Nanodiamonds (NDs) are the most biocompatible member of the carbon nanofamily which are widely researched for diagnostic and therapeutic applications. Unlike other carbon nanomaterials, the surface of NDs is innately reactive, hence capable of conjugating various chemical moieties for targeted actions. This work focuses on utilizing the surface reactivity of NDs for gene therapeutics and addressing the challenges associated with its application in the biological environment. Pristine carboxylated NDs were functionalized with basic amino acids (lysine and lysyl-histidine) through covalent conjugation via a three carbon chain linker. Amino acid functionalized NDs were characterized by infrared spectroscopy, thermogravimetry and size and zeta potential measurements. Lysine conjugation was evident through a marked change in the zeta potential of ND dispersion from negative to a high positive value (-54.6 mV to +26.3 mV). The thermogram of lysine functionalized NDs (Lys-NDs) revealed a significant weight loss from 150ᵒC to 700ᵒC confirming the functionalization through loss of amino acid conjugates from the surface and total loading was calculated as 1.97 mmols/g. Lys-NDs also showed optimum binding with pDNA and siRNA at weight ratios of 1:1 and 1:20 (pDNA/siRNA:ND), respectively. Functionalization of NDs with lysine contributed to limiting aggregation and enhancing the colloidal stability of ND dispersions in biological milieu. The aqueous dispersion of lys-NDs showed minimum sedimentation and remained stable over a period of 25 days. Average sizes under 100 nm and zeta potentials higher than +20 mV indicate a preservation of the cationic surface throughout the testing period. Moreover, size distributions and zeta potentials changed significantly upon incubation of lys-NDs with blood serum suggesting an interaction with biomolecules, mainly proteins and a possible formation of a protein corona. Cellular internalization of bare lys-NDs and their diamoplexes (i.e. complexes of NDs with nucleic acids) was assessed through scanning transmission X-ray microscopy and flow cytometry. Functional efficiency of lysine NDs was determined by flow cytometry monitoring the GFP knockdown through anti-GFP siRNA delivery. Results reveal a promising GFP knockdown of ~17% upon treating the cells with NDs/siRNA diamoplexes at a ratio of 20:1. Subsequent analyses regarding the effect of NDs to prevent cellular proliferation and to cause cellular apoptosis confirmed that they are innately biocompatible at a wide range of concentrations. Unlike lysine NDs, lysyl-histidine functionalization was limited and the surface loading of this conjugate on NDs was very low. Therefore, they were unable to bind pDNA and siRNA even at high weight ratios and hence demand design modifications. Overall this work demonstrates a novel approach of functionalizing NDs with basic amino acids capable of enhancing colloidal stability and delivering of therapeutic genes into mammalian cells. It represents an important step in the development of safe and efficient gene therapy for inherited and acquired diseases.

In this thesis nanoparticles consisting of a calcium phosphate core encapsulated by poly(lactic-co-glycolic) acid and polyethylenimine were developed for the delivery of siRNA in vivo. The nanoparticles were efficiently endocytosed by different cell types in vitro without exhibiting cytotoxic characteristics. Without possessing endogenous immune response activating properties, the nanoparticles had a highly preferable composition for the delivery of siRNA and subsequent gene knockdown. The delivery of siRNA with nanoparticles was tested in two different murine disease models: DSS-induced colitis as model for human IBD and a TH1-induced lung inflammation as model for COPD. In IBD and COPD chemokines and cytokines are predominant players in the progression of the inflammatory response. The local interference of cytokine signalling mediated by siRNA-loaded nanoparticles might therefore be a promising new therapeutic approach. In both murine models, the aim was to deliver siRNA directed against inflammation related cytokines by nanoparticles for the local treatment of mucosal inflammation. The local administration of nanoparticles loaded with siRNA to mice suffering from intestinal or lung inflammation led to significantly decreased target gene expression on mRNA as well as protein level in biopsies from the target tissues. Furthermore, reduced cytokine levels were accompanied by diminished inflammatory pathologies and augmented clinical signs of sickness. The results of this thesis indicate that a specific and local modulation of inflammatory responses by nanoparticle-based siRNA delivery is feasible and demonstrates a major therapeutic potential.

