Cocaine-related DNA methylation in neurons in the caudate nucleus alters the three dimensional structure of the IRXA gene cluster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA565243 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10107638.fastq.gz | Fastqsanger.gz | |||
| SRR10107639.fastq.gz | Fastqsanger.gz | |||
| SRR10107640.fastq.gz | Fastqsanger.gz | |||
| SRR10107641.fastq.gz | Fastqsanger.gz | |||
| SRR10107642.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 57 |
Similar Datasets
Project description:This study investigates differences in DNA methylation that are associated with chronic cociane dependence in post-mortem dorsolateral caudate tissue samples from human brain. The data were generated with reduced representation bisulfite sequencing (RRBS) and compared to data generated in caudate tissue from psychiatrically healthy controls.
2021-09-11 | GSE137364 | GEO
Project description:Epigenetic mechanisms, like those involving DNA methylation, are thought to mediate the relationship between chronic cocaine dependence and molecular changes in addiction-related neurocircuitry, but have been understudied in human brain. We initially used reduced representation bisulfite sequencing (RRBS) to generate a methylome-wide profile of cocaine dependence in human post-mortem caudate tissue. We focused on the Iroquois Homeobox A (IRXA) gene cluster, where hypomethylation in exon 3 of IRX2 in neuronal nuclei was associated with cocaine dependence. We replicated this finding in an independent cohort and found similar results in the dorsal striatum from cocaine self-administering mice. Using epigenome editing and 3C assays, we demonstrated a causal relationship between methylation within the IRX2 gene body, CTCF protein binding, three-dimensional (3D) chromatin interaction, and gene expression. Together, these findings suggest that cocaine-related hypomethylation of IRX2 contributes to the development and maintenance of cocaine dependence through alterations in 3D chromatin structure in the caudate nucleus.
| S-EPMC8039060 | biostudies-literature
Project description:The 10 samples below represent a study where gene expression levels were measured in 5 different parts of the rat brain under cocaine-treated (GSM4696, GSM4698 - GSM4701) and saline-treated control (GSM4702 - GSM4706) conditions. The regions studied were amygdala (amy), caudate putamen (cpu), nucleus acumbens (na), prefrontal cortex (cpu), and the ventral tegmental area (vta). The data were analyzed using two different computational techniques, viz. singular value decomposition (SVD) and self-organizing maps (SOM), to identify a common set of genes that were regulated by cocaine administration. Keywords = cocaine Keywords = oligonucleotide microarrays Keywords = svd Keywords = som Keywords: repeat sample
2003-03-13 | GSE340 | GEO
Project description:Cocaine use disorder (CUD) is an intractable syndrome, and rising overdose death rates represent a significant public health crisis that exacts tremendous personal and financial costs on patients and society. Sharp increases in cocaine use drive the urgent need for better mechanistic insight into this chronic relapsing brain disorder that currently lacks effective treatment options. To investigate the transcriptomic changes involved, we conducted RNA sequencing on two striatal brain regions that are heavily implicated in CUD, the nucleus accumbens and caudate nucleus, from postmortem brains of subjects with CUD and matched control subjects. Weighted gene co-expression analyses identified CUD-specific gene networks enriched in ionotropic receptors and associated with lowered neuroinflammation, contrasting the proinflammatory responses found in opioid use disorder. Integration of comprehensive transcriptomic datasets from mouse cocaine self-administration models revealed evolutionarily conserved gene networks in CUD that implicate especially D1 medium spiny neurons as drivers of cocaine-induced plasticity.
2022-12-19 | GSE214267 | GEO
Project description:The 10 samples below represent a study where gene expression levels were measured in 5 different parts of the rat brain under cocaine-treated (GSM4696, GSM4698 - GSM4701) and saline-treated control (GSM4702 - GSM4706) conditions. The regions studied were amygdala (amy), caudate putamen (cpu), nucleus acumbens (na), prefrontal cortex (cpu), and the ventral tegmental area (vta). The data were analyzed using two different computational techniques, viz. singular value decomposition (SVD) and self-organizing maps (SOM), to identify a common set of genes that were regulated by cocaine administration.
2007-10-10 | E-GEOD-340 | biostudies-arrayexpress
Project description:Global changes in gene expression that underlie the circuit and behavioral dysregulation associated with cocaine addiction remain incompletely understood. Here, we determined how a history of cocaine self-administration (SA) “re-programs” transcriptome-wide responses at baseline and in response to cocaine re-exposure after prolonged withdrawal (WD). We assigned male mice to one of six groups: saline or cocaine SA + 24 hr WD; or saline/cocaine SA + 30 d WD + an acute saline/cocaine challenge within the previous drug-paired context. RNA-seq was then conducted on six interconnected brain reward regions. We focused on patterns of gene expression that were altered by cocaine SA, in particular, molecular targets that show priming or desensitization upon re-exposure to cocaine. Genes that were affected uniquely by acute cocaine after cocaine SA+WD displayed region-specific regulation. The greatest number of regulated genes were seen in nucleus accumbens, dorsal striatum, and basolateral amygdala. Further analysis revealed several transcription factors as key upstream regulators in these three regions, including several not previously implicated in cocaine action. Regulation of subsets of these primed and desensitized genes correlated robustly with SA behavior displayed by individual mice. For example, analysis of transcriptome-wide expression changes revealed that genes associated with cocaine intake respond to contextual information in a region-specific manner. This comprehensive picture of transcriptome-wide regulation by cocaine SA and WD throughout the brain’s reward circuitry provides new insight into the molecular basis of cocaine addiction, which will guide future studies of the key molecular pathways involved.
