Divalent siRNAs are bioavailable in the lung and efficiently block SARS-CoV-2 infection.

The continuous evolution of SARS-CoV-2 variants complicates efforts to combat the ongoing pandemic, underscoring the need for a dynamic platform for the rapid development of pan-viral variant therapeutics. Oligonucleotide therapeutics are enhancing the treatment of numerous diseases with unprecedented potency, duration of effect, and safety. Through the systematic screening of hundreds of oligonucleotide sequences, we identified fully chemically stabilized siRNAs and ASOs that target regions of the SARS-CoV-2 genome conserved in all variants of concern, including delta and omicron. We successively evaluated candidates in cellular reporter assays, followed by viral inhibition in cell culture, with eventual testing of leads for in vivo antiviral activity in the lung. Previous attempts to deliver therapeutic oligonucleotides to the lung have met with only modest success. Here, we report the development of a platform for identifying and generating potent, chemically modified multimeric siRNAs bioavailable in the lung after local intranasal and intratracheal delivery. The optimized divalent siRNAs showed robust antiviral activity in human cells and mouse models of SARS-CoV-2 infection and represent a new paradigm for antiviral therapeutic development for current and future pandemics.

Di-valent siRNA-mediated silencing of MSH3 blocks somatic repeat expansion in mouse models of Huntington's disease.

Huntington's disease (HD) is a severe neurodegenerative disorder caused by the expansion of the CAG trinucleotide repeat tract in the huntingtin gene. Inheritance of expanded CAG repeats is needed for HD manifestation, but further somatic expansion of the repeat tract in non-dividing cells, particularly striatal neurons, hastens disease onset. Called somatic repeat expansion, this process is mediated by the mismatch repair (MMR) pathway. Among MMR components identified as modifiers of HD onset, MutS homolog 3 (MSH3) has emerged as a potentially safe and effective target for therapeutic intervention. Here, we identify a fully chemically modified short interfering RNA (siRNA) that robustly silences Msh3 in vitro and in vivo. When synthesized in a di-valent scaffold, siRNA-mediated silencing of Msh3 effectively blocked CAG-repeat expansion in the striatum of two HD mouse models without affecting tumor-associated microsatellite instability or mRNA expression of other MMR genes. Our findings establish a promising treatment approach for patients with HD and other repeat expansion diseases.

An interdisciplinary framework of youth participatory action research informed by curricula, youth, adults, and researchers.

Rarely are youth voices incorporated into program and policy development. Youth participatory action research (YPAR) is an opportunity for adolescents to develop research skills by completing projects relevant to their lives and allows participation and decision-making at systems and organizational levels. Attention to YPAR implementation detail, especially a curricular focus, is lacking in the literature. Specifically absent is an all-encompassing YPAR framework, a gap the current study addresses. The current study includes a review of existing YPAR curricula to develop the Youth Researcher Empowerment Framework, including research components, social emotional competencies, and assumptions necessary for completing a YPAR project that centers youth voice and shared power. The study includes a quantitative assessment of the YPAR curricula and qualitative reviews by adult practitioners. In addition, focus group data from youth and teacher audiences across multiple settings confirmed and clarified terms and concepts related to the framework. The study provides empirical evidence to support a revised framework for YPAR curricular implementation. Implications are discussed in terms of aspects of the research process needed for YPAR projects, attention to specific youth developmental skills as outcomes, and underlying principles needed to create a welcoming, contextual space allowing for empowerment, youth voice, and choice.

Imaging Net Retrograde Axonal Transport In Vivo: A Physiological Biomarker.

