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Ceapins block the unfolded protein response sensor ATF6α by inducing a neomorphic inter-organelle tether.
Torres SE, Gallagher CM, Plate L, Gupta M, Liem CR, Guo X, Tian R, Stroud RM, Kampmann M, Weissman JS, Walter P
(2019) Elife 8:
MeSH Terms: ATP-Binding Cassette Transporters, Activating Transcription Factor 6, CRISPR-Cas Systems, Endoplasmic Reticulum, HEK293 Cells, Hep G2 Cells, Humans, Organelles, Peroxisomes, Phenotype, Protein Binding, Small Molecule Libraries, Unfolded Protein Response
Show Abstract · Added March 3, 2020
The unfolded protein response (UPR) detects and restores deficits in the endoplasmic reticulum (ER) protein folding capacity. Ceapins specifically inhibit the UPR sensor ATF6α, an ER-tethered transcription factor, by retaining it at the ER through an unknown mechanism. Our genome-wide CRISPR interference (CRISPRi) screen reveals that Ceapins function is completely dependent on the ABCD3 peroxisomal transporter. Proteomics studies establish that ABCD3 physically associates with ER-resident ATF6α in cells and in vitro in a Ceapin-dependent manner. Ceapins induce the neomorphic association of ER and peroxisomes by directly tethering the cytosolic domain of ATF6α to ABCD3's transmembrane regions without inhibiting or depending on ABCD3 transporter activity. Thus, our studies reveal that Ceapins function by chemical-induced misdirection which explains their remarkable specificity and opens up new mechanistic routes for drug development and synthetic biology.
© 2019, Torres et al.
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NATF (Native and Tissue-Specific Fluorescence): A Strategy for Bright, Tissue-Specific GFP Labeling of Native Proteins in .
He S, Cuentas-Condori A, Miller DM
(2019) Genetics 212: 387-395
MeSH Terms: Animals, CRISPR-Cas Systems, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Fluorescence, Gene Editing, Green Fluorescent Proteins, Membrane Proteins, Nerve Tissue Proteins
Show Abstract · Added March 3, 2020
GFP labeling by genome editing can reveal the authentic location of a native protein, but is frequently hampered by weak GFP signals and broad expression across a range of tissues that may obscure cell-specific localization. To overcome these problems, we engineered a Native And Tissue-specific Fluorescence (NATF) strategy that combines genome editing and split-GFP to yield bright, cell-specific protein labeling. We use clustered regularly interspaced short palindromic repeats CRISPR/Cas9 to insert a tandem array of seven copies of the GFP11 β-strand ( ) at the genomic locus of each target protein. The resultant knock-in strain is then crossed with separate reporter lines that express the complementing split-GFP fragment () in specific cell types, thus affording tissue-specific labeling of the target protein at its native level. We show that NATF reveals the otherwise undetectable intracellular location of the immunoglobulin protein OIG-1 and demarcates the receptor auxiliary protein LEV-10 at cell-specific synaptic domains in the nervous system.
Copyright © 2019 by the Genetics Society of America.
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CRISPR/Cas9 engineering of a KIM-1 reporter human proximal tubule cell line.
Veach RA, Wilson MH
(2018) PLoS One 13: e0204487
MeSH Terms: Acute Kidney Injury, CRISPR-Cas Systems, Cell Line, Cisplatin, Gene Knock-In Techniques, Gene Targeting, Genes, Reporter, Genetic Engineering, Glucose, Green Fluorescent Proteins, Hepatitis A Virus Cellular Receptor 1, Homologous Recombination, Humans, Kidney Tubules, Proximal, Luciferases, Up-Regulation
Show Abstract · Added December 13, 2018
We used the CRISPR/Cas9 system to knock-in reporter transgenes at the kidney injury molecule-1 (KIM-1) locus and isolated human proximal tubule cell (HK-2) clones. PCR verified targeted knock-in of the luciferase and eGFP reporter at the KIM-1 locus. HK-2-KIM-1 reporter cells responded to various stimuli including hypoxia, cisplatin, and high glucose, indicative of upregulation of KIM-1 expression. We attempted using CRISPR/Cas9 to also engineer the KIM-1 reporter in telomerase-immortalized human RPTEC cells. However, these cells demonstrated an inability to undergo homologous recombination at the target locus. KIM-1-reporter human proximal tubular cells could be valuable tools in drug discovery for molecules inhibiting kidney injury. Additionally, our gene targeting strategy could be used in other cell lines to evaluate the biology of KIM-1 in vitro or in vivo.
