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 show that cells specific to a transcriptional state or spatial location are pivotal for CDK4/6 inhibitor, Palbociclib, treatment response. We integrated spatial gene expression with histological annotation and single-cell gene expression data from MB, developing an 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].…”

Heterogeneity and tumoral origin of medulloblastoma in the single-cell era

“… Hendrikse et al [ 102 ] Human Mouse scRNA-seq snRNA-seq SHH, G3, G4, G3 cell lines, Human cerebellum EGAS00001005826; GSE189238; GSE200791 Human specific split of RL to RL VZ and RL SVZ and Group 4/3 MBs tumors arise from UBC progenitors within the RL SVZ Smith et al [ 101 ] Human scRNA-seq snRNA-seq SHH, G3, G4, human cerebellum, human cerebellum organoids GSE207266 Human specific split of RL to RL VZ and RL SVZ , Group 3/4 MBs tumor cells arise from GlutaCN/UBC progenitors of the RL SVZ and are defined by the extent of their differentiation. Okonechnikov et al [ 98 ] Human scRNA-seq snRNA-seq SHH, G3, G4, human cerebellum www.brain-match.org Subgroup-specific resemblance of tumor cells to neuronal lineages of the developing human cerebellum Dang et al [ 120 ] Mouse scRNA-seq Mouse model of SHH GSE166691 TAMs heterogeneity in SHH MBs and increased TAM subpopulation after radiation along with decreased T cells and neutrophils infiltration Vo et al [ 126 ] PDOX ST-seq PDOX model of SHH https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-11720 CDK4/6 inhibition treatment with Palbociclib leads to reduced cellular heterogeneity and higher levels of neuronal differentiation within tumors Luo et al [ 103 ] Human scRNA-seq snATAC-seq SHH, G3, G4, Human cerebellum GSE198565; EGAD00001004435; CNP0002781 TCP is a putative cellular origin for Group 3 MBs and tumor-driver networks within TCP-like cells as the potential therapeutic avenues MFNs mossy fiber neuron, GNPs granule neuron progenitors, GlutaCN glutamatergic cerebellum nuclei, UBCs unipolar brush cells, TCPs transitional cerebellum progenitors, RL VZ rhombic lip ventricular zone, RL SVZ rhombic lip subventricular zone, TAMs tumor-associated macrophages, PDOX patient-derived orthotopic xenograft, ...…”

“…Recently, the spatial transcriptomics sequencing (ST-seq) technology has emerged as a powerful tool to address the limitations of scRNA-seq, providing whole transcriptome analysis across intact tissue sections without dissociation of cells from their in situ localization [ 121 – 125 ]. Vo et al performed ST-seq to investigate the spatial organization of cells in patient-derived orthotopic xenograft (PDOX) SHH MB sections [ 126 ]. ST-seq identified and accurately mapped cell subpopulations across the tumor regions and surrounding cerebellum cortex.…”

Drivers Underlying Metastasis and Relapse in Medulloblastoma and Targeting Strategies

“…Since then, the number of clinical trials investigating this treatment avenue for pediatric brain tumors has exploded and is most commonly combined with chemotherapy and exclusively for Rb-positive tumors; some are currently open (e.g., NCT03434262, NCT05429502, NCT03387020, NCT03709680, NCT03526250, NCT03155620, NCT04238819). Preclinical evidence supporting CDK4/6 inhibition for MB is rather strong [111,112] and the understanding of regrowth mechanisms and cell states has expanded to spatial-transcriptomics resolution [113]. The fact that MB tumors become more homogenous by differentiating towards the neuronal lineage but with some potential for self-renewal implies that drug combination regimens are the way to go, as also suggested in [111].…”