 on T cells by TSP1 regulates their differentiation and survival (Grimbert, et al. 2006; Lamy, et al. 2007) and inhibits T cell receptor signaling and antigen presentation by dendritic cells (DCs) (Kaur, et al. 2014; Li, et al. 2002; Liu, et al. 2015; Miller, et al. 2013; Soto-Pantoja, et al. 2014; Weng, et al. 2014). TSP1/CD47 signaling has similar inhibitory functions to limit NK cell activation (Kim, et al. 2008; Nath, et al. 2018; Nath, et al. 2019; Schwartz, et al. 2019) and IL1β production by macrophages (Stein, et al. 2016). CD47 is therefore a checkpoint that regulates both innate and adaptive immunity. The recent understanding of CD47 antagonism associated with increased antigen presentation by DCs (Liu, et al. 2016) and natural killer cell cytotoxicity (Nath, et al. 2019) contributes to the heightened interest in CD47 as a therapeutic target (Kaur, et al. 2020).
2022-09-21 | GSE198820 | GEO
Project description:In this work, we identify RBM41 as a novel unique protein component of the minor spliceosome. RBM41 has no previously recognized cellular function but has been identified as a paralog of the U11/U12-65K protein, a known unique component of the minor spliceosome that functions during the early steps of minor intron recognition as a component of the U11/U12 di-snRNP. We show that both proteins use their highly similar C-terminal RRMs to bind to 3'-terminal stem-loops in U12 and U6atac snRNAs with comparable affinity. Our BioID data indicate that the unique N-terminal domain of RBM41 is necessary for its association with complexes containing DHX8, an RNA helicase, which in the major spliceosome drives the release of mature mRNA from the spliceosome.
| MSV000092983 | MassIVE
Project description:DNA damage can promote altered RNA splicing and decreased gene expression (Gregersen and Svejstrup, 2018; Milek et al., 2017; Munoz et al., 2009; Shkreta and Chabot, 2015), and aberrant splicing is implicated in neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), Fragile X syndrome and spinal muscular atrophy (SMA) (Conlon et al., 2016; Jia et al., 2012; Loomis et al., 2014; Qiu et al., 2014; Scotti and Swanson, 2016). Therefore, we used RNA-seq data to assess RNA-splicing in double-mutant brain tissue using multivariate analysis of transcriptional splicing (rMATS) (Shen et al., 2014) and a splicing deficiency score algorithm (Bai et al., 2013) to assess intron retention.
2021-12-14 | GSE174841 | GEO
Project description:Recent studies using next-generation sequencing technology have uncovered mutational landscapes of various myeloid malignancies (Cancer Genome Atlas Research Network, 2013; Yoshida et al., 2011). These genetic data revealed novel classes of mutations that commonly occur in patients with myeloid malignancies, including epigenetic regulators and spliceosomal genes. In addition, co-occurrence and mutual exclusivity of these disease alleles suggest convergent cooperative roles or common biological effects of specific alleles in myeloid leukemogenesis (Shih et al., 2012). Somatic deletions and loss-of-function mutations in TET2, a member of the TET family which regulates DNA methylation, were identified in 10-20% of myelodysplastic syndromes (MDS) and myeloproliferative neoplasms (MPN) patients, 12-24% of acute myeloid leukemia (AML) patients and 40-50% of chronic myelomonocytic leukemia (CMML) patients (Abdel-Wahab et al., 2009; Delhommeau et al., 2009; Jankowska et al., 2009; Langemeijer et al., 2009). Analysis carried out in large AML cohorts has shown that TET2 mutations are associated with adverse outcome in patients with intermediate-risk, cytogenetically normal AML (Patel et al., 2012). TET proteins (TET1-3) are Fe(II)- and a-ketoglutarate-dependent enzymes that catalyze the conversion of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) leading to DNA demethylation (Guo et al., 2011; Tahiliani et al., 2009). Consistent with this notion, TET2 mutant AML patient samples show decreased 5-hmC levels and hypermethylation phenotype (Figueroa et al., 2010; Ko et al., 2010). Oncometabolite 2-hydroxyglutarate produced by IDH1/2 mutations inhibits TET2 function (Figueroa et al., 2010). Moreover, WT1 recruits TET2 to regulate its target gene expression (Wang et al., 2015) and WT1 mutations lead to reduced TET2 function and