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16 MeSH Terms
Arrestins and G proteins in cellular signaling: The coin has two sides.
Gurevich VV, Gurevich EV
(2018) Sci Signal 11:
MeSH Terms: Arrestins, CRISPR-Cas Systems, Phosphorylation, RNA, Small Interfering, beta-Arrestins
Show Abstract · Added March 18, 2020
Several studies have suggested that arrestin-mediated signaling by GPCRs requires G protein activation; however, in this issue of , Luttrell documented arrestin-dependent activation of ERK1/2 by a number of GPCRs. These studies do not contradict each other, but illustrate the complexity of cellular signaling that cannot and should not be reduced to simplistic models.
Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
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Disrupted structure and aberrant function of CHIP mediates the loss of motor and cognitive function in preclinical models of SCAR16.
Shi CH, Rubel C, Soss SE, Sanchez-Hodge R, Zhang S, Madrigal SC, Ravi S, McDonough H, Page RC, Chazin WJ, Patterson C, Mao CY, Willis MS, Luo HY, Li YS, Stevens DA, Tang MB, Du P, Wang YH, Hu ZW, Xu YM, Schisler JC
(2018) PLoS Genet 14: e1007664
MeSH Terms: Animals, Behavior, Animal, CRISPR-Cas Systems, Cognition, Disease Models, Animal, Female, Humans, Male, Mice, Mice, Inbred C57BL, Models, Molecular, Motor Activity, Mutagenesis, Site-Directed, Phenotype, Point Mutation, Protein Domains, Protein Multimerization, Rats, Rats, Sprague-Dawley, Spinocerebellar Ataxias, Ubiquitin-Protein Ligases
Show Abstract · Added March 26, 2019
CHIP (carboxyl terminus of heat shock 70-interacting protein) has long been recognized as an active member of the cellular protein quality control system given the ability of CHIP to function as both a co-chaperone and ubiquitin ligase. We discovered a genetic disease, now known as spinocerebellar autosomal recessive 16 (SCAR16), resulting from a coding mutation that caused a loss of CHIP ubiquitin ligase function. The initial mutation describing SCAR16 was a missense mutation in the ubiquitin ligase domain of CHIP (p.T246M). Using multiple biophysical and cellular approaches, we demonstrated that T246M mutation results in structural disorganization and misfolding of the CHIP U-box domain, promoting oligomerization, and increased proteasome-dependent turnover. CHIP-T246M has no ligase activity, but maintains interactions with chaperones and chaperone-related functions. To establish preclinical models of SCAR16, we engineered T246M at the endogenous locus in both mice and rats. Animals homozygous for T246M had both cognitive and motor cerebellar dysfunction distinct from those observed in the CHIP null animal model, as well as deficits in learning and memory, reflective of the cognitive deficits reported in SCAR16 patients. We conclude that the T246M mutation is not equivalent to the total loss of CHIP, supporting the concept that disease-causing CHIP mutations have different biophysical and functional repercussions on CHIP function that may directly correlate to the spectrum of clinical phenotypes observed in SCAR16 patients. Our findings both further expand our basic understanding of CHIP biology and provide meaningful mechanistic insight underlying the molecular drivers of SCAR16 disease pathology, which may be used to inform the development of novel therapeutics for this devastating disease.
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Alteration of BDNF in the medial prefrontal cortex and the ventral hippocampus impairs extinction of avoidance.
Rosas-Vidal LE, Lozada-Miranda V, Cantres-Rosario Y, Vega-Medina A, Melendez L, Quirk GJ
(2018) Neuropsychopharmacology 43: 2636-2644
MeSH Terms: Animals, Avoidance Learning, Brain-Derived Neurotrophic Factor, CRISPR-Cas Systems, Cell Line, Tumor, Extinction, Psychological, Hippocampus, Male, Neural Pathways, Neuronal Plasticity, Prefrontal Cortex, Rats, Rats, Sprague-Dawley
Show Abstract · Added March 3, 2020
Brain-derived neurotrophic factor (BDNF) is critical for establishing activity-related neural plasticity. There is increasing interest in the mechanisms of active avoidance and its extinction, but little is known about the role of BDNF in these processes. Using the platform-mediated avoidance task combined with local infusions of an antibody against BDNF, we show that blocking BDNF in either prelimbic (PL) or infralimbic (IL) medial prefrontal cortex during extinction training impairs subsequent recall of extinction of avoidance, differing from extinction of conditioned freezing. By combining retrograde tracers with BDNF immunohistochemistry, we show that extinction of avoidance increases BDNF expression in ventral hippocampal (vHPC) neurons, but not amygdala neurons, projecting to PL and IL. Using the CRISPR/Cas9 system, we further show that reducing BDNF production in vHPC neurons impairs recall of avoidance extinction. Thus, the vHPC may mediate behavioral flexibility in avoidance by driving extinction-related plasticity via BDNFergic projections to both PL and IL. These findings add to the growing body of knowledge implicating the hippocampal-prefrontal pathway in anxiety-related disorders and extinction-based therapies.