Applications of nanotechnology in medicine, also known as nanomedicine, is a rapidly growing field as it holds great potential in the development of novel therapeutics toward treatment of various diseases. Shell crosslinked knedel-like nanoparticles (SCKs) that are self assembled from amphiphilic block copolymers into polymeric micelles followed by crosslinking selectively throughout the shell domain have been investigated as theranostic agents for the delivery of nucleic acids and incorporation of imaging probes. The main focus of this dissertation is to design and develop unique multifunctional bio-synthetic hybrid nanoparticles that can carry agents for radiolabeling, moieties for inducing stealth properties to minimize protein adsorption in vivo, ligands for site-specific targeting, therapeutic payloads, and are optimized for efficient delivery of cargoes intracellularly and to the target sites toward constructing novel nanoscopic objects for therapy and diagnosis. Alteration of polymeric building blocks of the nanoparticles provides opportunities for precise control over the sizes, shapes, compositions, structures and properties of the nanoparticles. To ensure ideal performance of nanoparticles as theranostic agents, it is critical to ensure high intracellular bioavailability of the therapeutic payload conjugated to nanoparticles. Special efforts were made by employing well-defined multi-step polymerization and polymer modification reactions that involved conjugation of peptide nucleic acids (PNAs) to chain terminus of poly(ethylene glycol) (PEG) chain grafts such that they were presented at the outermost surface of SCKs. Additionally, chemical modification reactions were performed on the polymer backbone to integrate positive charges onto the shell of the nanoparticles to afford cationic SCKs (cSCKs) for facilitating cellular entry and electrostatic interactions with negatively charged nucleic acids. Covalent conjugation of F3, a tumor homing peptide, post-assembly of the nanoparticles enhanced cellular uptake and knockdown of nucleolin (a shuttling protein overexpressed at the sites of angiogenesis) and thus inhibiting tumor cell growth. Furthermore, these polymer precursors of the cSCKs were modified with partial to full incorporation of histamines to facilitate their endosomal escape for efficient delivery into the cytosol. The cSCKs were further templated onto high aspect ratio anionic cylinders to form hierarchically-assembled nanostructures that bring together individual components with unique functions, such as one carrying a therapeutic payload and the other with sites for radiolabeling. These higher order nanoobjects enhance circulation in vivo, have capabilities to package nucleic acids electrostatically and contain sites for radiolabeling, providing an overall advantage over the individual components, which could each facilitate only one or the other of the combined functions. Hierarchically-assembled nanostructures were investigated for their cellular uptake, transfection behavior and radiolabeling efficiency, as the next generation of theranostic agents.

abstract: Gene manipulation techniques, such as RNA interference (RNAi), offer a powerful method for elucidating gene function and discovery of novel therapeutic targets in a high-throughput fashion. In addition, RNAi is rapidly being adopted for treatment of neurological disorders, such as Alzheimer's disease (AD), Parkinson's disease, etc. However, a major challenge in both of the aforementioned applications is the efficient delivery of siRNA molecules, plasmids or transcription factors to primary cells such as neurons. A majority of the current non-viral techniques, including chemical transfection, bulk electroporation and sonoporation fail to deliver with adequate efficiencies and the required spatial and temporal control. In this study, a novel optically transparent biochip is presented that can (a) transfect populations of primary and secondary cells in 2D culture (b) readily scale to realize high-throughput transfections using microscale electroporation and (c) transfect targeted cells in culture with spatial and temporal control. In this study, delivery of genetic payloads of different sizes and molecular characteristics, such as GFP plasmids and siRNA molecules, to precisely targeted locations in primary hippocampal and HeLa cell cultures is demonstrated. In addition to spatio-temporally controlled transfection, the biochip also allowed simultaneous assessment of a) electrical activity of neurons, b) specific proteins using fluorescent immunohistochemistry, and c) sub-cellular structures. Functional silencing of GAPDH in HeLa cells using siRNA demonstrated a 52% reduction in the GAPDH levels. In situ assessment of actin filaments post electroporation indicated a sustained disruption in actin filaments in electroporated cells for up to two hours. Assessment of neural spike activity pre- and post-electroporation indicated a varying response to electroporation. The microarray based nature of the biochip enables multiple independent experiments on the same culture, thereby decreasing culture-to-culture variability, increasing experimental throughput and allowing cell-cell interaction studies. Further development of this technology will provide a cost-effective platform for performing high-throughput genetic screens. / Dissertation/Thesis / Ph.D. Bioengineering 2012

