Upregulation of PHLDA2 in Dicer knockdown HEK293 cells

It has been reported that RNAi-dependent chromatin silencing in vertebrates is not restricted to the centromeres. To address whether RNAi machinery could regulate the chromatin structure of imprinted genes, we knocked down Dicer in HEK293 cells and found that the expression of PHLDA2, one of the several genes in the imprinted gene domain of 11p15.5, was specifically upregulated. This was accompanied by a shift towards more activated chromatin at PHLDA2 locus as indicated by change in H3K9 acetylation, however, the methylation state at this locus was not affected. Furthermore, we found that PHLDA2 was downregulated in growth-arrested HEK293 cells induced by either serum deprivation or contact inhibition. This suggests that PHLDA2 upregulation might be a direct result of Dicer depletion rather than the consequence of growth arrest induced by Dicer knockdown. Considering the reports that there is consistent placental outgrowth in PHLDA2 knockout mice and that PHLDA2 overexpression in mice causes growth inhibition, we speculate that PHLDA2 may be a candidate for contributing to the reduced growth rate of Dicer-deficient cells and the very early embryonic lethality in Dicer knockout mice.     

High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension

Background

Dicer is a 219-kDa protein that plays key roles in gene regulation, particularly as the ribonuclease III enzyme responsible for cleaving precursor miRNA substrates. Its enzymatic activity is highly regulated by protein factors, and this regulation can impact on the levels of miRNAs and modulate the behavior of a cell. To better understand the underlying mechanisms of regulation, detailed enzymatic and structural characterization of Dicer are needed. However, these types of studies generally require several milligrams of recombinant protein, and efficient preparation of such quantities of pure human Dicer remains a challenge. To prepare large quantities of human Dicer, we have optimized transfection in HEK293-6E cells grown in suspension and streamlined a purification procedure.

Results

Transfection conditions were first optimized to achieve expression levels between 10 and 18?mg of recombinant Dicer per liter of culture. A three-step purification protocol was then developed that yields 4–9?mg of purified Dicer per liter of culture in a single day. From SEC-MALS/RI analysis and negative stain TEM, we confirmed that the purified protein is monomerically pure ( ≥ 98%) and folds with the characteristic L-shape geometry. Using an electrophoretic mobility shift assay, a dissociation constant (K_d) of 5?nM was measured for Dicer binding to pre-let-7a-1, in agreement with previous reports. However, when probing the cleavage activity of Dicer for pre-let-7a-1, we measured k_cat (7.2?±?0.5?min^??1) and K_M (1.2?±?0.3?μM) values that are much higher than previously reported due to experimental conditions that better respect the steady-state assumption.

Conclusions

The expression and purification protocols described here provide high yields of monomerically pure and active human Dicer. Cleavage studies of a pre-let-7 substrate with this purified Dicer reveal higher k_cat and K_M values than previously reported and support the current view that conformational changes are associated with substrate binding. Large quantities of highly pure Dicer will be valuable for future biochemical, biophysical and structural investigations of this key protein of the miRNA pathway.

     

Dicer knockdown induces fibronectin-1 expression in HEK293T cells via induction of Egr1

Background

Dicer is a multidomain ribonuclease III enzyme involved in the biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs); depletion of Dicer was found to impair the migration of endothelial cells.

Methods

siRNA transfection, cell migration assay, real-time RT–PCR, chromatin immunoprecipitation, Western blotting, ELISA, caspase-3 activity assay, and annexin-V–FITC assay were utilized.

Results

Knockdown of Dicer impairs the migratory capacity of HEK293T cells and induces fibronectin-1. The upregulation of fibronectin-1 is dependent on Egr1. Fibronectin-1/Dicer double-knockdown cells showed a marked increase in apoptosis compared with fibronectin-1 single knockdown cells.

Conclusions

Decreased Dicer expression induces fibronectin-1 expression via an Egr1-dependent manner.

General significance

Our data suggest that upregulation of fibronectin-1 protects Dicer knockdown HEK293T cells against apoptosis.     

