Skeletal Class II malocclusion is a common dentofacial deformity often associated with dysregulation in the growth and remodeling of periodontal tissues. Understanding the cellular heterogeneity and molecular pathways of periodontal ligament (PDL) cells is crucial for identifying novel therapeutic targets. However, traditional bulk sequencing methods lack the resolution to distinguish cell-type-specific gene expression and epigenetic regulation, limiting insights into the pathogenesis of this condition. To address these limitations, we propose an integrated framework utilizing 5200 high-quality PDL Single-Cell RNA combined with Assay for Transposase-Accessible Chromatin using sequencing (scRNA-ATAC-seq) to perform a multi-omics dissection of PDL cells in Class II malocclusion. This approach enables the simultaneous profiling of transcriptomic and chromatin accessibility landscapes at single-cell resolution, uncovering cell-specific regulatory networks. Using this scRNA-ATAC-seq method, we successfully identified 12 distinct PDL cell subpopulations and revealed key transcription factors and signaling pathways involved in aberrant skeletal development. Data integration achieved a 0.94 accuracy score, enabling confident regulatory mapping. The findings provide critical insights into the gene regulatory architecture underlying Class II malocclusion and highlight potential cell-specific therapeutic targets for clinical intervention.
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