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22660号 / 工博第4744号 / 新制||工||1741(附属図書館) / 京都大学大学院工学研究科高分子化学専攻 / (主査)教授 秋吉 一成, 教授 大内 誠, 准教授 佐々木 善浩 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

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Telomerase, discovered in 1985, is considered a near-universal marker of malignancy and therefore has a potential use in cancer therapeutics and diagnostics. In this study, I used several approaches to gain a better understanding of telomerase and its potential applications in the canine context, for both cancer therapeutics and diagnosis. Having already developed an effective siRNA viral vector in vitro, the challenge still remained to deliver it efficiently in vivo. Thus, I initially investigated two possible approaches for in vivo delivery. First, I investigated a cell-based system for direct delivery to the tumours. Specifically I optimised a system for efficient gene-transfer to endothelial cells using a green fluorescent protein plasmid vector, and monitored systemic delivery by ex vivo imaging of dye-labelled cells in a canine xenograft tumour mouse model. In parallel, in vitro I investigated the gene transfer mediated by a novel dendrimer vector that can form nanoparticles with DNA and accumulate in tumour sites in vivo after i.v. administration. In order to utilize these delivery systems, I developed a DNA plasmid-based siRNA vector and tested its efficacy on canine tumour cells. To investigate telomerase as a cancer biomarker, I conducted a study that aimed to detect circulating telomerase reverse transcriptase (TERT) mRNA in serum taken from canine cancer patients. For this I developed several systems for effective RNA isolation from serum and used both conventional and quantitative PCR assays to detect TERT expression. Although for the first time I can confirm the existence of mRNA in serum of canine cancer patients, in this clinical study, I could only detect telomerase transcripts in a very small proportion of canine cancer patients. In a final pilot study to investigate anti-ageing technologies, I looked at the potential for drug-dependant telomerase induction rather than inhibition. For this I investigated the ability of three candidate drugs to induce TERT mRNA activation in canine embryonic fibroblasts. In this study, telomerase induction was measured using the quantitative PCR method that I had developed for serum detection. In summary, I have demonstrated that a cell-based delivery vehicle has a potential application in cancer therapy, but that more development is required before it can be applied clinically. I have also reported here that PPIG3 dendrimer-based gene transfer in vitro is low in canine cancer cells and thus require more optimisation and development before it can be utilised as an efficient systemic delivery vehicle. For the siRNA experiment, unfortunately, I did not observe any telomerase genesilencing in canine cancer cells using the plasmid-based siRNA expression vector, and therefore the gene sequence of cTR that we were targeting as well as the siRNA plasmid-vector that we used needs further validation in canine cells. I also suggest that TERT mRNA may not be a good serum biomarker for canine cancer diagnostics as I did not find TERT transcript in most of our serum samples from canine cancer patients, although circulating mRNA of a housekeeping gene was detected. Finally, in a pilot study, I have demonstrated that telomerase can be induced in normal canine somatic cells using small molecules. However, the long-term effects of telomerase induction on ageing must be determined in future studies.

