ArticleNature communications2025
Investigative needle core biopsies support multimodal deep-data generation in glioblastoma.
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Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17citing papers in PubMed
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Who cites it
17 citing papers in PubMed.
- Comparative evaluation of oncolytic viruses reveals opposing preferences for glioblastoma subtypes.Molecular therapy. Oncology · 2026Article
- Multi-sampling allows intra-tumoral heterogeneity querying and vulnerability profiling in glioblastoma.Neuro-oncology · 2026Article
- The Invasive Margin of Glioblastoma as a Molecular Ecosystem: Spatial Heterogeneity, Tumor-Host Interactions, and Therapeutic Opportunities.International journal of molecular sciences · 2026Review
- Spatial ecotype in tumor immune exclusion: from spatial architecture to therapeutic strategies.Molecular cancer · 2026Review
- Engineering autoimmune disease models using organoids: Harnessing microenvironmental engineering for precision medicine and immunological recapitulation.Bioengineering & translational medicine · 2026Review
- Integrative spatial multi-omics reveals the tumor ecosystem: From mechanistic insights to therapeutic strategies.iScience · 2026Review
- Oncolytic viruses and cytokine-based gene therapies reprogram the tumor microenvironment.Nature cancer · 2026Review
- Article
- The Extracellular Matrix, the Silent 'Architect' of Glioma.Biomedicines · 2026Review
- Critical role of cell competition in gliomagenesis.bioRxiv : the preprint server for biology · 2026Article
- Prostate-specific membrane antigen in malignant brain tumors: vascular heterogeneity, imaging promise, and therapeutic challenges.Frontiers in oncology · 2026Review
- Integrating single-cell RNA-Seq and machine learning to dissect a novel Palmitoylation-related prognostic signature of glioblastoma.BMC neurology · 2025Article
- Serial multiomics uncovers anti-glioblastoma responses not evident by routine clinical analyses.Science translational medicine · 2025Article
- Oncolytic virus-mediated immunomodulation in glioblastoma: Insights from clinical trials and challenges.Seminars in immunology · 2025Review
- Use of Tissue Specimens from Stereotactic Biopsies for Patient-Derived GBM Organoid-Based Drug Testing.Cells · 2025Article
- Leveraging Single-Cell Multi-Omics to Decode Tumor Microenvironment Diversity and Therapeutic Resistance.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Mapping TAM-tumor crosstalk in glioma via ligand-receptor multi-omics: mechanisms of immune evasion.Frontiers in immunology · 2025Review
Corrections and comments
- Update of
Authors and funding
50 authors.
Kenny K H Yu *Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-2394-4990
Sreyashi Basu *Immunotherapy Platform and James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0002-5028-3833
Gerard Baquer *Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-4433-4972
Ryuhjin Ahn *MIT-Harvard Health Sciences and Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9788-4401
Jennifer Gantchev *Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Sonali Jindal *Immunotherapy Platform and James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0002-3911-6815
Michael S ReganDepartment of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-5252-2829
Zaki Abou-MradDepartment of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-6387-8396
Michael C PrabhuDepartment of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Marc J WilliamsDepartment of Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-5524-4174
Alicia D D'SouzaMIT-Harvard Health Sciences and Technology, Cambridge, MA, USA.
Seth W MalinowskiDepartment of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Kelsey HoplandDepartment of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Yuval ElhanatiDepartment of Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-4354-8864
Sylwia A StopkaDepartment of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-3761-6899
Alexei StortchevoiKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Charles CouturierDepartment of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Zhong HeImmunotherapy Platform and James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Jingjing SunImmunotherapy Platform and James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Yulong ChenImmunotherapy Platform and James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Alexsandra B EspejoImmunotherapy Platform and James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0002-8841-7219
Kin Hoe ChowDepartment of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Smitha YerrumDepartment of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Pei-Lun KaoDepartment of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Brittany Parker KerriganDepartment of Neurosurgery, The Brain Tumor Center, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Lisa NorbergDepartment of Anatomic Pathology, The Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Douglas NielsenDepartment of Anatomic Pathology, The Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
GBM TeamLab
Vinay K PuduvalliDepartment of Neuro-Oncology, The Brain Tumor Center, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0001-8396-9500
Jason HuseDepartment of Anatomic Pathology, Division of Pathology-Lab Medicine Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0003-4514-0640
Rameen BeroukhimBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6303-3609
Betty Y S KimDepartment of Neurosurgery, The Brain Tumor Center, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0001-6890-8355
Sangeeta GoswamiDepartment of Genitourinary Medical Oncology, Division of Cancer Medicine, and James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0001-9201-4503
Adrienne BoireDepartment of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-9029-1248
Sarah FriskenDepartment of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Michael J CimaDepartment of Materials Science and Engineering, Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-2379-6139
Matthias HoldhoffThe Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Calixto-Hope G LucasDepartment of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-8347-9592
Chetan BettegowdaDepartment of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-9991-7123
Stuart S LevineKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-7363-562X
Tejus A BaleDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Cameron BrennanDepartment of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
David A ReardonDepartment of Medical Oncology, Center for Neuro-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-6674-0157
Frederick F LangDepartment of Neurosurgery, The Brain Tumor Center, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0003-3747-873X
E Antonio ChioccaDepartment of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-5183-1670
Keith L LigonDepartment of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Forest M WhiteMIT-Harvard Health Sciences and Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-1545-1651
Padmanee SharmaImmunotherapy Platform and James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. PadSharma@mdanderson.org.ORCID http://orcid.org/0000-0003-4658-055X
Viviane TabarDepartment of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA. tabarv@mskcc.org.ORCID http://orcid.org/0000-0002-1284-1670
Nathalie Y R AgarDepartment of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Nathalie_Agar@dfci.harvard.edu.ORCID http://orcid.org/0000-0003-3149-3146
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4MVIRUS PRODUCTION COREP30CA014051 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Jacqueline A. Lees · 1985 to 2026
$93.9MGenetic evolution of glioblastomas during radiation and temozolomide therapyR01CA188228 · NCI · DANA-FARBER CANCER INST · PI BEROUKHIM, RAMEEN, CHAKRAVARTI, ARNAB · 2015 to 2025
$6.9MUltrasound based neurosurgical navigation with uncertainty visualizationR01EB032387 · NIBIB · BRIGHAM AND WOMEN'S HOSPITAL · PI FRISKEN, SARAH, GOLBY, ALEXANDRA J · 2022 to 2025
$2.0MContinuous Compensation of Brain Shift during NeurosurgeryR01EB027134 · NIBIB · BRIGHAM AND WOMEN'S HOSPITAL · PI FRISKEN, SARAH · 2018 to 2021
$1.8MNCI NIH HHS P30 CA008748NCI NIH HHS P30 CA014051NCI NIH HHS R01 CA188228NIBIB NIH HHS R01 EB027134NIBIB NIH HHS R01 EB032387
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.
Indexed as
Brain NeoplasmsGlioblastomaAnimalsBiopsy, Large-Core NeedleFemaleHumansMetabolomicsMiceProteomicsSingle-Cell AnalysisStereotaxic TechniquesTranscriptomeXenograft Model Antitumor Assays
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LicenceCC BY-NC-ND
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.