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Key Points Major depression encompasses heterogeneous disorders in humans that are associated with abnormalities in reward-related brain structures such as the nucleus accumbens, prefrontal cortex, amygdala and hippocampus. Changes in the activity and functional connectivity of these sites leads to abnormalities in the perception and interpretation of reward valence, in the motivation for rewards, and in subsequent decision-making. Recent drug development efforts and other new treatment approaches such as deep brain stimulation offer the potential to more effectively treat depression. However, the field still faces major difficulties. The heterogeneity of depression symptoms suggests that its aetiology is diverse, there are still no known or accepted biomarkers to diagnose major depression — let alone its many subtypes — and promising new treatments have yet to gain approval by the US Food and Drug Administration (FDA). Increasing evidence indicates that precipitating factors such as chronic stress induce changes in the functional connectivity within the brain's reward regions, and that such changes mediate reward-related depression-like behavioural symptoms in animal models, including social avoidance and anhedonia. The molecular and cellular bases of these behavioural abnormalities include changes in glutamatergic and GABAergic synaptic plasticity, dopamine neuron excitability, epigenetic and transcriptional mechanisms, and neurotrophic factors. The nucleus accumbens is central in processing and responding to rewarding and aversive stimuli. It has been extensively implicated in reward-related behavioural abnormalities that characterize depression and associated syndromes. Chronic exposure to stress alters gene expression patterns in and the morphology (and ultimately the functional activity and connectivity) of nucleus accumbens neurons — neuroadaptations that contribute importantly to depression-like behaviours. Advanced experimental tools, such as inducible mutations in mice, virus-mediated gene transfer and optogenetics, have made it possible for the first time to directly delineate the role of specific proteins acting within specific cell types within reward-related brain structures in mediating depression-like behavioural abnormalities in animal models. For example, medium spiny neurons (MSNs) that predominantly express D1 dopamine receptors have a very different effect on reward from MSNs that predominantly express D2 dopamine receptors. It will be important for future studies to examine the molecular and cellular underpinnings of depression-like behaviours in females. Depression is twice as likely to occur in women than in men, but animal studies have mostly been conducted in males. There is evidence that females use different cognitive strategies, exhibit increased stress sensitivity and show variations in reward-related behaviours throughout the oestrus cycle that may render them more sensitive to the deleterious effects of stress. Recent evidence suggests that mood disorders are associated with altered reward function. Russo and Nestler review studies that have shown alterations in the brain reward circuitry in patients with, and animal models of, depression, and discuss the cellular and molecular underpinnings of these alterations. Mood disorders are common and debilitating conditions characterized in part by profound deficits in reward-related behavioural domains. A recent literature has identified important structural and functional alterations within the brain's reward circuitry — particularly in the ventral tegmental area–nucleus accumbens pathway — that are associated with symptoms such as anhedonia and aberrant reward-associated perception and memory. This Review synthesizes recent data from human and rodent studies from which emerges a circuit-level framework for understanding reward deficits in depression. We also discuss some of the molecular and cellular underpinnings of this framework, ranging from adaptations in glutamatergic synapses and neurotrophic factors to transcriptional and epigenetic mechanisms.