Differential expression of Dicer and Argonaute genes duringthe differentiation of human neuroblastoma cells

Dicer and Argonaute 1-4 proteins are key components of the cytoplasmic enzyme machinery responsible for biogenesis and performance of microRNAs. To gain insight into the roles of these proteins in cell differentiation, we investigated possible changes in the expression levels of Dicer and Argonaute 1-4 genes during the differentiation of cultured neural and glial cells. The results show that the 5 genes are differentially expressed along the 2 differentiation pathways and suggest a prevalent role of Dicer and Argonaute 4 in neural cell differentiation.     

Effects of Wnt proteins on cell proliferation and apoptosis in HEK293 cells

Wnt proteins and Wnt signalings have been implicated in a variety of development and cell processes, while aberrant activation of Wnt signaling is linked to a range of cancers in many tissues. In this study, we used the HEK293 cell line to investigate the effects of Wnt3a and Wnt5a on proliferation and apoptosis in a serum starvation culture. After Wnt3a and Wnt5a proteins were expressed, they both promoted the proliferation of HEK293 cells under serum starvation. After 48h of serum starvation, both Wnt3a and Wnt5a inhibited serum starvation-induced apoptosis of HEK293 cells and continued up to 96h. We demonstrated that Wnt3a and Wnt5a can promote proliferation of HEK293 cells and inhibit serum starvation-induced apoptosis, which implies that Wnt3a and Wnt5a can maintain the survival of HEK293 cells under stress, and also provide a novel insight into the role of Wnt3a and Wnt5a and their related signalings in carcinogenesis.     

Elevation of gamma-glutamyltransferase activity in 293 HEK cells constitutively expressing antisense glutaminase mRNA

Previous studies have shown that the use of dynamic nutrient feeding to maintain glutamine at low levels in fed-batch cultures reduced the overflow of glutamine metabolism. This strategy resulted in the shift of metabolism towards an energetically more efficient state signified by reduced lactate and ammonia production and thus achieving a higher cell density for enhanced productivity. In an effort to mimic the metabolic changes effected by this fed-batch strategy at the molecular level, 293 HEK cells were engineered via stable transfection with an antisense fragment of the rat phosphate-dependent glutaminase (PDG) gene. PDG is localized in the mitochondria and catalyzes the deamination of glutamine to glutamate with the release of ammonia. Stable single cell clones were isolated from the transfected populations. Characterization of these transfectants revealed indications of an altered glutamine metabolism affected by the antisense strategy. Contrary to our expectations, glutamine consumption and ammonia production in the antisense cells did not deviate significantly from that of untransfected cells. Glutamate was also observed to accumulate to high level extracellularly, as opposed to a consumption pattern normally observed in non-transfected cells. Subsequent analyses show that gamma-glutamyltransferase (gamma-GT) may be a significant pathway that resulted in the formation of glutamate and ammonia from glutamine catabolism extracellularly. gamma-GT has been widely investigated in renal glutamine metabolism, but has rarely been implicated in cultured cell metabolism. This study highlights the importance of this alternative glutamine metabolism pathway in cell culture.     

Subcellular localization of human neutral ceramidase expressed in HEK293 cells

We previously reported that rat and mouse neutral ceramidases were mainly localized to plasma membranes as a type II integral membrane protein and partly detached from the cells via processing of the N-terminal/anchor sequence when expressed in HEK293 cells [M. Tani, H. Iida, M. Ito, O-glycosylation of mucin-like domain retains the neutral ceramidase on the plasma membranes as a type II integral membrane protein, J. Biol. Chem. 278 (2003) 10523-10530]. In contrast, the human homologue was exclusively detected in mitochondria when expressed in HEK293 and MCF7 cells as a fusion protein with green fluorescent protein at the N-terminal of the enzyme [S.E. Bawab, P. Roddy, T. Quian, A. Bielawska, J.J. Lemasters, Y.A. Hannun, Molecular cloning and characterization of a human mitochondrial ceramidase, J. Biol. Chem. 275 (2000) 21508-21513]. Given this discrepancy, we decided to clone the neutral ceramidase from human kidney cDNA and re-examine the intracellular localization of the enzyme when expressed in HEK293 cells. The putative amino acid sequence of the newly cloned enzyme was identical to that reported for human neutral ceramidase except at the N-terminal; the new protein was 19 amino acids longer at the N-terminal. We found that the putative full-length human neutral ceramidase was transported to plasma membranes, but not to mitochondria, possibly via a classical ER/Golgi pathway and localized mainly in plasma membranes when expressed in HEK293 cells. The N-terminal-truncated mutant, previously reported as a human mitochondrial ceramidase, was also weakly expressed in HEK293 cells but mainly released into the medium possibly due to the insufficient signal/anchor sequence.     

