Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition

SATB2 organizes the 3D genome architecture of cognition in cortical neurons

The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on the three-dimensional (3D) epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal-activity-regulated genes, thus influencing their expression. It also alters A/B compartments, topologically associating domains, and frequently interacting regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with a SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence, and schizophrenia. Our data establish SATB2 as a cell-type-specific 3D genome modulator, which operates both independently and in cooperation with CCCTC-binding factor (CTCF) to set up the chromatin landscape of pyramidal neurons for cognitive processes.

Environmental Enrichment for Stroke and Traumatic Brain Injury: Mechanisms and Translational Implications

Acquired brain injuries, such as ischemic stroke, intracerebral hemorrhage (ICH), and traumatic brain injury (TBI), can cause severe neurologic damage and even death. Unfortunately, currently, there are no effective and safe treatments to reduce the high disability and mortality rates associated with these brain injuries. However, environmental enrichment (EE) is an emerging approach to treating and rehabilitating acquired brain injuries by promoting motor, sensory, and social stimulation. Multiple preclinical studies have shown that EE benefits functional recovery, including improved motor and cognitive function and psychological benefits mediated by complex protective signaling pathways. This article provides an overview of the enriched environment protocols used in animal models of ischemic stroke, ICH, and TBI, as well as relevant clinical studies, with a particular focus on ischemic stroke. Additionally, we explored studies of animals with stroke and TBI exposed to EE alone or in combination with multiple drugs and other rehabilitation modalities. Finally, we discuss the potential clinical applications of EE in future brain rehabilitation therapy and the molecular and cellular changes caused by EE in rodents with stroke or TBI. This article aims to advance preclinical and clinical research on EE rehabilitation therapy for acquired brain injury. © 2024 American Physiological Society. Compr Physiol 14:5291-5323, 2024.

DNA Instability in Neurons: Lifespan Clock and Driver of Evolution

In the last ten years, the discovery of neuronal DNA postmitotic instability has changed the theoretical landscape in neuroscience and, more broadly, biology. In 2003, A. M. Olovnikov suggested that neuronal DNA is the "initial substrate of aging". Recent experimental data have significantly increased the likelihood of this hypothesis. How does neuronal DNA accumulate damage and in what genome regions? What factors contribute to this process and how are they associated with aging and lifespan? These questions will be discussed in the review. In the course of Metazoan evolution, the instability of neuronal DNA has been accompanied by searching for the pathways to reduce the biological cost of brain activity. Various processes and activities, such as sleep, evolutionary increase in the number of neurons in the vertebrate brain, adult neurogenesis, distribution of neuronal activity, somatic polyploidy, and RNA editing in cephalopods, can be reconsidered in the light of the trade-off between neuronal plasticity and DNA instability in neurons. This topic is of considerable importance for both fundamental neuroscience and translational medicine.

Chromosomal contacts change with age

The three-dimensional organization of the genome is remodeled throughout life.

Reduction of restricted repetitive behavior by environmental enrichment: Potential neurobiological mechanisms

Restricted repetitive behaviors (RRB) are one of two diagnostic criteria for autism spectrum disorder and common in other neurodevelopmental and psychiatric disorders. The term restricted repetitive behavior refers to a wide variety of inflexible patterns of behavior including stereotypy, self-injury, restricted interests, insistence on sameness, and ritualistic and compulsive behavior. However, despite their prevalence in clinical populations, their underlying causes remain poorly understood hampering the development of effective treatments. Intriguingly, numerous animal studies have demonstrated that these behaviors are reduced by rearing in enriched environments (EE). Understanding the processes responsible for the attenuation of repetitive behaviors by EE should offer insights into potential therapeutic approaches, as well as shed light on the underlying neurobiology of repetitive behaviors. This review summarizes the current knowledge of the relationship between EE and RRB and discusses potential mechanisms for EE's attenuation of RRB based on the broader EE literature. Existing gaps in the literature and future directions are also discussed.

