Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition

Abstract

Background: Medulloblastoma (MB) is a malignant tumour of the cerebellum which can be classified into four major subgroups based on gene expression and genomic features. Single cell transcriptome studies have defined the cellular states underlying each MB subgroup, however the spatial organisation of these diverse cell states and how this impacts response to therapy remains to be determined. Methods: Here, we used spatially resolved transcriptomics to define the cellular diversity within a sonic hedgehog (SHH) patient-derived model of MB and identify how cells specific to a transcriptional state or spatial location are pivotal in responses to treatment with the CDK4/6 inhibitor, Palbociclib. We integrated spatial gene expression with histological annotation and single cell gene expression data from MB, developing a analysis strategy to spatially map cell type responses within the hybrid system of human and mouse cells and their interface within an intact brain tumour section. Results: We distinguish neoplastic and non-neoplastic cells within tumours and from the surrounding cerebellar tissue, further refining pathological annotation. We identify a regional response to Palbociclib, with reduced proliferation and induced neuronal differentiation in both treated tumours. Additionally, we resolve at a cellular resolution a distinct tumour interface where the tumour contacts neighbouring mouse brain tissue consisting of abundant astrocytes and microglia and continues to proliferate despite Palbociclib treatment. Conclusions: Our data highlight the power of using spatial transcriptomics to characterise the response of a tumour to a targeted therapy and provide further insights into the molecular and cellular basis underlying the response and resistance to CDK4/6 inhibitors in SHH MB.

An imbalance between proliferation and differentiation underlies the development of microRNA-defective pineoblastoma

“…CDK4/6 inhibitors are clinically approved for use in hormone receptor-positive breast cancer and under investigation for treatment of other undifferentiated pediatric and adult tumors that retain intact RB1-E2F responses [20, 40, 64, 65]. Specifically, CDK4/6 inhibitors have been found to induce differentiation in neuroblastoma [66], rhabdomyosarcoma [22], medulloblastoma [67], and prostate cancer [68]. To date, the only known genomic predictors of sensitivity to CDK4/6 inhibition directly drive overexpression of CCND1 , CCND2 , or CCND3 [69].…”

Regulation of Primary Cilia Disassembly Through HUWE1-Mediated TTBK2 Degradation Plays a Crucial Role in Cerebellar Development and Medulloblastoma Growth

“…Given TTBK2's crucial role in stabilizing primary cilia and supporting GNP proliferation, we explored its potential role in SHH-MB. Utilizing spatially resolved transcriptomics from SHH patient-derived orthotopic xenograft MBs (PDOX MBs) (samples 1 and 2) 39 , we investigated the connection between TTBK2 expression and SHH-MB molecular characteristics. PDOX MB cells were separated into TTBK2-positive and negative clusters (Fig.…”

Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery

“…ST also provides a promising tool for identifying spatially relevant regions of drug action within the tumor microenvironment that have biological and therapeutic implications [131]. In the first study that mapped spatially resolved gene expression in Sonic hedgehog (SHH) patient-derived orthotopic xenograft (PDOX) medulloblastoma, a reduction in cellular diversity within the tumor following treatment with the CDK4/6 inhibitor palbociclib was revealed [132]. Interestingly, despite palbociclib treatment, cells at the tumormicroenvironment interface continue to proliferate, suggesting that cells specific to transcriptional states or spatial positions play a critical role in the response to palbociclib therapy.…”