OBJECTIVE: The objective of this study is to develop a novel method for monitoring the integrity of motor neurons in vivo by quantifying net retrograde axonal transport. METHODS: The method uses single photon emission computed tomography to quantify retrograde transport to spinal cord of tetanus toxin fragment C (125 I-TTC) following intramuscular injection. We characterized the transport profiles in 3 transgenic mouse models carrying amyotrophic lateral sclerosis (ALS)-associated genes, aging mice, and SOD1G93A transgenic mice following CRISPR/Cas9 gene editing. Lastly, we studied the effect of prior immunization of tetanus toxoid on the transport profile of TTC. RESULTS: This technique defines a quantitative profile of net retrograde axonal transport of TTC in living mice. The profile is distinctly abnormal in transgenic SOD1G93A mice as young as 65 days (presymptomatic) and worsens with disease progression. Moreover, this method detects a distinct therapeutic benefit of gene editing in transgenic SOD1G93A mice well before other clinical parameters (eg, grip strength) show improvement. Symptomatic transgenic PFN1C71G/C71G ALS mice display gross reductions in net retrograde axonal transport, which is also disturbed in asymptomatic mice harboring a human C9ORF72 transgene with an expanded GGGGCC repeat motif. In wild-type mice, net retrograde axonal transport declines with aging. Lastly, prior immunization with tetanus toxoid does not preclude use of this assay. INTERPRETATION: This assay of net retrograde axonal transport has broad potential clinical applications and should be particularly valuable as a physiological biomarker that permits early detection of benefit from potential therapies for motor neuron diseases. ANN NEUROL 2022;91:716-729.

Application of entropy and signal energy for ultrasound-based classification of three-dimensional printed polyetherketoneketone components.

This paper describes a preliminary method for the classification of annealed and unannealed polyetherketoneketone (PEKK) components manufactured using a material extrusion three-dimensional (3D) printing process. PEKK is representative of a class of high-performance thermoplastics that are increasingly employed as feedstocks for use in 3D printing. PEKK components may be used continuously at elevated temperatures, are chemically resistant, and able to withstand large mechanical loads. These properties render PEKK suitable as a metal component replacement in aerospace applications, high-temperature industrial applications, and surgical implants. The structure of PEKK is semi-crystalline with the specific crystallinity correlating to the final properties during application, making determination of this property crucial. This study compares three different signal processing techniques intended to distinguish annealed (high crystallinity) from unannealed (low crystallinity) components using backscattered ultrasound. The first is energy-based and is unable to detect annealing. The second two are based on different entropies of the backscattered signal: a limiting form of Renyi's entropy and a limiting form of joint entropy. The joint entropy values for the annealed and unannealed specimens fall into two non-overlapping intervals and have a statistical separation of two standard deviations.

Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice.

BACKGROUND & AIMS: It has been a challenge to identify liver tumor suppressors or oncogenes due to the genetic heterogeneity of these tumors. We performed a genome-wide screen to identify suppressors of liver tumor formation in mice, using CRISPR-mediated genome editing. METHODS: We performed a genome-wide CRISPR/Cas9-based knockout screen of P53-null mouse embryonic liver progenitor cells that overexpressed MYC. We infected p53-/-;Myc;Cas9 hepatocytes with the mGeCKOa lentiviral library of 67,000 single-guide RNAs (sgRNAs), targeting 20,611 mouse genes, and transplanted the transduced cells subcutaneously into nude mice. Within 1 month, all the mice that received the sgRNA library developed subcutaneous tumors. We performed high-throughput sequencing of tumor DNA and identified sgRNAs increased at least 8-fold compared to the initial cell pool. To validate the top 10 candidate tumor suppressors from this screen, we collected data from patients with hepatocellular carcinoma (HCC) using the Cancer Genome Atlas and COSMIC databases. We used CRISPR to inactivate candidate tumor suppressor genes in p53-/-;Myc;Cas9 cells and transplanted them subcutaneously into nude mice; tumor formation was monitored and tumors were analyzed by histology and immunohistochemistry. Mice with liver-specific disruption of p53 were given hydrodynamic tail-vein injections of plasmids encoding Myc and sgRNA/Cas9 designed to disrupt candidate tumor suppressors; growth of tumors and metastases was monitored. We compared gene expression profiles of liver cells with vs without tumor suppressor gene disrupted by sgRNA/Cas9. Genes found to be up-regulated after tumor suppressor loss were examined in liver cancer cell lines; their expression was knocked down using small hairpin RNAs, and tumor growth was examined in nude mice. Effects of the MEK inhibitors AZD6244, U0126, and trametinib, or the multi-kinase inhibitor sorafenib, were examined in human and mouse HCC cell lines. RESULTS: We identified 4 candidate liver tumor suppressor genes not previously associated with liver cancer (Nf1, Plxnb1, Flrt2, and B9d1). CRISPR-mediated knockout of Nf1, a negative regulator of RAS, accelerated liver tumor formation in mice. Loss of Nf1 or activation of RAS up-regulated the liver progenitor cell markers HMGA2 and SOX9. RAS pathway inhibitors suppressed the activation of the Hmga2 and Sox9 genes that resulted from loss of Nf1 or oncogenic activation of RAS. Knockdown of HMGA2 delayed formation of xenograft tumors from cells that expressed oncogenic RAS. In human HCCs, low levels of NF1 messenger RNA or high levels of HMGA2 messenger RNA were associated with shorter patient survival time. Liver cancer cells with inactivation of Plxnb1, Flrt2, and B9d1 formed more tumors in mice and had increased levels of mitogen-activated protein kinase phosphorylation. CONCLUSIONS: Using a CRISPR-based strategy, we identified Nf1, Plxnb1, Flrt2, and B9d1 as suppressors of liver tumor formation. We validated the observation that RAS signaling, via mitogen-activated protein kinase, contributes to formation of liver tumors in mice. We associated decreased levels of NF1 and increased levels of its downstream protein HMGA2 with survival times of patients with HCC. Strategies to inhibit or reduce HMGA2 might be developed to treat patients with liver cancer.

