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PubMed2004

Bnip3L is induced by p53 under hypoxia, and its knockdown promotes tumor growth.

p53-dependent apoptosis is a major determinant of its tumor suppressor activity and can be triggered by hypoxia. No p53 target is known to be induced by p53 or to mediate p53-dependent apoptosis during hypoxia. We report that p53 can directly upregulate expression of Bnip3L, a cell death inducer. During hypoxia, Bnip3L is highly induced in wild-type p53-expressing cells, in part due to increased recruitment of p53 and CBP to Bnip3L. Apoptosis is reduced in hypoxia-exposed cells with functional p53 following Bnip3L knockdown. In vivo, Bnip3L knockdown promotes tumorigenicity of wild-type versus mutant p53-expressing tumors. Thus, Bnip3L, capable of attenuating tumorigenicity, mediates p53-dependent apoptosis under hypoxia, which provides a novel understanding of p53 in tumor suppression.

Animals↗

PubMed2006

Knockdown of ribosomal protein S3 protects human cells from genotoxic stress.

Human ribosomal protein S3 (hS3) has a high apparent binding affinity for the oxidative lesion 7,8-dihydro-8-oxoguanine (8-oxoG). The hS3 ribosomal protein has also been found to inhibit the base excision repair (BER) enzyme hOGG1 from liberating 8-oxoG residing in a 5'-end-labeled oligonucleotide. To understand the in vivo involvement of hS3 in BER, we have turned to RNA interference to generate knockdown of hS3 in cells exposed to DNA damaging agents. Here we show that a 40% knockdown of hS3 resulted in as much as a seven-fold increase in the 24h survival-rate of HEK293 cells exposed to hydrogen peroxide. Significant protection to the alkylating agent methyl methanesulfonate (MMS) was also observed. Protection to the chemotherapeutic alkylating agent Thio-TEPA was only revealed at longer exposure times where the agent became more toxic to untransfected human cells. Overall, these results raise the possibility that hS3 interferes with the repair of the DNA lesions produced by genotoxic agents that potentially could play a role in the onset of cancer and other pathological states such as aging.

Alkylating Agents↗

PubMed2004

Pharmacologically selective block of mu opioid antinociception by peptide nucleic acid antisense in absence of detectable ex vivo knockdown.

The goal of this study was to determine the neuroanatomical extent of mu opioid receptor knockdown in central nervous system (CNS) following intracerebroventricular (i.c.v.) administration of peptide nucleic acid antisense. Rats received subchronic i.c.v. injections of anti-mu opioid receptor antisense, mismatch or vehicle, and were tested for paw pressure latency following i.c.v. mu opioid receptor agonist ([D-Ala2, N-Me-Phe4, Gly-ol5]-enkephalin; DAMGO) or delta opioid receptor agonist ((+)-4-[(aR)-a-((2S,5R)-4-allyl-2,5-dimethyl-1-piperazinyl)-3-methoxybenzyl]-N,N-diethylbenzamide; SNC80). The anti-mu opioid receptor antisense (but not mismatch) sequence abolished DAMGO-induced antinociception with no reduction in the delta opioid receptor-mediated response. In contrast, postmortem receptor autoradiographic analysis of CNS areas revealed no change in mu opioid receptor functional response ([35S]GTPgammaS assay) or receptor labelling ([125I]FK-33824 and mu opioid receptor immunoautoradiography). These results provide further evidence for antisense-induced knockdown at the behavioural level in the absence of clear changes at the tissue level.

Analgesics↗

PubMed2005

RNAi-mediated knockdown of P-glycoprotein using a transposon-based vector system durably restores imatinib sensitivity in imatinib-resistant CML cell lines.

OBJECTIVE: Resistance to therapeutic drugs is a frequent phenomenon in hematologic malignancies, causing treatment failure in patients with leukemias and lymphomas. Overexpression of the multidrug-resistance gene (MDR-1) and its translational product P-glycoprotein (PgP) represents one mechanism of fatal drug resistance. METHODS: We constructed a nonviral, transposon-based vector system for the stable knockdown of PgP in chronic myeloid leukemia cell lines resistant to imatinib and doxorubicin. RESULTS: Using this strategy, PgP expression was completely knocked down 72 hours after vector inoculation and lasted for several months. Cellular efflux of the PgP substates rhodamine and doxorubicin was abolished. Vector-treated cells were resensitized to imatinib- and doxorubicin-induced cell death. CONCLUSION: Using chronic myeloid leukemia as a model, we show that PgP-mediated resistance to imatinib and anthracyclines can be durably reversed by nonviral, transposon-based knockdown of PgP in malignant cells.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2005

Heritable and inducible gene knockdown in C. elegans using Wormgate and the ORFeome.

