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Series GSE186922 Query DataSets for GSE186922
Status Public on Nov 04, 2021
Title Identification of known and novel long non-coding RNAs potentially responsible for the effects of BMD GWAS loci
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Osteoporosis, characterized by low bone mineral density (BMD), is the most common complex disease affecting bone and constitutes a major societal health problem. Genome-wide association studies (GWASs) have identified over 1100 associations influencing BMD. It has been shown that perturbations to long non-coding RNAs (lncRNAs) influence BMD and the activities of bone cells; however, the extent to which lncRNAs are involved in the genetic regulation of BMD is unknown. Here, we combined the analysis of allelic imbalance (AI) in human acetabular bone fragments with a transcriptome-wide association study (TWAS) and expression quantitative trait loci (eQTL) colocalization analysis using data from the Genotype-Tissue Expression (GTEx) project to identify lncRNAs potentially responsible for GWAS associations. We identified 27 lncRNAs in bone that are located in proximity to a BMD GWAS association and harbor SNPs demonstrating AI. Using GTEx data we identified an additional 31 lncRNAs whose expression was associated (FDR correction<0.05) with BMD through TWAS and had a colocalizing eQTL (regional colocalization probability (RCP)>0.1). The 58 lncRNAs are located in 43 BMD associations. To further support a causal role for the identified lncRNAs, we show that 23 of the 58 lncRNAs are differentially expressed as a function of osteoblast differentiation. Our approach identifies lncRNAs that are potentially responsible for BMD GWAS associations and suggest that lncRNAs play a role in the genetics of osteoporosis.
 
Overall design Acetabular reaming from 17 Boston Medical Center (BMC) patients (ages 43-80 year) undergoing elective hip arthroplasty were collected: 12 Females and 5 Males; 8 Black, 8 White, and 1 Hispanic
 
Contributor(s) Abood A, Farber C
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Submission date Nov 01, 2021
Last update date Nov 06, 2021
Contact name Abdullah Abood
E-mail(s) aa9gj@virginia.edu
Phone 5712744329
Organization name University of Virginia
Lab Farber lab
Street address OMS, Room 3817B
City CHARLOTTESVILLE
State/province VA
ZIP/Postal code 22908
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (17)
GSM5663755 acentabular bone reamings [102]
GSM5663756 acentabular bone reamings [103]
GSM5663757 acentabular bone reamings [105]
Relations
BioProject PRJNA776822
SRA SRP344025

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
GSE186922_RAW.tar 398.8 Mb (http)(custom) TAR (of GTF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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