诱导表达p27对HEK293细胞生长代谢的影响

目的:研究诱导表达p27对HEK293细胞生长和代谢的影响。方法:将pTet-on载体和响应于Dox的p27诱导表达载体共转染HEK293细胞,随机挑选单克隆细胞株。以细胞周期分布和活细胞密度为主要观察指标,考察稳定转染的细胞在Dox诱导下的细胞生长;以Qglc、Qlac和Qgln为主要观察指标,考察转染细胞在Dox诱导下的细胞代谢。结果:p27基因的表达使HEK293细胞的增殖速度显著降低,G1期细胞比例显著升高,葡萄糖消耗和乳酸生产减少。结论:诱导表达p27基因是对HEK293细胞进行G1期阻滞的一种有效策略。     

诱导表达p27对HEK293细胞生长代谢的影响

目的：研究诱导表达p27对HEK293细胞生长和代谢的影响。方法：将pTet—on载体和响应于Dox的p27诱导表达载体共转染HEK293细胞,随机挑选单克隆细胞株。以细胞周期分布和活细胞密度为主要观察指标,考察稳定转染的细胞在Dox诱导下的细胞生长;以Qglc、Qlac和Qgln为主要观察指标,考察转染细胞在Dox诱导下的细胞代谢。结：p27基因的表达使HEK293细胞的增殖速度显著降低,G1期细胞比例显著升高,葡萄糖消耗和乳酸生产减少。结论：诱导表达p27基因是对HEK293细胞进行G1期阻滞的一种有效策略。     

Purification and characterization of the creatine transporter expressed at high levels in HEK293 cells

The bovine creatine transporter (CreaT) has been purified from membranes of HEK293 cells stably expressing high levels of the transporter. Membranes were solubilized with decyl maltoside and the CreaT was purified (90% pure) by affinity chromatography on wheat germ agglutinin (WGA)-Sepharose and gel-filtration. The CreaT was shown to be an approximately 70 kDa glycoprotein by SDS-polyacrylamide gel electrophoresis and Western blotting. Identification of the CreaT was confirmed by sequencing tryptic peptides by mass spectrometry. Laser light scattering showed the majority of the CreaT to be present as a 224 kDa species. Additional purification was obtained when the Creat was eluted from the WGA column and purified by gel-filtration in Fos-choline 12 instead of decyl maltoside, followed by a second WGA affinity step to exchange the detergent for sodium cholate. This resulted in a 30-fold purification (95% purity) of the approximately 70kDa CreaT, with a yield of 15%. From this, it is estimated that the CreaT comprises approximately 3% of total HEK293-CreaT membrane protein. Gel-filtration showed the transporter to migrate with an apparent molecular mass of 210 kDa. Circular dichroism showed a predominantly alpha-helical structure, consistent with the 12 transmembrane domains predicted for the transporter. This work has enabled the purification of the CreaT in amounts ( approximately 100 microg) that make it feasible to consider structural studies of a member of the Na(+)- and Cl(-)-dependent neurotransmitter transporter family.     

Effects of hormones on SBP mRNA levels in human cancer cells

The human plasma sex steroid binding protein (SBP) has been previously shown to be synthesized in liver cells. The hormonal regulation studies of hepatic SBP mRNA demonstrate that it is controlled by estradiol, antiestrogen tamoxifen, dihydrotestosterone, triiodothyronine and insulin in a similar way as secreted SBP. The metabolic inhibitor cycloheximide was unable to prevent the estrogen or thyroid hormone induced increase in SBP mRNA. The slight stimulation of SBP synthesis by estradiol suggests that non-steroidal factors may be involved in its regulation and that the estrogen regulatory mechanism could also be partly post-transcrptional. In endometrial (Ishikawa cells) and prostatic (LNCaP cells) carcinoma cells, SBP mRNA has been detected suggesting that SBP may play a role in the uptake and intracellular mechanism of action of sex steroid in target cells.     

