The multilayered transcriptional architecture of glioblastoma ecosystems

Masashi Nomura; Avishay Spitzer; Kevin C. Johnson; Luciano Garofano; Djamel Nehar-belaid; Noam Galili Darnell; Alissa C. Greenwald; Lillian Bussema; Young Taek Oh; Frederick S. Varn; Fulvio D’Angelo; Simon Gritsch; Kevin J. Anderson; Simona Migliozzi; L. Nicolas Gonzalez Castro; Tamrin ChowdhFury; Nicolas Robine; Catherine Reeves; Jong Bae Park; Anuja Lipsa; Frank Hertel; Anna Golebiewska; Simone P. Niclou; Labeeba Nusrat; Sorcha Kellet; Sunit Das; Hyo Eun Moon; Sun Ha Paek; Franck Bielle; Alice Laurenge; Anna Luisa Di Stefano; Bertrand Mathon; Alberto Picca; Marc Sanson; Shota Tanaka; Nobuhito Saito; David M. Ashley; Stephen T. Keir; Keith L. Ligon; Jason T. Huse; W. K.Alfred Yung; Anna Lasorella; Roel G.W. Verhaak; Antonio Iavarone; Mario L. Suvà; Itay Tirosh

doi:10.1038/s41588-025-02167-5

The multilayered transcriptional architecture of glioblastoma ecosystems

Masashi Nomura, Avishay Spitzer, Kevin C. Johnson, Luciano Garofano, Djamel Nehar-belaid, Noam Galili Darnell, Alissa C. Greenwald, Lillian Bussema, Young Taek Oh, Frederick S. Varn, Fulvio D’Angelo, Simon Gritsch, Kevin J. Anderson, Simona Migliozzi, L. Nicolas Gonzalez Castro, Tamrin ChowdhFury, Nicolas Robine, Catherine Reeves, Jong Bae Park, Anuja LipsaFrank Hertel, Anna Golebiewska, Simone P. Niclou, Labeeba Nusrat, Sorcha Kellet, Sunit Das, Hyo Eun Moon, Sun Ha Paek, Franck Bielle, Alice Laurenge, Anna Luisa Di Stefano, Bertrand Mathon, Alberto Picca, Marc Sanson, Shota Tanaka, Nobuhito Saito, David M. Ashley, Stephen T. Keir, Keith L. Ligon, Jason T. Huse, W. K.Alfred Yung, Anna Lasorella^*, Roel G.W. Verhaak^*, Antonio Iavarone^*, Mario L. Suvà^*, Itay Tirosh^*

^*Corresponding author for this work

NORLUX Neuro-Oncology Laboratory

Research output: Contribution to journal › Article › Research › peer-review

1 Citation (Scopus)

Abstract

In isocitrate dehydrogenase wildtype glioblastoma (GBM), cellular heterogeneity across and within tumors may drive therapeutic resistance. Here we analyzed 121 primary and recurrent GBM samples from 59 patients using single-nucleus RNA sequencing and bulk tumor DNA sequencing to characterize GBM transcriptional heterogeneity. First, GBMs can be classified by their broad cellular composition, encompassing malignant and nonmalignant cell types. Second, in each cell type we describe the diversity of cellular states and their pathway activation, particularly an expanded set of malignant cell states, including glial progenitor cell-like, neuronal-like and cilia-like. Third, the remaining variation between GBMs highlights three baseline gene expression programs. These three layers of heterogeneity are interrelated and partially associated with specific genetic aberrations, thereby defining three stereotypic GBM ecosystems. This work provides an unparalleled view of the multilayered transcriptional architecture of GBM. How this architecture evolves during disease progression is addressed in the companion manuscript by Spitzer et al.

Original language	English
Article number	3406
Pages (from-to)	1155-1167
Number of pages	37
Journal	Nature Genetics
Volume	57
Issue number	5
DOIs	https://doi.org/10.1038/s41588-025-02167-5
Publication status	Published - 9 May 2025

Keywords

Humans
Glioblastoma/genetics
Brain Neoplasms/genetics
Gene Expression Regulation, Neoplastic
Isocitrate Dehydrogenase/genetics
Transcription, Genetic
Transcriptome
Gene Expression Profiling

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Nomura, M., Spitzer, A., Johnson, K. C., Garofano, L., Nehar-belaid, D., Galili Darnell, N., Greenwald, A. C., Bussema, L., Oh, Y. T., Varn, F. S., D’Angelo, F., Gritsch, S., Anderson, K. J., Migliozzi, S., Gonzalez Castro, L. N., ChowdhFury, T., Robine, N., Reeves, C., Park, J. B., ... Tirosh, I. (2025). The multilayered transcriptional architecture of glioblastoma ecosystems. Nature Genetics, 57(5), 1155-1167. Article 3406. https://doi.org/10.1038/s41588-025-02167-5

