GeneSet Information

Tier IV GS404756 • Up regulated genes from caudate nucleus (from dorsal striatum) from postmortem human brain tissue with Alcohol Use Disorder (AUD)

DESCRIPTION:

Postmortem human brain tissue from the caudate nucleus region of a total of 48 individuals with Alcohol Use Disorder (AUD) and 51 control individuals were taken and RNA extracted from frozen tissue. Sequencing was carried out using the NovaSeq 6000 (Illumina) platform, and gene expression analysis was carried out with respect to AUD and control samples. Gene symbols from Entrez ids are used and Logbase2 FC as provided by the authors are annotated.

LABEL:

Up regulated genes from caudate nucleus

SCORE TYPE:

Effect

THRESHOLD:

<= 0.5

GENES IN THRESHOLD:

0

DATE ADDED:

2022-07-08

DATE UPDATED:

2024-10-22

SPECIES:

AUTHORS:

Lea Zillich, Eric Poisel, Josef Frank, Jerome C Foo, Marion M Friske, Fabian Streit, Lea Sirignano, Stefanie Heilmann-Heimbach, André Heimbach, Per Hoffmann, Franziska Degenhardt, Anita C Hansson, Georgy Bakalkin, Markus M Nöthen, Marcella Rietschel, Rainer Spanagel, Stephanie H Witt

TITLE:

Multi-omics signatures of alcohol use disorder in the dorsal and ventral striatum.

JOURNAL:

Translational psychiatry 05 2022, Vol 12, pp. 190

ABSTRACT:

Alcohol Use Disorder (AUD) is a major contributor to global mortality and morbidity. Postmortem human brain tissue enables the investigation of molecular mechanisms of AUD in the neurocircuitry of addiction. We aimed to identify differentially expressed (DE) genes in the ventral and dorsal striatum between individuals with AUD and controls, and to integrate the results with findings from genome- and epigenome-wide association studies (GWAS/EWAS) to identify functionally relevant molecular mechanisms of AUD. DNA-methylation and gene expression (RNA-seq) data was generated from postmortem brain samples of 48 individuals with AUD and 51 controls from the ventral striatum (VS) and the dorsal striatal regions caudate nucleus (CN) and putamen (PUT). We identified DE genes using DESeq2, performed gene-set enrichment analysis (GSEA), and tested enrichment of DE genes in results of GWASs using MAGMA. Weighted correlation network analysis (WGCNA) was performed for DNA-methylation and gene expression data and gene overlap was tested. Differential gene expression was observed in the dorsal (FDR < 0.05), but not the ventral striatum of AUD cases. In the VS, DE genes at FDR < 0.25 were overrepresented in a recent GWAS of problematic alcohol use. The ARHGEF15 gene was upregulated in all three brain regions. GSEA in CN and VS pointed towards cell-structure associated GO-terms and in PUT towards immune pathways. The WGCNA modules most strongly associated with AUD showed strong enrichment for immune response and inflammation pathways. Our integrated analysis of multi-omics data sets provides further evidence for the importance of immune- and inflammation-related processes in AUD. PUBMED: 35523767
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Annotation Information

No sequence read archive data associated with this GeneSet.


Brain (D001921)
RNA (D012313)
Humans (D006801)
DNA (D004247)
Caudate Nucleus (D002421)
Putamen (D011699)
Immunity (D007109)
Genome (D016678)
Gene Expression Profiling (D020869)
Gene Expression (D015870)
Morbidity (D009017)
Tissues (D014024)
Genes (D005796)
Inflammation (D007249)
Cells (D002477)
Id (D007060)
Mortality (D009026)
Association (D001244)
Alcoholism (D000437)
Methylation (D008745)
striatum (MA:0000891)
putamen (MA:0000895)
caudate nucleus (MA:0000894)
dorsal striatum (MA:0002971)
brain (MA:0000168)
ventral striatum (MA:0002972)
addiction (MP:0002555)
abnormal inflammatory response (MP:0001845)
methylation (GO:0032259)
inflammatory response (GO:0006954)
immune response (GO:0006955)
nucleus (GO:0005634)
gene expression (GO:0010467)
RNA (EDAM_topic:0099)
Structure (EDAM_data:0883)
Gene expression analysis (EDAM_operation:2410)
Analysis (EDAM_operation:2945)
Genetics (EDAM_topic:3053)
Gene expression profile annotation (EDAM_operation:2436)
dna (EDAM_format:1212)
Sequencing (EDAM_topic:3168)
Microarray data (EDAM_data:2603)
Pathway or network (EDAM_data:2600)
Transcriptomics (EDAM_topic:0203)
Data (EDAM_data:0006)
Gene expression data processing (EDAM_operation:2495)
Evidence (EDAM_data:2042)
Pathways, networks and models (EDAM_topic:0602)
RNA-Seq (EDAM_topic:3170)
rna (EDAM_format:1213)
DNA (EDAM_topic:0654)
deoxyribonucleic acid (CHEBI:16991)
ethanol (CHEBI:16236)
alcohol (CHEBI:30879)
ribonucleic acid (CHEBI:33697)
atomic nucleus (CHEBI:33252)
developmental similarity evidence (ECO:0000067)
evidence (ECO:0000000)
alcohol abuse (DOID:1574)
disease (EFO:0000408)
mortality (EFO:0004352)
ventral (EFO:0001662)
transcription profiling by high throughput sequencing (EFO:0002770)
dorsal (EFO:0001656)
control (EFO:0001461)
RNA-seq assay (MMO:0000659)
putamen (UBERON:0001874)
caudate nucleus (UBERON:0001873)
brain (UBERON:0000955)
tissue (UBERON:0000479)
neural nucleus (UBERON:0000125)
caudate-putamen (UBERON:0005383)
dorsal striatum (UBERON:0005382)
anatomical projection (UBERON:0004529)
adult cerebral ganglion (UBERON:6110636)
striatum (UBERON:0002435)
ventral striatum (UBERON:0005403)
tissue (MA:0003002)

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