Programmable DNA Nanodevices for Applications in Neuroscience

Endocytic pathways of pathogenic protein aggregates in neurodegenerative diseases

Endocytosis is the fundamental uptake process through which cells internalize extracellular materials and species. Neurodegenerative diseases (NDs) are characterized by a progressive accumulation of intrinsically disordered protein species, leading to neuronal death. Misfolding in many proteins leads to various NDs such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS) and other disorders. Despite the significance of disordered protein species in neurodegeneration, their spread between cells and the cellular uptake of extracellular species is not entirely understood. This review discusses the major internalization mechanisms of the different conformer species of these proteins and their endocytic mechanisms. We briefly introduce the broad types of endocytic mechanisms found in cells and then summarize what is known about the endocytosis of monomeric, oligomeric and aggregated conformations of tau, Aβ, α-Syn, Huntingtin, Prions, SOD1, TDP-43 and other proteins associated with neurodegeneration. We also highlight the key players involved in internalizing these disordered proteins and the several techniques and approaches to identify their endocytic mechanisms. Finally, we discuss the obstacles involved in studying the endocytosis of these protein species and the need to develop better techniques to elucidate the uptake mechanisms of a particular disordered protein species.

Structural, kinetic, and thermodynamic aspects of insulin aggregation

Given the significance of protein aggregation in proteinopathies and the development of therapeutic protein pharmaceuticals, revamped interest in assessing and modelling the aggregation kinetics has been observed. Quantitative analysis of aggregation includes data of gradual monomeric depletion followed by the formation of subvisible particles. Kinetic and thermodynamic studies are essential to gain key insights into the aggregation process. Despite being the medical marvel in the world of diabetes, insulin suffers from the challenge of aggregation. Physicochemical stresses are experienced by insulin during industrial formulation, storage, delivery, and transport, considerably impacting product quality, efficacy, and effectiveness. The present review briefly describes the pathways, mathematical kinetic models, and thermodynamics of protein misfolding and aggregation. With a specific focus on insulin, further discussions include the structural heterogeneity and modifications of the intermediates incurred during insulin fibrillation. Finally, different model equations to fit the kinetic data of insulin fibrillation are discussed. We believe that this review will shed light on the conditions that induce structural changes in insulin during the lag phase of fibrillation and will motivate scientists to devise strategies to block the initialization of the aggregation cascade. Subsequent abrogation of insulin fibrillation during bioprocessing will ensure stable and globally accessible insulin for efficient management of diabetes.

Red emitting fluorescent carbon nanoparticles to track spatio-temporal dynamics of endocytic pathways in model neuroblastoma neurons

One of the biggest challenges limiting the biological applications of fluorescent carbon-based nanoparticles is their capacity to emit in the red region of the spectrum and simultaneously maintaining the smaller size. These two parameters always go in inverse proportion, thus lagging their applications in biological imaging. Endocytic pathways play important roles in regulating major cellular functions such as cellular differentiation. The Spatio-temporal dynamics of endocytic pathways adopted by various ligands (including nanoparticles) over longer durations in cellular differentiation remain unstudied. Here we have used red-emitting fluorescent carbon nanoparticles to study the endocytic pathways in neuronal cells at different stages of differentiation. These small-sized, bright, red-emitting carbon nanoparticles (CNPs) can be internalized by live cells and imaged for extended periods, thus capturing the Spatio-temporal dynamics of endocytic pathways in model SH-SY5Y derived neuroblastoma neurons. We find that these nanoparticles are preferably taken up via clathrin-mediated endocytosis and follow the classical recycling pathways at all the stages of neuronal differentiation. These nanoparticles hold immense potential for their size, composition, surface and fluorescence tunability, thus maximizing their applications in spatio-temporally tracking multiple cellular pathways in cells and tissues simultaneously.

