Blood Gene Expression Signature Correlates With Low Postmenopausal Bone Density

A cross-dataset transcriptomic analysis and clinical blood validation study identified reproducible osteoclastogenesis-associated gene signatures and confirmed six candidate genes whose expression levels progressively increase alongside deteriorating bone mineral density in postmenopausal women.

Osteoporosis is characterized by reduced bone mass and increased fracture risk, yet minimally invasive molecular correlates of postmenopausal low bone mineral density remain limited, prompting researchers to investigate osteoclastogenesis-related transcriptional programs.

The investigators independently reanalyzed two human osteoclastogenesis RNA-sequencing datasets, GSE225974 and GSE246769, employing differential-expression, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Hallmark gene set enrichment, and cross-dataset concordance analyses to evaluate gene expression changes.

Across the two RNA-sequencing datasets, 1,782 differentially expressed genes were shared, including 1,240 concordantly upregulated and 385 concordantly downregulated genes, exhibiting a strong cross-dataset effect-size correlation of r = 0.74. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses identified replicated sterol and lipid programs, skeletal development, adhesion and integrin pathways, and actin-cytoskeletal programs, while Hallmark gene set enrichment analysis identified 22 concordantly enriched gene sets, including oxidative phosphorylation, fatty acid metabolism, and cholesterol homeostasis.

All six candidate genes—LGALSL, FAXDC2, DHCR7, MYL9, RHOC, and ITGB5—were significantly and concordantly upregulated during osteoclastogenesis in both datasets. Subsequent RT-qPCR analysis in whole blood from 100 postmenopausal women, including 30 with normal bone mineral density, 30 with osteopenia, and 40 with osteoporosis, demonstrated progressively higher relative expression across the three groups for all six candidates, while serum analysis further validated elevated expression of LGALSL, RHOC, MYL9, and ITGB5 in osteoporosis cases.

Clinical evaluations in the study revealed that bone mineral density was positively correlated with calcium intake and physical activity, whereas deteriorating bone health was positively associated with high cholesterol, low body mass index, and early menopause. The researchers concluded that these findings identify reproducible osteoclastogenesis-associated transcriptional programs and support the six candidate genes as a signature correlating with postmenopausal bone mineral density status.

The bioinformatics workflow centered on establishing reproducibility between the GSE225974 and GSE246769 human osteoclastogenesis datasets through concordance and functional enrichment analyses. Among the 1,782 shared differentially expressed genes, 1,240 displayed concordant upregulation and 385 demonstrated concordant downregulation, yielding an effect-size correlation of r = 0.74. Functional annotation via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes confirmed recurring biological themes, specifically sterol and lipid regulation, skeletal system development, cell adhesion and integrin interactions, and actin-cytoskeletal dynamics. Furthermore, Hallmark gene set enrichment identified 22 concordant pathways, highlighting bioenergetic and metabolic alterations such as oxidative phosphorylation, fatty-acid metabolism, and cholesterol homeostasis during osteoclast differentiation.

To translate these transcriptomic signatures into potential minimally invasive indicators, six candidate genes, LGALSL, FAXDC2, DHCR7, MYL9, RHOC, and ITGB5, were examined in patient blood samples. All six targets had demonstrated significant, concordant upregulation in both osteoclastogenesis sequencing profiles. Experimental testing using RT-qPCR across 100 postmenopausal female subjects evaluated expression gradients across thirty participants with normal bone mineral density, thirty diagnosed with osteopenia, and forty with osteoporosis. Relative expression for each candidate gene increased in a stepwise manner from normal bone density through osteopenia to osteoporosis. In addition, serum-based expression profiling corroborated elevated levels of LGALSL, RHOC, MYL9, and ITGB5 specifically among participants with osteoporosis, supporting their relevance in peripheral circulation.

Alongside transcriptional measurements, clinical assessments documented distinct associations between bone health and participant characteristics. Higher bone mineral density was positively correlated with physical activity and dietary calcium intake. In contrast, compromised skeletal status was positively linked with high cholesterol, reduced body mass index, and early menopause. Together, the integration of public sequencing repositories with targeted blood assays provides evidence of shared molecular machinery in osteoclastogenesis while presenting a correlated gene signature for postmenopausal skeletal monitoring.

Subject of Research: Osteoclastogenesis gene signatures in postmenopausal low bone mineral density

Article Title: Osteoclastogenesis associated gene signatures in postmenopausal low bone mineral density: cross-dataset transcriptomics and whole-blood validation

Article References: Anbreen, N., Iqbal, M. J., Wahab, H., Manzoor, S., Tariq, A., Aruge, S., & Menotta, M. (2026). Osteoclastogenesis associated gene signatures in postmenopausal low bone mineral density: cross-dataset transcriptomics and whole-blood validation. Molecular Biology Reports, 53(1), Article 1895. https://doi.org/10.1007/s11033-026-13082-1

Image Credits: AI Generated

DOI: 10.1007/s11033-026-13082-1

Keywords: osteoporosis, bone mineral density, osteoclastogenesis, transcriptomics, RT-qPCR, gene expression, postmenopausal health, biomarkers, associated, gene, signatures, postmenopausal