Molecular mapping in head and neck adenoid cystic carcinoma by pathological grade using whole-exome sequencing and spatial transcriptome

Our previous study demonstrated that pathological grades of adenoid cystic carcinoma (ACC) correlate with distinct prognoses and treatment strategies. To explore the molecular alterations underlying these grades, we performed whole-exome sequencing (WES) on 20 head and neck ACC samples from 12 patients, categorized into grade I-II, grade III, and high-grade transformation (HGT). Comprehensive analyses, including somatic mutations, chromosomal structural variations, and phylogenetic tree construction, were conducted. Spatial transcriptome (ST) technology was further employed to analyze gene expression, pseudo-time trajectories, and copy number variations in a grade III sample. WES revealed that high-grade (grade III and HGT) ACC tissues frequently harbor mutations in TP53, PI3K pathway genes, and chromatin remodelers. Phylogenetic analysis showed that higher-grade regions exhibit more subclonal mutations or a larger proportion of intergenerational mutations. Copy number analysis identified recurrent deletions of 1p36.33 and amplifications of 8q24.21/9p24.1 in high-grade samples, along with significant deletions on chr12 in both WES and ST. ST pathway enrichment and cell trajectory analyses indicated that high-grade clusters are more primitive and proliferative, while low-grade clusters display greater microenvironmental stability and interstitial specialization. These findings highlight the complex spatial heterogeneity associated with ACC pathological grades, providing critical insights into disease progression and guiding therapeutic strategies.