Direct Functionalization of an Acid-Terminated Nanodiamond with Azide: Enabling Access to 4-Substituted-1,2,3-Triazole-Functionalized Particles.

Azides on the periphery of nanodiamond materials (ND) are of great utility because they have been shown to undergo Cu-catalyzed and Cu-free cycloaddition reactions with structurally diverse alkynes, affording particles tailored for applications in biology and materials science. However, current methods employed to access ND featuring azide groups typically require either harsh pretreatment procedures or multiple synthesis steps and use surface linking groups that may be susceptible to undesirable cleavage. Here we demonstrate an alternative single-step approach to producing linker-free, azide-functionalized ND. Our method was applied to low-cost, detonation-derived ND powders where surface carbonyl groups undergo silver-mediated decarboxylation and radical substitution with azide. ND with directly grafted azide groups were then treated with a variety of aliphatic, aromatic, and fluorescent alkynes to afford 1-(ND)-4-substituted-1,2,3-triazole materials under standard copper-catalyzed cycloaddition conditions. Surface modification steps were verified by characteristic infrared absorptions and elemental analyses. High loadings of triazole surface groups (up to 0.85 mmol g-1) were obtained as determined from thermogravimetric analysis. The azidation procedure disclosed is envisioned to become a valuable initial transformation in numerous future applications of ND.

Single-Step Synthesis of Small, Azide-Functionalized Gold Nanoparticles: Versatile, Water-Dispersible Reagents for Click Chemistry.

Nanoparticles possessing functional groups that can be readily conjugated (e.g., through click chemistry) are important precursors for the preparation of customized nanohybrid products. Such nanoparticles, if they are stable against agglomeration, are easily dispersible and have well-defined surface chemistry and size. As click-ready reagents, they can be stored until their time of use and then simply dispersed and reacted with an appropriate substrate. Gold nanoparticles (AuNPs) are excellent candidates for this purpose, and some clickable gold nanoparticles have been developed; however, AuNPs for use in aqueous systems are often prepared through difficult multistep processes and/or can be poorly dispersible in water. Here we report a single-step synthesis of clickable, water-dispersible AuNPs. The synthesis yields uniform, 3.5 nm diameter cores coated with a well-defined molecular ligand shell that makes the AuNPs stable and dispersible in water. The AuNP mixed ligand shell consists of hydroxyl-terminated ethylene glycol-based ligands to promote dispersion in water and a small number of azide-terminated ligands that readily undergo click reactions with alkynes. The use of a mesofluidic reactor affords fine control over the core size and ligand shell composition and ensures reproducible results (e.g., less than 0.1 nm variation in core diameter between batches). The purified reagents were successfully coupled to a variety of alkyne-containing substrates using both Cu-catalyzed and strain-promoted click reactions. Particle size, morphology, stability, and surface composition were thoroughly characterized using small-angle X-ray scattering, transmission electron microscopy, X-ray photoelectron spectroscopy, UV-vis, and 1H NMR before and after the click reactions. Both the parent nanoparticles and their click chemistry products are stable during storage and remained dispersible for over a year in water, suggesting their potential for environmental, biological, and biomedical applications.

