Deciphering the genomic mechanisms underlying the physiology of human brain stimulation

NIH RePORTER · NIH · RF1 · $211,227 · view on reporter.nih.gov ↗

Abstract

PROJECT SUMMARY The underlying mechanisms of brain stimulation in humans are poorly understood, especially at the level of gene expression. To address this gap in knowledge, in the parent award, we proposed a series of three experiments that take advantage of the opportunity to obtain high-quality human neural tissue from neurosurgical patients in order to measure the impact of brain stimulation on gene expression. Our experiments will generate data from human subjects that underwent neurostimulation and unstimulated control subjects to measure the impact of stimulation on brain circuit changes and their underlying gene expression signature. Our study team has seven years of experience analyzing gene expression using an established pipeline for studying human cortical tissue from neurosurgical patients, including application of cutting-edge methods for measuring gene expression. These methods include single nuclei RNA-sequencing (snRNA-seq) and the exciting addition of single nuclei ATAC-sequencing (snATAC-seq) to understand stimulation-related changes in transcription factors and chromatin remodeling. Our hypotheses regarding specific gene classes were developed from our published data correlating gene expression changes with neurophysiological signatures (brain oscillations) linked with successful memory formation. In this administrative supplement, we will integrate the multiomic datasets being generated in the parent award with available human brain genomic datasets from BRAIN Initiative mechanisms. We will determine how our stimulation paradigms both in vivo and in organotypic slice culture (OSC) mimic genomic features of other human brain datasets both over development and/or with underlying disease pathology. We will test if stimulation reverses gene expression programs relevant to disease. In Aim 1, we will integrate our datasets with those derived across development. In Aim 2, we will integrate our datasets with those derived from individuals with a number of brain disorders, and we will use the integrated data from Aim 1 as comparison. In Aim 3, we will directly examine whether stimulation mimics control or disease genomic states more closely. The experience of our research team and proven record in publishing data using neurosurgical tissue specimens, especially within the context of genomic analyses, supports our expectations of success.

Key facts

NIH application ID
10834634
Project number
3RF1NS126143-01A1S1
Recipient
UT SOUTHWESTERN MEDICAL CENTER
Principal Investigator
Genevieve Konopka
Activity code
RF1
Funding institute
NIH
Fiscal year
2024
Award amount
$211,227
Award type
3
Project period
2023-09-01 → 2025-08-31