Intensive RNAi with lentiviral vectors in mammalian cells

RNAi is a powerful technology for analyzing gene function in human cells. However, its utility can be compromised by inadequate knockdown of the target mRNA or by interpretation of effects without rigorous controls. We review lentiviral vector-based methods that enable transient or stable knockdowns to trace mRNA levels in human CD4+ T cell lines and other targets. Critical controls are reviewed, including rescue of the pre-knockdown phenotype by re-expression of the targeted gene. The time from thinking about a potential knockdown target to analysis of phenotypes can be as short as a few weeks.     

Etk敲除及过表达细胞株构建并探讨Etk对细胞增殖的影响

目的:利用CRISPR-Cas9技术在人脐静脉内皮细胞(Human umbilical vein endothelial cells,HUVECs)中构建Etk(Epithelial and endothelial tyrosine kinase)敲除稳定细胞株以及利用慢病毒构建Etk过表达稳定细胞株,并初步探讨Etk基因对HUVECs细胞增殖的影响。方法:利用CRISPR-Cas9技术,使用在线工具设计针对Etk的sgRNA (https://chopchop.rc.fas.harvard.edu/)。将sgRNA利用连接酶整合到病毒载体中,包被病毒并感染HUVECs敲除HUVECs中的内源性Etk。利用嘌呤霉素筛选得到Etk敲除的稳定细胞株。PCR扩增Etk基因序列,将其整合到pLEX-MCS慢病毒过表达载体中构建Etk过表达重组质粒。包被病毒并感染HUVECs,在HUVECs中过表达Etk,利用嘌呤霉素筛选得到Etk过表达的稳定细胞株。利用qRT-PCR和Western-Blotting检测Etk的敲除和过表达情况。利用CCK-8盒子检测两种稳定细胞株细胞增殖情况。结果:利用CRISPR-Cas9技术有效的敲除HUVECs中内源性Etk,同对照相比,Etk的mRNA和蛋白水平显著地降低(P0.01)。同时利用慢病毒在HUVECs中过表达Etk,同对照相比,在过表达Etk稳定细胞株中Etk的mRNA和蛋白表达显著上调(P0.01)。CCK-8检测发现,Etk敲除降低细胞增殖能力;而Etk过表达增加细胞增殖能力。结论:通过CRISPR-Cas9技术成功在HUVECs中敲除Etk,利用慢病毒过表达系统成功的在HUVECs中过表达Etk,并且初步验证了Etk促进HUVECs细胞增殖。     

Hypomorphic zebrafish models mimic the musculoskeletal phenotype of β4GalT7-deficient Ehlers-Danlos syndrome

β4GalT7 is a transmembrane Golgi enzyme, encoded by B4GALT7, that plays a pivotal role in the proteoglycan linker region formation during proteoglycan biosynthesis. Defects in this enzyme give rise to a rare autosomal recessive form of Ehlers-Danlos syndrome (EDS), currently known as ‘spondylodysplastic EDS (spEDS-B4GALT7)’. This EDS subtype is mainly characterized by short stature, hypotonia and skeletal abnormalities, thereby illustrating its pleiotropic importance during human development. Insights into the pathogenic mechanisms underlying this disabling disease are very limited, in part due to the lack of a relevant in vivo model.As the majority of mutations identified in patients with spEDS-B4GALT7 are hypomorphic, we generated zebrafish models with partial loss of B4galt7 function, including different knockdown (morphant) and mosaic knockout (crispant) b4galt7 zebrafish models and studied the morphologic, functional and molecular aspects in embryonic and larval stages.Morphant and crispant zebrafish show highly similar morphological abnormalities in early development including a small, round head, bowed pectoral fins, short body-axis and mild developmental delay. Several craniofacial cartilage and bone structures are absent or strongly misshapen. In addition, the total amount of sulfated glycosaminoglycans is significantly diminished and particularly heparan and chondroitin sulfate proteoglycan levels are greatly reduced. We also show impaired cartilage patterning and loss of chondrocyte organization in a cartilage-specific Tg(Col2a1aBAC:mcherry) zebrafish reporter line. The occurrence of the same abnormalities in the different models confirms these are specifically caused by B4galt7 deficiency. A disturbed actin pattern, along with a lack of muscle tone, was only noted in morphants in which translation of b4galt7 was blocked.In conclusion, we generated the first viable animal models for spEDS-B4GALT7, and show that in early development the human spEDS-B4GALT7 phenotype is faithfully mimicked in these zebrafish models. Our findings underscore a key role for β4GalT7 in early development of cartilage, bone and muscle. These models will lead to a better understanding of spEDS-B4GALT7 and can be used in future efforts focusing on therapeutic applications.     