Influence of Ligand Shell Composition upon Interparticle Interactions in Multifunctional Nanoparticles.

The interactions of nanoparticles with biomolecules, surfaces, or other nanostructures are dictated by the nanoparticle's surface chemistry. Thus, far, shortcomings of syntheses of nanoparticles with defined ligand shell architectures have limited our ability to understand how changes in their surface composition influence reactivity and assembly. We report new synthetic approaches to systematically control the number (polyvalency), length, and steric interactions of omega-functionalized (targeting) ligands within an otherwise passivating (diluent) ligand shell. A mesofluidic reactor was used to prepare nanoparticles with the same core diameter for each of the designed ligand architectures. When the targeting ligands are malonamide groups, the nanoparticles assemble via cross-linking in the presence of trivalent lanthanides. We examined the influence of ligand composition on assembly by monitoring the differences in optical properties of the cross-linked and free nanoparticles. Infrared spectroscopy, electron microscopy, and solution small-angle X-ray scattering provided additional insight into the assembly behavior. Lower (less than 33%) malonamide ligand densities (where the binding group extends beyond the periphery of diluent ethylene glycol ligands) produce the strongest optical responses and largest assemblies. Surprisingly, nanoparticles containing a higher surface number of targeting ligand did not produce an optical response or assemble, underscoring the importance of an informed mixed ligand strategy for highest nanoparticle performance.

Improved gene therapy for spinal muscular atrophy in mice using codon-optimized hSMN1 transgene and hSMN1 gene-derived promotor.

Physiological regulation of transgene expression is a major challenge in gene therapy. Onasemnogene abeparvovec (Zolgensma®) is an approved adeno-associated virus (AAV) vector gene therapy for infants with spinal muscular atrophy (SMA), however, adverse events have been observed in both animals and patients following treatment. The construct contains a native human survival motor neuron 1 (hSMN1) transgene driven by a strong, cytomegalovirus enhancer/chicken ß-actin (CMVen/CB) promoter providing high, ubiquitous tissue expression of SMN. We developed a second-generation AAV9 gene therapy expressing a codon-optimized hSMN1 transgene driven by a promoter derived from the native hSMN1 gene. This vector restored SMN expression close to physiological levels in the central nervous system and major systemic organs of a severe SMA mouse model. In a head-to-head comparison between the second-generation vector and a benchmark vector, identical in design to onasemnogene abeparvovec, the 2nd-generation vector showed better safety and improved efficacy in SMA mouse model.

Identification of selective and non-selective C9ORF72 targeting in vivo active siRNAs.

A hexanucleotide (G4C2) repeat expansion (HRE) within intron one of C9ORF72 is the leading genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). C9ORF72 haploinsufficiency, formation of RNA foci, and production of dipeptide repeat (DPR) proteins have been proposed as mechanisms of disease. Here, we report the first example of disease-modifying siRNAs for C9ORF72 driven ALS/FTD. Using a combination of reporter assay and primary cortical neurons derived from a C9-ALS/FTD mouse model, we screened a panel of more than 150 fully chemically stabilized siRNAs targeting different C9ORF72 transcriptional variants. We demonstrate the lack of correlation between siRNA efficacy in reporter assay versus native environment; repeat-containing C9ORF72 mRNA variants are found to preferentially localize to the nucleus, and thus C9ORF72 mRNA accessibility and intracellular localization have a dominant impact on functional RNAi. Using a C9-ALS/FTD mouse model, we demonstrate that divalent siRNAs targeting C9ORF72 mRNA variants specifically or non-selectively reduce the expression of C9ORF72 mRNA and significantly reduce DPR proteins. Interestingly, siRNA silencing all C9ORF72 mRNA transcripts was more effective in removing intranuclear mRNA aggregates than targeting only HRE-containing C9ORF72 mRNA transcripts. Combined, these data support RNAi-based degradation of C9ORF72 as a potential therapeutic paradigm.

Intrathecal Delivery of Therapeutic Oligonucleotides for Potent Modulation of Gene Expression in the Central Nervous System.

Therapeutic oligonucleotides hold tremendous potential for treating central nervous system (CNS) disorders. The route of administration of oligonucleotides significantly impacts both distribution and silencing efficiency. Here, we describe a technically simple, clinically relevant method to administer oligonucleotide compounds into the CNS via direct intrathecal injections. This method achieves distribution throughout the CNS rapidly and permits high-throughput testing of oligonucleotide efficacy and potency in mammals.

