A Discovery with Potential to Revitalize Hammerhead Ribozyme Therapeutics for Treatment of Inherited Retinal Degenerations.

Hammerhead ribozymes (hhRzs), RNA enzymes capable of site-specific cleavage of arbitrary target mRNAs, have faced significant hurdles in development and optimization as gene therapeutics for clinical translation. Chemical and biological barriers must be overcome to realize an effective therapeutic. A new Facilitated ribozyme has been identified with greatly enhanced kinetic properties that lead new insight on the capacity of ribozymes to target mutant genes to treat inherited retinal degenerations.

High-resolution microstrip NMR detectors for subnanoliter samples.

We present the numerical optimization and experimental characterization of two microstrip-based nuclear magnetic resonance (NMR) detectors. The first detector, introduced in our previous work, was a flat wire detector with a strip resting on a substrate, and the second detector was created by adding a ground plane on top of the strip conductor, separated by a sample-carrying capillary and a thin layer of insulator. The dimensional parameters of the detectors were optimized using numerical simulations with regards to radio frequency (RF) sensitivity and homogeneity, with particular attention given to the effect of the ground plane. The influence of copper surface finish and substrate surface on the spectral resolution was investigated, and a resolution of 0.8-1.5 Hz was obtained on 1 nL deionized water depending on sample positioning. For 0.13 nmol sucrose (0.2 M in 0.63 nL H2O) encapsulated between two Fluorinert plugs, high RF homogeneity (A810°/A90° = 70-80%) and high sensitivity (expressed in the limit of detection nLODm = 0.73-1.21 nmol s1/2) were achieved, allowing for high-performance 2D NMR spectroscopy of subnanoliter samples.

Toward high-resolution NMR spectroscopy of microscopic liquid samples.

A longstanding limitation of high-resolution NMR spectroscopy is the requirement for samples to have macroscopic dimensions. Commercial probes, for example, are designed for volumes of at least 5 µL, in spite of decades of work directed toward the goal of miniaturization. Progress in miniaturizing inductive detectors has been limited by a perceived need to meet two technical requirements: (1) minimal separation between the sample and the detector, which is essential for sensitivity, and (2) near-perfect magnetic-field homogeneity at the sample, which is typically needed for spectral resolution. The first of these requirements is real, but the second can be relaxed, as we demonstrate here. By using pulse sequences that yield high-resolution spectra in an inhomogeneous field, we eliminate the need for near-perfect field homogeneity and the accompanying requirement for susceptibility matching of microfabricated detector components. With this requirement removed, typical imperfections in microfabricated components can be tolerated, and detector dimensions can be matched to those of the sample, even for samples of volume ≪5 µL. Pulse sequences that are robust to field inhomogeneity thus enable small-volume detection with optimal sensitivity. We illustrate the potential of this approach to miniaturization by presenting spectra acquired with a flat-wire detector that can easily be scaled to subnanoliter volumes. In particular, we report high-resolution NMR spectroscopy of an alanine sample of volume 500 pL.

A cellular high-throughput screening approach for therapeutic trans-cleaving ribozymes and RNAi against arbitrary mRNA disease targets.

