Laser microdissection-based multi-omics integration unveils the pathological atlas and tumor differentiation network of adamantinomatous craniopharyngioma.

Although adamantinomatous craniopharyngioma (ACP) is a histologically benign intracranial tumor, its invasive growth pattern, characterized by finger-like protrusions, leads to a poor prognosis. In-depth analysis of the heterogeneity of the pathological structure of ACP and the development and evolution of tumor cells is crucial for expanding precision treatment strategies. However, a detailed understanding of the complex pathological structural characteristics of ACP is lacking. Here, we used laser microdissection to obtain 40 samples from 6 different pathological structures for Smart-Seq2 sequencing and conducted in-depth analysis of 6 single-nucleus RNA sequencing samples and 4 spatial transcriptome samples. We also performed comprehensive validation using 3 external single-cell databases. Through histopathological observation, multiomic analysis, and immunofluorescence staining, we resolved the single-cell expression profiles of two distinct functional subpopulations of the whorl-like cell clusters, providing insights into their potential biological roles in tumor progression. Additionally, we discovered the epithelial-mesenchymal transition (EMT) or partial EMT development direction of the stellate reticulum and different cell fates related to terminal keratinization. Moreover, we reported the presence of previously neglected cyst-wall epithelium and the constitutive epithelium within ACP. The latter was found to possess basal cell characteristics and act as a potential progenitor cell pool for tumor maintenance and evolution. Through pseudotime analysis combined with co-expression network analysis, we constructed a differentiation regulatory network based on the constitutive epithelium. Our research results complement existing knowledge and provide a comprehensive analysis of the pathological features of ACP, providing new concepts and targets for precision targeted therapy.