1
|
Faisal SM, Ravi VM, Miska JM. Editorial: Spatiotemporal heterogeneity in CNS tumors. Front Immunol 2024; 15:1430227. [PMID: 38868775 PMCID: PMC11167105 DOI: 10.3389/fimmu.2024.1430227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Affiliation(s)
- Syed M. Faisal
- Department of Pediatrics, Division of Hematology/Oncology, Children’s Mercy Research Institute, Kansas City, MO, United States
| | - Vidhya M. Ravi
- Department of Neurosurgery, Medical Center – University of Freiburg, Freiburg, Germany
| | - Jason M. Miska
- Lou and Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, United States
| |
Collapse
|
2
|
Vymola P, Garcia-Borja E, Cervenka J, Balaziova E, Vymolova B, Veprkova J, Vodicka P, Skalnikova H, Tomas R, Netuka D, Busek P, Sedo A. Fibrillar extracellular matrix produced by pericyte-like cells facilitates glioma cell dissemination. Brain Pathol 2024:e13265. [PMID: 38705944 DOI: 10.1111/bpa.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Gliomagenesis induces profound changes in the composition of the extracellular matrix (ECM) of the brain. In this study, we identified a cellular population responsible for the increased deposition of collagen I and fibronectin in glioblastoma. Elevated levels of the fibrillar proteins collagen I and fibronectin were associated with the expression of fibroblast activation protein (FAP), which is predominantly found in pericyte-like cells in glioblastoma. FAP+ pericyte-like cells were present in regions rich in collagen I and fibronectin in biopsy material and produced substantially more collagen I and fibronectin in vitro compared to other cell types found in the GBM microenvironment. Using mass spectrometry, we demonstrated that 3D matrices produced by FAP+ pericyte-like cells are rich in collagen I and fibronectin and contain several basement membrane proteins. This expression pattern differed markedly from glioma cells. Finally, we have shown that ECM produced by FAP+ pericyte-like cells enhances the migration of glioma cells including glioma stem-like cells, promotes their adhesion, and activates focal adhesion kinase (FAK) signaling. Taken together, our findings establish FAP+ pericyte-like cells as crucial producers of a complex ECM rich in collagen I and fibronectin, facilitating the dissemination of glioma cells through FAK activation.
Collapse
Affiliation(s)
- Petr Vymola
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Elena Garcia-Borja
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jakub Cervenka
- Laboratory of Applied Proteome Analyses, Research Center PIGMOD, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Laboratory of proteomics, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Eva Balaziova
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Barbora Vymolova
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Veprkova
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Vodicka
- Laboratory of Applied Proteome Analyses, Research Center PIGMOD, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
| | - Helena Skalnikova
- Laboratory of Applied Proteome Analyses, Research Center PIGMOD, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Laboratory of proteomics, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Robert Tomas
- Department of Neurosurgery, Na Homolce Hospital, Prague, Czech Republic
| | - David Netuka
- Department of Neurosurgery and Neurooncology, First Faculty of Medicine, Charles University and Military University Hospital, Prague, Czech Republic
| | - Petr Busek
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Aleksi Sedo
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| |
Collapse
|
3
|
Faisal SM, Clewner JE, Stack B, Varela ML, Comba A, Abbud G, Motsch S, Castro MG, Lowenstein PR. Spatiotemporal Insights into Glioma Oncostream Dynamics: Unraveling Formation, Stability, and Disassembly Pathways. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309796. [PMID: 38384234 PMCID: PMC11095212 DOI: 10.1002/advs.202309796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Glioblastoma (GBM) remains a challenge in Neuro-oncology, with a poor prognosis showing only a 5% survival rate beyond two years. This is primarily due to its aggressiveness and intra-tumoral heterogeneity, which limits complete surgical resection and reduces the efficacy of existing treatments. The existence of oncostreams-neuropathological structures comprising aligned spindle-like cells from both tumor and non-tumor origins- is discovered earlier. Oncostreams are closely linked to glioma aggressiveness and facilitate the spread into adjacent healthy brain tissue. A unique molecular signature intrinsic to oncostreams, with overexpression of key genes (i.e., COL1A1, ACTA2) that drive the tumor's mesenchymal transition and malignancy is also identified. Pre-clinical studies on genetically engineered mouse models demonstrated that COL1A1 inhibition disrupts oncostreams, modifies TME, reduces mesenchymal gene expression, and extends survival. An in vitro model using GFP+ NPA cells to investigate how various treatments affect oncostream dynamics is developed. Analysis showed that factors such as cell density, morphology, neurotransmitter agonists, calcium chelators, and cytoskeleton-targeting drugs influence oncostream formation. This data illuminate the patterns of glioma migration and suggest anti-invasion strategies that can improve GBM patient outcomes when combined with traditional therapies. This work highlights the potential of targeting oncostreams to control glioma invasion and enhance treatment efficacy.
