Single-cell and spatial transcriptomics unveils key regulators governing cell differentiation for Schistosoma sexual development

Abstract Schistosomiasis remains a major global health challenge, primarily due to the large number of egg production by sexually mature parasites. The cellular basis and regulatory programs governing sexual development and egg production are poorly characterized, hindering the identification of effective targets for disease intervention. Here, we construct a dynamic single-cell atlas of Schistosoma japonicum (S. japonicum) covering key development stages of sexual maturation and egg production, and integrated it for the first time with spatial transcriptomics to map tissue-resolved cellular niches. Through bioinformatic analysis and experimental validation, we identify critical cell populations and regulatory networks that drive parasite development and egg laying. By mapping de novo identified transcription factors (TFs) onto these atlases, we generate a comprehensive spatiotemporal expression profile and define the regulatory programs of several tissue specific TFs including Zfp, Fbp3, and Lim. Integrated re-clustering further reveals and validates key regulators of germline stem cell differentiation. Finally, comparative analyses with S. mansoni single-cell datasets revealed both conserved and species-divergent cellular plasticity, providing unprecedented insights into their distinct biological traits. Collectively, our comprehensive study establishes a foundational resource for understanding schistosome biology, deciphers regulatory programs underlying cell differentiation and pathogenicity, and accelerates the identification of effective targets to combat this devastating disease. Competing Interest Statement The authors have declared no competing interest.