Major bottlenecks in development of therapeutic post transcriptional gene silencing (PTGS) agents (e.g. ribozymes, RNA interference, antisense) include the challenge of mapping rare accessible regions of the mRNA target that are open for annealing and cleavage, testing and optimization of agents in human cells to identify lead agents, testing for cellular toxicity, and preclinical evaluation in appropriate animal models of disease. Methods for rapid and reliable cellular testing of PTGS agents are needed to identify potent lead candidates for optimization. Our goal was to develop a means of rapid assessment of many RNA agents to identify a lead candidate for a given mRNA associated with a disease state. We developed a rapid human cell-based screening platform to test efficacy of hammerhead ribozyme (hhRz) or RNA interference (RNAi) constructs, using a model retinal degeneration target, human rod opsin (RHO) mRNA. The focus is on RNA Drug Discovery for diverse retinal degeneration targets. To validate the approach, candidate hhRzs were tested against NUH↓ cleavage sites (N = G,C,A,U; H = C,A,U) within the target mRNA of secreted alkaline phosphatase (SEAP), a model gene expression reporter, based upon in silico predictions of mRNA accessibility. HhRzs were embedded in a larger stable adenoviral VAI RNA scaffold for high cellular expression, cytoplasmic trafficking, and stability. Most hhRz expression plasmids exerted statistically significant knockdown of extracellular SEAP enzyme activity when readily assayed by a fluorescence enzyme assay intended for high throughput screening (HTS). Kinetics of PTGS knockdown of cellular targets is measureable in live cells with the SEAP reporter. The validated SEAP HTS platform was transposed to identify lead PTGS agents against a model hereditary retinal degeneration target, RHO mRNA. Two approaches were used to physically fuse the model retinal gene target mRNA to the SEAP reporter mRNA. The most expedient way to evaluate a large set of potential VAI-hhRz expression plasmids against diverse NUH↓ cleavage sites uses cultured human HEK293S cells stably expressing a dicistronic Target-IRES-SEAP target fusion mRNA. Broad utility of this rational RNA drug discovery approach is feasible for any ophthalmological disease-relevant mRNA targets and any disease mRNA targets in general. The approach will permit rank ordering of PTGS agents based on potency to identify a lead therapeutic compound for further optimization.

High-resolution zero-field NMR J-spectroscopy of aromatic compounds.

We report the acquisition and interpretation of nuclear magnetic resonance (NMR) J-spectra at zero magnetic field for a series of benzene derivatives, demonstrating the analytical capabilities of zero-field NMR. The zeroth-order spectral patterns do not overlap, which allows for straightforward determination of the spin interactions of substituent functional groups. Higher-order effects cause additional line splittings, revealing additional molecular information. We demonstrate resonance linewidths as narrow as 11 mHz, permitting resolution of minute frequency differences and precise determination of long-range J-couplings. The measurement of J-couplings with the high precision offered by zero-field NMR may allow further refinements in the determination of molecular structure and conformation.

Multiplets at zero magnetic field: the geometry of zero-field NMR.

For liquid samples at Earth's field or below, nuclear-spin motion within scalar-coupled networks yields multiplets as a spectroscopic signature. In weak fields, the structure of the multiplets depends on the magnitude of the Zeeman interaction relative to the scalar couplings; in Earth's field, for example, heteronuclear couplings are truncated by fast precession at distinct Larmor frequencies. At zero field, weak scalar couplings are truncated by the relatively fast evolution associated with strong scalar couplings, and the truncated interactions can be described geometrically. When the spin system contains a strongly coupled subsystem A, an average over the fast evolution occurring within the subsystem projects each strongly coupled spin onto FA, the summed angular momentum of the spins in A. Weakly coupled spins effectively interact with FA, and the coupling constants for the truncated interactions are found by evaluating projections. We provide a formal description of zero-field spin systems with truncated scalar couplings while also emphasizing visualization based on a geometric model. The theoretical results are in good agreement with experimental spectra that exhibit second-order shifts and splittings.

Parahydrogen-induced polarization at zero magnetic field.

We use symmetry arguments and simple model systems to describe the conversion of the singlet state of parahydrogen into an oscillating sample magnetization at zero magnetic field. During an initial period of free evolution governed by the scalar-coupling Hamiltonian HJ, the singlet state is converted into scalar spin order involving spins throughout the molecule. A short dc pulse along the z axis rotates the transverse spin components of nuclear species I and S through different angles, converting a portion of the scalar order into vector order. The development of vector order can be described analytically by means of single-transition operators, and it is found to be maximal when the transverse components of I are rotated by an angle of ±π∕2 relative to those of S. A period of free evolution follows the pulse, during which the vector order evolves as a set of oscillating coherences. The imaginary parts of the coherences represent spin order that is not directly detectable, while the real parts can be identified with oscillations in the z component of the molecular spin dipole. The dipole oscillations are due to a periodic exchange between Iz and Sz, which have different gyromagnetic ratios. The frequency components of the resulting spectrum are imaginary, since the pulse cannot directly induce magnetization in the sample; it is only during the evolution under HJ that the vector order present at the end of the pulse evolves into detectable magnetization.