Importance of Control Groups for Evaluating Long-Term Behavioral and Cognitive Outcomes of Controlled Cortical Impact in Immature Rats

Therapies are limited for pediatric traumatic brain injury (TBI), especially for the very young who can experience long-term consequences to learning, memory, and social behavior. Animal models of pediatric TBI have yielded mechanistic insights, but demonstration of clinically relevant long-term behavioral and/or cognitive deficits has been challenging. We characterized short- and long-term outcomes in a controlled cortical impact (CCI) model of pediatric TBI using a panel of tests between 2 weeks and ∼4 months after injury. Male rats with CCI at postnatal Day (PND) 10 were compared with three control groups: Naïve, Anesthesia, and Craniotomy. Motor testing (PND 25-33), novel object recognition (NOR; PND 40-50), and multiple tasks in water maze (WM; PND 65-100) were followed by social interaction tests (PND 120-140). Anesthesia rats performed the same as Naïve rats in all tasks. TBI rats, when compared with Naïve controls, had functional impairments across most tests studied. The most sensitive cognitive processes affected by TBI included those that required fast one-trial learning (NOR, WM), flexibility of acquired memory traces (reversals in WM), response strategies (WM), or recognition memory in the setting of reciprocal social interactions. Both TBI and Craniotomy groups demonstrated increased rates of decision making across several WM tasks, suggesting disinhibition of motor responses. When the TBI group was compared with the Craniotomy group, however, deficits were detected in a limited number of outcomes. The latter included learning speed (WM), cognitive flexibility (WM), and social recognition memory. Notably, effects of craniotomy, when compared with Naïve controls, spanned across multiple tasks, and in some tasks, could reach the effect sizes observed in TBI. These results highlight the importance of appropriate control groups in pediatric CCI models. In addition, the study demonstrates the high sensitivity of comprehensive cognitive testing to detect long-term effects of early-age craniotomy and TBI and provides a template for future testing of experimental therapies.

Neurodynamical Computing at the Information Boundaries of Intelligent Systems

Artificial intelligence has not achieved defining features of biological intelligence despite models boasting more parameters than neurons in the human brain. In this perspective article, we synthesize historical approaches to understanding intelligent systems and argue that methodological and epistemic biases in these fields can be resolved by shifting away from cognitivist brain-as-computer theories and recognizing that brains exist within large, interdependent living systems. Integrating the dynamical systems view of cognition with the massive distributed feedback of perceptual control theory highlights a theoretical gap in our understanding of nonreductive neural mechanisms. Cell assemblies—properly conceived as reentrant dynamical flows and not merely as identified groups of neurons—may fill that gap by providing a minimal supraneuronal level of organization that establishes a neurodynamical base layer for computation. By considering information streams from physical embodiment and situational embedding, we discuss this computational base layer in terms of conserved oscillatory and structural properties of cortical-hippocampal networks. Our synthesis of embodied cognition, based in dynamical systems and perceptual control, aims to bypass the neurosymbolic stalemates that have arisen in artificial intelligence, cognitive science, and computational neuroscience.

3D Genome Plasticity in Normal and Diseased Neurodevelopment

Non-random spatial organization of the chromosomal material inside the nuclei of brain cells emerges as an important regulatory layer of genome organization and function in health and disease. Here, we discuss how integrative approaches assessing chromatin in context of the 3D genome is providing new insights into normal and diseased neurodevelopment. Studies in primate (incl. human) and rodent brain have confirmed that chromosomal organization in neurons and glia undergoes highly dynamic changes during pre- and early postnatal development, with potential for plasticity across a much wider age window. For example, neuronal 3D genomes from juvenile and adult cerebral cortex and hippocampus undergo chromosomal conformation changes at hundreds of loci in the context of learning and environmental enrichment, viral infection, and neuroinflammation. Furthermore, locus-specific structural DNA variations, such as micro-deletions, duplications, repeat expansions, and retroelement insertions carry the potential to disrupt the broader epigenomic and transcriptional landscape far beyond the boundaries of the site-specific variation, highlighting the critical importance of long-range intra- and inter-chromosomal contacts for neuronal and glial function.