2018-08-22 | GSE110344 | GEO
Project description:To identify specific cell populations that respond to acute cocaine exposure, we analyzed single cell transcriptional responses in duplicate samples of flies that consumed fixed amounts of sucrose or sucrose supplemented with cocaine, in both sexes. Unsupervised clustering of the transcriptional profiles of a total of 86,224 cells yielded 36 distinct clusters. Annotation of clusters based on gene markers revealed that all major cell types (neuronal and glial) as well as neurotransmitter types from most brain regions were represented. The brain transcriptional responses to cocaine showed profound sexual dimorphism and were considerably more pronounced in males than females. Differential expression analysis within individual clusters indicated cluster-specific responses to cocaine. Clusters corresponding to glia and Kenyon cells of the mushroom bodies showed especially large transcriptional responses following cocaine exposure. Cluster specific co-expression networks and global interaction networks revealed a diverse array of cellular processes affected by acute cocaine exposure. These results provide an atlas of sexually dimorphic cocaine-modulated gene expression in a model brain.
2021-01-29 | GSE152495 | GEO
Project description:Gut-microbiota membership is associated with diverse neuropsychological-diseases, including substance use disorders (SUDs). Unravelling mechanistic interactions between gut microbes and the host during psychostimulant use remains challenging. Here we show that cocaine exposure increases intestinal levels of norepinephrine, sensed through the bacterial adrenergic receptor QseC, promoting intestinal colonization of g-Proteobacteria. Gut colonization by g-Proteobacteria depletes the neuroactive metabolite glycine (used as a nitrogen source) both in the gut and cerebrospinal fluid, enhancing host cocaine-induced behaviors. Glycine repletion reversed this response, and intestinal colonization by g-Proteobacteria unable to uptake glycine did not alter the host response to cocaine. Transcriptomic profiling indicates a role of g-Proteobacteria modulated glycine levels in cocaine induced transcriptional plasticity in the nucleus accumbens through the glutamatergic transmission. Altogether, we introduce a mechanism by which intestinal bacteria alter the host’s brain responses to cocaine that could be exploited to modulate reward-related brain circuits that contribute to SUDs.
2022-09-07 | GSE212421 | GEO
Project description:Prior research demonstrated that environmental enrichment creates individual differences in behavior leading to a protective addiction phenotype in rats. Understanding the mechanisms underlying this phenotype will guide selection of targets for much-needed novel pharmacotherapeutics. The current study investigates basal differences in proteome expression in the nucleus accumbens of enriched and isolated rats and the proteomic response to cocaine self-administration using a liquid chromatography mass spectrometry (LCMS) technique to quantify 1917 proteins. Results of complementary Ingenuity Pathways Analyses (IPA) and gene set enrichment analyses (GSEA) demonstrate that cocaine increases vesicular transporters for dopamine and glutamate, as well as increasing proteins in the RhoA pathway. Further, cocaine regulates proteins related to ERK, CREB and AKT signaling. Environmental enrichment altered expression of a large number of proteins with diverse functions, including mood disorders, energy production, ubiquitination, splicing, transport, kinases and neurodegenerative diseases. Most of the biological functions and pathways listed above were also identified in the Cocaine X Enrichment interaction analysis, providing clear evidence that enriched and isolated rats respond quite differently to cocaine exposure. The overall impression of the current results is that enriched saline-administering rats have a unique proteomic complement compared to enriched cocaine-administering rats as well as saline and cocaine-taking isolated rats. These results identify possible mechanisms of the protective phenotype and provide fertile soil for developing novel pharmacotherapeutics.
2014-07-22 | PXD000990 | Pride
Project description:Cocaine is one of the most abused psychostimulants in the United States. In addition to its established roles in the regulation of dopaminergic circuitries, cocaine has a broader mechanism of action, including global alterations in brain metabolism and mitochondrial homeostasis. Our group recently identified a subpopulation of non-microvesicular, non-exosomal extracellular vesicles of mitochondrial origin, mitovesicles (mtVs), and provided a method to isolate mtVs from brain parenchyma. Given their origin, we hypothesized that mtVs could be affected by mitochondrial abnormalities induced by chronic cocaine exposure. Therefore, we analyzed mtVs from hemibrains of 3-month-old mice that received for two weeks intraperitoneal injections of cocaine or saline as control. MtVs from the brain extracellular space of cocaine-intoxicated mice were enlarged and more numerous when compared to controls. Moreover, cocaine stimulated higher intracellular mitochondrial fission and higher levels of upstream (but not downstream) mitophagy pathways, suggesting increased mitochondrial fragmentation and a block in mitophagy flux. Lastly, cocaine impaired brain mtV cargo loading as revealed by Mass Spec analysis, causing an alteration in mtV ATP production capacity. These data suggest that mtVs are a previously unidentified player in the biology of cocaine addiction and that target therapies to fine tune brain mtV functionality may be beneficial to mitigate chronic cocaine pathology.
2022-04-27 | MSV000089323 | MassIVE