Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA

Relationship between reduction in rice (Nipponbare) leaf blade size under elevated CO2 and miR396-GRF module

Elevated CO₂ (eCO₂; 1000 ppm) influences developing rice leaf formation, reducing leaf blade length and width as compared to rice grown under ambient CO₂ (aCO₂; 400 ppm). Since micro RNAs (miRNAs) are known to play multiple roles in plant development, we hypothesized that miRNAs might be involved in modulating leaf size under eCO₂ conditions. To identify miRNAs responding to eCO₂, we profiled miRNA levels in developing rice leaves (P4; plastochron number of the fourth-youngest leaf) under eCO₂ using small RNA-seq. We detected 18 mature miRNA sequences for which expression levels varied more than two-fold between the eCO₂ and aCO₂ conditions. Among them, only miR396e and miR396f significantly differed between the two conditions. Additionally, the expression of growth-regulating factors (GRFs), potential target mRNA of miR396s, were repressed under the eCO₂ condition. We used an antisense oligonucleotide approach to confirm that single-strand DNA corresponding to the miR396e sequence effectively downregulated GRF expression in developing leaves, reducing the leaf blade length, such as for rice grown under eCO₂. These results suggest that the miR396-GRF module is crucially relevant to controlling rice leaf blade length in eCO₂ environments.

A novel nonviral gene delivery system: multifunctional envelope-type nano device

In this review we introduce a new concept for developing a nonviral gene delivery system which we call "Programmed Packaging." Based on this concept, we succeeded in developing a multifunctional envelope-type nano device (MEND), which exerts high transfection activities equivalent to those of an adenovirus in a dividing cell. The use of MEND has been extended to in vivo applications. PEG/peptide/DOPE ternary conjugate (PPD)-MEND, a new in vivo gene delivery system for the targeting of tumor cells that dissociates surface-modified PEG in tumor tissue by matrix metalloproteinase (MMP) and exerts significant transfection activities, was developed. In parallel with the development of MEND, a quantitative gene delivery system, Confocal Image-assisted 3-dimensionally integrated quantification (CIDIQ), also was developed. This method identified the rate-limiting step of the nonviral gene delivery system by comparing it with adenoviral-mediated gene delivery. The results of this analysis provide a new direction for the development of rational nonviral gene delivery systems.

Assessing uncertainty in model parameters based on sparse and noisy experimental data

To perform parametric identification of mathematical models of biological events, experimental data are rare to be sufficient to estimate target behaviors produced by complex non-linear systems. We performed parameter fitting to a cell cycle model with experimental data as an in silico experiment. We calibrated model parameters with the generalized least squares method with randomized initial values and checked local and global sensitivity of the model. Sensitivity analyses showed that parameter optimization induced less sensitivity except for those related to the metabolism of the transcription factors c-Myc and E2F, which are required to overcome a restriction point (R-point). We performed bifurcation analyses with the optimized parameters and found the bimodality was lost. This result suggests that accumulation of c-Myc and E2F induced dysfunction of R-point. We performed a second parameter optimization based on the results of sensitivity analyses and incorporating additional derived from recent in vivo data. This optimization returned the bimodal characteristics of the model with a narrower range of hysteresis than the original. This result suggests that the optimized model can more easily go through R-point and come back to the gap phase after once having overcome it. Two parameter space analyses showed metabolism of c-Myc is transformed as it can allow cell bimodal behavior with weak stimuli of growth factors. This result is compatible with the character of the cell line used in our experiments. At the same time, Rb, an inhibitor of E2F, can allow cell bimodal behavior with only a limited range of stimuli when it is activated, but with a wider range of stimuli when it is inactive. These results provide two insights; biologically, the two transcription factors play an essential role in malignant cells to overcome R-point with weaker growth factor stimuli, and theoretically, sparse time-course data can be used to change a model to a biologically expected state.

Toxicity and efficacy evaluation of multiple targeted polymalic acid conjugates for triple-negative breast cancer treatment

Engineered nanoparticles are widely used for delivery of drugs but frequently lack proof of safety for cancer patient's treatment. All-in-one covalent nanodrugs of the third generation have been synthesized based on a poly(β-L-malic acid) (PMLA) platform, targeting human triple-negative breast cancer (TNBC). They significantly inhibited tumor growth in nude mice by blocking synthesis of epidermal growth factor receptor, and α4 and β1 chains of laminin-411, the tumor vascular wall protein and angiogenesis marker. PMLA and nanodrug biocompatibility and toxicity at low and high dosages were evaluated in vitro and in vivo. The dual-action nanodrug and single-action precursor nanoconjugates were assessed under in vitro conditions and in vivo with multiple treatment regimens (6 and 12 treatments). The monitoring of TNBC treatment in vivo with different drugs included blood hematologic and immunologic analysis after multiple intravenous administrations. The present study demonstrates that the dual-action nanoconjugate is highly effective in preclinical TNBC treatment without side effects, supported by hematologic and immunologic assays data. PMLA-based nanodrugs of the Polycefin™ family passed multiple toxicity and efficacy tests in vitro and in vivo on preclinical level and may prove to be optimized and efficacious for the treatment of cancer patients in the future.