@article{18ef09dff2324bb9b43d4aa50bbf26cc,

title = "The multilayered transcriptional architecture of glioblastoma ecosystems",

abstract = "In isocitrate dehydrogenase wildtype glioblastoma (GBM), cellular heterogeneity across and within tumors may drive therapeutic resistance. Here we analyzed 121 primary and recurrent GBM samples from 59 patients using single-nucleus RNA sequencing and bulk tumor DNA sequencing to characterize GBM transcriptional heterogeneity. First, GBMs can be classified by their broad cellular composition, encompassing malignant and nonmalignant cell types. Second, in each cell type we describe the diversity of cellular states and their pathway activation, particularly an expanded set of malignant cell states, including glial progenitor cell-like, neuronal-like and cilia-like. Third, the remaining variation between GBMs highlights three baseline gene expression programs. These three layers of heterogeneity are interrelated and partially associated with specific genetic aberrations, thereby defining three stereotypic GBM ecosystems. This work provides an unparalleled view of the multilayered transcriptional architecture of GBM. How this architecture evolves during disease progression is addressed in the companion manuscript by Spitzer et al.",

keywords = "Humans, Glioblastoma/genetics, Brain Neoplasms/genetics, Gene Expression Regulation, Neoplastic, Isocitrate Dehydrogenase/genetics, Transcription, Genetic, Transcriptome, Gene Expression Profiling",

author = "Masashi Nomura and Avishay Spitzer and Johnson, {Kevin C.} and Luciano Garofano and Djamel Nehar-belaid and {Galili Darnell}, Noam and Greenwald, {Alissa C.} and Lillian Bussema and Oh, {Young Taek} and Varn, {Frederick S.} and Fulvio D{\textquoteright}Angelo and Simon Gritsch and Anderson, {Kevin J.} and Simona Migliozzi and {Gonzalez Castro}, {L. Nicolas} and Tamrin ChowdhFury and Nicolas Robine and Catherine Reeves and Park, {Jong Bae} and Anuja Lipsa and Frank Hertel and Anna Golebiewska and Niclou, {Simone P.} and Labeeba Nusrat and Sorcha Kellet and Sunit Das and Moon, {Hyo Eun} and Paek, {Sun Ha} and Franck Bielle and Alice Laurenge and {Di Stefano}, {Anna Luisa} and Bertrand Mathon and Alberto Picca and Marc Sanson and Shota Tanaka and Nobuhito Saito and Ashley, {David M.} and Keir, {Stephen T.} and Ligon, {Keith L.} and Huse, {Jason T.} and Yung, {W. K.Alfred} and Anna Lasorella and Verhaak, {Roel G.W.} and Antonio Iavarone and Suv{\`a}, {Mario L.} and Itay Tirosh",

note = "Funding: This work was supported by a GBM CARE grant (supplemented to no. P30CA006516-56S6 (to M.L.S.)); M.L.S. is also supported by National Institutes of Health (NIH)-National Cancer Institute (NCI) grant nos. R01CA276765, R37CA245523, R01CA258763 and P50CA165962, the Mark Foundation Emerging Leader Award, the MGH Research Scholars Award, the Sontag Foundation Distinguished Scientist Alumni Award and the National Foundation for Cancer Research. I.T. is supported by a European Research Council consolidator grant no. 101044318, the Zuckerman STEM Leadership Program and a Mexican Friends New Generation grant, and he is the incumbent of the Dr. Celia Zwillenberg-Fridman and Dr. Lutz Zwillenberg Career Development Chair. A.I. is supported by NIH grant nos. R35CA253183, P30CA013696-46S1 and P30CA240139. R.G.W.V. is supported by NIH grant nos. R01CA237208, R21NS114873, R21CA256575 and P30CA034196, and by the Luxembourg National Research Fund. A. Lipsa, A.G. and S.P.N. are supported by C20/ BM/14646004/GLASSLUX. A. Lasorella is supported by NIH grant nos. R01CA268592, R01CA280560 and R01CA239721. M.N. is supported by the JSPS Overseas Research Fellowship from the Japan Society for the Promotion of Science and the Overseas Research Fellowship from Uehara Memorial Foundation. A.S. is partially supported by the Israeli Council for Higher Education via the Weizmann Data Science Research Center. A. Lipsa, A.G. and S.P.N. are supported by the Luxembourg National Research Fund and TRANSCAN3 grants (C20/ BM/14646004/GLASSLUX, INTER/TRANSCAN22/17612718/PLASTIG). L.N.G.C. has received honoraria from Elsevier, BMJ Best Practice, Oakstone Publishing and Servier, as well as research support from Merck, Conquer Cancer (The ASCO Foundation), the Robert Wood Johnson Foundation and the NCI. We thank the PROACTIVE team at MD Anderson for their assistance in procuring patient material. We gratefully acknowledge the contribution of The Jackson Laboratory Single Cell Biology service, S. Bessonett in particular, the Genome Technologies service and the Cyberinfrastructure high performance computing resources at The Jackson Laboratory for expert assistance related to processing the NORLUX/SNU samples and data analysis. These shared services are supported in part by The Jackson Laboratory Cancer Center (no. P30CA034196). We thank R. Matsuura in the neurosurgery laboratory, Tokyo University Hospital, for the technical assistance in preparing the clinical samples. We thank SciStories for the figure schematics. We thank the patients and their families for their generous donation to biomedical research. {\textcopyright} 2025. The Author(s).",

