Stomach-Selective Gene Transfer Following the Administration of Naked Plasmid DNA onto the Gastric Serosal Surface in Mice

Omics community detection using multi-resolution clustering

MOTIVATION

The discovery of biologically interpretable and clinically actionable communities in heterogeneous omics data is a necessary first step towards deriving mechanistic insights into complex biological phenomena. Here we present a novel clustering approach, omeClust, for community detection in omics profiles by simultaneously incorporating similarities among measurements and the overall complex structure of the data.

RESULTS

We show that omeClust outperforms published methods in inferring the true community structure as measured by both sensitivity and misclassification rate on simulated datasets. We further validated omeClust in diverse, multiple omics datasets, revealing new communities and functionally related groups in microbial strains, cell line gene expression patterns, and fetal genomic variation. We also derived enrichment scores attributable to putatively meaningful biological factors in these datasets that can serve as hypothesis generators facilitating new sets of testable hypotheses.

AVAILABILITY

omeClust is open-source software, and the implementation is available online at http://github.com/omicsEye/omeClust.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Monitoring method for transgene expression in target tissue by blood sampling

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Transgene expressions of simultaneously-administered two plasmid DNA in muscle correlated each other.

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Transgene expressions of secretable luciferase in muscle and plasma also correlated each other.

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It was possible to monitor transgene expression in tissues by blood sampling.

In this study, we have developed a novel method to monitor transgene expression in tissues by blood sampling. We administered plasmid DNA (pDNA) encoding non-secretory form of firefly luciferase as a reporter gene and pDNA encoding secretable Gaussia princeps luciferase as a monitor gene simultaneously into mice. Good positive correlations were found between log-transgene expression of the reporter gene and the monitor gene in the treated muscle, between the monitor gene in the treated muscle and plasma, and consequently between the reporter gene in the treated muscle and the monitor gene in plasma after naked pDNA transfer into the muscle of mice. Such positive correlations were also found with gastric serosal surface instillation of naked pDNA, intravenous injection of lipoplex, and hydrodynamics-based injection of naked pDNA. We developed monitoring method of transgene expression in tissues by blood sampling, which was named ‘Therapeutic transgene monitoring (TTM)’, after ‘Therapeutic drug monitoring (TDM)’.

Pretreatment with epidermal growth factor enhances naked plasmid DNA transfer onto gastric serosal surface in mice

We have developed a simple administration method, which is gastric serosal surface instillation of naked plasmid DNA (pDNA) in experimental animals. The purpose of this study was to improve gastric gene transfer efficiency by pre-treatment with a macropinocytosis enhancer, such as fetuin or epidermal growth factor (EGF), in mice. A series of concentrations of fetuin were instilled onto gastric serosal surface prior to instillation of naked pDNA in mice; however, fetuin did not improve transgene expression in the stomach 6 h after administration of pDNA. EGF also did not affect transgene expression in the stomach when pDNA was instilled immediately after EGF instillation. On the other hand, when pDNA was instilled onto gastric serosal surface 24 h after EGF treatment, transgene expression in the stomach was significantly improved by 2.6-fold. In addition, transgene-positive cells were increased 5.3-fold by EGF pre-treatment. High transgene expression in the stomach lasted for 48 h in the EGF pre-treatment group in comparison with that in the no pre-treatment group. These findings are valuable to develop an effective method of in vivo gene transfer to the stomach.

Rubbing gastric serosal surface enhances naked plasmid DNA transfer in rats and mice

We have developed in vivo gene transfer to mesothelial cells on the peritoneal organs, including the stomach. Simple instillation of naked plasmid DNA onto the gastric serosal surface in mice resulted in effective but transient transgene expression. Here, we developed a simple method to improve not only the transfection efficiency but also the duration of transgene expression. Rubbing the gastric serosal surface using a medical spoon immediately after instillation of naked plasmid DNA onto the gastric serosal surface resulted in 59-fold higher transgene expression 24 h after administration in rats. Without rubbing, transgene expression decreased under the detection limit 7 d after administration. On the other hand, rubbing the gastric serosal surface with a medical spoon after instillation of plasmid DNA prolonged transgene expression for one month. Mechanistic study in mice revealed that improved transfection should not be due to stimulation of cell function such as macropinocytosis by rubbing because rubbing before instillation of plasmid DNA did not improve transfection. Plasmid DNA should enter effectively into cells during rubbing. These findings are valuable to develop an effective method of in vivo gene transfer into peritoneal organs.