Carbon nanotubes (CNTs) are of special interest to industry and they have been increasingly utilised as advanced nanovectors in drug/gene delivery systems. They possess significant advantages including high surface area, welldefined morphologies, unique optical property, superior mechanical strength and thermal conductivity. However, despite their unique and advanced physicochemical properties, the low compatibility of some of those materials [e.g. multiwalled CNTs (MWCNTs)] in most biological and chemical environments has also generated some serious health and environment concerns. Chemical functionalization broadens CNT applications, conferring new functions, and at the same time was found potentially altering toxicity. Although considerable experimental data related to functionalised CNT toxicity, at the molecular and cellular levels, have been reported, there is very limited information available for the corresponding mechanism involved (e.g. cell apoptosis, genotoxicity. The toxicity of carbon nanotubes has been confirmed on many cell lines including A549 (lung cancer cell line) and MRC-5 (lung fibroblasts). However, the sensitivity of each cell line in terms of cellular morphology, apoptosis and DNA damage are still unknown. In this report the different levels of cellular response to oxidative stress and phagocytosis have been investigated in A549, MCF-7 and MRC-5 cell lines to better understand the mechanisms of the toxicity pathway. siRNA as an ideal personalized therapeutics can specifically regulate gene expression, but efficient delivery of siRNA is difficult while it has been shown that MWCNTs protect siRNA, facilitate entry into cells. In this study, we comprehensively evaluated the in vitro cytotoxicity of pristine and functionalized (-OH, -COOH) multi-wall carbon nanotubes (MWCNTs), via cell viability test, reactive oxygen species (ROS) generation test, cell apoptosis and DNA mutation detection, to investigate the non-toxic dose and influence of functional group in A549, MCF-7 and MRC-5 cells exposed to 1-1000 μg/mL MWCNTs from 6 to 72 hours. In addition, 84 toxicity related genes have been detected to investigate the change of RNA regulation after treatment with MWCNTs. The research findings suggest that functionalized MWCNTs are more genotoxic compared to their pristine form, and the level of both dose and dispersion in the matrix used should be taken into consideration before applying further clinical applications of MWCNTs. Among all three cell lines, MCF-7 was the most sensitive to cell death and DNA damage induced by pristine carbon nanotubes. The majority of MCF-7 cell death was in necrotic. In A549 cells, apoptosis played a notable role in cytotoxicity. MRC-5 didn’t show significant cell loss or membrane damage, which might be explained by its low cell growth rate, notably however, a great reduction of the F-actin and attachment points was observed after treatment which indicates that MRC-5 cells are under very unhealthy condition and less attached to the bottom of flasks. Despite their toxicity, which is still being researched, carbon nanotubes have a great potential in clinical medicine. Thus, understanding the sensitivity of different cell lines could offer a more individualized approach for future treatment regimes. In regards to gene delivery, MWCNTs were found to be less toxic than chemical agents (positive control) without weakening the delivery efficiency, which proves that MWCNTs have a good potential in medicine area.

RNA silencing is a cellular mechanism of post-transcriptional gene regulation which is highly conserved among the plant and animal kingdoms of life, and plays a critical part of developmental biology, maintenance of homeostasis, and host-pathogen interactions. The pathway is engaged by small double-stranded (ds)RNA molecules (small RNAs), which effect sequence specific gene silencing by targeting complementary RNA sequences. There are several classes of small RNAs which engage the pathway. MicroRNAs (miRNAs) are expressed in the genome as endogenous regulators of gene expression. Short-interfering RNAs (siRNAs) are usually from exogenous sources such as viral-derived short-interfering RNAs, or synthetic siRNAs which are applied to cells or organisms to inhibit expression of specific genes. The p19 protein is a viral suppressor of RNA silencing (VSRS) endogenous to tombusviruses, which binds small RNA duplexes of any sequence with extremely high affinity. Because of its unique binding properties, recombinant p19 proteins are an excellent platform for tool development surrounding the RNA silencing pathway and are used extensively in novel applications for modulating the activity of small RNAs in living systems and for detecting small RNAs in biological samples. Herein we present work that has increased the breadth of p19’s utility as a biotechnology tool in three distinct realms. First, we present a chemical biology approach which combines p19 and small molecules for potent inhibition of the RNA silencing pathway in human cells. Secondly, we present the development of a novel fusion protein between p19 and a cell penetrating peptide (CPP), which functions as an siRNA delivery agent to allow gene knockdown in human cells. Thirdly, we have improved the utility of p19 for detecting and sequestering human miRNAs through rationally designing the binding surface; we describe mutations which dramatically enhance p19's affinity for human miRNA-122. The work presented here adds to the growing repertoire of engineered RNA binding proteins (RBPs) as tools for studying small RNA molecules and modulating their activity for applications in human therapeutics.