Spatiotemporal patterns of gene expression around implanted silicon electrode arrays

Abstract

Objective.Intracortical brain interfaces are an ever evolving technology with growing potential for clinical and research applications. The chronic tissue response to these devices traditionally has been characterized by glial scarring, inflammation, oxidative stress, neuronal loss, and blood-brain barrier disruptions. The full complexity of the tissue response to implanted devices is still under investigation.Approach.In this study, we have utilized RNA-sequencing to identify the spatiotemporal gene expression patterns in interfacial (within 100µm) and distal (500µm from implant) brain tissue around implanted silicon microelectrode arrays. Naïve, unimplanted tissue served as a control.Main results.The data revealed significant overall differential expression (DE) in contrasts comparing interfacial tissue vs naïve (157 DE genes), interfacial vs distal (94 DE genes), and distal vs naïve tissues (21 DE genes). Our results captured previously characterized mechanisms of the foreign body response, such as astroglial encapsulation, as well as novel mechanisms which have not yet been characterized in the context of indwelling neurotechnologies. In particular, we have observed perturbations in multiple neuron-associated genes which potentially impact the intrinsic function and structure of neurons at the device interface. In addition to neuron-associated genes, the results presented in this study identified significant DE in genes which are associated with oligodendrocyte, microglia, and astrocyte involvement in the chronic tissue response.Significance. The results of this study increase the fundamental understanding of the complexity of tissue response in the brain and provide an expanded toolkit for future investigation into the bio-integration of implanted electronics with tissues in the central nervous system.

Keywords: Michigan probe; RNA-sequencing; inflammation; neural prostheses; tissue response.

Figure 1:. RNA-sequencing of cortical tissue reveals spatiotemporal gene expression at the device interface.

Volcano plots illustrate overall DE of genes at near-device relative to naïve tissue ((A) 157 DE genes), near relative to far tissue ((B) 94 DE genes), and far relative to naïve tissue ((C) 21 DE genes). “Overall” expression represents the group comparisons of samples pooled across time points. Significance was thresholded at Log2FC ≥ 0.6 and P ≤ 0.05 (dashed red lines). (Red: Upregulated DE, Blue: Downregulated DE, Black: Detected not DE)

Figure 2:. Transcriptomic analysis of interfacial and distal tissue at the device interface.

(A) Representative heatmap of differential gene expression for each contrast for previously characterized cell types and their known roles in tissue response to implanted devices. (I) neurons, (II) astrocytes, (III) microglia, and (IV) oligodendrocytes. (B) Representative heatmap showing differential gene expression of each contrast in our analysis for (V) oxidative stress, (VI) inflammation, and (VII) blood-brain barrier. Color bar indicates Log2FC. “NaN” indicates non-detection. Significance was thresholded at Log2FC ≥ 0.6 and P ≤ 0.05. Asterisks* denote statistically significant differentially expressed genes.

Figure 3:. Differential expression of genes associated with the neuronal synaptic architecture at the device interface relative to naïve tissue.

The table and representative graphs that illustrate the downregulation of synaptic associated genes at 24 hours, 1-week and 6-weeks post-implantation. “Overall” expression represents the group comparisons of samples pooled across time points. Significance was thresholded at Log2FC ≥ 0.6 and P ≤ 0.05. Asterisks (*) denote statistically significant differentially expressed genes.

Figure 4:. Differential expression of genes associated with the cytoskeletal architecture of neurons at the device interface relative to naïve tissue.

The table and representative graphs above show fluctuations in neuronal genes associated with cytoskeleton and motor proteins at 24 hours, 1-week and 6-weeks post-implantation. “Overall” expression represents the group comparisons of samples pooled across time points. Significance was thresholded at Log2FC ≥ 0.6 and P ≤ 0.05. Asterisks* denote significantly differentially expressed genes.

Figure 5:. Differential expression of genes associated with astrocyte activity at the device interface relative to naïve tissue.

The table and representative graphs that outline the general upregulation of astrocyte associated genes at 24 hours, 1-week and 6-weeks post-implantation. “Overall” expression represents the group comparisons of samples pooled across time points. Significance was thresholded at Log2FC ≥ 0.6 and P ≤ 0.05. Asterisks (*) denote statistically significant differentially expressed genes.

Figure 6:. Differential expression of genes associated with inflammation and microglial activity at the device interface relative to naïve tissue.

The table and representative graphs that show the generalized upregulation of microglial and inflammation associated genes at 24 hours, 1-week and 6-weeks post-implantation. “Overall” expression represents the group comparisons of samples pooled across time points. Significance was thresholded at Log2FC ≥ 0.6 and P ≤ 0.05. Asterisks (*) denote statistically significant differentially expressed genes.

Figure 7:. Differential expression of genes associated with oligodendrocytes at the device interface relative to naïve tissue.

The table and representative graphs illustrate the upregulation of key genes associated with oligodendrocytes at 24 hours, 1-week and 6-weeks post-implantation. “Overall” expression represents the group comparisons of samples pooled across time points. Significance was thresholded at Log2FC ≥ 0.6 and P ≤ 0.05. Asterisks (*) denote statistically significant differentially expressed genes.

Figure 8:. Differential expression of genes associated with blood brain barrier integrity at the device interface relative to naïve tissue.

The table and representative graphs illustrate fluctuations of blood brain barrier associated genes at 24 hours, 1-week and 6-weeks post-implantation. “Overall” expression represents the group comparisons of samples pooled across time points. Significance was thresholded at Log2FC ≥ 0.6 and P ≤ 0.05. No genes were identified as significantly DE in this group.

Figure 9:. Differential expression of genes associated with oxidative stress at the device interface relative to naïve tissue.

The table and representative graphs illustrate fluctuations of oxidative stress associated genes at 24 hours, 1-week and 6-weeks post-implantation. “Overall” expression represents the group comparisons of samples pooled across time points. Significance was thresholded at Log2FC ≥ 0.6 and P ≤ 0.05. Asterisks (*) denote significant differentially expressed genes.