Correlation of mRNA Expression and Signal Variability in Chronic Intracortical Electrodes

Abstract

Objective: The goal for this research was to identify molecular mechanisms that explain animal-to-animal variability in chronic intracortical recordings.

Approach: Microwire electrodes were implanted into Sprague Dawley rats at an acute (1 week) and a chronic (14 weeks) time point. Weekly recordings were conducted, and action potentials were evoked in the barrel cortex by deflecting the rat's whiskers. At 1 and 14 weeks, tissue was collected, and mRNA was extracted. mRNA expression was compared between 1 and 14 weeks using a high throughput multiplexed qRT-PCR. Pearson correlation coefficients were calculated between mRNA expression and signal-to-noise ratios at 14 weeks.

Main results: At 14 weeks, a positive correlation between signal-to-noise ratio (SNR) and NeuN and GFAP mRNA expression was observed, indicating a relationship between recording strength and neuronal population, as well as reactive astrocyte activity. The inflammatory state around the electrode interface was evaluated using M1-like and M2-like markers. Expression for both M1-like and M2-like mRNA markers remained steady from 1 to 14 weeks. Anti-inflammatory markers, CD206 and CD163, however, demonstrated a significant positive correlation with SNR quality at 14 weeks. VE-cadherin, a marker for adherens junctions, and PDGFR-β, a marker for pericytes, both partial representatives of blood-brain barrier health, had a positive correlation with SNR at 14 weeks. Endothelial adhesion markers revealed a significant increase in expression at 14 weeks, while CD45, a pan-leukocyte marker, significantly decreased at 14 weeks. No significant correlation was found for either the endothelial adhesion or pan-leukocyte markers.

Significance: A positive correlation between anti-inflammatory and blood-brain barrier health mRNA markers with electrophysiological efficacy of implanted intracortical electrodes has been demonstrated. These data reveal potential mechanisms for further evaluation to determine potential target mechanisms to improve consistency of intracortical electrodes recordings and reduce animal-to-animal/implant-to-implant variability.

Keywords: blood–brain barrier; chronic recordings; correlation analysis; intracortical microelectrodes; neuro-inflammatory response; signal-to-noise ratio.

Figure 1

(A) Implantation of microwire array and electrode site map. (B) Representative image of barrel cortex craniotomy and anchoring/grounding screws. (C) Average waveforms for a single unit. (D) Acquired raw waveforms from recording system with example threshold setting.

Figure 2

(A) Animal variability at 14 weeks demonstrated through signal-to-noise ratio (SNR) and percentage of active electrodes. (B) Average SNR and (C) average percentage of active electrodes over time for individual animals.

Figure 3

Representative images of 16 electrode microwire arrays at 1 week with * representing electrode location for (A) CD68, (B) GFAP, and (C) NeuN antibody staining (scale bar = 100 µm). Fold change comparison between 1 and 14 weeks for (D) NeuN, (E) GFAP, and (F) CD68 (*p < 0.05, Student’s t-test, Bonferroni corrected). Each time point was compared to age-matched naïve controls to calculate fold change. (G) Pearson correlation values for CD68, GFAP, and CD68 (*p < 0.05).

Figure 4

Fold change comparisons between 1 and 14 weeks for M1-like pro-inflammatory markers (A) CD32, (B) CD64, (C) CD80, (D) CD86, and (E) CCR7, and M2-like anti-inflammatory markers (F) CD206, (G) CD163, and (H) Arg-1 (*p < 0.05, Student’s t-test, Bonferroni corrected). Each time point was compared to age-matched naïve controls to calculate fold change. Pearson correlations for (I) M1-like and (J) M2-like markers (*p < 0.05).

Figure 5

Fold change comparisons between 1 and 14 weeks for tight junction proteins (A) Cldn-5, (B) occluding (Ocln), and (C) zona-occludens-1 (ZO-1) and other blood–brain barrier (BBB) markers, (E) cdh-5, (F) PDGFR-β, and (G) AQP-4 (*p < 0.05, Student’s t-test, Bonferroni corrected). Each time point was compared to age-matched naïve controls to calculate fold change. Pearson correlations for (D) tight junction protein markers and (H) other BBB markers (*p < 0.05).

Figure 6

Fold change comparisons between 1 and 14 weeks for endothelial adhesion markers (A) ACAM, (B) ICAM1, (C) ICAM2, (D) sel-e, (E) sel-p, (F) VCAM1 and pan-leukocyte marker, (G) CD45 (*p < 0.05, Student’s t-test, Bonferroni corrected). Each time point was compared to age-matched naïve controls to calculate fold change. (H) Pearson correlation for endothelial adhesion and pan-leukocyte markers (*p < 0.05).