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This research aims to identify the role of the autophagy-related gene ATG7 in osteoporosis by integrating single-cell and microarray data.

March 21, 2026Open Access

Integrating Single-Cell and Microarray Data to Explore the Role of Autophagy-Related Gene Atg7 in Osteoporosis

Key Points

This research aims to identify the role of the autophagy-related gene ATG7 in osteoporosis by integrating single-cell and microarray data.
Integrated single-cell RNA sequencing and microarray datasets to identify relevant genes.
Used an ovariectomized mouse model for in vivo experiments.
Conducted micro-CT and immunohistochemistry to verify findings.
Performed qRT-PCR and Western blot to assess gene expression levels.
Applied pseudotime analysis to explore cell differentiation trajectories.
Found a strong correlation between ATG7 expression and EYA1 mesenchymal stem cell subpopulations.
Observed decreased ATG7 expression as osteoporosis progressed.
Identified reduced expression of autophagy and osteogenesis-related markers in MSCs from OVX mice.
Restored expression levels of markers through ATG7 overexpression, indicating its role in autophagy and osteogenesis.

Abstract

Purpose: Osteoporosis is a metabolic bone disorder characterized by reduced bone mass, impaired microarchitecture, and diminished bone strength, resulting in a significantly elevated risk of fractures. It is especially prevalent among older adults, particularly postmenopausal females, and profoundly impacts quality of life. In this study, we integrated osteoporosis-related single-cell RNA sequencing (scRNA-seq) and microarray datasets, to identify the autophagy-related gene ATG7 , which is associated with osteoporosis. Methods: By integrating single-cell transcriptomics with chip data, autophagy-related genes associated with osteoporosis were screened, and cell-cell interactions and developmental trajectories were explored using cell communication and pseudotime analysis. An ovariectomized (OVX) mouse model was established, and verification was performed using micro-CT and immunohistochemistry techniques. Dual-labeled three-color fluorescence technology was employed to further validate the pseudotime analysis results. Additionally, qRT-PCR, Western blot, and other experiments were conducted to assess the expression levels of related genes. Further, ATG7 was overexpressed in OVX mouse BMSCs to investigate its impact on the autophagy process and osteogenic marker proteins. Results: Pseudotime trajectory analysis revealed a strong link between ATG7 expression and the EYA1 mesenchymal stem cell (MSC) subpopulation. The proportion of EYA1-positive cells and ATG7 expression decreased as osteoporosis progressed.MSCs isolated from OVX mice exhibited diminished expression of autophagy- and osteogenesis-related marker proteins compared to those from normal mice. ATG7 overexpression effectively restored the expression levels of these markers, suggesting its functional role in promoting autophagy and osteogenesis under OP conditions. Conclusion: These findings highlight ATG7 as a critical regulator of MSC differentiation, suggesting that it may serve as a promising therapeutic target for osteoporosis. Modulation of autophagy pathways through ATG7 holds potential for future clinical applications in osteoporosis prevention and treatment. Keywords: osteoporosis, autophagy, single-cell analysis, microarray data, pseudotime trajectory

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