Zero-field NMR enhanced by parahydrogen in reversible exchange.

We have recently demonstrated that sensitive and chemically specific NMR spectra can be recorded in the absence of a magnetic field using hydrogenative parahydrogen induced polarization (PHIP) (1-3) and detection with an optical atomic magnetometer. Here, we show that non-hydrogenative parahydrogen-induced polarization (4-6) (NH-PHIP) can also dramatically enhance the sensitivity of zero-field NMR. We demonstrate the detection of pyridine, at concentrations as low as 6 mM in a sample volume of 250 µL, with sufficient sensitivity to resolve all identifying spectral features, as supported by numerical simulations. Because the NH-PHIP mechanism is nonreactive, operates in situ, and eliminates the need for a prepolarizing magnet, its combination with optical atomic magnetometry will greatly broaden the analytical capabilities of zero-field and low-field NMR.

A first-principles description of proton-driven spin diffusion.

Herein we design a reduced Liouville space for the simulation of proton-driven spin diffusion. Using this approach, the experimentally observed carbon-13 polarisation transfer in a powder sample undergoing magic-angle spinning is quantitatively described, directly from crystal geometry and without any adjustable parameters.

Nanoscale torsional resonator for polarization and spectroscopy of nuclear spins.

We propose a torsional resonator that couples to the transverse spin dipole of an attached sample. The absence of relative motion eliminates a source of friction that would otherwise hinder nanoscale implementation. Enhanced spontaneous emission induced by the resonator relaxes the longitudinal spin dipole at a rate of ∼1 s⁻¹ in the low-temperature limit. With signal averaging, single-proton magnetic resonance spectroscopy appears feasible at ∼10 mK and a high magnetic field, while single-shot sensitivity is practical for samples with at least tens of protons in a volume of ∼5 nm³.

Ab initio simulation of proton spin diffusion.

The many-body nature of the ubiquitous spin diffusion phenomenon makes it difficult to predict accurately from first principles. We show how the use of reduced Liouville spaces makes it possible to reproduce experimental proton spin diffusion measurements directly from crystalline geometry for powdered solids under magic-angle spinning.

Numerical simulation of free evolution in solid-state nuclear magnetic resonance using low-order correlations in Liouville space.

The design of simulations of free evolution in dipolar-coupled nuclear-spin systems using low-order correlations in Liouville space (LCL) is discussed, and a computational scheme relying on the Suzuki-Trotter algorithm and involving minimal memory requirements is described. The unusual nature of the approximation introduced by Liouville-space reduction in a spinning solid is highlighted by considering the accuracy of LCL simulations at different spinning frequencies, the quasiequilibria achieved by spin systems in LCL simulations, and the growth of high-order coherences in the exact dynamics. In particular, it is shown that accurate LCL simulations of proton spin diffusion occur in a regime where the reduced space excludes the coherences that make the dominant contribution to ∥σ∥(2), the norm-squared of the density matrix.

Retinal Degeneration Caused by Rod-Specific Dhdds Ablation Occurs without Concomitant Inhibition of Protein N-Glycosylation.

