Cocaine addiction-like behaviors are associated with long-term changes in gene regulation, energy metabolism, and GABAergic inhibition within the amygdala

Abstract

The amygdala contributes to negative emotional states associated with relapse to drug seeking, but the cell type-specific gene regulatory programs that are involved in addiction are unknown. Here we generate an atlas of single nucleus gene expression and chromatin accessibility in the amygdala of outbred rats with low and high cocaine addiction-like behaviors following a prolonged period of abstinence. Between rats with different addiction indexes, there are thousands of cell type-specific differentially expressed genes and these are enriched for molecular pathways including GABAergic synapse in astrocytes, excitatory, and somatostatin neurons. We find that rats with higher addiction severity have excessive GABAergic inhibition in the amygdala, and that hyperpolarizing GABAergic transmission and relapse-like behavior are reversed by pharmacological manipulation of the metabolite methylglyoxal, a GABAA receptor agonist. By analyzing chromatin accessibility, we identify thousands of cell type-specific chromatin sites and transcription factor (TF) motifs where accessibility is associated with addiction-like behaviors, most notably at motifs for pioneer TFs in the FOX, SOX, and helix-loop-helix families.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

“…snRNA-seq data used for the alignment metrics were obtained from rat amygdala using the Droplet-based Chromium Single-Cell 3′ solution (10x Genomics, v3 chemistry), as previously described. 96 Briefly, nuclei were isolated from frozen brain tissues and purified by flow cytometry. Sorted nuclei were counted and 12,000 were loaded onto a Chromium Controller (10x Genomics).…”

Cocaine-Induced Gene Regulation in D1 and D2 Neuronal Ensembles of the Nucleus Accumbens Revealed by Single-Cell RNA Sequencing

“…Our TF motif analysis further implicated the involvement of the RFX family of transcription factors, including RFX2 (Figure 5G). RFX2 is known to play a role in regulating genes involved in ciliary function and neuronal signaling 70,71 , suggesting its potential impact on the structural and functional adaptations in response to cocaine. Additionally, prominent zinc finger motifs, such as ZNF7, also emerged from this analysis.…”

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

“…94 Single nuclei (sn) RNA-seq data. snRNA-seq data used for the alignment metrics were obtained from rat amygdala using the Droplet-based Chromium Single-Cell 3' solution (10x Genomics, v3 chemistry), as previously described 95 . Briefly, nuclei were isolated from frozen brain tissues and purified by flow cytometry.…”