Transcriptional and epigenetic regulation of microglia in substance use disorders

Abstract

Microglia are widely known for their role in immune surveillance and for their ability to refine neurocircuitry during development, but a growing body of evidence suggests that microglia may also play a complementary role to neurons in regulating the behavioral aspects of substance use disorders. While many of these efforts have focused on changes in microglial gene expression associated with drug-taking, epigenetic regulation of these changes has yet to be fully understood. This review provides recent evidence supporting the role of microglia in various aspects of substance use disorder, with particular focus on changes to the microglial transcriptome and the potential epigenetic mechanisms driving these changes. Further, this review discusses the latest technical advances in low-input chromatin profiling and highlights the current challenges for studying these novel molecular mechanisms in microglia.

Keywords: Chromatin; Craving; Epigenetics; Genomics; Histone; Microglia; Opioids; Self-administration; Stimulants; Substance use disorders; Transcription.

Figure 1.. Microglia regulate drug-related behaviors as a result of transcriptional changes throughout Substance Use Disorders.

Proposed mechanisms for microglial activation following exposure to various drugs of abuse. Microglia may be activated through both direct and indirect means. Following activation, microglia maintain an altered state, with possible changes to morphology, gene expression and epigenetic modifications that lead to functional deficits such as aberrant pruning of synapses and hyperexcitability. These changes are underscored by altered behavior across numerous paradigms. However, treatment with known anti-inflammatory drugs like AV-411 and the tetracycline antibiotic minocycline, as well as complete microglial depletion can mitigate these drug-induced changes both molecularly and behaviorally.

Figure 2.. Methodologies for studying microglial genomics.

A number of novel technologies have enhanced the ability to sequence the genome and epigenome of microglia. As an initial barrier to profiling microglia, isolation of pure populations has recently been made easier with developments in both FACS and magnetic bead based affinity purification, with both methods achieving similar results. For RNA sequencing, the advent of low input and single cell, kits capable of creating complex libraries for sequencing has enabled investigators to reduce the number of microglia needed to understand their response to certain stimuli and delineate sub-populations within different brain regions. To study chromatin dynamics, methods such as CUT&RUN and CUT&Tag allow for regional microglial populations to be analyzed for various histone marks and transcription factors with very low cellular input, including single cells, at a fraction of the cost of ChIP-sequencing assays. These more recent advances can generate robust datasets comparable to those generated by ChIP-sequencing. ATAC-seq is a convenient method for profiling chromatin accessibility, however its utility is hampered by its limited ability to recognize gene enhancer loci. (FACS: Fluorescence Assisted Cellular Sorting, AFP: Affinity purification, scRNA: Single-cell RNA, CUT&RUN: Cleavage Under Targets & Release Using Nuclease, CUT&Tag: Cleavage Under Targets & Tagmentation, ATAC: Assay for Transposase-Accessible Chromatin) Created with BioRender.