year = "2025",

month = may,

day = "9",

doi = "10.1038/s41588-025-02167-5",

language = "English",

volume = "57",

pages = "1155--1167",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Research",

number = "5",

}

Nomura, M, Spitzer, A, Johnson, KC, Garofano, L, Nehar-belaid, D, Galili Darnell, N, Greenwald, AC, Bussema, L, Oh, YT, Varn, FS, D’Angelo, F, Gritsch, S, Anderson, KJ, Migliozzi, S, Gonzalez Castro, LN, ChowdhFury, T, Robine, N, Reeves, C, Park, JB, Lipsa, A, Hertel, F, Golebiewska, A, Niclou, SP, Nusrat, L, Kellet, S, Das, S, Moon, HE, Paek, SH, Bielle, F, Laurenge, A, Di Stefano, AL, Mathon, B, Picca, A, Sanson, M, Tanaka, S, Saito, N, Ashley, DM, Keir, ST, Ligon, KL, Huse, JT, Yung, WKA, Lasorella, A, Verhaak, RGW, Iavarone, A, Suvà, ML & Tirosh, I 2025, 'The multilayered transcriptional architecture of glioblastoma ecosystems', Nature Genetics, vol. 57, no. 5, 3406, pp. 1155-1167. https://doi.org/10.1038/s41588-025-02167-5

TY - JOUR

T1 - The multilayered transcriptional architecture of glioblastoma ecosystems

AU - Nomura, Masashi

AU - Spitzer, Avishay

AU - Johnson, Kevin C.

AU - Garofano, Luciano

AU - Nehar-belaid, Djamel

AU - Galili Darnell, Noam

AU - Greenwald, Alissa C.

AU - Bussema, Lillian

AU - Oh, Young Taek

AU - Varn, Frederick S.

AU - D’Angelo, Fulvio

AU - Gritsch, Simon

AU - Anderson, Kevin J.

AU - Migliozzi, Simona

AU - Gonzalez Castro, L. Nicolas

AU - ChowdhFury, Tamrin

AU - Robine, Nicolas

AU - Reeves, Catherine

AU - Park, Jong Bae

AU - Lipsa, Anuja

AU - Hertel, Frank

AU - Golebiewska, Anna

AU - Niclou, Simone P.

AU - Nusrat, Labeeba

AU - Kellet, Sorcha

AU - Das, Sunit

AU - Moon, Hyo Eun

AU - Paek, Sun Ha

AU - Bielle, Franck

AU - Laurenge, Alice

AU - Di Stefano, Anna Luisa

AU - Mathon, Bertrand

AU - Picca, Alberto

AU - Sanson, Marc

AU - Tanaka, Shota

AU - Saito, Nobuhito

AU - Ashley, David M.

AU - Keir, Stephen T.

AU - Ligon, Keith L.

AU - Huse, Jason T.

AU - Yung, W. K.Alfred

AU - Lasorella, Anna

AU - Verhaak, Roel G.W.

AU - Iavarone, Antonio

AU - Suvà, Mario L.

