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Series GSE71620 Query DataSets for GSE71620
Status Public on Dec 31, 2015
Title The effects of aging on circadian patterns of gene expression in the human prefrontal cortex
Organism Homo sapiens
Experiment type Expression profiling by array
Summary With aging, significant changes in circadian rhythms occur, including a shift in phase toward a “morning” chronotype and a loss of rhythmicity in circulating hormones. However, the effects of aging on molecular rhythms in the human brain have remained elusive. Here we employed a previously-described time-of-death analyses to identify transcripts throughout the genome that have a significant circadian rhythm in expression in the human prefrontal cortex (Brodmann’s areas (BA) 11 and 47). Expression levels were determined by microarray analysis in 146 individuals. Rhythmicity in expression was found in ~10% of detected transcripts (p<0.05). Using a meta-analysis across the two brain areas, we identified a core set of 235 genes (q<0.05) with significant circadian rhythms of expression. These 235 genes showed 92% concordance in the phase of expression between the two areas. In addition to the canonical core circadian genes, a number of other genes were found to exhibit rhythmic expression in the brain. Notably, we identified more than one thousand genes (1186 in BA11; 1591 in BA47) that exhibited age-dependent rhythmicity or alterations in rhythmicity patterns with aging. Interestingly, a set of transcripts gained rhythmicity in older individuals, which may represent a compensatory mechanism due to a loss of canonical clock function. Thus, we confirm that rhythmic gene expression can be reliably measured in human brain and identified for the first time significant changes in molecular rhythms with aging that may contribute to altered cognition, sleep and mood in later life.
 
Overall design Using the resources of the University of Pittsburgh’s Brain Tissue Donation Program, 210 subjects were identified. Samples were obtained after consent from next-of-kin during autopsies conducted at the Allegheny County Medical Examiner’s Office (Pittsburgh, USA). The absence of lifetime psychiatric disorders was determined by an independent committee of experienced clinical research scientists using information from clinical records, toxicology results and a standardized psychological autopsy. Subjects of unwitnessed death were removed from the study. A total of 146 individuals with the following characteristics were analyzed in this study: mean (range) age of 50.7 (16-96) years, 78% male, 85% Caucasian, mean postmortem interval (PMI) for brain collection 17.3 (4.8-28) hours, mean pH 6.7 (5.8-7.6) and RNA integrity number (RIN) 8.0 (5.9-9.6).
For each subject, the right hemisphere was blocked coronally, frozen and stored at -80C. Blocks containing Brodmann area 11 (BA11) or Brodmann area 47 (BA47) of the orbital PFC were cut on a cryostat, and cortical gray matter was collected for RNA extraction as previously described. All procedures were approved by the University of Pittsburgh’s Institutional Review Board for Biomedical Research and Committee for Research Involving the Dead.
 
Citation(s) 26699485, 28611654
Submission date Jul 31, 2015
Last update date Oct 24, 2019
Contact name Etienne Sibille
E-mail(s) etienne.sibille@camh.ca
Phone 412-624-0804
Organization name University of Pittsburgh
Department Psychiatry
Street address 450 Technology Drive, Suite 231
City Pittsburgh
State/province PA
ZIP/Postal code 15219
Country USA
 
Platforms (1)
GPL11532 [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]
Samples (420)
GSM1841348 BA47 sample #1
GSM1841349 BA47 sample #2
GSM1841350 BA47 sample #3
Relations
BioProject PRJNA291629

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE71620_Phenotype_GEO.txt.gz 2.8 Kb (ftp)(http) TXT
GSE71620_RAW.tar 1.6 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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