Micromanipulation of Gene Expression in the Adult Zebrafish Brain Using Cerebroventricular Microinjection of Morpholino Oligonucleotides

Manipulation of gene expression in tissues is required to perform functional studies. In this paper, we demonstrate the cerebroventricular microinjection (CVMI) technique as a means to modulate gene expression in the adult zebrafish brain. By using CVMI, substances can be administered into the cerebroventricular fluid and be thoroughly distributed along the rostrocaudal axis of the brain. We particularly focus on the use of antisense morpholino oligonucleotides, which are potent tools for knocking down gene expression in vivo. In our method, when applied, morpholino molecules are taken up by the cells lining the ventricular surface. These cells include the radial glial cells, which act as neurogenic progenitors. Therefore, knocking down gene expression in the radial glial cells is of utmost importance to analyze the widespread neurogenesis response in zebrafish, and also would provide insight into how vertebrates could sustain adult neurogenesis response. Such an understanding would also help the efforts for clinical applications in human neurodegenerative disorders and central nervous system regeneration. Thus, we present the cerebroventricular microinjection method as a quick and efficient way to alter gene expression and neurogenesis response in the adult zebrafish forebrain. We also provide troubleshooting tips and other useful information on how to carry out the CVMI procedure.     

Knockdown of gene expression by antisense morpholino oligos in preimplantation mouse embryos cultured in vitro

Knockdown of gene expression by antisense morpholino oligos (MOs) is a simple and effective method for analyzing the roles of genes in mammalian cells. Here, we demonstrate the efficient delivery of MOs by Endo-Porter (EP), a special transfection reagent for MOs, into preimplantation mouse embryos cultured in vitro. A fluorescein-labeled control MO was applied for monitoring the incorporation of MOs into developing 2-cell embryos in the presence of varying amounts of EP and bovine serum albumin. In optimized conditions, fluorescence was detected in 2-cell embryos within a 3-h incubation period. In order to analyze the validity of the optimized conditions, an antisense Oct4 MO was applied for knockdown of the synthesis of OCT4 protein in developing embryos from the 2-cell stage. In blastocysts, the antisense Oct4 MO induced a decrease in the amount in OCT4 protein to less than half. An almost complete absence of OCT4-positive cells and nearly complete disappearance of the inner cell mass in the outgrowths of blastocysts were also noted. These phenotypes corresponded with those of Oct4-deficient mouse embryos. Overall, we suggest that the delivery of MOs using EP is useful for the knockdown of gene expression in preimplantation mouse embryos cultured in vitro.     

Analysis of gene function in the zebrafish retina

Mutagenesis screens in zebrafish have uncovered several hundred mutant alleles affecting the development of the retina and established the zebrafish as one of the leading models of vertebrate eye development. In addition to forward genetic mutagenesis approaches, gene function in the zebrafish embryo is being studied using several reverse genetic techniques. Some of these rely on the overexpression of a gene product, others take advantage of antisense oligonucleotides to block function of selected loci. Here we describe these methods in the context of the developing eye.     

The contribution of cacao agroforests to the conservation of lower canopy ant and beetle diversity in Indonesia