Dehydrodolichyl diphosphate synthase (DHDDS) catalyzes the committed step in dolichol synthesis. Recessive mutations in DHDDS cause retinitis pigmentosa (RP59), resulting in blindness. We hypothesized that rod photoreceptor-specific ablation of Dhdds would cause retinal degeneration due to diminished dolichol-dependent protein N-glycosylation. Dhddsflx/flx mice were crossed with rod-specific Cre recombinase-expressing (Rho-iCre75) mice to generate rod-specific Dhdds knockout mice (Dhddsflx/flx iCre+). In vivo morphological and electrophysiological evaluation of Dhddsflx/flx iCre+ retinas revealed mild retinal dysfunction at postnatal (PN) 4 weeks, compared with age-matched controls; however, rapid photoreceptor degeneration ensued, resulting in almost complete loss of rods and cones by PN 6 weeks. Retina dolichol levels were markedly decreased by PN 4 weeks in Dhddsflx/flx iCre+ mice, relative to controls; despite this, N-glycosylation of retinal proteins, including opsin (the dominant rod-specific glycoprotein), persisted in Dhddsflx/flx iCre+ mice. These findings challenge the conventional mechanistic view of RP59 as a congenital disorder of glycosylation.

Systematic Screening, Rational Development, and Initial Optimization of Efficacious RNA Silencing Agents for Human Rod Opsin Therapeutics.

PURPOSE: To systematically evaluate human rod opsin (hRHO) mRNA for potential target sites sensitive to posttranscriptional gene silencing (PTGS) by hammerhead ribozyme (hhRz) or RNA interference (RNAi) in human cells. To develop a comprehensive strategy to identify and optimize lead candidate agents for PTGS gene therapeutics. METHODS: In multidisciplinary RNA drug discovery, computational mRNA accessibility and in vitro experimental methods using reverse transcription-polymerase chain reaction (RT-PCR) were used to map accessibility in full-length hRHO transcripts. HhRzs targeted predicted accessible and inaccessible sites and were screened for cellular knockdown using a bicistronic reporter construct. Lead hhRz and RNAi PTGS agents were rationally optimized for target knockdown in human cells. RESULTS: Systematic screening of hRHO mRNA targeting agents resulted in lead candidate identification of a novel hhRz embedded in an RNA scaffold. Rational optimization strategies identified a minimal 725 hhRz as the most active agent. Recently identified tertiary accessory elements did not enhance activity. A 725-short-hairpin RNA (shRNA) agent exerts log-order knockdown. Silent modulation of the 725-hhRz target site in hRHO mRNA resulted in resistance to knockdown. CONCLUSIONS: Combining rational RNA drug design with cell-based screening allowed rapid identification of lead agents targeting hRHO. Optimization strategies identified the agent with highest intracellular activity. These agents have therapeutic potential in a mutation-independent strategy for adRP, or other degenerations where hRHO is a target. This approach can be broadly applied to any validated target mRNA, regardless of the disease. TRANSLATIONAL RELEVANCE: This work establishes a platform approach to develop RNA biologicals for the treatment of human disease.

Bottlenecks in development of retinal therapeutic post-transcriptional gene silencing agents.

Development of post-transcriptional gene silencing (PTGS) agents for therapeutic purposes is an immense challenge in modern biology. Established technologies used to knockdown a specific target RNA and its cognate protein: antisense, ribozyme, RNAi, all conditionally depend upon an initial, critical annealing event of the PTGS ligand to a target RNA. In this review we address the nature of the bottlenecks, emphasizing the biocomplexity of target RNA structure, that currently limit PTGS therapeutic development. We briefly review existing and emerging technologies designed to release these constraints to realize the potential of PTGS agents in gene based therapies.

Ultrahigh Resolution Mouse Optical Coherence Tomography to Aid Intraocular Injection in Retinal Gene Therapy Research.