AU - Tirosh, Itay

N1 - Funding: This work was supported by a GBM CARE grant (supplemented to no. P30CA006516-56S6 (to M.L.S.)); M.L.S. is also supported by National Institutes of Health (NIH)-National Cancer Institute (NCI) grant nos. R01CA276765, R37CA245523, R01CA258763 and P50CA165962, the Mark Foundation Emerging Leader Award, the MGH Research Scholars Award, the Sontag Foundation Distinguished Scientist Alumni Award and the National Foundation for Cancer Research. I.T. is supported by a European Research Council consolidator grant no. 101044318, the Zuckerman STEM Leadership Program and a Mexican Friends New Generation grant, and he is the incumbent of the Dr. Celia Zwillenberg-Fridman and Dr. Lutz Zwillenberg Career Development Chair. A.I. is supported by NIH grant nos. R35CA253183, P30CA013696-46S1 and P30CA240139. R.G.W.V. is supported by NIH grant nos. R01CA237208, R21NS114873, R21CA256575 and P30CA034196, and by the Luxembourg National Research Fund. A. Lipsa, A.G. and S.P.N. are supported by C20/ BM/14646004/GLASSLUX. A. Lasorella is supported by NIH grant nos. R01CA268592, R01CA280560 and R01CA239721. M.N. is supported by the JSPS Overseas Research Fellowship from the Japan Society for the Promotion of Science and the Overseas Research Fellowship from Uehara Memorial Foundation. A.S. is partially supported by the Israeli Council for Higher Education via the Weizmann Data Science Research Center. A. Lipsa, A.G. and S.P.N. are supported by the Luxembourg National Research Fund and TRANSCAN3 grants (C20/ BM/14646004/GLASSLUX, INTER/TRANSCAN22/17612718/PLASTIG). L.N.G.C. has received honoraria from Elsevier, BMJ Best Practice, Oakstone Publishing and Servier, as well as research support from Merck, Conquer Cancer (The ASCO Foundation), the Robert Wood Johnson Foundation and the NCI. We thank the PROACTIVE team at MD Anderson for their assistance in procuring patient material. We gratefully acknowledge the contribution of The Jackson Laboratory Single Cell Biology service, S. Bessonett in particular, the Genome Technologies service and the Cyberinfrastructure high performance computing resources at The Jackson Laboratory for expert assistance related to processing the NORLUX/SNU samples and data analysis. These shared services are supported in part by The Jackson Laboratory Cancer Center (no. P30CA034196). We thank R. Matsuura in the neurosurgery laboratory, Tokyo University Hospital, for the technical assistance in preparing the clinical samples. We thank SciStories for the figure schematics. We thank the patients and their families for their generous donation to biomedical research. © 2025. The Author(s).

PY - 2025/5/9

Y1 - 2025/5/9

N2 - In isocitrate dehydrogenase wildtype glioblastoma (GBM), cellular heterogeneity across and within tumors may drive therapeutic resistance. Here we analyzed 121 primary and recurrent GBM samples from 59 patients using single-nucleus RNA sequencing and bulk tumor DNA sequencing to characterize GBM transcriptional heterogeneity. First, GBMs can be classified by their broad cellular composition, encompassing malignant and nonmalignant cell types. Second, in each cell type we describe the diversity of cellular states and their pathway activation, particularly an expanded set of malignant cell states, including glial progenitor cell-like, neuronal-like and cilia-like. Third, the remaining variation between GBMs highlights three baseline gene expression programs. These three layers of heterogeneity are interrelated and partially associated with specific genetic aberrations, thereby defining three stereotypic GBM ecosystems. This work provides an unparalleled view of the multilayered transcriptional architecture of GBM. How this architecture evolves during disease progression is addressed in the companion manuscript by Spitzer et al.

AB - In isocitrate dehydrogenase wildtype glioblastoma (GBM), cellular heterogeneity across and within tumors may drive therapeutic resistance. Here we analyzed 121 primary and recurrent GBM samples from 59 patients using single-nucleus RNA sequencing and bulk tumor DNA sequencing to characterize GBM transcriptional heterogeneity. First, GBMs can be classified by their broad cellular composition, encompassing malignant and nonmalignant cell types. Second, in each cell type we describe the diversity of cellular states and their pathway activation, particularly an expanded set of malignant cell states, including glial progenitor cell-like, neuronal-like and cilia-like. Third, the remaining variation between GBMs highlights three baseline gene expression programs. These three layers of heterogeneity are interrelated and partially associated with specific genetic aberrations, thereby defining three stereotypic GBM ecosystems. This work provides an unparalleled view of the multilayered transcriptional architecture of GBM. How this architecture evolves during disease progression is addressed in the companion manuscript by Spitzer et al.

KW - Humans

KW - Glioblastoma/genetics

KW - Brain Neoplasms/genetics

KW - Gene Expression Regulation, Neoplastic

KW - Isocitrate Dehydrogenase/genetics

KW - Transcription, Genetic

KW - Transcriptome

KW - Gene Expression Profiling

UR - http://www.scopus.com/inward/record.url?scp=105004431760&partnerID=8YFLogxK

UR - https://pubmed.ncbi.nlm.nih.gov/40346361/

U2 - 10.1038/s41588-025-02167-5

DO - 10.1038/s41588-025-02167-5

M3 - Article

C2 - 40346361

AN - SCOPUS:105004431760

SN - 1061-4036

VL - 57

SP - 1155

EP - 1167

JO - Nature Genetics

JF - Nature Genetics

IS - 5

M1 - 3406

ER -

The multilayered transcriptional architecture of glioblastoma ecosystems

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Keywords

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