Double-stranded RNA (dsRNA) mediated gene silencing (RNA interference; RNAi) is a powerful tool for investigating gene function. It is usually performed in Caenorhabditis elegans via the injection or oral delivery of dsRNA, but an alternative approach, the expression of RNA hairpins from introduced DNA (hairpin RNAi; hpRNAi) has several advantages: (1) it can be induced systemically or in a tissue-specific manner; (2) because it is heritable, it allows consistent RNAi silencing across a whole population of genetically identical animals; and (3) it can be applied in refractory tissue such as neurons. hpRNAi has not been widely used to investigate gene function because a number of steps are relatively inefficient and labour-intensive. We describe Wormgate, a new cloning system, which facilitates the efficient high-throughput production of hpRNAi constructs using clones from the C. elegans ORFeome library. The combined use of pWormgate2 and the ORFeome library, with a recently developed particle bombardment transformation system, expedites hpRNAi gene silencing. This will be particularly useful for studying those genes that are refractory to the effects of injected or fed dsRNA, such as neural genes. We report the efficient production of hpRNAi constructs using pWormgate2 and also the knockdown of selected genes, including neurally expressed genes that have previously been refractory to RNAi. Further, when combined with the rrf-3 RNAi hypersensitive strain, the Wormgate approach delivered a highly penetrant knockdown phenotype in nearly 100% of worms for a gene that was completely refractory to other RNAi delivery methods.

Administration, Oral↗

PubMed2026

Spacer-engineered donor DNA enhances CRISPR-Cas9-mediated knockin to establish a chemical knockdown platform for endogenous proteins.

Precise installation of functional protein domains at endogenous loci is a powerful approach for interrogating protein functions, but its broad application is limited by the low efficiency of homology-directed repair (HDR)-mediated knockin during Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 gene editing. Here, we investigated a simple donor DNA engineering strategy that enhances HDR-mediated gene knockin by appending additional gRNA-recognizable spacer sequences to donor templates. Systematic analysis of linear dsDNA and plasmid donors showed that spacer position, length, and orientation influenced HDR efficiency, and that spacer-containing donors improved knockin across multiple genomic loci, insertion sizes, cell types and delivery modalities. Mechanistic analyses revealed that spacer-containing donors formed stable complexes with Cas9/gRNA and showed increased nuclear localization, supporting nuclear delivery as a key contributor to improved editing outcomes. We then applied this gene-editing strategy to establish a chemical knockdown platform by installing drug-responsive degrons at endogenous loci, generating cell lines in which GSK3β or Lin28A protein could be rapidly, potently and reversibly depleted by drug treatment. These platforms enable selective modulation of endogenous proteins and reveal cellular responses that may differ from those obtained using conventional genetic perturbation. Together, this work establishes a readily implementable framework that integrates improved gene editing with on-demand chemical knockdown of endogenous proteins.

CRISPR-Cas9↗

PubMed2004

Transfection microarray of human mesenchymal stem cells and on-chip siRNA gene knockdown.

The transfection efficiency of primary cells is the bottleneck for their use with miniaturized formats for gene validation assays. We have found that when formulations containing various reporter plasmids were microarrayed on glass slides (chips), hMSCs cultivated on the chip incorporated and expressed the microarrayed plasmid DNAs with high efficiency and virtually total spatial resolution. Fibronectin, as the key formulation component, was found to significantly increase the on-chip transfection efficiency in hMSCs as well as many other cells. Further, we have conclusively proven that when siRNA was co-arrayed with the target plasmid DNA, a concentration-dependent gene knockdown was observed. Thus, massively miniaturized RNAi gene knockdown experiments can now be performed in primary cells, previously unusable with transfection microarrays (TMA).

Animals↗

PubMed2005

Expression profiles of genes in DJ-1-knockdown and L 166 P DJ-1 mutant cells.

