Spatiotemporal expression of RNA-seq identified proteins at the electrode interface

Area of Science:

• Neuroscience
• Biomaterials Science
• Molecular Biology

Background:

• Brain electrode implantation is crucial for treating neurological conditions but is limited by tissue response.
• RNA sequencing (RNA-seq) reveals numerous genes altered by microelectrode insertion, impacting neural tissue.
• Understanding protein-level changes is vital to validate transcriptomic data and assess device impact.

Purpose of the Study:

• To validate RNA-seq identified proteins (RSIPs) at the protein level using quantitative immunofluorescence.
• To investigate the spatiotemporal distribution of RSIPs around implanted microelectrodes over time.
• To develop a method for quantifying protein distribution within specific cell types at the device interface.

Main Methods:

• Quantitative immunofluorescence was used to evaluate a subset of RSIPs at 24 hours, 1 week, and 6 weeks post-implantation.
• A MATLAB-based approach quantified immunofluorescence intensity within specific cell types (neurons, astrocytes, microglia, oligodendrocytes).
• Expression and distribution of proteins related to glial activation, neuronal structure, and iron metabolism were analyzed.

Main Results:

• Protein expression of RSIPs related to glial activation (GFAP, Ptbp1), neuronal structure (Nefh, Plp1, MBP), and iron metabolism (TF, Fth1) confirmed transcriptional data.
• Ptbp1, TF, and Fth1 showed specific spatiotemporal distribution within various neural cell types at the device interface.
• Altered protein distribution was primarily localized within 100µm of the device injury site.

Conclusions:

• RNA sequencing is a reliable predictor of protein-level changes in cortical tissue following electrode implantation.
• RSIPs provide insights into the spatiotemporal dynamics of the tissue response to brain implants.
• The identified proteins and quantification methodology can serve as biomarkers for device performance and therapeutic interventions.