[Organ-, region- and cell-selective gene transfer using non-viral vectors]

Safety in gene therapy is an important issue since both viral and non-viral vectors have toxic side effects. Not only vectors themselves, but also distributions of produced proteins affect safety in gene therapy; thus, development of target-selective gene transfer methods is rational. We have developed organ-, region- and cell-selective gene transfer methods using non-viral vectors. To deliver foreign gene to liver parenchymal cells (hepatocytes), galactosylation of cationic liposome/plasmid DNA complex is useful strategy. Based on analyses for intrahepatic disposition characteristics and interaction with blood components, we formulated novel galactosylated lipoplex with regulated salt concentration to reduce particle size of lipoplex and to stabilize lipoplex simultaneously; as a consequence, we succeeded in improvement of hepatocyte-selective gene transfer after intraportal injection of the lipoplex in mice. On the other hand, administration routes are important for target-selective gene transfer. We discovered that simple instillation of naked plasmid DNA onto organ surface (the liver, kidney, spleen, stomach and lung) in mice and rats could result in effective and region-selective transgene expression. Neither physical force nor carriers are necessary for gene transfer onto organ surface mesothelial cells. To rationally improve transfection efficiency, mechanism of gene transfer should be elucidated. We clarified that Rac-mediated macropinocytosis was required for naked plasmid DNA transfer in gastric mesothelial cells.

Liver- and lobe-specific gene transfer following the continuous microinstillation of Plasmid DNA onto the liver surface in mice: effect of instillation speed

Development of technology to deliver foreign gene(s) to a specific organ/tissue is one of the major challenges in gene therapy. Here, we show liver- and lobe-specific gene transfer following the continuous microinstillation of plasmid DNA (pDNA) onto the liver surface in mice. Naked pDNA was continuously instilled onto the right medial liver lobe using syringe pump in male ddY mice. Our previous studies showed liver- and lobe-selective gene expression after instillation of 30 mul of pDNA solution onto the liver surface, but gene expression was also found in the other liver lobe, kidney and spleen. To improve target site selectivity of gene expression, the instillation volume was decreased; however, non-specific gene expression in the other liver lobe and diaphragm was still detected. To prevent immediate diffusion of the pDNA solution, we performed continuous microinstillation of pDNA using a syringe pump; as a result, target site selectivity was greatly improved. As for instillation speed, 5 min infusion was enough to prevent diffusion of pDNA solution. Furthermore, transfection efficiency in the target site was maintained when instillation speed was slowed. Wiping off residual pDNA solution from the applied liver lobe resulted in a further improvement in selectivity, suggesting not only immediate diffusion, but also gradual diffusion, are important factors for successful target site-specific gene transfer. Information in this study will be useful for further development of an effective gene delivery system targeted to a specific organ/tissue by use of other non-viral or viral vectors.

[Development of drug delivery system by utilizing absorption from liver surface and its application]

Because it is difficult to achieve local drug activity following administration by the conventional intravenous and oral routes, I sought to develop a new route of administration utilizing drug absorption from the liver surface in order to target that organ. Although direct application to the liver surface should yield local drug distribution, drug absorption from the liver surface has not been reported in the literature. Therefore, we analyzed, as a model, the efficiency of absorption of several organic anions and dextrans of various molecular weights following application to the rat liver surface in vivo using a cylindrical diffusion cell. Each compound appeared gradually in the plasma, followed by excretion into the bile and/or urine, indicating the possibility of drug absorption from the liver surface. The absorption process from the liver surface may not involve a specific transport system because dose and transport inhibitors had no detectable effect. In addition, molecular weight was found to be a determinant of absorption through the liver surface. The efficiency of targeting desired region in the liver was enhanced considerably by application to the liver surface, compared to intravenous administration. Moreover, I have obtained several promising results from the application of this new drug delivery system to anticancer drugs and gene therapy. On the other hand, I have also clarified the characteristics of drug absorption from the surfaces of the kidney, stomach, cecum and small intestine, and plan to apply the physiological findings to other fields.

Highly stomach-selective gene transfer following gastric serosal surface instillation of naked plasmid DNA in rats

BACKGROUND

The purpose of this study was to achieve stomach-selective gene transfer in rats by our simple and novel administration method, which is gastric serosal surface instillation of naked plasmid DNA (pDNA).

METHODS

Naked pDNA encoding firefly luciferase as a reporter gene was instilled onto the gastric serosal surface in male Wistar rats. As controls, we performed intraperitoneal, intragastric and intravenous administration of naked pDNA. At appropriate time intervals, we measured luciferase activities in the stomach and other tissues.

RESULTS

Gene expression in the stomach 6 h after gastric serosal surface instillation of naked pDNA (5 microg) was significantly higher than that after using other administration methods. The present study is the first report on stomach-selective gene transfer following instillation of naked pDNA onto the gastric serosal surface in rats. Also, the gene expression level in the stomach 6 h after gastric serosal surface instillation of naked pDNA was markedly higher than that in other tissues. In a dose-dependent study, the gene expression level was saturated over 5 microg. Gene expression in the stomach was detected 3 h after gastric serosal surface instillation of naked pDNA. The gene expression level peaked 12-24 h after instillation of naked pDNA, then decreased to a level similar to 3 h at 48 h.

CONCLUSIONS

Gastric serosal surface in stillation of naked pDNA can be a highly stomach-selective gene transfer method in rats.