PSORS1C1 may be involved in rheumatoid arthritis

PSORS1C1/CDSN is a susceptibility gene for psoriasis. Both psoriasis and rheumatoid arthritis (RA) are autoimmune diseases. This study investigated whether PSORS1C1/CDSN was involved in RA. The TagSNPs rs3130983, rs3778638 and rs4959053 in the PSORS1C1/CDSN locus were shown to predict susceptibility to RA in two independent RA cohorts using a TaqMan genotyping assay and Sequenom MassARRAY. The expression of PSORS1C1/CDSN was determined with western blotting and ELISA. Cultured synovial fibroblasts from RA patients (RASF) were treated with anti-PSORS1C1 siRNA. The TaqMan genotyping assay demonstrated significant differences in the rs3130983 and rs4959053 allele frequencies (p = 0.002001 and 1.74E-07, respectively) and genotype frequencies (0.010503 and 1.07E-06, respectively) between the RA patients and controls. Sequenom MassARRAY results indicated that SNP rs3778638 allele frequency and genotype frequency were significantly associated with RA (p = 7.35E-05 and 0.000357, respectively). Western blotting revealed a significant increase in expression of PSORS1C1 in RA synovial tissues, and ELISA detected high levels of PSORS1C1 and CDSN in the blood of RA patients. PSORS1C1-siRNA treatment significantly decreased the PSORS1C1 expression, IL-17 level, Il-1β level and cell proliferation in RASF. These results suggest that PSORS1C1 might play an important role in the development of RA.

Design of multifunctional non-viral gene vectors to overcome physiological barriers: dilemmas and strategies

Gene-based therapeutics hold great promise for medical advancement and have been used to treat various human diseases with mixed success. However, their therapeutic application in vivo is limited due largely to several physiological barriers. The design of non-viral gene vectors with the ability to overcome delivery obstacles is currently under extensive investigation. These efforts have placed an emphasis on the development of multifunctional vectors able to execute multiple tasks to simultaneously overcome both extracellular and intracellular obstacles. However, the assembly of these different functionalities into a single system to create multifunctional gene vectors faces many conflicts that largely limit the safe and efficient application of lipoplexes and polyplexes in a systemic delivery. In the review, we have described the dilemmas inherent in the design of a viable, non-viral gene vector equipped with multiple functionalities. The strategies directed towards individual delivery barriers are first summarized, followed by a focus on the design of so-called smart multifunctional vectors with the capability to overcome the delivery difficulties of gene medicines, including the so-called the "polycation dilemma", the "PEG dilemma" and the "package and release dilemma".

Comparison of three techniques for generation of tolerogenic dendritic cells: siRNA, oligonucleotide antisense, and antibody blocking

In recent years, a new view of dendritic cells (DCs) as a main regulator of immunity to induce and maintain tolerance has been established. In vitro manipulation of their development and maturation is a topic of DC therapeutic application, which utilizes their inherent tolerogenicity. In this field, the therapeutic potential of antisense, siRNA, and blocking antibody are an interesting goal. In the present study, the efficiency of these three methods--siRNA, antisense, and blocking antibody--against CD40 molecule and its function in DCs and BCL1 cell line are compared. DCs were separated from mouse spleen and then cultured in vitro using Lipofectamine 2000 to deliver both silencers; the efficacy of transfection was estimated by flow cytometry. mRNA expression and protein synthesis were assessed by real time-PCR and flow cytometry, respectively. By Annexin V and propidium iodine staining, we could evaluate the viability of transfected cells. Knocking down the CD40 gene into separate groups of DCs by siRNA, antisense, and blocking antibody treated DCs can cause an increase in IL-4, decrease in IL-12, IFN-γ production, and allostimulation activity. Our results indicated that, in comparison to antisense and blocking antibody, siRNAs appear to be quantitatively more efficient in CD40 downregulation and their differences are significant.

