29 research outputs found
Downregulation of MicroRNA-9 in iPSC-Derived Neurons of FTD/ALS Patients with TDP-43 Mutations
Transactive response DNA-binding protein 43 (TDP-43) is a major pathological protein in frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). There are many disease-associated mutations in TDP-43, and several cellular and animal models with ectopic overexpression of mutant TDP-43 have been established. Here we sought to study altered molecular events in FTD and ALS by using induced pluripotent stem cell (iPSC) derived patient neurons. We generated multiple iPSC lines from an FTD/ALS patient with the TARDBP A90V mutation and from an unaffected family member who lacked the mutation. After extensive characterization, two to three iPSC lines from each subject were selected, differentiated into postmitotic neurons, and screened for relevant cell-autonomous phenotypes. Patient-derived neurons were more sensitive than control neurons to 100 nM straurosporine but not to other inducers of cellular stress. Three disease-relevant cellular phenotypes were revealed under staurosporine-induced stress. First, TDP-43 was localized in the cytoplasm of a higher percentage of patient neurons than control neurons. Second, the total TDP-43 level was lower in patient neurons with the A90V mutation. Third, the levels of microRNA-9 (miR-9) and its precursor pri-miR-9-2 decreased in patient neurons but not in control neurons. The latter is likely because of reduced TDP-43, as shRNA-mediated TDP-43 knockdown in rodent primary neurons also decreased the pri-miR-9-2 level. The reduction in miR-9 expression was confirmed in human neurons derived from iPSC lines containing the more pathogenic TARDBP M337V mutation, suggesting miR-9 downregulation might be a common pathogenic event in FTD/ALS. These results show that iPSC models of FTD/ALS are useful for revealing stress-dependent cellular defects of human patient neurons containing rare TDP-43 mutations in their native genetic contexts
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CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion
CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exons. For example, CRISPR-mediated editing of β-catenin exon 3, which encodes an autoinhibitory domain, induces partial skipping of the in-frame exon and nuclear accumulation of β-catenin. A single sgRNA can induce small insertions or deletions that partially alter splicing or unexpected larger deletions that remove exons. Exon skipping adds to the unexpected outcomes that must be accounted for, and perhaps taken advantage of, in CRISPR experiments. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1237-8) contains supplementary material, which is available to authorized users
CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion
Facile Morphology and Porosity Regulation of Zeolite ZSM-5 Mesocrystals with Synergistically Enhanced Catalytic Activity and Shape Selectivity
The morphology and mesoporosity of zeolite are two vital properties to determine its performance in diverse applications involving adsorption and catalysis; while it remains a big challenge for the synthesis and regulation of zeolites with exceptional morphology/porosity only through inorganic-ions-based modification. Herein, by simply optimizing the alkali metal type (K+ or Na+), as well as alkali/water ratio and crystallization temperature, the zeolite ZSM-5 mesocrystals with diverse mesostructures are simply and controllably prepared via fine-tuning the crystallization mechanism in an organotemplate-free, ions-mediated seed-assisted system. Moreover, the impacts of these key parameters on the evolution of seed crystals, the development and assembly behavior of aluminosilicate species and the solution-phase process during zeolite crystallization are investigated by means of directional etching in NH4F or NaOH solutions. Except for the morphology/mesoporosity modulation, their physical and chemical properties, such as particle size, microporosity, Si/Al ratio and acidity, can be well maintained at a similar level. As such, the p/o-xylene adsorption and catalytic performance of o-xylene isomerization are used to exhaustively evaluate the synergistically enhanced catalytic activity and shape selectivity of the obtained products. This work demonstrates the possibility of effectively constructing novel zeolite mesostructures by simply altering parameters on simple ions-controlled crystallization and provides good models to inspect the impacts of mesoporosity or morphology on their catalytic performances
Comparative Analysis of the Reported Animal-Vehicle Collisions Data and Carcass Removal Data for Hotspot Identification