DJ-1 is a novel oncogene and a causative gene for the familial form of Parkinson's disease (PD). DJ-1 has been shown to play roles in anti-oxidative stress by eliminating reactive oxygen species and in transcriptional regulation of genes. Loss of these functions of DJ-1 is thought to trigger the onset of PD. In this study, to identify genes for which expressions are regulated by DJ-1, DNA microarray analyses were carried out using two mouse NIH3T3 cell lines, DJ-1-knockdown cells and cells harboring an exogenously added L 166 P DJ-1 mutant found in PD patients. In both cell lines, drastic changes in expressions of genes, including genes related to stress, apoptosis, oxidative stress and neurotoxicity, were observed and changes in expressions were confirmed by RT-PCR. Of the genes identified, expression level of the extracellular superoxide dismutase (SOD 3) gene was found to decrease in DJ-1-knockdown cells, while expressions of SOD 1 and SOD 2 genes did not change. Furthermore, expression of the tau gene, a gene whose product gives cells neurotoxicity by aggregation, was found to increase at its promoter level in L 166 P DJ-1 cells. These findings suggest that DJ-1 regulates expressions of genes for which functions are thought to be related to cell death or neurodegeneration.

Amino Acid Substitution↗

PubMed2006

Motor deficits and hyperactivity in Dyt1 knockdown mice.

The DYT1 gene containing a trinucleotide deletion (DeltaGAG) is linked to early-onset dystonia, a neurological movement disorder of involuntary muscle contractions. To understand DYT1's contribution to dystonia, we produced and analyzed Dyt1 knockdown (KD) mice that expressed a reduced level of torsinA protein encoded by Dyt1. Knockdown mice exhibited deficits in motor control and a decreased trend in dopamine with a significant reduction in 3,4-dihydroxyphenylacetic acid. These alterations are similar to those displayed by previously reported Dyt1 DeltaGAG knockin heterozygous mice, suggesting that the partial loss of torsinA function contributes to the pathology of the disease.

3,4-Dihydroxyphenylacetic Acid↗

PubMed2006

The effects of the members of growth hormone family knockdown in zebrafish development.

Growth hormone (GH), prolactin (PRL), and somatolactin (SL) are members of GH/PRL superfamily. These hormones are involved in the regulation of an array of physiological processes, including growth, lactation, and osmoregulation. While recent evidence has shown the GH, PRL, and SL gene transcripts and protein products are expressed during early zebrafish development, their functions at this time of embryogenesis remain unknown. In the current study, antisense morpholino oligonucleotide (MO) inhibition of gh, prl, and sl gene translation was used to examine the effects of gene knockdown on hormone function in zebrafish development. We observed that PRL, SLalpha and SLbeta MO treatment all affected development. PRL MO-treated embryos showed defects in gas bladder inflation, reduced head and eye size, shorter body length and fewer melanophores than untreated controls, whereas SLalpha and SLbeta MO-treated embryos were only defective in gas bladder inflation, GH MO-inhibition of GH specific translation did not lead to any discernable morphological changes within 10 days post fertilization (dpf). The effects of PRL knockdown were further verified using a second PRL morpholino antisense and by a rescue experiment with in vitro transcribed prl mRNA containing 5 nucleotide mismatch within the PRL-MO binding region. These results provide the first evidence that members of the GH/PRL superfamily play a role in proper development of various structures including the head, eyes, melanophores and the gas bladder in zebrafish.

Air Sacs↗

PubMed2003

Antisense hippocampal knockdown of NMDA-NR1 by HVJ-liposome vector induces deficit of prepulse inhibition but not of spatial memory.

Considerable evidence suggests that an N-methyl-D-aspartate (NMDA) receptor plays a crucial role in memory and cognitive function. To identify the role of this receptor in higher functions of the brain, we delivered antisense oligonucleotides against an NMDA-NR1 subunit (NR1) to the hippocampus in rats using the HVJ-liposome-mediated gene-transfer method. NR1 hippocampal knockdown was performed by the focal injection of the NR1 antisense-HVJ-liposome complex into the bilateral hippocampus. The blocking effect of NR1-antisense on the expression of NR1 was confirmed by Western blot analysis. Spatial memory was tested by a water maze task, and sensorimotor gating was examined by prepulse inhibition (PPI). Western blot analysis demonstrated that the NR1-antisense treatment specifically provided the down-regulation (about 30%) of NR1 protein levels in the hippocampus. The water maze task showed that the antisense treatment did not affect spatial memory, while the PPI test revealed that NR1 hippocampal knockdown caused a deficit in sensorimotor gating. We conclude that mild dysfunction of hippocampal NMDA receptor causes sensorimotor gating deficit and relatively intact in spatial memory.

