Spatial Transcriptomics as a Novel Approach to Redefine Electrical Stimulation Safety

Abstract

Current standards for safe delivery of electrical stimulation to the central nervous system are based on foundational studies which examined post-mortem tissue for histological signs of damage. This set of observations and the subsequently proposed limits to safe stimulation, termed the “Shannon limits,” allow for a simple calculation (using charge per phase and charge density) to determine the intensity of electrical stimulation that can be delivered safely to brain tissue. In the three decades since the Shannon limits were reported, advances in molecular biology have allowed for more nuanced and detailed approaches to be used to expand current understanding of the physiological effects of stimulation. Here, we demonstrate the use of spatial transcriptomics (ST) in an exploratory investigation to assess the biological response to electrical stimulation in the brain. Electrical stimulation was delivered to the rat visual cortex with either acute or chronic electrode implantation procedures. To explore the influence of device type and stimulation parameters, we used carbon fiber ultramicroelectrode arrays (7 μm diameter) and microwire electrode arrays (50 μm diameter) delivering charge and charge density levels selected above and below reported tissue damage thresholds (range: 2–20 nC, 0.1–1 mC/cm2). Spatial transcriptomics was performed using Visium Spatial Gene Expression Slides (10x Genomics, Pleasanton, CA, United States), which enabled simultaneous immunohistochemistry and ST to directly compare traditional histological metrics to transcriptional profiles within each tissue sample. Our data give a first look at unique spatial patterns of gene expression that are related to cellular processes including inflammation, cell cycle progression, and neuronal plasticity. At the acute timepoint, an increase in inflammatory and plasticity related genes was observed surrounding a stimulating electrode compared to a craniotomy control. At the chronic timepoint, an increase in inflammatory and cell cycle progression related genes was observed both in the stimulating vs. non-stimulating microwire electrode comparison and in the stimulating microwire vs. carbon fiber comparison. Using the spatial aspect of this method as well as the within-sample link to traditional metrics of tissue damage, we demonstrate how these data may be analyzed and used to generate new hypotheses and inform safety standards for stimulation in cortex.

Fabrication Methods and Chronic In Vivo Validation of Mechanically Adaptive Microfluidic Intracortical Devices

“…However, the drug may also be swapped out for any therapeutic designed to improve brain tissue health and function. The flexibility of our design lends itself ‘flexible’ to the discovery of additional targets with the recent use of more sophisticated analysis methods of the neuroinflammatory response to IMEs [ 13 , 77 , 78 , 79 , 80 , 81 , 82 ]. The ability for this probe to be a platform device makes it a powerful tool that may help improve patient quality of life.…”

Structural, Functional, and Genetic Changes Surrounding Electrodes Implanted in the Brain

“…24 We are employing RNA sequencing (RNA-seq) and spatial transcriptomics techniques to map transcriptional changes in cells surrounding devices, 39 which has revealed new information about both recording and stimulating electrodes. 2,3,30,40 In our initial study, RNA sequencing of interfacial (≤100 μm from device site) and distal tissue (∼500 μm from device site) samples collected via laser capture microscopy yielded hundreds of DEGs in tissue proximal to implanted electrodes relative to non-implanted nai ̈ve tissues (Figure 5). 3 Genes were grouped based on previously identified associations of cellular interactions and expression (Figure 5E).…”

“…However, histology is relatively low throughput and provides limited information on the biological mechanisms affecting signal quality . We are employing RNA sequencing (RNA-seq) and spatial transcriptomics techniques to map transcriptional changes in cells surrounding devices, which has revealed new information about both recording and stimulating electrodes. ,,, …”

“…A. Koo, B. Celik, M. E. Evans, B. M. Weiland, J. D. Purcell, E. K. 202216937923 . The application of new techniques in spatial transcriptomics to the investigation of electrical stimulation effects on brain tissue revealed new sets of genes associated with inflammation, cell cycle progression, and plasticity. ThompsonC.…”

“…Historically, the tissue response to brain implants has been understood through histological assays, which have revealed observations of insertional trauma, inflammation, neuronal loss, and the formation of an encapsulating glial sheath around the inserted probe. − Our research focuses on the biological effects of electrode implantation in the brain, and our recent work has uncovered unexpected effects of the device presence on the structure, function, and gene expression of neighboring brain cells. , Using whole-cell electrophysiology and two-photon imaging, we observed that implanted recording electrodes are accompanied by reduced excitatory postsynaptic currents, altered dendritic structure, a reduction of spine density, and changes in the spine morphologies and intrinsic excitability of neurons within the recordable radius of implanted electrodes . In parallel, our transcriptomics data revealed hundreds of differentially expressed genes (DEGs) around the implant site, indicative of disruptions in synaptic transmission, astrogliosis, oligodendrocyte dysfunction, and microglial activation. , Spatial transcriptomics on tissue following electrical stimulation showed induction of the genetic signatures of cell death, plasticity, and activity in a manner dependent on the intensity of the applied stimulus . Recently, our group has implemented computational approaches with the goal to identify the genes most strongly predictive of changes in recording performance.…”