The Promise of Emergent Nanobiotechnologies for In Vivo Applications and Implications for Safety and Security.

Nanotechnology, the multidisciplinary field based on the exploitation of the unique physicochemical properties of nanoparticles (NPs) and nanoscale materials, has opened a new realm of possibilities for biological research and biomedical applications. The development and deployment of mRNA-NP vaccines for COVID-19, for example, may revolutionize vaccines and therapeutics. However, regulatory and ethical frameworks that protect the health and safety of the global community and environment are lagging, particularly for nanotechnology geared toward biological applications (ie, bionanotechnology). In this article, while not comprehensive, we attempt to illustrate the breadth and promise of bionanotechnology developments, and how they may present future safety and security challenges. Specifically, we address current advancements to streamline the development of engineered NPs for in vivo applications and provide discussion on nano-bio interactions, NP in vivo delivery, nanoenhancement of human performance, nanomedicine, and the impacts of NPs on human health and the environment.

PK-modifying anchors significantly alter clearance kinetics, tissue distribution, and efficacy of therapeutics siRNAs.

Effective systemic delivery of small interfering RNAs (siRNAs) to tissues other than liver remains a challenge. siRNAs are small (∼15 kDa) and therefore rapidly cleared by the kidneys, resulting in limited blood residence times and tissue exposure. Current strategies to improve the unfavorable pharmacokinetic (PK) properties of siRNAs rely on enhancing binding to serum proteins through extensive phosphorothioate modifications or by conjugation of targeting ligands. Here, we describe an alternative strategy for enhancing blood and tissue PK based on dynamic modulation of the overall size of the siRNA. We engineered a high-affinity universal oligonucleotide anchor conjugated to a high-molecular-weight moiety, which binds to the 3' end of the guide strand of an asymmetric siRNA. Data showed a strong correlation between the size of the PK-modifying anchor and clearance kinetics. Large 40-kDa PK-modifying anchors reduced renal clearance by ∼23-fold and improved tissue exposure area under the curve (AUC) by ∼26-fold, resulting in increased extrahepatic tissue retention (∼3- to 5-fold). Furthermore, PK-modifying oligonucleotide anchors allowed for straightforward and versatile modulation of blood residence times and biodistribution of a panel of chemically distinct ligands. The effects were more pronounced for conjugates with low lipophilicity (e.g., N-Acetylgalactosamine [GalNAc]), where significant improvement in uptake by hepatocytes and dose-dependent silencing in the liver was observed.

Pearlescent Mica-Doped Alginate as a Stable, Vibrant Medium for Two-Dimensional and Three-Dimensional Art.

Emergent technologies are driving forces in the development of innovative art media that progress the field of modern art. Recently, artists have capitalized on the versatility of a new technology to create, restore, and modify art: additive manufacturing or three-dimensional (3D) printing. Additively manufactured art relies heavily on plastic-based materials, which typically require high heat to induce melting for workability. The necessity for heat limits plastic media to dedicated 3D printers. In contrast, biologically derived polymers such as polysaccharides used to create "bioinks" often do not require heating the material for workability, broadening the types of techniques available for printing. Here, we detail the formulation of a bioink consisting of mica pigments suspended in alginate as a new, vibrant art medium for 2D and 3D compositions. The properties that make alginate an ideal colorant binder are detailed: low cost with wide availability, nontoxicity and biocompatibility, minimal color, and an array of attractive physicochemical properties that offer workability and processing into 2D and 3D structures. Further, the chemical composition, morphology, and dispersibility of an array of mica pigment additives are characterized in detail as they pertain to the quality of an art medium. Alginate-based media with eight mica colors were formulated, where mica addition resulted in vibrantly colored inks with moderate hiding power and coverage of substrates necessary for 2D printing with thin horizontal and vertical lines. The utility of the media is demonstrated via the generation of 2D and 3D vibrant structures.

CRISPR-SONIC: targeted somatic oncogene knock-in enables rapid in vivo cancer modeling.