Animals↗

PubMed2003

Inwardly rectifying Kir3.1 subunit knockdown impairs learning and memory in an olfactory associative task in rat.

Inward-rectifier potassium channels gated by the direct action of G proteins are activated or inhibited by numerous neurotransmitters and they modulate neuronal excitability. Using an olfactory associative task, the effect of Kir3.1 subunit knockdown was tested on learning and memory. Repeated intracerebroventricular injections of antisense oligodeoxyribonucleotide to the Kir3.1 subunit significantly reduced hippocampal expression of its mRNA target determined by Western blotting. The antisense knockdown had no effect on locomotor and drinking activity or on attention processes. The reduction in Kir3.1 subunit impaired the learning of the odor associations and the procedural side of the task. This reduction correlated with the performance impairment. The results suggest that Kir3.1 channel activity is implicated in the memory processes.

Animals↗

PubMed1998

GluR2 hippocampal knockdown reveals developmental regulation of epileptogenicity and neurodegeneration.

In adult rats, kainic acid-induced status epilepticus reduces GluR2 subunit expression prior to neurodegeneration of hippocampal CA3 neurons. Increased formation of Ca2+ permeable AMPA receptors may contribute to the delayed neurodegenerative process. In rat pups, highly prone to seizures but resistant to seizure-induced hippocampal damage, GluR2 mRNA and protein expression remain constant in CA3 neurons possibly contributing to their survival. To investigate whether reduced GluR2 expression in hippocampus may lead to enhanced hippocampal vulnerability in an age-dependent manner and whether changes correspond to altered electroencephalography (EEG) patterns, unilateral microinfusion of GluR2 antisense oligodeoxynucleotides (AS-ODNs) into hippocampus was performed at three ages (postnatal (P8), P13, and adult). At P13, GluR2 knockdown resulted in spontaneous seizure-like behavioral manifestations and neurodegeneration of CA3 neurons lateral and distal from the cannula infusion site. EEG recordings revealed high rhythmic activity associated with seizure-like behavior. In P8 pups and adult rats, there were no behavioral manifestations; distant hippocampal damage of the CA3 was not observed. Results indicate that unilateral knockdown of hippocampal GluR2 subunit expression induces age-dependent seizure-like behavioral manifestations, altered EEG recording patterns, and reduces the survival of CA3 neurons in the hippocampus of young rats during a specific postnatal period (3rd week), when GluR2 expression peaks in development and glutamatergic inputs are maturing.

Animals↗

PubMed2000

Novel point mutations in the German cockroach para sodium channel gene are associated with knockdown resistance (kdr) to pyrethroid insecticides.

Knockdown resistance (kdr) to pyrethroid insecticides has been attributed to point mutations in the para sodium channel gene in more than a half dozen insect pest species. In this study, we identified two novel para mutations in five highly resistant kdr-type German cockroach strains. The two mutations, from glutamic acid (E434) to lysine (K434) and from cysteine (C764) to arginine (R764), respectively, are located in the first intracellular linker connecting domains I and II. E434K is located near the beginning of the linker (closest to domain I), whereas C764R is found toward the end of the linker (closest to domain II). Two additional mutations from aspartic acid (D58) to glycine (G58), and from proline (P1880) to leucine (L1888), respectively, were found in one of the resistant strains. The four mutations coexist with the previously identified leucine to phenylalanine (L993F) kdr mutation in IIS6, and are present only in the highly resistant individuals of a given strain. These findings suggest that these mutations might be responsible for high levels of knockdown resistance toward pyrethroid insecticides in the German cockroach.

Amino Acid Sequence↗

PubMed1987

Genetic divergence under uniform selection. III. Selection for knockdown resistance to ethanol in Drosophila pseudoobscura populations and their replicate lines.

Replicate D. pseudoobscura lines from populations collected at different geographic locations were selected for increased knockdown resistance to ethanol. Population background affected the initial rate of response but not the extent that lines responded. Lines were tested for physiological traits contributing to increased knockdown resistance. Populations showed different correlated responses for two traits (tolerance of ethanol, and of acetone), suggesting that they had responded to selection by different mechanisms. Replicate lines had diverged for most traits. The results indicate that drift and/or differences in genetic background can lead to divergence under uniform selection, even when fairly large population sizes are maintained.

