Investigative needle core biopsies support multimodal deep-data generation in glioblastoma

Kenny K. H. Yu, Sreyashi Basu, Gerard Baquer, Ryuhjin Ahn, Jennifer Gantchev, Sonali Jindal, Michael S. Regan, Zaki Abou-Mrad, Michael C. Prabhu, Marc J. Williams, Alicia D. D’Souza, Seth W. Malinowski, Kelsey Hopland, Yuval Elhanati, Sylwia A. Stopka, Alexei Stortchevoi, Charles Couturier, Zhong He, Jingjing Sun, Yulong Chen, Alexsandra B. Espejo, Kin Hoe Chow, Smitha Yerrum, Pei-Lun Kao, Brittany Parker Kerrigan, Lisa Norberg, Douglas Nielsen, Vinay K. Puduvalli, Jason Huse, Rameen Beroukhim, Betty Y. S. Kim, Sangeeta Goswami, Adrienne Boire, Sarah Frisken, Michael J. Cima, Matthias Holdhoff, Calixto-Hope G. Lucas, Chetan Bettegowda, Stuart S. Levine, Tejus A. Bale, Cameron Brennan, David A. Reardon, Frederick F. Lang, E. Antonio Chiocca, Keith L. Ligon, Forest M. White, Padmanee Sharma (), Viviane Tabar () and Nathalie Y. R. Agar ()
Additional contact information
Kenny K. H. Yu: Memorial Sloan Kettering Cancer Center
Sreyashi Basu: The University of Texas MD Anderson Cancer Center
Gerard Baquer: Harvard Medical School
Ryuhjin Ahn: MIT-Harvard Health Sciences and Technology
Jennifer Gantchev: Harvard Medical School
Sonali Jindal: The University of Texas MD Anderson Cancer Center
Michael S. Regan: Harvard Medical School
Zaki Abou-Mrad: Memorial Sloan Kettering Cancer Center
Michael C. Prabhu: Harvard Medical School
Marc J. Williams: Memorial Sloan Kettering Cancer Center
Alicia D. D’Souza: MIT-Harvard Health Sciences and Technology
Seth W. Malinowski: Harvard Medical School
Kelsey Hopland: Memorial Sloan Kettering Cancer Center
Yuval Elhanati: Memorial Sloan Kettering Cancer Center
Sylwia A. Stopka: Harvard Medical School
Alexei Stortchevoi: Massachusetts Institute of Technology
Charles Couturier: Harvard Medical School
Zhong He: The University of Texas MD Anderson Cancer Center
Jingjing Sun: The University of Texas MD Anderson Cancer Center
Yulong Chen: The University of Texas MD Anderson Cancer Center
Alexsandra B. Espejo: The University of Texas MD Anderson Cancer Center
Kin Hoe Chow: Harvard Medical School
Smitha Yerrum: Harvard Medical School
Pei-Lun Kao: Harvard Medical School
Brittany Parker Kerrigan: The University of Texas MD Anderson Cancer Center
Lisa Norberg: The University of Texas MD Anderson Cancer Center
Douglas Nielsen: The University of Texas MD Anderson Cancer Center
Vinay K. Puduvalli: The University of Texas MD Anderson Cancer Center
Jason Huse: The University of Texas MD Anderson Cancer Center
Rameen Beroukhim: Broad Institute of MIT and Harvard
Betty Y. S. Kim: The University of Texas MD Anderson Cancer Center
Sangeeta Goswami: The University of Texas MD Anderson Cancer Center
Adrienne Boire: Memorial Sloan Kettering Cancer Center
Sarah Frisken: Harvard Medical School
Michael J. Cima: Koch Institute for Integrative Cancer Research
Matthias Holdhoff: Johns Hopkins University School of Medicine
Calixto-Hope G. Lucas: Johns Hopkins University School of Medicine
Chetan Bettegowda: Johns Hopkins University School of Medicine
Stuart S. Levine: Massachusetts Institute of Technology
Tejus A. Bale: Memorial Sloan Kettering Cancer Center
Cameron Brennan: Memorial Sloan Kettering Cancer Center
David A. Reardon: Harvard Medical School
Frederick F. Lang: The University of Texas MD Anderson Cancer Center
E. Antonio Chiocca: Harvard Medical School
Keith L. Ligon: Harvard Medical School
Forest M. White: MIT-Harvard Health Sciences and Technology
Padmanee Sharma: The University of Texas MD Anderson Cancer Center
Viviane Tabar: Memorial Sloan Kettering Cancer Center
Nathalie Y. R. Agar: Harvard Medical School

Nature Communications, 2025, vol. 16, issue 1, 1-23

Abstract: Abstract Glioblastoma (GBM) is an aggressive primary brain cancer with few effective therapies. Stereotactic needle biopsies are routinely used for diagnosis; however, the feasibility and utility of investigative biopsies to monitor treatment response remains ill-defined. Here, we demonstrate the depth of data generation possible from routine stereotactic needle core biopsies and perform highly resolved multi-omics analyses, including single-cell RNA sequencing, spatial transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics on standard biopsy tissue obtained intra-operatively. We also examine biopsies taken from different locations and provide a framework for measuring spatial and genomic heterogeneity. Finally, we investigate the utility of stereotactic biopsies as a method for generating patient-derived xenograft (PDX) models. Multimodal dataset integration highlights spatially mapped immune cell-associated metabolic pathways and validates inferred cell-cell ligand-receptor interactions. In conclusion, investigative biopsies provide data-rich insight into disease processes and may be useful in evaluating treatment responses.

Date: 2025
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-58452-8 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58452-8

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-58452-8

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().