Beneficial effects and neurobiological aspects of environmental enrichment associated to major depressive disorder and autism spectrum disorder

A suitable enriched environment favors development but can also influence behavior and neuronal circuits throughout development. Studies have shown that environmental enrichment (EE) can be used as an essential tool or combined with conventional treatments to improve psychiatric and neurological symptoms, including major depressive disorder (MDD) and autism spectrum disorder (ASD). Both disorders affect a significant percentage of the world's population and have complex pathophysiology. Moreover, the available treatments for MDD and ASD are still inadequate for many affected individuals. Experimental models demonstrate that EE has significant positive effects on behavioral modulation. In addition, EE has effects on neurobiology, including improvement in synaptic connections and neuroplasticity, modulation of neurotransmissions, a decrease in inflammation and oxidative stress, and other neurobiology effects that can be involved in the pathophysiology of MDD and ASD. Thus, this review aims to describe the leading behavioral and neurobiological effects associated with EE in MDD and ASD.

DNA methylation as a mediator of genetic and environmental influences on Parkinson's disease susceptibility: Impacts of alpha-Synuclein, physical activity, and pesticide exposure on the epigenome

Parkinson's disease (PD) is a neurodegenerative disorder with a complex etiology and increasing prevalence worldwide. As PD is influenced by a combination of genetic and environment/lifestyle factors in approximately 90% of cases, there is increasing interest in identification of the interindividual mechanisms underlying the development of PD as well as actionable lifestyle factors that can influence risk. This narrative review presents an outline of the genetic and environmental factors contributing to PD risk and explores the possible roles of cytosine methylation and hydroxymethylation in the etiology and/or as early-stage biomarkers of PD, with an emphasis on epigenome-wide association studies (EWAS) of PD conducted over the past decade. Specifically, we focused on variants in the SNCA gene, exposure to pesticides, and physical activity as key contributors to PD risk. Current research indicates that these factors individually impact the epigenome, particularly at the level of CpG methylation. There is also emerging evidence for interaction effects between genetic and environmental contributions to PD risk, possibly acting across multiple omics layers. We speculated that this may be one reason for the poor replicability of the results of EWAS for PD reported to date. Our goal is to provide direction for future epigenetics studies of PD to build upon existing foundations and leverage large datasets, new technologies, and relevant statistical approaches to further elucidate the etiology of this disease.

Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions

Regulatory mechanisms associated with repeat-rich sequences and chromosomal conformations in mature neurons remain unexplored. Here, we map cell-type specific chromatin domain organization in adult mouse cerebral cortex and report strong enrichment of Endogenous Retrovirus 2 (ERV2) repeat sequences in the neuron-specific heterochromatic B₂^NeuN+ megabase-scaling subcompartment. Single molecule long-read sequencing and comparative Hi-C chromosomal contact mapping in wild-derived SPRET/EiJ (Mus spretus) and laboratory inbred C57BL/6J (Mus musculus) reveal neuronal reconfigurations tracking recent ERV2 expansions in the murine germline, with significantly higher B₂^NeuN+ contact frequencies at sites with ongoing insertions in Mus musculus. Neuronal ablation of the retrotransposon silencer Kmt1e/Setdb1 triggers B₂^NeuN+ disintegration and rewiring with open chromatin domains enriched for cellular stress response genes, along with severe neuroinflammation and proviral assembly with infiltration of dendrites . We conclude that neuronal megabase-scale chromosomal architectures include an evolutionarily adaptive heterochromatic organization which, upon perturbation, results in transcriptional dysregulation and unleashes ERV2 proviruses with strong neuronal tropism.