decreased 5-hmC levels (Rampal et al., 2014). Together, IDH1/2 mutations and WT1 mutations share, at least partially, common epigenetic pathogenesis in AML as TET2 mutations through altered DNA hydroxymethylation. A number of studies have shown that TET2 is a key regulator of hematopoietic stem cell (HSC) self-renewal and myeloid differentiation. Conditional loss of Tet2 in mouse hematopoietic compartment leads to expansion of hematopoietic stem/progenitor cells (HSPCs, LSK, lin- Sca1+ cKit+) and enhanced repopulating capacity in vivo (Li et al., 2011; Moran-Crusio et al., 2011; Quivoron et al., 2011). In addition, Tet2-mutant mice show myeloproliferation in vivo and TET2-silenced human cord blood cells show skewed differentiation towards CD14+ myelomonocytic lineage in vitro (Pronier et al., 2011), which is compatible with a high frequency of TET2 mutations in CMML patients. More recently, mutations in TET2 and in other epigenetic regulators, such as DNMT3A and ASXL1, are reported in individuals with clonal hematopoiesis without hematological malignancies (Busque et al., 2012; Xie et al., 2014). Analysis of AML and patients with nonhematologic malignancies suggest mutations in TET2 and in other epigenetic modifiers may represent early premalignant events that cause clonal hematopoietic expansion (Genovese et al., 2014; Jaiswal et al., 2014; Jan et al., 2012). These data indicate that TET2 inactivation contributes to selective clonal advantages in early leukemia initiation but requires additional genetic events to induce myeloid transformation. Ras proteins are small GTPases that cycle between active guanosine triphosphate (GTP)-bound (Ras-GTP) and inactive guanosine diphosphate (GDP)-bound (Ras-GDP) conformations (Schubbert et al., 2007). Ras-GTP binds to and activates downstream signaling effectors, such as Raf and phosphoinositide 3-kinase (PI3K), thereby transducing signals from activated growth factor receptors to the nucleus. Thus, Ras-mediated signal transduction critically regulates fundamental cellular behaviors, including proliferation, differentiation and survival (Schubbert et al., 2007). The three cellular Ras genes encode 4 highly homologous proteins, Hras, Kras4A, Kras4B and Nras, that share conserved effector binding domains and the P-loop, which binds the g-phosphate of GTP (Zhou et al., 2016). Cancer-associated RAS mutations encode proteins that accumulate in the active GTP-bound conformation due to defective intrinsic hydrolysis and resistance to guanosine triphosphatase-activating proteins (Schubbert et al., 2007). Among these isoforms, NRAS is the most common target of oncogenic signaling mutations in myeloid leukemia, including 10-15% of AML and CMML cases (Bacher et al., 2006; Ball et al., 2016). Moreover, recent study identified NRAS as one of the somatic gene mutations with adverse prognostic relevance in CMML (Elena et al., 2016). Consistent with human data, mice with hematopoietic tissue specific conditional NrasG12D allele develop fatal myeloproliferative disease in vivo (Li et al., 2011). These data underscore critical role of oncogenic NRAS mutations in myeloid leukemogenesis. Recent studies have shown that mutations in epigenetic modifiers and signaling factors commonly co-occur in AML, including the co-occurrence of TET2 mutations and NRAS mutations (Papaemmanuil et al., 2016; Patel et al., 2012). Analysis of the clonal architecture in CMML patients suggests TET2/NRAS double-mutant clones expand both within stable disease time course and in relapse after allogeneic stem cell transplantation (Itzykson et al., 2013). These evidences imply TET2 and NRAS mutation likely function together in myeloid transformation. Although previous study has shown that knockdown of Tet2 does not accelerate NrasG12D induced transplant myeloproliferative disease model (Chang et al., 2014), to date there have been no studies of the mechanistic impact caused by the combination of these high risk genetic lesions using physiologic in vivo model. Moreover, how the combination of myeloid leukemia-associated disease alleles affect sensitivity to targeted therapy has not been elucidated. Here we investigate loss of Tet2 together with NrasG12D in CMML development and specifically how they interact to affect sensitivity to targeted therapy.
