Investigation of candidate genes and mechanisms underlying postmenopausal osteoporosis using bioinformatics analysis

RANK signaling in osteoclast precursors results in a more permissive epigenetic landscape and sexually divergent patterns of gene expression

Background

Sex is an important risk factor in the development of osteoporosis and other bone loss disorders, with women often demonstrating greater susceptibility than men. While variation in sex steroids, such as estradiol, accounts for much of the risk, there are likely additional non-endocrine factors at transcriptional and epigenetic levels that result in a higher rate of bone loss in women. Identification of these factors could improve risk assessment and therapies to preserve and improve bone health.

Methods

Osteoclast precursors were isolated male and female C57Bl/6 mice and cultured with either MCSF alone or MCSF and RANKL. Following the culture period RNA was isolated for RNA sequencing and DNA was isolated for tagmentation and ATAC sequencing. RNA-Seq and ATAC-seq were evaluated via pathway analysis to identify sex- and RANKL-differential transcription and chromatin accessibility.

Results

Osteoclasts demonstrated significant alterations in gene expression compared to macrophages with both shared and differential pathways between the sexes. Transcriptional pathways differentially regulated between male and female cells were associated with immunological functions with evidence of greater sensitivity in male macrophages and female osteoclasts. ATAC-Seq revealed a large increase in chromatin accessibility following RANKL treatment with few alterations attributable to sex. Comparison of RNA-Seq and ATAC-seq data revealed few common pathways suggesting that many of the transcriptional changes of osteoclastogenesis occur independently of chromatin remodeling.

Identification of Serum Exosome-Derived circRNA-miRNA-TF-mRNA Regulatory Network in Postmenopausal Osteoporosis Using Bioinformatics Analysis and Validation in Peripheral Blood-Derived Mononuclear Cells

BACKGROUND

Osteoporosis is one of the most common systemic metabolic bone diseases, especially in postmenopausal women. Circular RNA (circRNA) has been implicated in various human diseases. However, the potential role of circRNAs in postmenopausal osteoporosis (PMOP) remains largely unknown. The study aims to identify potential biomarkers and further understand the mechanism of PMOP by constructing a circRNA-associated ceRNA network.

METHODS

The PMOP-related datasets GSE161361, GSE64433, and GSE56116 were downloaded from the Gene Expression Omnibus (GEO) database and were used to obtain differentially expressed genes (DEGs). Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied to determine possible relevant functions of differentially expressed messenger RNAs (mRNAs). The TRRUST database was used to predict differential transcription factor (TF)-mRNA regulatory pairs. Afterwards, combined CircBank and miRTarBase, circRNA-miRNA as well as miRNA-TF pairs were constructed. Then, a circRNA-miRNA-TF-mRNA network was established. Next, the correlation of mRNAs, TFs, and PMOP was verified by the Comparative Toxicogenomics Database. And expression levels of key genes, including circRNAs, miRNAs, TFs, and mRNAs in the ceRNA network were further validated by quantitative real-time PCR (qRT-PCR). Furthermore, to screen out signaling pathways related to key mRNAs of the ceRNA network, Gene Set Enrichment Analysis (GSEA) was performed.

RESULTS

A total of 1201 DE mRNAs, 44 DE miRNAs, and 1613 DE circRNAs associated with PMOP were obtained. GO function annotation showed DE mRNAs were mainly related to inflammatory responses. KEGG analysis revealed DE mRNAs were mainly enriched in osteoclast differentiation, rheumatoid arthritis, hematopoietic cell lineage, and cytokine-cytokine receptor interaction pathways. We first identified 26 TFs and their target mRNAs. Combining DE miRNAs, miRNA-TF/mRNA pairs were obtained. Combining DE circRNAs, we constructed the ceRNA network contained 6 circRNAs, 4 miRNAs, 4 TFs, and 12 mRNAs. The expression levels of most genes detected by qRT-PCR were generally consistent with the microarray results. Combined with the qRT-PCR validation results, we eventually identified the ceRNA network that contained 4 circRNAs, 3 miRNAs, 3 TFs, and 9 mRNAs. The GSEA revealed that 9 mRNAs participate in many important signaling pathways, such as "olfactory transduction", "T cell receptor signaling pathway", and "neuroactive ligand-receptor interaction". These pathways have been reported to the occurrence and development of PMOP. To sum up, key mRNAs in the ceRNA network may participate in the development of osteoporosis by regulating related signal pathways.

CONCLUSIONS

A circRNA-associated ceRNA network containing TFs was established for PMOP. The study may help further explore the molecular mechanisms and may serve as potential biomarkers or therapeutic targets for PMOP.