Effects of calcium ion on adenovirus production with high densities of HEK293 cells

One of the major restrictions on the production of adenoviral vectors (AdV) is due to the decrease in virus concentration concomitant with an increase in cell concentration at infection (CCI) which is known as “cell density effect”, this could be because of the limited access to the nutrients or significant accumulation of toxic by-products. However, current strategies, such as developing robust serum-free medium and performing nutrient feeding, will partially address this issue. Therefore, the objective of this study was to further optimize serum-free culture medium by exploring the influence of calcium ion on virus production. Our studies showed that an optimal concentration of calcium ion significantly enhances AdV production, especially at a high CCI. During the virus infection process, a high concentration of calcium ion (≥ 1 mM) caused a reduction in virus infection efficiency, possibly as a result of cell aggregation. However, by optimizing the timing of the addition of calcium ion (i.e., 12 hours post-infection [hpi]), high virus infection efficiency could be maintained. The addition of 0.1 to 2 mM calcium ion at 12 hpi increased virus proliferation dose-dependently. Therefore, the optimal selection of both the concentration and the supplementation time of calcium ion during the process of AdV production could minimize the “cell density effect,” and a 2.6- and 3.2-fold increase in virus concentration could be achieved at CCI3 and CCI4, respectively.     

Effects of cannabinoids on endogenous K+ and Ca2+ currents in HEK293 cells

Effects of cannabinoids on endogenous potassium and calcium currents in HEK293 cells were studied using the whole-cell variant of the patch-clamp technique. The cannabinoid agonists WIN 55,212-2, methanandamide, and anandamide (1 microM) decreased the calcium current by 53.1 +/- 2.6, 47.5 +/- 1.2, and 38.8 +/- 3.1%, respectively, after transfection of human CB1 cannabinoid receptor (hCB1) cDNA into HEK293 cells. The delayed rectifier-like current was not changed after application of these agonists, but the inward rectifier was increased by 94.0 +/- 3.6, 83.7 +/- 5.1, and 63.0 +/- 2.5% after application of WIN 55,212-2, methanandamide, and anandamide, respectively. The effects of the cannabinoid antagonists (AM251, AM281, and AM630) on the inward rectifier and calcium currents were the opposite of those seen with cannabinoid agonists; thus, these compounds act as inverse agonists in this preparation. These results suggest that endogenous inward rectifier and calcium currents are modulated by cannabinoids in HEK293 cells, and that some expressed receptors may be constitutively active.     

Phorbol ester-regulated cleavage of normal prion protein in HEK293 human cells and murine neurons

Cellular prion protein (PrP(c)) undergoes a proteolytic attack at the 110/111 downward arrow112 peptide bond, whereas the PrP isoform (PrP(res)) that accumulates in the brain tissue in Creutzfeldt-Jakob disease reveals an alternate cleavage site at about residue 90. Interestingly, the normal processing of PrP occurs inside the 106-126 amino acid region thought to be responsible for the neurotoxicity of the pathogenic prions, whereas PrP(res) cleavage preserves this potentially toxic domain. Therefore, any molecular mechanisms leading to enhanced cleavage at the 110/111 downward arrow112 peptide bond could be of potential interest. We set up TSM1 neurons and HEK293 stable transfectants overexpressing the wild-type or 3F4-tagged murine PrP(c), respectively. Both mock-transfected and PrP(c)-expressing cell lines produced an 11-12-kDa PrP fragment (referred to as N1), the immunological characterization of which strongly suggests that it corresponds to the N-terminal PrP(c) fragment derived from normal processing. We have established that the recovery of secreted N1 is increased by the protein kinase C agonists PDBu and PMA in a time- and dose-dependent manner in both cell lines. In contrast, secretion of N1 remains unaffected by the inactive PDBu analog alphaPDD and by the protein kinase A effectors dibutyryl cAMP and forskolin. Overall, our data indicate that the normal processing of PrP(c) is up-regulated by protein kinase C but not protein kinase A in human cells and murine neurons.     

