Multi-omics and Machine Learning Identify Senescence Targets Linked to CXCL12–CXCR4 T-Cell Responses in Periodontitis

Objectives To characterise senescence-associated fibroblast alterations in periodontitis (PD), identify relevant molecular targets, and examine the relationship between CXCL12–CXCR4 signalling and T-cell responses. Methods We integrated single-cell RNA-sequencing of 26 human gingival samples with bulk and spatial transcriptomics, Xenium in situ profiling, weighted gene coexpression network analysis, five machine-learning algorithms, tissue imaging, and cell-based assays. H₂O₂-induced senescent human gingival fibroblasts and their conditioned medium were used to assess CXCL12 expression, Jurkat-cell migration, and inflammatory gene expression in the presence or absence of the CXCR4 antagonist LY2510924. Results Fibroblasts exhibited the highest senescence scores among the major gingival cell populations, with elevated scores in PD. High-senescence fibroblasts showed inflammatory, chemokine, extracellular-matrix-remodelling and metabolic alterations, together with enhanced predicted communication with immune cells. Integrated analyses prioritised CXCL12, PECAM1 and PLAT as PD- and senescence-associated candidate genes. Their combined signature yielded areas under the receiver operating characteristic curve of 0.944 and 0.902 in the discovery and validation datasets, respectively. CXCL12 was predominantly expressed by fibroblasts, enriched in high-senescence fibroblasts and spatially associated with CXCR4-positive T cells. H₂O₂-induced fibroblast senescence increased CXCL12 expression. Conditioned medium from H₂O₂-treated fibroblasts increased Jurkat-cell migration and inflammatory-gene expression, whereas LY2510924 attenuated these responses. Conclusions Multiomics and machine-learning analyses identified senescence-associated molecular alterations in PD. The findings associate fibroblast CXCL12 expression with a CXCR4-antagonist-sensitive component of Jurkat-cell migration and inflammatory transcription in vitro, supporting further investigation of this pathway as a potential host-directed target.