Collapse
Affiliation(s)
- Syed M. Faisal
- Department of NeurosurgeryUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Department of Cell and Developmental BiologyUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Rogel Cancer CentreUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
| | - Jarred E. Clewner
- Department of NeurosurgeryUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Department of Cell and Developmental BiologyUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Rogel Cancer CentreUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
| | - Brooklyn Stack
- Department of NeurosurgeryUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Department of Cell and Developmental BiologyUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Rogel Cancer CentreUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
| | - Maria L. Varela
- Department of NeurosurgeryUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Department of Cell and Developmental BiologyUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Rogel Cancer CentreUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
| | - Andrea Comba
- Department of NeurosurgeryUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Department of Cell and Developmental BiologyUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Rogel Cancer CentreUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
| | - Grace Abbud
- Department of NeurosurgeryUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Department of Cell and Developmental BiologyUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Rogel Cancer CentreUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
| | - Sebastien Motsch
- Department of Statistics and Mathematical SciencesArizona State UniversityTempeArizona85287USA
| | - Maria G. Castro
- Department of NeurosurgeryUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Department of Cell and Developmental BiologyUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Rogel Cancer CentreUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
| | - Pedro R. Lowenstein
- Department of NeurosurgeryUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Department of Cell and Developmental BiologyUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Rogel Cancer CentreUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
- Department of Biomedical EngineeringUniversity of Michigan Medical SchoolAnn ArborMichigan48108USA
| |
Collapse
|
4
|
Licón-Muñoz Y, Avalos V, Subramanian S, Granger B, Martinez F, Varela S, Moore D, Perkins E, Kogan M, Berto S, Chohan M, Bowers C, Piccirillo S. Single-nucleus and spatial landscape of the sub-ventricular zone in human glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590852. [PMID: 38712234 PMCID: PMC11071523 DOI: 10.1101/2024.04.24.590852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The sub-ventricular zone (SVZ) is the most well-characterized neurogenic area in the mammalian brain. We previously showed that in 65% of patients with glioblastoma (GBM), the SVZ is a reservoir of cancer stem-like cells that contribute to treatment resistance and emergence of recurrence. Here, we built a single-nucleus RNA-sequencing-based microenvironment landscape of the tumor mass (T_Mass) and the SVZ (T_SVZ) of 15 GBM patients and 2 histologically normal SVZ (N_SVZ) samples as controls. We identified a mesenchymal signature in the T_SVZ of GBM patients: tumor cells from the T_SVZ relied on the ZEB1 regulatory network, whereas tumor cells in the T_Mass relied on the TEAD1 regulatory network. Moreover, the T_SVZ microenvironment was predominantly characterized by tumor-supportive microglia, which spatially co-exist and establish heterotypic interactions with tumor cells. Lastly, differential gene expression analyses, predictions of ligand-receptor and incoming/outgoing interactions, and functional assays revealed that the IL-1β/IL-1RAcP and Wnt-5a/Frizzled-3 pathways are therapeutic targets in the T_SVZ microenvironment. Our data provide insights into the biology of the SVZ in GBM patients and identify specific targets of this microenvironment.
Collapse
Affiliation(s)
- Y. Licón-Muñoz
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - V. Avalos
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - S. Subramanian
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - B. Granger
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - F. Martinez
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - S. Varela
- University of New Mexico School of Medicine, Albuquerque, NM
| | - D. Moore
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - E. Perkins
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, MS
| | - M. Kogan
- Department of Neurosurgery, University of New Mexico Hospital, Albuquerque, NM
| | - S. Berto
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - M.O. Chohan
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, MS
| | - C.A. Bowers
- Department of Neurosurgery, University of New Mexico Hospital, Albuquerque, NM
| | - S.G.M. Piccirillo
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| |
Collapse
|
5
|
Bao Q, Yu X, Qi X. Integrated analysis of single-cell sequencing and weighted co-expression network identifies a novel signature based on cellular senescence-related genes to predict prognosis in glioblastoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:643-656. [PMID: 37565732 DOI: 10.1002/tox.23921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Glioblastoma (GBM) is a highly aggressive cancer with heavy mortality rates and poor prognosis. Cellular senescence exerts a pivotal influence on the development and progression of various cancers. However, the underlying effect of cellular senescence on the outcomes of patients with GBM remains to be elucidated. METHODS Transcriptome RNA sequencing data with clinical information and single-cell sequencing data of GBM cases were obtained from CGGA, TCGA, and GEO (GSE84465) databases respectively. Single-sample gene set enrichment analysis (ssGSEA) analysis was utilized to calculate the cellular senescence score. WGCNA analysis was employed to ascertain the key gene modules and identify differentially expressed genes (DEGs) associated with the cellular senescence score in GBM. The prognostic senescence-related risk model was developed by least absolute shrinkage and selection operator (LASSO) regression analyses. The immune infiltration level was calculated by microenvironment cell populations counter (MCPcounter), ssGSEA, and xCell algorithms. Potential anti-cancer small molecular compounds of GBM were estimated by "oncoPredict" R package. RESULTS A total of 150 DEGs were selected from the pink module through WGCNA analysis. The risk-scoring model was constructed based on 5 cell senescence-associated genes (CCDC151, DRC1, C2orf73, CCDC13, and WDR63). Patients in low-risk group had a better prognostic value compared to those in high-risk group. The nomogram exhibited excellent predictive performance in assessing the survival outcomes of patients with GBM. Top 30 potential anti-cancer small molecular compounds with higher drug sensitivity scores were predicted. CONCLUSION Cellular senescence-related genes and clusters in GBM have the potential to provide valuable insights in prognosis and guide clinical decisions.