CRISPR/Cas9 has revolutionized cancer mouse models. Although loss-of-function genetics by CRISPR/Cas9 is well-established, generating gain-of-function alleles in somatic cancer models is still challenging because of the low efficiency of gene knock-in. Here we developed CRISPR-based Somatic Oncogene kNock-In for Cancer Modeling (CRISPR-SONIC), a method for rapid in vivo cancer modeling using homology-independent repair to integrate oncogenes at a targeted genomic locus. Using a dual guide RNA strategy, we integrated a plasmid donor in the 3'-UTR of mouse ß-actin, allowing co-expression of reporter genes or oncogenes from the ß-actin promoter. We showed that knock-in of oncogenic Ras and loss of p53 efficiently induced intrahepatic cholangiocarcinoma in mice. Further, our strategy can generate bioluminescent liver cancer to facilitate tumor imaging. This method simplifies in vivo gain-of-function genetics by facilitating targeted integration of oncogenes.

Systematic determination of the relationship between nanoparticle core diameter and toxicity for a series of structurally analogous gold nanoparticles in zebrafish.

Predictive models for the impact of nanomaterials on biological systems remain elusive. Although there is agreement that physicochemical properties (particle diameter, shape, surface chemistry, and core material) influence toxicity, there are limited and often contradictory, data relating structure to toxicity, even for core diameter. Given the importance of size in determining nanoscale properties, we aimed to address this data gap by examining the biological effects of a defined series of gold nanoparticles (AuNPs) on zebrafish embryos. Five AuNPs samples with narrowly spaced core diameters (0.8-5.8 nm) were synthesized and functionalized with positively charged N,N,N-trimethylammonium ethanethiol (TMAT) ligands. We assessed the bioactivity of these NPs in a high-throughput developmental zebrafish assay at eight concentrations (0.5-50 µg/mL) and observed core diameter-dependent bioactivity. The smaller diameter AuNPs were the most toxic when expressing exposures based on an equal mass. However, when expressing exposures based on total surface area, toxicity was independent of the core diameter. When holding the number of nanoparticles per volume constant (at 6.71 × 1013/mL) in the exposure medium across AuNPs diameters, only the 5.8 nm AuNPs exhibited toxic effects. Under these exposure conditions, the uptake of AuNPs in zebrafish was only weakly associated with core diameter, suggesting that differential uptake of TMAT-AuNPs was not responsible for toxicity associated with the 5.8 nm core diameter. Our results indicate that larger NPs may be the most toxic on a per particle basis and highlight the importance of using particle number and surface area, in addition to mass, when evaluating the size-dependent bioactivity of NPs.

Polysaccharide-based liquid storage and transport media for non-refrigerated preservation of bacterial pathogens.

The preservation of biological samples for an extended time period of days to weeks after initial collection is important for the identification, screening, and characterization of bacterial pathogens. Traditionally, preservation relies on cold-chain infrastructure; however, in many situations this is impractical or not possible. Thus, our goal was to develop alternative bacterial sample preservation and transport media that are effective without refrigeration or external instrumentation. The viability, nucleic acid stability, and protein stability of Bacillus anthracis Sterne 34F2, Francisella novicida U112, Staphylococcus aureus ATCC 43300, and Yersinia pestis KIM D27 (pgm-) was assessed for up to 28 days. Xanthan gum (XG) prepared in PBS with L-cysteine maintained more viable F. novicida U112 cells at elevated temperature (40°C) compared to commercial reagents and buffers. Viability was maintained for all four bacteria in XG with 0.9 mM L-cysteine across a temperature range of 22-40°C. Interestingly, increasing the concentration to 9 mM L-cysteine resulted in the rapid death of S. aureus. This could be advantageous when collecting samples in the built environment where there is the potential for Staphylococcus collection and stabilization rather than other organisms of interest. F. novicida and S. aureus DNA were stable for up to 45 days upon storage at 22°C or 40°C, and direct analysis by real-time qPCR, without DNA extraction, was possible in the XG formulations. XG was not compatible with proteomic analysis via LC-MS/MS due to the high amount of residual Xanthomonas campestris proteins present in XG. Our results demonstrate that polysaccharide-based formulations, specifically XG with L-cysteine, maintain bacterial viability and nucleic acid integrity for an array of both Gram-negative and Gram-positive bacteria across ambient and elevated temperatures.