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Knockdown of survivin results in inhibition of epithelial to mesenchymal transition in retinal pigment epithelial cells by attenuating the TGFβ pathway.
Zhang P, Zhao G, Ji L, Yin J, Lu L, Li W, Zhou G, Chaum E, Yue J
(2018) Biochem Biophys Res Commun 498: 573-578
MeSH Terms: CRISPR-Cas Systems, Cell Line, Cell Proliferation, Epithelial-Mesenchymal Transition, Humans, Inhibitor of Apoptosis Proteins, Retinal Pigment Epithelium, Signal Transduction, Survivin, Transforming Growth Factor beta, Vitreoretinopathy, Proliferative
Show Abstract · Added June 11, 2018
Proliferative vitreoretinopathy (PVR) is a common complication of open globe injury and the most common cause of failed retinal detachment surgery. The response by retinal pigment epithelial (RPE) cells liberated into the vitreous includes proliferation and migration; most importantly, epithelial to mesenchymal transition (EMT) of RPE plays a central role in the development and progress of PVR. For the first time, we show that knockdown of BIRC5, a member of the inhibitor of apoptosis protein family, using either lentiviral vector based CRISPR/Cas9 nickase gene editing or inhibition of survivin using the small-molecule inhibitor YM155, results in the suppression of EMT in RPE cells. Knockdown of survivin or inhibition of survivin significantly reduced TGFβ-induced cell proliferation and migration. We further demonstrated that knockdown or inhibition of survivin attenuated the TGFβ signaling by showing reduced phospho-SMAD2 in BIRC5 knockdown or YM155-treated cells compared to controls. Inhibition of the TGFβ pathway using TGFβ receptor inhibitor also suppressed survivin expression in RPE cells. Our studies demonstrate that survivin contributes to EMT by cross-talking with the TGFβ pathway in RPE cells. Targeting survivin using small-molecule inhibitors may provide a novel approach to treat PVR disease.
Copyright © 2018 Elsevier Inc. All rights reserved.
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11 MeSH Terms
Gene-edited MLE-15 Cells as a Model for the Hermansky-Pudlak Syndromes.
Kook S, Qi A, Wang P, Meng S, Gulleman P, Young LR, Guttentag SH
(2018) Am J Respir Cell Mol Biol 58: 566-574
MeSH Terms: Alveolar Epithelial Cells, Animals, CRISPR-Associated Protein 9, CRISPR-Cas Systems, Cell Line, Clustered Regularly Interspaced Short Palindromic Repeats, Disease Models, Animal, Gene Editing, Genetic Markers, Genetic Predisposition to Disease, Hermanski-Pudlak Syndrome, Humans, Mice, Inbred C57BL, Mice, Transgenic, Mutation, Phenotype
Show Abstract · Added April 1, 2019
Defining the mechanisms of cellular pathogenesis in rare lung diseases such as Hermansky-Pudlak syndrome (HPS) is often complicated by loss of the differentiated phenotype of cultured primary alveolar type 2 (AT2) cells, as well as by a lack of durable cell lines that are faithful to both AT2-cell and rare disease phenotypes. We used CRISPR/Cas9 gene editing to generate a series of HPS-specific mutations in the MLE-15 cell line. The resulting MLE-15/HPS cell lines exhibit preservation of AT2 cellular functions, including formation of lamellar body-like organelles, complete processing of surfactant protein B, and known features of HPS specific to each trafficking complex, including loss of protein targeting to lamellar bodies. MLE-15/HPS1 and MLE-15/HPS2 (with a mutation in Ap3β1) express increased macrophage chemotactic protein-1, a well-described mediator of alveolitis in patients with HPS and in mouse models. We show that MLE-15/HPS9 and pallid AT2 cells (with a mutation in Bloc1s6) also express increased macrophage chemotactic protein-1, suggesting that mice and humans with BLOC-1 mutations may also be susceptible to alveolitis. In addition to providing a flexible platform to examine the role of HPS-specific mutations in trafficking AT2 cells, MLE-15/HPS cell lines provide a durable resource for high-throughput screening and studies of cellular pathophysiology that are likely to accelerate progress toward developing novel therapies for this rare lung disease.