Bi-Directional Relationship Between Autophagy and Inflammasomes in Neurodegenerative Disorders

The innate immune system, as the first line of cellular defense, triggers a protective response called inflammation when encountered with invading pathogens. Inflammasome is a multi-protein cytosolic signaling complex that induces inflammation and is critical for inflammation-induced pyroptotic cell death. Inflammasome activation has been found associated with neurodegenerative disorders (NDs), inflammatory diseases, and cancer. Autophagy is a crucial intracellular quality control and homeostasis process which removes the dysfunctional organelles, damaged proteins, and pathogens by sequestering the cytosolic components in a double-membrane vesicle, which eventually fuses with lysosome resulting in cargo degradation. Autophagy disruption has been observed in many NDs presented with persistent neuroinflammation and excessive inflammasome activation. An interplay between inflammation activation and the autophagy process has been realized over the last decade. In the case of NDs, autophagy regulates neuroinflammation load and cellular damage either by engulfing the misfolded protein deposits, dysfunctional mitochondria, or the inflammasome complex itself. A healthy two-way regulation between both cellular processes has been realized for cell survival and cell defense during inflammatory conditions. Therefore, clinical interest in the modulation of inflammasome activation by autophagy inducers is rapidly growing. In this review, we discuss the structural basis of inflammasome activation and the mechanistic ideas of the autophagy process in NDs. Along with comments on multiple ways of neuroinflammation regulation by microglial autophagy, we also present a perspective on pharmacological opportunities in this molecular interplay pertaining to NDs.

Peptide functionalized DNA hydrogel enhances neuroblastoma cell growth and differentiation

Designing programmable biomaterials that could act as extracellular matrices and permit functionalization is a current need for tissue engineering advancement. DNA based hydrogels are gaining significant attention owing to their self-assembling properties, biocompatibility, chemical robustness and low batch to batch variability. The real potential of DNA hydrogels in the biomedical domain remains to be explored. In this work, a DNA hydrogel was coated on a glass surface and coupled to a synthetic IKVAV peptide by a chemical crosslinker. We observe enhanced neuronal differentiation, prolonged neurite length, dynamic movement of microtubules and cytoskeleton, and altered endocytic mechanisms in neuroblastoma-based stem cells for the peptide modified DNA hydrogel compared to the unmodified DNA hydrogel and controls. We anticipate that a peptide-modified DNA hydrogel could emerge as a promising scaffold coating material to develop nerve tissue conduits in the future for application in neuroscience and neuroregeneration.

Biology-guided engineering of bioelectrical interfaces

Bioelectrical interfaces that bridge biotic and abiotic systems have heightened the ability to monitor, understand, and manipulate biological systems and are catalyzing profound progress in neuroscience research, treatments for heart failure, and microbial energy systems. With advances in nanotechnology, bifunctional and high-density devices with tailored structural designs are being developed to enable multiplexed recording or stimulation across multiple spatial and temporal scales with resolution down to millisecond-nanometer interfaces, enabling efficient and effective communication with intracellular electrical activities in a relatively noninvasive and biocompatible manner. This review provides an overview of how biological systems guide the design, engineering, and implementation of bioelectrical interfaces for biomedical applications. We investigate recent advances in bioelectrical interfaces for applications in nervous, cardiac, and microbial systems, and we also discuss the outlook of state-of-the-art biology-guided bioelectrical interfaces with high biocompatibility, extended long-term stability, and integrated system functionality for potential clinical usage.

Spatiotemporal Dynamics of Endocytic Pathways Adapted by Small DNA Nanocages in Model Neuroblastoma Cell-Derived Differentiated Neurons

Multiple endocytic pathways operate on the plasma membrane of cells at any moment with diverse but specific cellular functions. Knowledge of uptake of synthetic nanoparticles and ligands with respect to endocytic pathways is crucial to device the appropriate ligands for therapeutic delivery into differentiated neurons for targeting neuronal diseases. We herein explore the mechanisms of cellular uptake of 3D tetrahedral DNA nanocages at different stages of differentiating neurons. We monitored the uptake, kinetics, and dynamics of DNA cages of different geometries, and interestingly we find a specific pattern and adaptability of the uptake of DNA devices with respect to the geometry of the ligand and specific endocytic pathways. We find that tetrahedral DNA nanocages get endocytosed mostly via clathrin-mediated endocytosis in fully mature neurons. This endocytic uptake and intracellular choreography of DNA nanodevices will help us design the smartly targeted biotherapeutics for targeting neuronal disorders.