The ongoing destruction of tropical rainforests has increased the interest in the potential value of tropical agroforests for the conservation of biodiversity. Traditional, shaded agroforests may support high levels of biodiversity, for some groups even approaching that of undisturbed tropical forests. However, it is unclear to what extent forest fauna is represented in this diversity and how management affects forest fauna in agroforests. We studied lower canopy ant and beetle fauna in cacao agroforests and forests in Central Sulawesi, Indonesia, a region dominated by cacao agroforestry. We compared ant and beetle species richness and composition in forests and cacao agroforests and studied the impact of two aspects of management intensification (the decrease in shade tree diversity and in shade canopy cover) on ant and beetle diversity. The agroforests had three types of shade that represented a decrease in tree diversity (high, intermediate and low diversity). Species richness of ants and beetles in the canopies of the cacao trees was similar to that found in lower canopy forest trees. However, the composition of ant and beetle communities differed greatly between the agroforest and forest sites. Forest beetles suffered profoundly from the conversion to agroforests: only 12.5% of the beetle species recorded in the forest sites were also found in the agroforests and those species made up only 5% of all beetles collected from cacao. In contrast, forest ants were well represented in agroforests, with 75% of all species encountered in the forest sites also occurring on cacao. The reduction of shade tree diversity had no negative effect on ants and beetles on cacao trees. Beetle abundances and non-forest ant species richness even increased with decreasing shade tree diversity. Thinning of the shade canopy was related to a decrease in richness of forest ant species on cacao trees but not of beetles. The contrasting responses of ants and beetles to shade tree management emphasize that conservation plans that focus on one taxonomic group may not work for others. Overall ant and beetle diversity can remain high in shaded agroforests but the conservation of forest ants and beetles in particular depends primarily on the protection of natural forests, which for forest ants can be complemented by the conservation of adjacent shaded cacao agroforests.     

Integrin α9β1-mediated cell migration in glioblastoma via SSAT and Kir4.2 potassium channel pathway

The α9β1 integrin accelerates cell migration through binding of the α9 cytoplasmic domain to SSAT, which catalyzes the catabolism of higher order polyamines, spermidine and spermine, to the lower order polyamine, putrescine. SSAT levels were downregulated at both the mRNA and protein levels by shRNA-mediated simultaneous knockdown of MMP-9 and uPAR/cathepsin B. In addition, we noted a prominent reduction in the expression of SSAT with MMP-9 and uPAR/cathepsin B knockdown in the tumor regions of 5310 injected nude mice brains. Further, SSAT knockdown in glioma xenograft cells significantly reduced their migration potential. Interestingly, MMP-9, uPAR and cathepsin B overexpression in these xenograft cells significantly elevated SSAT mRNA and protein levels. The migratory potential of MMP-9/uPAR/cathepsin B-overexpressed 4910 and 5310 cells was not affected by either glybenclamide (Kir 6.x inhibitor) or tertiapin-Q (Kir 1.1 and 3.x inhibitor) but instead was significantly inhibited by either barium or Kir4.2 siRNA treatments. Co-localization of α9 integrin with Kir4.2 was observed in both 4910 and 5310 xenograft cells. However, MMP-9 and uPAR/cathepsin B knockdown in these cells prominently reduced the co-localization of α9 with Kir4.2. Taken together, our results clearly demonstrate that α9β1 integrin-mediated cell migration utilizes SSAT and the Kir4.2 potassium channel pathway, and inhibition of the migratory potential of these glioma xenograft cells by simultaneous knockdown of MMP-9 and uPAR/cathepsin B could be attributed to the reduced SSAT levels and co-localization of α9 integrin with Kir4.2 inward rectifier potassium channels.     

Lysophosphatidylcholine acyltransferase 3 deficiency impairs 3T3L1 cell adipogenesis through activating Wnt/β-catenin pathway

Levels of polyunsaturated phosphatidylcholine (PC) influence plasma membrane structure and function. Phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and then undergoes extensive deacylation/reacylation remodeling via Lands' cycle (non-Kennedy pathway). The reacylation is catalyzed by lysophosphatidylcholine acyltransferase (LPCAT), which adds a polyunsaturated fatty acid at the sn-2 position. Four LPCAT isoforms have been described to date, among which we found LPCAT3 to be the major isoform in adipose tissue, but its exact role in adipogenesis is unclear. In this study, we aimed to investigate whether LPCAT3 activity affects 3T3L1 cell adipogenic differentiation potential and its underline mechanism. Lentivirus-mediated LPCAT3 shRNA expression stably knocked down LPCAT3 in 3T3L1 preadipocytes and LPCAT3 deficiency dramatically reduced the levels of cellular polyunsaturated PCs. Importantly, we found that this deficiency activated the β-catenin dependent Wnt signaling pathway, which suppressed the expression of adipogenesis-related genes, thereby inhibiting 3T3L1 preadipocyte differentiation and lipid accumulation. Moreover, three different Wnt/β-catenin pathway inhibitors reversed the effect of LPCAP3 deficiency, suggesting that Wnt/β-catenin pathway activation is one of the causes for the observed phenotypes. To the best of our knowledge, we show here for the first time that PC remodeling is an important regulator of adipocyte differentiation.