Key Points We propose that changes in the transcriptional potential of genes, through the actions of drug-regulated transcription factors, chromatin modifications and non-coding RNAs, contribute substantially to the neuroadaptations that underlie addiction. This Review highlights key examples of such transcriptional and epigenetic mechanisms of addiction, and identifies some of the novel potential targets for therapeutic intervention during the addiction process. The nucleus accumbens, a region that is central to the processing of reward and the addicting actions of virtually all drugs of abuse, contains a complex milieu of cell types. It receives input from, and sends signals to various brain regions. Chronic exposure to drugs of abuse alters gene expression patterns, as well as the morphology (and ultimately the functional activity) of nucleus accumbens neurons — neuroadaptations that contribute importantly to the addiction process. Chronic exposure to drugs of abuse alters the expression or activity of numerous transcription factors, including ΔFOSB, cyclic AMP-responsive element binding (CREB), nuclear factor-κB (NF-κB) and myocyte-specific enhancer factor 2 (MEF2). Manipulation of these factors, specifically in the nucleus accumbens or other parts of the brain's reward circuitry, alters specific molecular, cellular and behavioural responses in rodent models of addiction, which points to the functional role of these factors and their target genes in addiction. Epigenetic regulation underlies many adaptations of an adult organism to environmental stimuli, such as those seen in drug addiction. Post-translational modification of histone tails and direct modification of DNA, as well as altered levels or activity of a host of other chromatin remodelling proteins, mediate the ability of drugs of abuse, after chronic exposure, to alter the expression of specific genes in the brain's reward circuitry. Ongoing studies of chromatin regulation in addiction models support the view that epigenetic changes at individual genes alter not only the steady-state levels of their expression but also their inducibility in response to a subsequent stimulus. We propose that these latent epigenetic changes, termed gene 'priming' and 'desensitization', alter an individual's adaptability and contribute substantially to the addicted state. Several recent studies have implicated microRNAs in addiction-related behaviours in animal models, and several specific microRNAs, whose expression is altered by drugs of abuse in brain reward regions, have been shown to regulate the expression of several proteins strongly linked to addiction. Among the key questions for future research are: what controls the recruitment or expulsion of individual transcriptional and chromatin-regulatory proteins to a particular target gene? What controls the formation and maintenance of distinct epigenetic states at particular genes? How are the actions of drugs of abuse, all of which initially target the synapse, transduced to the neuronal nucleus to regulate the epigenetic state and transcriptional potential of individual genes? Chronic drug exposure induces long-term changes in the brain, which are partly due to alterations in gene expression. Robison and Nestler review the mechanisms by which drugs of abuse alter the transcriptional potential of genes through the regulation of transcription factors and epigenetic mechanisms, including the regulation of gene expression by non-coding RNAs. Investigations of long-term changes in brain structure and function that accompany chronic exposure to drugs of abuse suggest that alterations in gene regulation contribute substantially to the addictive phenotype. Here, we review multiple mechanisms by which drugs alter the transcriptional potential of genes. These mechanisms range from the mobilization or repression of the transcriptional machinery — including the transcription factors ΔFOSB, cyclic AMP-responsive element binding protein (CREB) and nuclear factor-κB (NF-κB) — to epigenetics — including alterations in the accessibility of genes within their native chromatin structure induced by histone tail modifications and DNA methylation, and the regulation of gene expression by non-coding RNAs. Increasing evidence implicates these various mechanisms of gene regulation in the lasting changes that drugs of abuse induce in the brain, and offers novel inroads for addiction therapy.

Regulation of gene expression is considered a plausible mechanism of drug addiction, given the stability of behavioural abnormalities that define an addicted state. Among many transcription factors known to influence the addiction process, one of the best characterized is ΔFosB, which is induced in the brain's reward regions by chronic exposure to virtually all drugs of abuse and mediates sensitized responses to drug exposure. Since ΔFosB is a highly stable protein, it represents a mechanism by which drugs produce lasting changes in gene expression long after the cessation of drug use. Studies are underway to explore the detailed molecular mechanisms by which ΔFosB regulates target genes and produces its behavioural effects. We are approaching this question using DNA expression arrays coupled with the analysis of chromatin remodelling-changes in the posttranslational modifications of histones at drug-regulated gene promoters-to identify genes that are regulated by drugs of abuse via the induction of ΔFosB and to gain insight into the detailed molecular mechanisms involved. Our findings establish chromatin remodelling as an important regulatory mechanism underlying drug-induced behavioural plasticity, and promise to reveal fundamentally new insight into how ΔFosB contributes to addiction by regulating the expression of specific target genes in brain reward pathways.

Major depressive disorder is a chronic, remitting syndrome involving widely distributed circuits in the brain. Stable alterations in gene expression that contribute to structural and functional changes in multiple brain regions are implicated in the heterogeneity and pathogenesis of the illness. Epigenetic events that alter chromatin structure to regulate programs of gene expression have been associated with depression-related behavior, antidepressant action, and resistance to depression or 'resilience' in animal models, with increasing evidence for similar mechanisms occurring in postmortem brains of depressed humans. In this review, we discuss recent advances in our understanding of epigenetic contributions to depression, in particular the role of histone acetylation and methylation, which are revealing novel mechanistic insight into the syndrome that may aid in the development of novel targets for depression treatment.

ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs. control, and identify regions that show differences in ChIP enrichment. We have developed a powerful and easy to use program, called diffReps, to detect those differential sites from ChIP-seq data, with or without biological replicates. In addition, we have developed two useful tools for ChIP-seq analysis in the diffReps package: one for the annotation of the differential sites and the other for finding chromatin modification \"hotspots\". diffReps is developed in PERL programming language and runs on all platforms as a command line script. We tested diffReps on two different datasets. One is the comparison of H3K4me3 between two human cell lines from the ENCODE project. The other is the comparison of H3K9me3 in a discrete region of mouse brain between cocaine- and saline-treated conditions. The results indicated that diffReps is a highly sensitive program in detecting differential sites from ChIP-seq data.

There has been increasing interest in the possibility that behavioral experience--in particular, exposure to stress--can be passed on to subsequent generations through heritable epigenetic modifications. The possibility remains highly controversial, however, reflecting the lack of standardized definitions of epigenetics and the limited empirical support for potential mechanisms of transgenerational epigenetic inheritance. Nonetheless, growing evidence supports a role for epigenetic regulation as a key mechanism underlying lifelong regulation of gene expression that mediates stress vulnerability. This Perspective provides an overview of the multiple meanings of the term epigenetic, discusses the challenges of studying epigenetic contributions to stress susceptibility--and the experimental evidence for and against the existence of such mechanisms--and outlines steps required for future investigations.

Key Points Resilient individuals demonstrate adaptive psychological and physiological stress responses to acute stress, trauma or more chronic forms of adversity. Resilience is an active process, not simply the absence of changes induced by stress. Examining stress responses at multiple phenotypic levels can help to delineate an integrative model of resilience. Positive emotions and cognitive reappraisal promote adaptive coping strategies and resilience. Complex interactions between an individual's genetic make-up and their history of exposure to environmental stressors influence the adaptability of stress response systems and neural circuitry function. Progress is being made in identifying the neural circuits in the brain that mediate resilience. Recent work has begun to identify specific changes in gene expression and chromatin remodelling (that is, epigenetic adaptations) that underlie resilience. Although stress is associated with many physical and mental illnesses, most individuals cope well with it. Feder and colleagues review the factors that underlie stress resilience, showing that it involves adaptive changes in specific neural circuits, neuromodulator levels and molecular pathways. Every individual experiences stressful life events. In some cases acute or chronic stress leads to depression and other psychiatric disorders, but most people are resilient to such effects. Recent research has begun to identify the environmental, genetic, epigenetic and neural mechanisms that underlie resilience, and has shown that resilience is mediated by adaptive changes in several neural circuits involving numerous neurotransmitter and molecular pathways. These changes shape the functioning of the neural circuits that regulate reward, fear, emotion reactivity and social behaviour, which together are thought to mediate successful coping with stress.

Drug discovery for psychiatric conditions is stagnating. Behavioral changes could be used as a primary phenotypic screen for new drug candidates, if enough useful data can be generated from behavioral models. Could machine learning be the answer to extracting the data we need?

Abuse, neglect, and other forms of early life stress (ELS) significantly increase risk for psychiatric disorders including depression. In this study, we show that ELS in a postnatal sensitive period increases sensitivity to adult stress in female mice, consistent with our earlier findings in male mice. We used RNA-sequencing in the ventral tegmental area, nucleus accumbens, and prefrontal cortex of male and female mice to show that adult stress is distinctly represented in the brain’s transcriptome depending on ELS history. We identify: 1) biological pathways disrupted after ELS and associated with increased behavioral stress sensitivity, 2) putative transcriptional regulators of the effect of ELS on adult stress response, and 3) subsets of primed genes specifically associated with latent behavioral changes. We also provide transcriptomic evidence that ELS increases sensitivity to future stress through enhancement of known programs of cortical plasticity. Early life stress alters behavioural response to adult stress in female mice. Here authors transcriptionally profile three brain regions involved in reward (ventral tegmental area, nucleus accumbens, and prefrontal cortex) in both male and female adult mice after early life and/or adult stress

Early life stress increases risk for depression. Here we establish a “two-hit” stress model in mice wherein stress at a specific postnatal period increases susceptibility to adult social defeat stress and causes long-lasting transcriptional alterations that prime the ventral tegmental area (VTA)—a brain reward region—to be in a depression-like state. We identify a role for the developmental transcription factor orthodenticle homeobox 2 (Otx2) as an upstream mediator of these enduring effects. Transient juvenile—but not adult—knockdown of Otx2 in VTA mimics early life stress by increasing stress susceptibility, whereas its overexpression reverses the effects of early life stress. This work establishes a mechanism by which early life stress encodes lifelong susceptibility to stress via long-lasting transcriptional programming in VTA mediated by Otx2.