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16 MeSH Terms
DNPEP is not the only peptidase that produces SPAK fragments in kidney.
Koumangoye R, Delpire E
(2017) Physiol Rep 5:
MeSH Terms: Animals, CRISPR-Cas Systems, Female, Glutamyl Aminopeptidase, Kidney, Male, Mice, Mice, Knockout, Peptide Hydrolases, Protein-Serine-Threonine Kinases
Show Abstract · Added February 15, 2018
SPAK (STE20/SPS1-related proline/alanine-rich kinase) regulates Na and Cl reabsorption in the distal convoluted tubule, and possibly in the thick ascending limb of Henle. This kinase phosphorylates and activates the apical Na-Cl cotransporter in the DCT. Western blot analysis reveals that SPAK in kidney exists as a full-length protein as well as shorter fragments that might affect NKCC2 function in the TAL. Recently, we showed that kidney lysates exerts proteolytic activity towards SPAK, resulting in the formation of multiple SPAK fragments with possible inhibitory effects on the kinase. The proteolytic activity is mediated by a Zn metalloprotease inhibited by 1,10-phenanthroline, DTT, and EDTA. Size exclusion chromatography demonstrated that the protease was a high-molecular-weight protein. Protein identification by mass-spectrometry analysis after ion exchange and size exclusion chromatography identified multiple proteases as possible candidates and aspartyl aminopeptidase, DNPEP, shared all the properties of the kidney lysate activity. Furthermore, recombinant GST-DNPEP produced similar proteolytic pattern. No mouse knockout model was, however, available to be used as negative control. In this study, we used a DNPEP-mutant mouse generated by EUCOMM as well as a novel CRISPR/cas9 mouse knockout to assess the activity of their kidney lysates towards SPAK. Two mouse models had to be used because different anti-DNPEP antibodies provided conflicting data on whether the EUCOMM mouse resulted in a true knockout. We show that in the absence of DNPEP, the kidney lysates retain their ability to cleave SPAK, indicating that DNPEP might have been misidentified as the protease behind the kidney lysate activity, or that the aspartyl aminopeptidase might not be the only protease cleaving SPAK in kidney.
© 2017 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.
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10 MeSH Terms
RADX Promotes Genome Stability and Modulates Chemosensitivity by Regulating RAD51 at Replication Forks.
Dungrawala H, Bhat KP, Le Meur R, Chazin WJ, Ding X, Sharan SK, Wessel SR, Sathe AA, Zhao R, Cortez D
(2017) Mol Cell 67: 374-386.e5
MeSH Terms: A549 Cells, Animals, BRCA2 Protein, CRISPR-Cas Systems, DNA Breaks, Double-Stranded, DNA Repair, DNA, Neoplasm, Dose-Response Relationship, Drug, Drug Resistance, Neoplasm, Gene Expression Regulation, Neoplastic, Genomic Instability, HEK293 Cells, Humans, Mice, Models, Molecular, Mutation, Neoplasms, Poly(ADP-ribose) Polymerase Inhibitors, Protein Binding, RNA Interference, Rad51 Recombinase, Replication Origin, Transfection
Show Abstract · Added March 24, 2018
RAD51 promotes homology-directed repair (HDR), replication fork reversal, and stalled fork protection. Defects in these functions cause genomic instability and tumorigenesis but also generate hypersensitivity to cancer therapeutics. Here we describe the identification of RADX as an RPA-like, single-strand DNA binding protein. RADX is recruited to replication forks, where it prevents fork collapse by regulating RAD51. When RADX is inactivated, excessive RAD51 activity slows replication elongation and causes double-strand breaks. In cancer cells lacking BRCA2, RADX deletion restores fork protection without restoring HDR. Furthermore, RADX inactivation confers chemotherapy and PARP inhibitor resistance to cancer cells with reduced BRCA2/RAD51 pathway function. By antagonizing RAD51 at forks, RADX allows cells to maintain a high capacity for HDR while ensuring that replication functions of RAD51 are properly regulated. Thus, RADX is essential to achieve the proper balance of RAD51 activity to maintain genome stability.
Copyright © 2017 Elsevier Inc. All rights reserved.
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23 MeSH Terms