Ricca, D. | bioRxiv Science

bioRxiv2025

Glioblastoma stem cell morphotypes convey distinct cell states and clinically relevant functions

Glioblastoma (GBM) is an aggressive brain tumor and an unmet clinical need due to its invasiveness and therapy-resistance. These features are driven by glioblastoma stem cells (GSCs), which exhibit remarkable functional heterogeneity. However, GSC transcriptional profiling alone cannot predict clinically relevant behaviors. Here, we developed CellShape-seq, a spatial transcriptomics platform that integrates cell morphology with transcriptome. This identified three GSC morphoclasses corresponding to distinct transcriptomic states and functions: (1) nonpolar cells show differentiation and therapy sensitivity, (2) elongated cells are invasive, and (3) multipolar cells form intercellular networks. Importantly, chemoresistance is morphoclass-specific: elongated GSCs depend on YAP/TEAD1 signaling, while multipolar GSCs rely on gap junction-mediated networks. Targeting these vulnerabilities with specific inhibitors sensitized resistant GSC morphoclasses to temozolomide (TMZ) in patient-derived organoids. Our findings demonstrate that morphology provides critical insights into GSC behavior and establish a rationale for morphology-informed therapies to overcome resistance and improve outcomes in GBM. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/644884v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@141e698org.highwire.dtl.DTLVardef@18a238corg.highwire.dtl.DTLVardef@23ef62org.highwire.dtl.DTLVardef@1390c07_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single cell resolution

The combination of brain organoid and single cell omic technologies holds transformative potential to dissect human neurobiology at high resolution and with mechanistic precision. Delivering this promise in the context of human neurodiversity, physiological and pathological alike, requires however a major leap in scalability, given the need for experimental designs that include multiple individuals and, prospectively, population cohorts. To lay the foundation for this, we implemented and benchmarked complementary strategies to multiplex brain organoids. Following an extended longitudinal design with a uniquely informative set of timepoints, we pooled cells from different induced pluripotent stem cell lines either during organoids generation (upstream multiplexing in mosaic models) or before single cell-RNAseq library preparation (downstream multiplexing). We developed a new method, SCanSNP, and an aggregated call to deconvolve organoids cell identities, overcoming current criticalities in doublets prediction and low quality cells identification and improving accuracy over state of the art algorithms. Integrating single cell transcriptomes and analysing cell types across neurodevelopmental stages and multiplexing modalities, we validated the feasibility of both multiplexing methods in charting neurodevelopmental trajectories at high resolution, linking their specificity to genetic variation between individual lines. Together, this multiplexing suite of experimental and computational methods provides an enabling resource for disease modelling at scale and paves the way towards an in vitro epidemiology paradigm.

neuroscience↗