Search for: All records

Objective: We developed 3-dimensional spatially resolved gene neighborhood network embedding (3D-spaGNN-E) to find subcellular gene proximity relationships and identify key subcellular motifs in cell–cell communication (CCC). Impact Statement: The pipeline combines 3D imaging-based spatial transcriptomics and graph-based deep learning to identify subcellular motifs. Introduction: Advancements in imaging and experimental technology allow the study of 3D spatially resolved transcriptomics and capture better spatial context than approximating the samples as 2D. However, the third spatial dimension increases the data complexity and requires new analyses. Methods: 3D-spaGNN-E detects single transcripts in 3D cell culture samples and identifies subcellular gene proximity relationships. Then, a graph autoencoder projects the gene proximity relationships into a latent space. We then applied explainability analysis to identify subcellular CCC motifs. Results: We first applied the pipeline to mesenchymal stem cells (MSCs) cultured in hydrogel. After clustering the cells based on the RNA count, we identified cells belonging to the same cluster as homotypic and those belonging to different clusters as heterotypic. We identified changes in local gene proximity near the border between homotypic and heterotypic cells. When applying the pipeline to the MSC–peripheral blood mononuclear cell (PBMC) coculture system, we identified CD4+ and CD8+ T cells. Local gene proximity and autoencoder embedding changes can distinguish strong and weak suppression of different immune cells. Lastly, we compared astrocyte–neuron CCC in mouse hypothalamus and cortex by analyzing 3D multiplexed-error-robust fluorescence insitu hybridization (MERFISH) data and identified regional gene proximity differences. Conclusion: 3D-spaGNN-E distinguished distinct CCCs in cell culture and tissue by examining subcellular motifs 

Abstract Emergent trends in the device development for neural prosthetics have focused on establishing stimulus localization, improving longevity through immune compatibility, reducing energy re-quirements, and embedding active control in the devices. Ultrasound stimulation can single-handedly address several of these challenges. Ultrasonic stimulus of neurons has been studied extensively from 100 kHz to 10 MHz, with high penetration but less localization. In this paper, a chip-scale device consisting of piezoelectric Aluminum Nitride ultrasonic transducers was engineered to deliver gigahertz (GHz) ultrasonic stimulus to the human neural cells. These devices provide a path towards complementary metal oxide semiconductor (CMOS) integration towards fully controllable neural devices. At GHz frequencies, ultrasonic wavelengths in water are a few microns and have an absorption depth of 10–20 µm. This confinement of energy can be used to control stimulation volume within a single neuron. This paper is the first proof-of-concept study to demonstrate that GHz ultrasound can stimulate neuronsin vitro. By utilizing optical calcium imaging, which records calcium ion flux indicating occurrence of an action potential, this paper demonstrates that an application of a nontoxic dosage of GHz ultrasonic waves$$(\ge 0.05\frac{W}{c{m}^{2}})$$ $\left(\ge 0.05\frac{W}{c{m}^2}\right)$caused an average normalized fluorescence intensity recordings >1.40 for the calcium transients. Electrical effects due to chip-scale ultrasound delivery was discounted as the sole mechanism in stimulation, with effects tested atα = 0.01 statistical significance amongst all intensities and con-trol groups. Ionic transients recorded optically were confirmed to be mediated by ion channels and experimental data suggests an insignificant thermal contributions to stimulation, with a predicted increase of 0.03^oCfor$$1.2\frac{W}{c{m}^{2}}\cdot $$ $1.2\frac{W}{c{m}^2}\cdot$This paper paves the experimental framework to further explore chip-scale axon and neuron specific neural stimulation, with future applications in neural prosthetics, chip scale neural engineering, and extensions to different tissue and cell types. 

Abstract Osteoarthritis (OA) of the knee joint is a degenerative disease initiated by mechanical stress that affects millions of individuals. The disease manifests as joint damage and synovial inflammation. Post-traumatic osteoarthritis (PTOA) is a specific form of OA caused by mechanical trauma to the joint. The progression of PTOA is prevented by immediate post-injury therapeutic intervention. Intra-articular injection of anti-inflammatory therapeutics (e.g. corticosteroids) is a common treatment option for OA before end-stage surgical intervention. However, the efficacy of intra-articular injection is limited due to poor drug retention time in the joint space and the variable efficacy of corticosteroids. Here, we endeavored to characterize a four-arm maleimide-functionalized polyethylene glycol (PEG-4MAL) hydrogel system as a ‘mechanical pillow’ to cushion the load-bearing joint, withstand repetitive loading and improve the efficacy of intra-articular injections of nanoparticles containing dexamethasone, an anti-inflammatory agent. PEG-4MAL hydrogels maintained their mechanical properties after physiologically relevant cyclic compression and released therapeutic payload in an on-demand manner under in vitro inflammatory conditions. Importantly, the on-demand hydrogels did not release nanoparticles under repetitive mechanical loading as experienced by daily walking. Although dexamethasone had minimal protective effects on OA-like pathology in our studies, the PEG-4MAL hydrogel functioned as a mechanical pillow to protect the knee joint from cartilage degradation and inhibit osteophyte formation in an in vivo load-induced OA mouse model. 

Abstract Nanoparticle shape has emerged as a key regulator of nanoparticle transport across physiological barriers, intracellular uptake, and biodistribution. We report a facile approach to synthesize ellipsoidal nanoparticles through self‐assembly of poly(glycerol sebacate)‐co‐poly(ethylene glycol) (PGS‐co‐PEG). The PGS‐PEG nanoparticle system is highly tunable, and the semiaxis length of the nanoparticles can be modulated by changing PGS‐PEG molar ratio and incorporating therapeutics. As both PGS and PEG are highly biocompatible, the PGS‐co‐PEG nanoparticles show high hemo‐, immuno‐, and cytocompatibility. Our data suggest that PGS‐co‐PEG nanoparticles have the potential for use in a wide range of biomedical applications including regenerative medicine, stem cell engineering, immune modulation, and cancer therapeutics. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 2048–2058, 2018.