Single cell mass spectrometry reveals intercellular compartmentalization of camptothecin biosynthesis in the tree Camptotheca acuminata

Abstract The medicinal tree Camptotheca acuminata produces camptothecin, a monoterpenoid indole al- kaloid (MIA) precursor for several leading chemotherapeutic agents (Lorence and Nessler 2004). Alt- hough the biosynthesis of camptothecin remains poorly understood, a putative route has been hypothe- sized based on in planta metabolite profiling and feeding studies (Fig. 1a) (Sheriha and Rapoport 1976; Sadre et al. 2016). However, pathways proposed on whole-tissue or organ-level metabolomic and tran- scriptomic data lack resolution on the intricate, cell-specific compartmentalization of natural products biosynthesis. Such gaps could be addressed by single cell technologies, which have recently shown tremendous potential to transform gene discovery in herbaceous plants (Li et al. 2023; Zhan et al. 2023; Vu et al. 2024; Wu et al. 2024; McClune et al. 2025). Nevertheless, single cell mass spectrometry (scMS) has not been adapted for woody species, largely due to the challenges associated with their highly lignified tissue and complex cellular architecture. In this study, we developed an scMS pipeline for the woody tree C. acuminata to investigate the intercellular organization of camptothecin biosynthesis.