Integrative multi-omics landscape of fluoxetine action across 27 brain regions reveals global increase in energy metabolism and region-specific chromatin remodelling

Abstract

Depression and anxiety are major global health burdens. Although SSRIs targeting the serotonergic system are prescribed over 200 million times annually, they have variable therapeutic efficacy and side effects, and mechanisms of action remain incompletely understood. Here, we comprehensively characterise the molecular landscape of gene regulatory changes associated with fluoxetine, a widely-used SSRI. We performed multimodal analysis of SSRI response in 27 mammalian brain regions using 310 bulk RNA-seq and H3K27ac ChIP-seq datasets, followed by in-depth characterisation of two hippocampal regions using single-cell RNA-seq (20 datasets). Remarkably, fluoxetine induced profound region-specific shifts in gene expression and chromatin state, including in the nucleus accumbens shell, locus coeruleus and septal areas, as well as in more well-studied regions such as the raphe and hippocampal dentate gyrus. Expression changes were strongly enriched at GWAS loci for depression and antidepressant drug response, stressing the relevance to human phenotypes. We observed differential expression at dozens of signalling receptors and pathways, many of which are previously unknown. Single-cell analysis revealed stark differences in fluoxetine response between the dorsal and ventral hippocampal dentate gyri, particularly in oligodendrocytes, mossy cells and inhibitory neurons. Across diverse brain regions, integrative omics analysis consistently suggested increased energy metabolism via oxidative phosphorylation and mitochondrial changes, which we corroborated in vitro; this may thus constitute a shared mechanism of action of fluoxetine. Similarly, we observed pervasive chromatin remodelling signatures across the brain. Our study reveals unexpected regional and cell type-specific heterogeneity in SSRI action, highlights under-studied brain regions that may play a major role in antidepressant response, and provides a rich resource of candidate cell types, genes, gene regulatory elements and pathways for mechanistic analysis and identifying new therapeutic targets for depression and anxiety.

Transcriptional changes in specific subsets of Drosophila neurons following inhibition of the serotonin transporter

“…A large number of previous reports have investigated transcriptomic changes in response to SSRI-like perturbations, but most have used peripheral samples or highly heterogenous brain tissue as input. More recently, specific subtypes of neurons have been targeted using molecular-genetic strategies employed in rodents such as RiboTag [21,73] and untargeted scRNA-seq [14]. We have now employed similar strategies in the fly with an additional purification step -FACS sorting of GFP labeled cells to isolate a genetically-labeled neuronal subtype: the KCs of the mushroom bodies.…”

“…Widespread prescription of these drugs has motivated many studies of their long-term effects utilizing peripheral samples [11][12][13] or highly heterogeneous brain tissue [14,15]. However, deeper understanding of serotonergic circuits and their responses to therapeutic interventions remains elusive due in part to the heterogeneity of serotonergic neurons themselves and the cells that they innervate.…”

“…Several reports have investigated changes in ribosome-loaded RNA in a particular cell-type after environmental/behavioral perturbations and/or SSRI administration [20,21]. Another recent study has generated multi-omic datasets on fluoxetine vs. sham-treated mice across multiple brain regions, including two datasets utilizing scRNA-seq to analyze specific hippocampal cell types [14]. The complexity of these findings suggests that further, detailed analysis of the response that occurs in different subtypes of neurons will be necessary to fully understand the molecular effects of SERT inhibition.…”

Transcriptomic Studies of Antidepressant Action in Rodent Models of Depression: A First Meta-Analysis

“…Although it has been observed for one of the experiments we included that similar gene expression responses to FLX were found in dorsal and ventral dentate gyrus [ 51 ], more recent investigations show that the ventral hippocampus was particularly sensitive to the effects of stress. Therefore, it was proposed to consider the dorsal and ventral hippocampus separately when conducting high-throughput molecular analyses [ 24 , 70 ]. We are aware of this caveat, but we had no choice if we wanted to keep enough power in our analysis.…”

“…As in humans, animal models reveal absence of homogeneous response, which offers the possibility of selecting animals that respond well to AD treatment to study the biological pathways involved in the recovery of normal social, emotional, hedonic, affective, mnemonic, exploratory, and feeding behaviors [ 21 ]. Going a step beyond, recent convergence studies have been undertaken from human and animal transcriptomes and should advance our knowledge of the pathophysiology of major depression [ 16 , 22 , 23 , 24 , 25 ]. Concerning the identification of signatures of AD treatments, several teams have tried to gather common features of genome-wide transcriptional variations induced by the action of ADs in patients suffering from affective disorders [ 11 , 12 , 26 ], but to our knowledge, studies carried out in rodent models are very scarce and fragmented.…”