Engineered PAM-flexible FnCas9 variants for robust and specific genome editing and diagnostics

The clinical success of CRISPR therapies is dependent on the safety and efficacy ofCas proteins. The Cas9 from Francisella novicida (FnCas9) has negligible affinity formismatched substrates enabling it to discriminate off-targets in DNA with very highprecision even at the level of binding. However, its cellular targeting efficiency is low,limiting its use in therapeutic applications. Here, we rationally engineer the protein todevelop engineered(enFnCas9) variants with enhanced activity and expand its cellularediting activity to genomic loci previously inaccessible. Notably, some of the variantsrelease the protospacer adjacent motif (PAM) constraint from NGG to NGR/NRGmaking them rank just below SpCas9-RY and SpCas9-NG in their accessibility acrosshuman genomic sites. The enFnCas9 proteins, similar to Cas12a and Cas12f, harborhigh intrinsic specificity and can diagnose single nucleotide variants accurately.Importantly, they provide superior outcomes in terms of editing efficiency, knock-inrates, and off-target specificity over other engineered high-fidelity versions of SpCas9(SpCas9-HF1 and eSpCas9). Broad targeting range coupled with remarkablespecificity of DNA interrogation underscores the utility of these variants for safe andefficient therapeutic gene correction across multiple cell lines and target loci.

Biophysical Considerations in the Rational Design and Cellular Targeting of Flexible Polymeric Nanoparticles

Physicochemical characteristics of nanoparticles (NPs) can be engineered for tuning their biological function in cellular delivery. How NP mechanical properties impact multivalent ligand-receptor mediated binding to cell surfaces, the avidity of NP adhesion to cells, propensity for internalization, and effects due to crowding remain unknown or unquantified. We report computational analyses of binding mechanisms of three distinct NPs that differ in type and rigidity (core-corona flexible NP, rigid NP, and rigid-tethered NP) but are otherwise similar in size and ligand surface density; moreover, for the case of flexible NP, we tune NP stiffness by varying the internal crosslinking density. We employ biophysical modeling of NP binding to membranes together with thermodynamic analysis powered by free energy calculations and show that efficient cellular targeting and uptake of NP functionalized with targeting ligand molecules can be shaped by factors including NP flexibility and crowding, receptor-ligand binding avidity, state of the membrane cytoskeleton, and curvature inducing proteins. Owing to this multitude of factors, we demonstrate that the binding avidity of a flexible NP depends on engineered changes in NP flexibility governed by significant enthalpy entropy compensations arising from multiple competing terms associated with NP, receptor density, and membrane. Analyses of the individual enthalpic and entropic contributions associated with NP, membrane, and receptor-ligand binding and receptor diffusion collectively illuminate this complex dependence of avidity on crosslinking. These findings provide strong evidence that NP flexibility is an important design parameter for rationally engineering NP targeting and uptake in a crowded cellular adhesion microenvironment.

Biophysical Considerations in the Rational Design and Cellular Targeting of Flexible Polymeric Nanoparticles

It is becoming evident that engineered physicochemical characteristics of nanoparticles (NPs) are essential to improve their biological function for their cellular delivery and uptake. How NP mechanical properties impact multivalent ligand-receptor mediated binding to cell surfaces, the avidity of NP adhesion to cells, and cooperative effects due to crowding remain largely unknown or unquantified, and how tuning NPs' stiffness impacts their propensity for internalization is not clear. Here we focus on exploring the binding mechanisms of three distinct NPs that differ in type and rigidity (core-corona flexible NP, rigid NP, and rigid-tethered NP) but are otherwise similar in size and ligand surface density; moreover, for the case of flexible NP, we tune NP stiffness by varying the internal crosslinking density. We employed our recent spatial biophysical modeling of NP binding to membranes together with thermodynamic analysis powered by free energy calculations and show that efficient cellular targeting and uptake of NP functionalized with targeting ligand molecules can be shaped by factors including NP flexibility and crowding, receptor-ligand binding avidity, state of the membrane cytoskeleton, and curvature inducing proteins. Owing to this multitude of factors, we demonstrate that the binding avidity of a flexible NP depends on engineered changes in NP flexibility in a non-intuitive fashion because of significant enthalpy entropy compensations arising from multiple competing terms associated with NP, receptor density, and membrane. Analyses of the individual enthalpic and entropic contributions associated with NP, membrane, and receptor-ligand binding and receptor diffusion collectively illuminate this complex dependence of avidity on crosslinking. We find that the NP binding avidity can be engineered in a crowded environment by tuning their flexibility. We also find that when the cell membrane is bound to the cytoskeletal proteins via the pinning sites, the pinning sites' presence does not limit the binding avidity of both flexible and rigid-tethered NPs. Furthermore, we show that the membrane tension and pinning density, and the stiffness of flexible NPs can be tuned to alter the adhesion energy landscape and eventually improve the adhesion efficiency of flexible NPs. We also probed the effects of curvature-inducing proteins and receptor-ligand binding interactions on NP uptake. We found that complete uptake of both rigid-tethered NPs, and flexible NPs can be achieved by tuning NP stiffness and membrane tension even under moderate levels of ligand-densities in use for physiologically relevant applications. These findings provide strong evidence that NP flexibility is an important design parameter for rationally engineering NP targeting and uptake in a crowded cellular adhesion microenvironment.

Cellular Targeting of Oligonucleotides by Conjugation with Small Molecules

Drug candidates derived from oligonucleotides (ON) are receiving increased attention that is supported by the clinical approval of several ON drugs. Such therapeutic ON are designed to alter the expression levels of specific disease-related proteins, e.g., by displaying antigene, antisense, and RNA interference mechanisms. However, the high polarity of the polyanionic ON and their relatively rapid nuclease-mediated cleavage represent two major pharmacokinetic hurdles for their application in vivo. This has led to a range of non-natural modifications of ON structures that are routinely applied in the design of therapeutic ON. The polyanionic architecture of ON often hampers their penetration of target cells or tissues, and ON usually show no inherent specificity for certain cell types. These limitations can be overcome by conjugation of ON with molecular entities mediating cellular ‘targeting’, i.e., enhanced accumulation at and/or penetration of a specific cell type. In this context, the use of small molecules as targeting units appears particularly attractive and promising. This review provides an overview of advances in the emerging field of cellular targeting of ON via their conjugation with small-molecule targeting structures.

Retinal ganglion cell interactions shape the developing mammalian visual system

ABSTRACTRetinal ganglion cells (RGCs) serve as a crucial communication channel from the retina to the brain. In the adult, these cells receive input from defined sets of presynaptic partners and communicate with postsynaptic brain regions to convey features of the visual scene. However, in the developing visual system, RGC interactions extend beyond their synaptic partners such that they guide development before the onset of vision. In this Review, we summarize our current understanding of how interactions between RGCs and their environment influence cellular targeting, migration and circuit maturation during visual system development. We describe the roles of RGC subclasses in shaping unique developmental responses within the retina and at central targets. Finally, we highlight the utility of RNA sequencing and genetic tools in uncovering RGC type-specific roles during the development of the visual system.

Luminescent silicon nanoparticles for distinctive tracking of cellular targeting and trafficking

We demonstrate tracking of silicon nanoparticles through intrinsic photoluminescence during the course of cellular targeting and uptake.