Ifi27l2a is a Candidate Gene Associated With Osteoclast-Related Transcriptional Remodeling in the Aging Bone Marrow

Age-related bone loss is closely linked to inflammaging in the bone marrow microenvironment, but the molecular factors connecting immune remodeling to bone metabolic imbalance remain incompletely defined. This study aimed to identify aging-associated genes related to inflammatory remodeling in the bone marrow and to provide preliminary cellular evidence for a prioritized candidate.

Public bulk RNA-seq (GSE132040) and single-cell RNA-seq (GSE132042) datasets from physiologically aging mice were analyzed using an integrated workflow. Differentially expressed genes (DEGs) were identified from bulk RNA-seq data, followed by Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA). Candidate genes were prioritized using least absolute shrinkage and selection operator (LASSO) regression and support vector machine-recursive feature elimination (SVM-RFE). Single-cell RNA-seq was used to examine the cellular distribution of the candidate gene within bone marrow cell populations. For cellular validation, Ifi27l2a was knocked down in RAW264.7 cells using lentiviral shRNA, followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR) and transcriptomic analysis. Primary bone marrow-derived macrophages (BMMs) were further used for TRAP staining-based assessment under M-CSF/RANKL-induced osteoclastogenic conditions.

A total of 313 DEGs were identified between young and aged bone marrow samples, with enrichment mainly in antiviral, host-defense, and immune-related processes. Integrated LASSO and SVM-RFE screening prioritized Ifi27l2a for further analysis. Whole-bone-marrow bulk RNA-seq analysis showed an age-associated decline in Ifi27l2a expression, whereas single-cell analysis showed a monocyte-enriched distribution. In RAW264.7 cells, Ifi27l2a knockdown reduced Il6 and Tnf expression and was accompanied by broader transcriptomic remodeling involving inflammatory programs and osteoclast-related transcriptional changes. Pathway analysis showed significant positive enrichment of the rheumatoid arthritis pathway and suggestive enrichment of the osteoclast differentiation pathway. In primary BMMs, TRAP staining showed that Ifi27l2a knockdown was associated with altered osteoclast-like morphology under M-CSF/RANKL stimulation.

These findings identify Ifi27l2a as a bone marrow aging-associated candidate gene with monocyte-enriched expression and a potential link to inflammatory and osteoclast-lineage remodeling. The current study supports an association between Ifi27l2a reduction, macrophage-lineage transcriptional remodeling, and osteoclast-like morphological changes, rather than definitive causality. Further in vivo validation of bone phenotypes and pathway-level studies are needed to clarify its role in age-related bone remodeling.