RELT induces cellular death in HEK 293 epithelial cells

RELT is a recently identified Tumor Necrosis Factor Receptor that possess two homologues in humans named RELL1 and RELL2. We investigated whether RELT and its homologues could induce cellular death when transiently transfected into HEK 293 epithelial cells. Transfection of RELT family members into HEK 293 epithelial cells induced cell death characterized by rounding and lifting of cells accompanied by DNA fragmentation, characteristics that are consistent with the activation of an apoptotic pathway. Overexpression of RELT in COS-7 cells resulted in cell rounding and lifting without DNA fragmentation, suggesting that the effects of RELT signaling may vary among different cell types. In summary, we report that overexpression of RELT or its homologues RELL1 and RELL2 in HEK 293 epithelial cells results in cell death with morphological characteristics consistent with the activation of an apoptotic pathway.     

Prestin-prestin and prestin-GLUT5 interactions in HEK293T cells

The remarkable hearing sensitivity and frequency selectivity in mammals is attributed to cochlear amplifier in the outer hair cells (OHCs). Prestin, a membrane protein in the lateral wall of OHC plasma membrane, is required for OHC electromotility and cochlear amplifier. In addition, GLUT5, a fructose transporter, is reported to be abundant in the plasma membrane of the OHC lateral wall and has been originally proposed as the OHC motor protein. Here we provide evidence of interactions between prestin/prestin and prestin/GLUT5 in transiently transfected HEK293T cells. We used a combination of techniques: (1) membrane colocalization by confocal microscopy, (2) fluorescence resonance energy transfer (FRET) by fluorescence activated cell sorting (FACS), (3) FRET by acceptor photobleaching, (4) FRET by fluorescence lifetime imaging (FRET-FLIM), and (5) coimmunoprecipitation. Our results suggest that homomeric and heteromeric prestin interactions occur in native OHCs to facilitate its electromotile function and that GLUT5 interacts with prestin for its elusive function.     

Transient gene expression in HEK293 and vero cells immobilised on microcarriers

The upscale of transient gene expression (TGE) gained popularity over the last decade as it drastically shortens timelines for the production of recombinant proteins. Bottlenecks of the method turned out to be media composition and media exchange, which is usually required as conditioned medium drastically reduces the transfection efficiency. Media exchanges are typically done by centrifugation, which limits upscale, is prone to contamination or is a high cost factor when continuous centrifuges are used. In this work HEK/EBNA cells were grown and transfected on microcarriers. Cell immobilisation allows easy media exchange after sedimentation. The transfection method was optimised regarding polyethylenimine (PEI) concentration, optimal DNA:PEI ratio, type of PEI, incubation time and polyplex formation time. In addition to HEK, Vero cells were also transfected using the same protocol. The method was established in spinner flasks and scaled up to a 1.5 litre stirred tank reactor. Transfection efficiencies of up to 33% with pCEP4 and 98% with pMAX were reached. Additionally immobilisation on microcarriers was used to retain the cells during cultivation, thus allowing media replacement and prolonging cultivation time from one to two weeks with continuous expression of the recombinant protein.     

Altering TET dioxygenase levels within physiological range affects DNA methylation dynamics of HEK293 cells

The TET family of dioxygenases (TET1/2/3) can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and has been shown to be involved in active and passive DNA demethylation. Here, we demonstrate that altering TET dioxygenase levels within physiological range can affect DNA methylation dynamics of HEK293 cells. Overexpression of TET1 increased global 5hmC levels and was accompanied by mild DNA demethylation of promoters, gene bodies and CpG islands. Conversely, the simultaneous knockdown of TET1, TET2, and TET3 led to decreased global 5hmC levels and mild DNA hypermethylation of above-mentioned regions. The methylation changes observed in the overexpression and knockdown studies were mostly non-reciprocal and occurred with different preference depending on endogenous methylation and gene expression levels. Single-nucleotide 5hmC profiling performed on a genome-wide scale revealed that TET1 overexpression induced 5mC oxidation without a distribution bias among genetic elements and structures. Detailed analysis showed that this oxidation was related to endogenous 5hmC levels. In addition, our results support the notion that the effects of TET1 overexpression on gene expression are generally unrelated to its catalytic activity.