Two common types of animal-vehicle collision data (reported animal-vehicle collision (AVC) data and carcass removal data) are usually recorded by transportation management agencies. Previous studies have found that these two datasets often demonstrate different characteristics. To accurately identify the higher-risk animal-vehicle collision sites, this study compared the differences in hotspot identification and the effect of explanation variables between carcass removal and reported AVCs. To complete the objective, both the Negative Binomial (NB) model and the generalized Negative Binomial (GNB) are applied in calculating the Empirical Bayesian (EB) estimates using the animal collision data collected on ten highways in Washington State. The important findings can be summarized as follows. (1) The explanatory variables have different effects on the occurrence of carcass removal data and reported AVC data. (2) The ranking results from EB estimates when using carcass removal data and reported AVC data differ significantly. (3) The results of hotspot identification are different between carcass removal data and reported AVC data. However, the ranking results of GNB models are better than those of NB models in terms of consistency. Thus, transportation management agencies should be cautious when using either carcass removal data or reported AVC data to identify hotspots
Analysing the Impact of Traffic Incidents on the Travel Time Reliability of Freeway High-Occupancy Vehicle Lanes
NEAT1 is Required for Survival of Breast Cancer Cells Through FUS and miR-548
Increasing evidence shows that long noncoding RNAs (lncRNAs) have important roles in the regulation of multiple cellular processes, including cell division, cell growth, and apoptosis, as well as cancer metastasis and neurological disease progression; however, the mechanism of how lncRNAs regulate these processes is not well established. In this study, we demonstrated that downregulating the expression of the lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) in breast cancer cells inhibited cell growth and induced cell apoptosis. In addition, the RNA-binding protein fused in sarcoma/translocated in liposarcoma (FUS/TLS) physically interacted with NEAT1, and reducing the expression of FUS/TLS also induced cell apoptosis. Multiple miRNAs were identified as regulators of NEAT1, but only overexpression of miR-548ar was able to decrease NEAT1 expression and promote apoptosis. These results indicate a novel interaction between NEAT1, miR-548ar-3p, and FUS and their role in the regulation of breast cancer cell apoptosis
NEAT1 is Required for Survival of Breast Cancer Cells through FUS and miR-548
Increasing evidence shows that long noncoding RNAs (lncRNAs) have important roles in the regulation of multiple cellular processes, including cell division, cell growth, and apoptosis, as well as cancer metastasis and neurological disease progression; however, the mechanism of how lncRNAs regulate these processes is not well established. In this study, we demonstrated that downregulating the expression of the lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) in breast cancer cells inhibited cell growth and induced cell apoptosis. In addition, the RNA-binding protein fused in sarcoma/translocated in liposarcoma (FUS/TLS) physically interacted with NEAT1, and reducing the expression of FUS/TLS also induced cell apoptosis. Multiple miRNAs were identified as regulators of NEAT1, but only overexpression of miR-548ar was able to decrease NEAT1 expression and promote apoptosis. These results indicate a novel interaction between NEAT1, miR-548ar-3p, and FUS and their role in the regulation of breast cancer cell apoptosis
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Mutant and Wild-Type Isocitrate Dehydrogenase 1 Share Enhancing Mechanisms Involving Distinct Tyrosine Kinase Cascades in Cancer
Isocitrate dehydrogenase 1 (IDH1) is important for reductive carboxylation in cancer cells, and the IDH1 R132H mutation plays a pathogenic role in cancers including acute myeloid leukemia (AML). However, the regulatory mechanisms modulating mutant and/or wild-type (WT) IDH1 function remain unknown. Here, we show that two groups of tyrosine kinases (TK) enhance the activation of mutant and WT IDH1 through preferential Y42 or Y391 phosphorylation. Mechanistically, Y42 phosphorylation occurs in IDH1 monomers, which promotes dimer formation with enhanced substrate (isocitrate or α-ketoglutarate) binding, whereas Y42-phosphorylated dimers show attenuated disruption to monomers. Y391 phosphorylation occurs in both monomeric and dimeric IDH1, which enhances cofactor (NADP+ or NADPH) binding. Diverse oncogenic TKs phosphorylate IDH1 WT at Y42 and activate Src to phosphorylate IDH1 at Y391, which contributes to reductive carboxylation and tumor growth, whereas FLT3 or the FLT3-ITD mutation activates JAK2 to enhance mutant IDH1 activity through phosphorylation of Y391 and Y42, respectively, in AML cells. SIGNIFICANCE: We demonstrated an intrinsic connection between oncogenic TKs and activation of WT and mutant IDH1, which involves distinct TK cascades in related cancers. In particular, these results provide an additional rationale supporting the combination of FLT3 and mutant IDH1 inhibitors as a promising clinical treatment of mutant IDH1-positive AML.See related commentary by Horton and Huntly, p. 699.This article is highlighted in the In This Issue feature, p. 681