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Series GSE190675 Query DataSets for GSE190675
Status Public on Dec 14, 2021
Title Blood-based miRNA biomarkers as correlates of brain-based miRNA expression
Organism Papio hamadryas
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary To better understand the relationship between peripheral blood- and brain-based epigenetic activity, we conducted a pilot study on captive baboons (Papio hamadryas) to investigate correlations between miRNA expression in peripheral blood mononuclear cells (PBMCs) and 14 different cortical and subcortical brain regions, represented by two study groups comprised of 4 and 6 animals. Using next-generation sequencing, we identified 362 miRNAs expressed at ≥10 read counts in 80% or more of the brain samples analyzed. Nominally significant pairwise correlations (one-sided P<0.05) between peripheral blood and mean brain expression levels of individual miRNAs were observed for 39 and 44 miRNAs in each group. When miRNA expression levels were averaged across animals within the groups, pairwise correlations between PBMCs and individual brain regions are all highly significant (P<2.2x10^-16), although correlations between brain regions are markedly stronger (rs=0.86-0.99) than those between blood and brain (rs=0.47-0.57). Principal component analysis revealed differentiation in miRNA expression between peripheral blood and the brain regions for the first component (accounting for ~75% of variance). Linear mixed effects modeling attributed most of the variance in expression to differences between miRNAs (>70%), with non-significant 7.5% and 13.1% assigned to differences between blood and brain-based samples in the two study groups. Hierarchical UPGMA clustering revealed two major co-expression branches that are evident in both groups, with one comprised of miRNAs hyper-expressed in blood relative to the brain samples, exhibiting an enrichment of miRNAs expressed in immune cells (CD14+, CD15+, CD19+, CD3+, and CD56+ leukocytes) among the top blood-brain correlates. In the other major branch, hypo-expression in the blood samples was observed, with enrichment for miRNAs associated with Alzheimer’s Disease among its top correlates. Although some differentiation was observed between tissue types, these preliminary findings reveal wider correlated patterns between blood- and brain-expressed miRNAs, suggesting the utility of blood-based miRNA profiling for investigating by proxy the epigenetic underpinnings of neurological and neuroinflammatory processes in the brain.
 
Overall design miRNAseq characterization and comparison of peripheral blood mononuclear cells and brain samples obtained from captive baboons.
 
Contributor(s) Carless MA, Kos MZ
Citation(s) 35392269
Submission date Dec 10, 2021
Last update date Apr 19, 2022
Contact name Melanie Anita Carless
E-mail(s) melanie.carless@utsa.edu
Organization name The University of Texas at San Antonio
Street address One UTSA Circle
City San Antonio
State/province Texas
ZIP/Postal code 78249
Country USA
 
Platforms (1)
GPL15440 Illumina Genome Analyzer IIx (Papio hamadryas)
Samples (160)
GSM5728687 Animal 11641, PBMC, index ACAGTG, 1st run [B1_PBMC]
GSM5728688 Animal 11641, PBMC, index ACAGTG, 2nd run [B1_PBMC]
GSM5728689 Animal 11641, cerebellum, index GCCAAT, 1st run [B1_Cb]
Relations
BioProject PRJNA787946
SRA SRP350276

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
GSE190675_Processed_miRNA_expression_data.xlsx 237.2 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record
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