Development of a targeted siRNA delivery system using FOL-PEG-PEI conjugate

Receptor mediated delivery of siRNA enables silencing of target genes in specific tissues. Folate receptor (FR) is an attractive target for tumor-selective gene delivery. The focus of this study was to deliver the dihydrofolate reductase (DHFR) siRNA expressing plasmid and to silence the DHFR gene in FR positive KB cells, by complexing the plasmid with a folate-polyethylene glycol-polyethylenimine (FOL-PEG-PEI) conjugate, as a gene carrier. A DHFR siRNA sequence was cloned into a pSUPER-RNAi vector and complexed with the FOL-PEG-PEI conjugate. The complex was characterized by particle size analyzer, gel retardation and DNase protection assay. The FOL-PEG-PEI/pSUPER-siDHFR complex was transfected to FR overexpressing (KB) and FR negative (A549) cells. The transfection effiencies and gene inhibition were analyzed by fluorescence microscopy and RT-PCR. The pSUPER-siDHFR/PEI-PEG-FOL complex delivered the siRNA vector and inhibited DHFR gene in KB cells, while A549 cells were unaffected. Lipofectamine mediated transfection of pSUPER-siDHFR, delivered the vector and inhibited the DHFR gene in both KB and A549 cells. FR mediated delivery of siDHFR complexed with PEI-PEG-FOL conjugate inhibits the DHFR expression in FR positive cells alone. This strategy can be extended to deliver a wide range of drugs and post-transcriptional gene silencing therapeutics.

Octaarginine-modified multifunctional envelope-type nano device for siRNA

The multifunctional envelope-type nano device (MEND) is a novel non-viral gene delivery system for plasmid DNA (pDNA) and oligodeoxynucleotides (ODN). We showed previously that octaarginine-modified MEND (R8-MEND) produces a high transfection activity without cytotoxicity via macropinocytosis and efficient release of a condensed DNA core to the cytosol. In the present study, we succeeded in developing an efficient method for packaging siRNA into the R8-MEND, and its silencing effect was compared with that of transfection reagent TransIT-TKO. A polycation able to condense siRNA was screened for by measuring the size and zeta-potential of complexes formed between siRNA and the polycations poly-l-lysine (PLL), stearyl octaarginine (STR-R8) and protamine. Only STR-R8 was able to condense siRNA to form nano particles (<100 nm), whereas all three polycations were able to condense pDNA or ODN. The siRNA packaged in R8-MEND inhibited luciferase activity by more than 80% in HeLa cells stably expressing luciferase. Much amount of siRNA was internalized into the cells as R8-MEND, and siRNA was effectively released from lipid envelope of MEND to cytoplasm near the nucleus. Consequently, R8-MEND can deliver condensed siRNA into cells to produce an efficient and persistent silencing effect with minimum cytotoxicity.

PFKFB3 gene silencing decreases glycolysis, induces cell-cycle delay and inhibits anchorage-independent growth in HeLa cells

The high rate of glycolysis despite the presence of oxygen in tumor cells (Warburg effect) suggests an important role for this process in cell division. The glycolytic rate is dependent on the cellular concentration of fructose 2,6-bisphosphate (Fru-2,6-P2), which, in turn, is controlled by the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFK-2). The ubiquitous PFK-2 isoenzyme (uPFK-2, alternatively named UBI2K5 or ACG) coded by the pfkfb3 gene is induced by different stimuli (serum, progesterone, insulin, hypoxia, etc.) and has the highest kinase/phosphatase activity ratio amongst all PFK-2 isoenzymes discovered to date, which is consistent with its role as a powerful activator of glycolysis. uPFK-2 is expressed in brain, placenta, transformed cells and proliferating cells. In the present work, we analyze the impact of small interfering RNA (siRNA)-induced silencing of uPFK-2 on the inhibition of cell proliferation. HeLa cells treated with uPFK-2 siRNA showed a decrease in uPFK-2 RNA levels measured at 24h. uPFK-2 protein levels were severely depleted at 48-72h when compared with cells treated with an unrelated siRNA, correlating with decreased glycolytic activity, Fru-2,6-P2, lactate and ATP concentrations. These metabolic changes led to reduced viability, cell-cycle delay and an increase in the population of apoptotic cells. Moreover, uPFK-2 suppression inhibited anchorage-independent growth. The results obtained highlight the importance of uPFK-2 on the regulation of glycolysis, on cell viability and proliferation and also on anchorage-independent growth. These data underscore the potential for uPFK-2 as an effective tumor therapeutic target.