Animals↗

PubMed2003

Local gene knockdown in the brain using viral-mediated RNA interference.

Conditional mutant techniques that allow spatial and temporal control over gene expression can be used to create mice with restricted genetic modifications. These mice serve as powerful disease models in which gene function in adult tissues can be specifically dissected. Current strategies for conditional genetic manipulation are inefficient, however, and often lack sufficient spatial control. Here we use viral-mediated RNA interference (RNAi) to generate a specific knockdown of Th, the gene encoding the dopamine synthesis enzyme tyrosine hydroxylase, within midbrain neurons of adult mice. This localized gene knockdown resulted in behavioral changes, including a motor performance deficit and reduced response to a psychostimulant. These results underscore the potential of using viral-mediated RNAi for the rapid production and testing of new genetic disease models. Similar strategies may be used in other model species, and may ultimately find applications in human gene therapy.

Animals↗

PubMed2006

Enhanced selenium effect on growth arrest by BiP/GRP78 knockdown in p53-null human prostate cancer cells.

Redox modification of thiol/disulfide interchange in proteins by selenium could lead to protein unfolding. When this occurs in the endoplasmic reticulum (ER), a process known as unfolded protein response (UPR) is orchestrated for survival through activation of PERK-eIF2alpha (PERK: double-stranded RNA-activated protein kinase-like ER kinase; eIF2alpha: eucaryotic initiation factor 2alpha), ATFalpha (ATFalpha: activating transcription factor 6) and inositol requiring 1 (IRE1)-x-box-binding protein 1 (XBP1) signalings. All three UPR transducer pathways were upregulated very rapidly when PC-3 cells were exposed to selenium. These changes were accompanied by increased expression of UPR target genes, including immunoglobulin heavy chain-binding protein/glucose-regulated protein, 78 kDa and CCAAT/enhancer binding protein-homologous protein/growth arrest- and DNA damage-inducible gene (CHOP/GADD153). Induction of BiP/GRP78, an ER-resident chaperone, is part of the damage control mechanism, while CHOP/GADD153 is a transcription factor associated with growth arrest and apoptosis in the event of prolonged ER stress. Knocking down BiP/GRP78 induction by small interference RNA produced a differential response of the three transducers to selenium, suggesting that the signaling intensity of each transducer could be fine-tuned depending on BiP/GRP78 availability. In the presence of selenium, CHOP/GADD153 expression was raised even higher by BiP/GRP78 knockdown. Under this condition, the selenium effect on wild-type p53-activated fragment p21 (p21(WAF)), cyclin-dependent kinase (CDK)1 and CDK2 was also magnified in a manner consistent with enhanced cell growth arrest. Additional experiments with CHOP/GADD153 siRNA knockdown strongly suggested that CHOP/GADD153 may play a positive role in upregulating the expression of p21(WAF) in a p53-independent manner (PC-3 cells are p53 null). Collectively, the above findings support the idea that UPR could be an important mechanism in mediating the anticancer activity of selenium.

CDC2 Protein Kinase↗

PubMed2006

Induction of apoptosis in human cells by RNAi-mediated knockdown of hARD1 and NATH, components of the protein N-alpha-acetyltransferase complex.

Protein N-epsilon-acetylation is recognized as an important modification influencing many biological processes, and protein deacetylase inhibitors leading to N-epsilon-hyperacetylation of histones are being clinically tested for their potential as anticancer drugs. In contrast to N-epsilon-acetyltransferases, the N-alpha-acetyltransferases transferring acetyl groups to the alpha-amino groups of protein N-termini have only been briefly described in mammalians. Human arrest defective 1 (hARD1), the only described human enzyme in this class, complexes with N-acetyltransferase human (NATH) and cotranslationally transfers acetyl groups to the N-termini of nascent polypeptides. Here, we demonstrate that knockdown of NATH and/or hARD1 triggers apoptosis in human cell lines. Knockdown of hARD1 also sensitized cells to daunorubicin-induced apoptosis, potentially pointing at the NATH-hARD1 acetyltransferase complex as a novel target for chemotherapy. Our results argue for an essential role of the NATH-hARD1 complex in cell survival and underscore the importance of protein N-alpha-acetylation in mammalian cells.

Acetyltransferases↗