2018-03-17 | GSE96758 | GEO
Project description:Recent studies using next-generation sequencing technology have uncovered mutational landscapes of various myeloid malignancies (Cancer Genome Atlas Research Network, 2013; Yoshida et al., 2011). These genetic data revealed novel classes of mutations that commonly occur in patients with myeloid malignancies, including epigenetic regulators and spliceosomal genes. In addition, co-occurrence and mutual exclusivity of these disease alleles suggest convergent cooperative roles or common biological effects of specific alleles in myeloid leukemogenesis (Shih et al., 2012). Somatic deletions and loss-of-function mutations in TET2, a member of the TET family which regulates DNA methylation, were identified in 10-20% of myelodysplastic syndromes (MDS) and myeloproliferative neoplasms (MPN) patients, 12-24% of acute myeloid leukemia (AML) patients and 40-50% of chronic myelomonocytic leukemia (CMML) patients (Abdel-Wahab et al., 2009; Delhommeau et al., 2009; Jankowska et al., 2009; Langemeijer et al., 2009). Analysis carried out in large AML cohorts has shown that TET2 mutations are associated with adverse outcome in patients with intermediate-risk, cytogenetically normal AML (Patel et al., 2012). TET proteins (TET1-3) are Fe(II)- and a-ketoglutarate-dependent enzymes that catalyze the conversion of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) leading to DNA demethylation (Guo et al., 2011; Tahiliani et al., 2009). Consistent with this notion, TET2 mutant AML patient samples show decreased 5-hmC levels and hypermethylation phenotype (Figueroa et al., 2010; Ko et al., 2010). Oncometabolite 2-hydroxyglutarate produced by IDH1/2 mutations inhibits TET2 function (Figueroa et al., 2010). Moreover, WT1 recruits TET2 to regulate its target gene expression (Wang et al., 2015) and WT1 mutations lead to reduced TET2 function and decreased 5-hmC levels (Rampal et al., 2014). Together, IDH1/2 mutations and WT1 mutations share, at least partially, common epigenetic pathogenesis in AML as TET2 mutations through altered DNA hydroxymethylation. A number of studies have shown that TET2 is a key regulator of hematopoietic stem cell (HSC) self-renewal and myeloid differentiation. Conditional loss of Tet2 in mouse hematopoietic compartment leads to expansion of hematopoietic stem/progenitor cells (HSPCs, LSK, lin- Sca1+ cKit+) and enhanced repopulating capacity in vivo (Li et al., 2011; Moran-Crusio et al., 2011; Quivoron et al., 2011). In addition, Tet2-mutant mice show myeloproliferation in vivo and TET2-silenced human cord blood cells show skewed differentiation towards CD14+ myelomonocytic lineage in vitro (Pronier et al., 2011), which is compatible with a high frequency of TET2 mutations in CMML patients. More recently, mutations in TET2 and in other epigenetic regulators, such as DNMT3A and ASXL1, are reported in individuals with clonal hematopoiesis without hematological malignancies (Busque et al., 2012; Xie et al., 2014). Analysis of AML and patients with nonhematologic malignancies suggest mutations in TET2 and in other epigenetic modifiers may represent early premalignant events that cause clonal hematopoietic expansion (Genovese et al., 2014; Jaiswal et al., 2014; Jan et al., 2012). These data indicate that TET2 inactivation contributes to selective clonal advantages in early leukemia initiation but requires additional genetic events to induce myeloid transformation. Ras proteins are small GTPases that cycle between active guanosine triphosphate (GTP)-bound (Ras-GTP) and inactive guanosine diphosphate (GDP)-bound (Ras-GDP) conformations (Schubbert et al., 2007). Ras-GTP binds to and activates downstream signaling effectors, such as Raf and phosphoinositide 3-kinase (PI3K), thereby transducing signals from activated growth factor receptors to the nucleus. Thus, Ras-mediated signal transduction critically regulates fundamental cellular behaviors, including proliferation, differentiation and survival (Schubbert et al., 2007). The three cellular Ras genes encode 4 highly homologous proteins, Hras, Kras4A, Kras4B and Nras, that share conserved effector binding domains and the P-loop, which binds the g-phosphate of GTP (Zhou et al., 2016). Cancer-associated RAS mutations encode proteins that accumulate in the active GTP-bound conformation due to defective intrinsic hydrolysis and resistance to guanosine triphosphatase-activating proteins (Schubbert et al., 2007). Among these isoforms, NRAS is the most common target of oncogenic signaling mutations in myeloid leukemia, including 10-15% of AML and CMML cases (Bacher et al., 2006; Ball et al., 2016). Moreover, recent study identified NRAS as one of the somatic gene mutations with adverse prognostic relevance in CMML (Elena et al., 2016). Consistent with human data, mice with hematopoietic tissue specific conditional NrasG12D allele develop fatal myeloproliferative disease in vivo (Li et al., 2011). These data underscore critical role of oncogenic NRAS mutations in myeloid leukemogenesis. Recent studies have shown that mutations in epigenetic modifiers and signaling factors commonly co-occur in AML, including the co-occurrence of TET2 mutations and NRAS mutations (Papaemmanuil et al., 2016; Patel et al., 2012). Analysis of the clonal architecture in CMML patients suggests TET2/NRAS double-mutant clones expand both within stable disease time course and in relapse after allogeneic stem cell transplantation (Itzykson et al., 2013). These evidences imply TET2 and NRAS mutation likely function together in myeloid transformation. Although previous study has shown that knockdown of Tet2 does not accelerate NrasG12D induced transplant myeloproliferative disease model (Chang et al., 2014), to date there have been no studies of the mechanistic impact caused by the combination of these high risk genetic lesions using physiologic in vivo model. Moreover, how the combination of myeloid leukemia-associated disease alleles affect sensitivity to targeted therapy has not been elucidated. Here we investigate loss of Tet2 together with NrasG12D in CMML development and specifically how they interact to affect sensitivity to targeted therapy.
2018-03-17 | GSE96759 | GEO