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bioRxiv · 10.1101/2025.07.29.667532

Cellular heterogeneity and therapeutic response profiling of human IDH+ glioma stem cell cultures

Chambwe, N.·Kennedy, S. R.·Kohrn, B. F.·Lazarchuk, P.·Leutert, M.·Qin, G.·Tercan, B.·Sanchez-Contreras, M.·Tang, W.·Graber, J.·PADDISON, P.·Villen, J.·Shmulevich, I.·Monnat, R. J.
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Abstract

Summary/AbstractGlioblastoma stem cell (GSC) cultures are initiated from glioblastoma (GBM) surgical resection tissue. They can capture and propagate key GBM primary tumor molecular and cellular features. We have deeply characterized four isocitrate dehydrogenase (IDH)-expressing (or IDH+) GSC cultures from unrelated adults to serve as cellular models for the majority of adult primary GBM. We demonstrate that GSC cultures can be continuously propagated in defined, serum-free media and 5% oxygen without requiring specialized growth substrates; have well-defined genomic and mtDNA variants and gene/protein expression profiles; and highly reproducible dose-survival curves when treated with the GBM standard-of-care therapies of ionizing radiation (IR) and temozolomide (TMZ). We also illustrate how expressed lentiviral barcodes, mtDNA variants and single cell gene expression profiling can be used to define and track cellular heterogeneity over 40 days after IR treatment. These well-characterized IDH+ GSC cultures can support many high throughput in vitro assay formats, including xenograft, organoid and other GBM disease modeling protocols. They should prove a useful resource to better understand GBM biology, and to identify new and more effective GBM therapies and treatment regimens. HighlightsO_LIGlioblastoma (GBM)-derived IDH-expressing Glioma Stem Cell (GSC) cultures can capture and propagate GBM genomic variants, gene and protein expression programs. C_LIO_LIMitochondrial DNA (mtDNA) variants identified by high accuracy Duplex DNA sequencing are abundant and sub-clonally organized in GSC cultures. C_LIO_LIGSC cultures have highly reproducible dose-survival curves for ionizing radiation and temozolomide, the GBM standard-of-care therapies. C_LIO_LIGSC culture cellular heterogeneity can be captured, characterized and tracked by using expressed lentiviral barcodes, mtDNA variants and scRNA sequencing. C_LI eTOC blurbIDH-expressing glioma stem cell cultures (GSCs) are experimentally tractable and versatile glioblastoma (GBM) cellular disease models. Deeply characterized GSC cultures can enable new work to understand GBM biology, and help identify new and more effective GBM therapies and treatment regimens. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/667532v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@82aceeorg.highwire.dtl.DTLVardef@1277c18org.highwire.dtl.DTLVardef@144188eorg.highwire.dtl.DTLVardef@1a84bb3_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Chambwe, N., Kennedy, S. R., Kohrn, B. F., Lazarchuk, P., Leutert, M., Qin, G., Tercan, B., Sanchez-Contreras, M., Tang, W., Graber, J., PADDISON, P., Villen, J., Shmulevich, I., Monnat, R. J.. 2025-08-01. Cellular heterogeneity and therapeutic response profiling of human IDH+ glioma stem cell cultures. https://doi.org/10.1101/2025.07.29.667532

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