Exth-66. single-cell spatiotemporal genomics reveals clonal evolution and therapeutic target in recurrent disseminated medulloblastoma

Abstract Despite the cellular heterogeneity observed in single-cell studies of medulloblastoma, limited knowledge exists regarding the genetic features and spatiotemporal states of specific cell populations following tumor relapse and dissemination, leading to a lack of effective treatment strategies. In this study, we conducted single-cell transcriptomic, chromatin accessibility, and spatial transcriptomic analyses on 15 primary and recurrent Group 3 medulloblastomas, along with two PDX models (including a lung metastasis model). Subsequently, we deconvoluted our findings with our RNA-seq cohort to further validate cell cluster-specific gene expression associated with relapse and its prognostic significance. We analyzed malignant cells, including cancer stem cells (MB-CSCs), proliferating cells, and differentiated cell populations, and examined gene expression features closely associated with clinical prognosis. To elucidate the origin and maturation process of these malignant cells accurately, we compared tumor cell profiles with early human cerebellar cell-types. Furthermore, we described the spatiotemporal transitions from MB-CSCs to terminal states, with a particular emphasis on the extensive spatial heterogeneity within the tumor during the processes of primary, local relapse, and dissemination. Through computational non-negative matrix factorization (cNMF) analysis, we identified a group of tumor cells in recurrent Group 3 medulloblastoma with high cellular plasticity (HCP), demonstrating strong stemness and proliferative capabilities, as well as the ability to differentiate into multiple functional tumor cell subgroups. This cell population exhibited elevated expression of PTPRZ1, which phosphorylates downstream molecules to promote tumor progression. Through single-cell transcriptomic and chromatin accessibility analyses, we validated the expression of PTPRZ1 in human samples, PDX samples, and transgenic mouse samples. In vitro and in vivo inhibition of PTPRZ1 function using small molecule inhibitors effectively suppressed tumor proliferation and metastatic activity. By employing single-cell spatiotemporal genomics, we elucidated the evolutionary states and subclonal events of primary and recurrent medulloblastoma, and identified PTPRZ1 as a target for effectively inhibiting tumor progression.