HR-SD-OCT is utilized to monitor the progression of photoreceptor degeneration in live mouse models, assess the delivery of therapeutic agents into the subretinal space, and to evaluate toxicity and efficacy in vivo. HR-SD-OCT uses near infrared light (800-880 nm) and has optics specifically designed for the unique optics of the mouse eye with sub-2-micron axial resolution. Transgenic mouse models of outer retinal (photoreceptor) degeneration and controls were imaged to assess the disease progression. Pulled glass microneedles were used to deliver sub retinal injections of adeno-associated virus (AAV) or nanoparticles (NP) via a trans-scleral and trans-choroidal approach. Careful positioning of the needle into the subretinal space was required prior to a calibrated pressure injection, which delivers fluid into the sub retinal space. Real time subretinal surgery was conducted on our retinal imaging system (RIS). HR-SD-OCT demonstrated progressive uniform retinal degeneration due to expression of a toxic mutant human mutant rhodopsin (P347S) (RHOP347S) transgene in mice. HR-SD-OCT allows rigorous quantification of all the retinal layers. Outer nuclear layer (ONL) thickness and photoreceptor outer segment length (OSL) measurements correlate with photoreceptor vitality, degeneration, or rescue. The RIS delivery system allows real-time visualization of subretinal injections in neonatal (~P10-14) or adult mice, and HR-SD-OCT immediately determines success of delivery and maps areal extent. HR-SD-OCT is a powerful tool that can evaluate the success of subretinal surgery in mice, in addition to measuring vitality of photoreceptors in vivo. HR-SD-OCT can also be used to identify uniform animal cohorts to evaluate the extent of retinal degeneration, toxicity, and therapeutic rescue in preclinical gene therapy research studies.

A Novel, Real-Time, In Vivo Mouse Retinal Imaging System.

PURPOSE: To develop an efficient, low-cost instrument for robust real-time imaging of the mouse retina in vivo, and assess system capabilities by evaluating various animal models. METHODS: Following multiple disappointing attempts to visualize the mouse retina during a subretinal injection using commercially available systems, we identified the key limitation to be inadequate illumination due to off axis illumination and poor optical train optimization. Therefore, we designed a paraxial illumination system for Greenough-type stereo dissecting microscope incorporating an optimized optical launch and an efficiently coupled fiber optic delivery system. Excitation and emission filters control spectral bandwidth. A color coupled-charged device (CCD) camera is coupled to the microscope for image capture. Although, field of view (FOV) is constrained by the small pupil aperture, the high optical power of the mouse eye, and the long working distance (needed for surgical manipulations), these limitations can be compensated by eye positioning in order to observe the entire retina. RESULTS: The retinal imaging system delivers an adjustable narrow beam to the dilated pupil with minimal vignetting. The optic nerve, vasculature, and posterior pole are crisply visualized and the entire retina can be observed through eye positioning. Normal and degenerative retinal phenotypes can be followed over time. Subretinal or intraocular injection procedures are followed in real time. Real-time, intravenous fluorescein angiography for the live mouse has been achieved. CONCLUSIONS: A novel device is established for real-time viewing and image capture of the small animal retina during subretinal injections for preclinical gene therapy studies.

A high-throughput biophotonics instrument to screen for novel ocular photosensitizing therapeutic agents.

PURPOSE: High-throughput techniques are needed to identify and optimize novel photodynamic therapy (PDT) agents with greater efficacy and to lower toxicity. Novel agents with the capacity to completely ablate pathologic angiogenesis could be of substantial utility in diseases such as wet age-related macular degeneration (AMD). METHODS: An instrument and approach was developed based on light-emitting diode (LED) technology for high-throughput screening (HTS) of libraries of potential chemical and biological photosensitizing agents. Ninety-six-well LED arrays were generated at multiple wavelengths and under rigorous intensity control. Cell toxicity was measured in 96-well culture arrays with the nuclear dye SYTOX Green (Invitrogen-Molecular Probes, Eugene, OR). RESULTS: Rapid screening of photoactivatable chemicals or biological molecules has been realized in 96-well arrays of cultured human cells. This instrument can be used to identify new PDT agents that exert cell toxicity on presentation of light of the appropriate energy. The system is further demonstrated through determination of the dose dependence of model compounds having or lacking cellular phototoxicity. Killer Red (KR), a genetically encoded red fluorescent protein expressed from transfected plasmids, is examined as a potential cellular photosensitizing agent and offers unique opportunities as a cell-type-specific phototoxic protein. CONCLUSIONS: This instrument has the capacity to screen large chemical or biological libraries for rapid identification and optimization of potential novel phototoxic lead candidates. KR and its derivatives have unique potential in ocular gene therapy for pathologic angiogenesis or tumors.