Collapse
Affiliation(s)
- Qingquan Bao
- Department of Neurosurgery, Shaoxing People's Hospital, Shaoxing, China
| | - Xuebin Yu
- Department of Neurosurgery, Shaoxing People's Hospital, Shaoxing, China
| | - Xuchen Qi
- Department of Neurosurgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
6
|
Lee S, Kim G, Lee J, Lee AC, Kwon S. Mapping cancer biology in space: applications and perspectives on spatial omics for oncology. Mol Cancer 2024; 23:26. [PMID: 38291400 PMCID: PMC10826015 DOI: 10.1186/s12943-024-01941-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
Technologies to decipher cellular biology, such as bulk sequencing technologies and single-cell sequencing technologies, have greatly assisted novel findings in tumor biology. Recent findings in tumor biology suggest that tumors construct architectures that influence the underlying cancerous mechanisms. Increasing research has reported novel techniques to map the tissue in a spatial context or targeted sampling-based characterization and has introduced such technologies to solve oncology regarding tumor heterogeneity, tumor microenvironment, and spatially located biomarkers. In this study, we address spatial technologies that can delineate the omics profile in a spatial context, novel findings discovered via spatial technologies in oncology, and suggest perspectives regarding therapeutic approaches and further technological developments.
Collapse
Affiliation(s)
- Sumin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea
| | - Gyeongjun Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - JinYoung Lee
- Division of Engineering Science, University of Toronto, Toronto, Ontario, ON, M5S 3H6, Canada
| | - Amos C Lee
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, 08826, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| |
Collapse
|
7
|
Zheng Y, Pizurica M, Carrillo-Perez F, Noor H, Yao W, Wohlfart C, Marchal K, Vladimirova A, Gevaert O. Digital profiling of cancer transcriptomes from histology images with grouped vision attention. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.28.560068. [PMID: 37808782 PMCID: PMC10557714 DOI: 10.1101/2023.09.28.560068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Cancer is a heterogeneous disease that demands precise molecular profiling for better understanding and management. Recently, deep learning has demonstrated potentials for cost-efficient prediction of molecular alterations from histology images. While transformer-based deep learning architectures have enabled significant progress in non-medical domains, their application to histology images remains limited due to small dataset sizes coupled with the explosion of trainable parameters. Here, we develop SEQUOIA, a transformer model to predict cancer transcriptomes from whole-slide histology images. To enable the full potential of transformers, we first pre-train the model using data from 1,802 normal tissues. Then, we fine-tune and evaluate the model in 4,331 tumor samples across nine cancer types. The prediction performance is assessed at individual gene levels and pathway levels through Pearson correlation analysis and root mean square error. The generalization capacity is validated across two independent cohorts comprising 1,305 tumors. In predicting the expression levels of 25,749 genes, the highest performance is observed in cancers from breast, kidney and lung, where SEQUOIA accurately predicts the expression of 11,069, 10,086 and 8,759 genes, respectively. The accurately predicted genes are associated with the regulation of inflammatory response, cell cycles and metabolisms. While the model is trained at the tissue level, we showcase its potential in predicting spatial gene expression patterns using spatial transcriptomics datasets. Leveraging the prediction performance, we develop a digital gene expression signature that predicts the risk of recurrence in breast cancer. SEQUOIA deciphers clinically relevant gene expression patterns from histology images, opening avenues for improved cancer management and personalized therapies.
Collapse
Affiliation(s)
- Yuanning Zheng
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
| | - Marija Pizurica
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
- Internet technology and Data science Lab (IDLab), Ghent University, Technologiepark-Zwijnaarde 126, Ghent, 9052, Gent, Belgium
| | - Francisco Carrillo-Perez
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
| | - Humaira Noor
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
| | - Wei Yao
- Roche Information Solutions, Roche Diagnostics Corporation, Santa Clara, California, USA
| | | | - Kathleen Marchal
- Internet technology and Data science Lab (IDLab), Ghent University, Technologiepark-Zwijnaarde 126, Ghent, 9052, Gent, Belgium
| | - Antoaneta Vladimirova
- Roche Information Solutions, Roche Diagnostics Corporation, Santa Clara, California, USA
| | - Olivier Gevaert
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, 94305, USA
| |
Collapse
|
8
|
Mathur R, Wang Q, Schupp PG, Nikolic A, Hilz S, Hong C, Grishanina NR, Kwok D, Stevers NO, Jin Q, Youngblood MW, Stasiak LA, Hou Y, Wang J, Yamaguchi TN, Lafontaine M, Shai A, Smirnov IV, Solomon DA, Chang SM, Hervey-Jumper SL, Berger MS, Lupo JM, Okada H, Phillips JJ, Boutros PC, Gallo M, Oldham MC, Yue F, Costello JF. Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective. Cell 2024; 187:446-463.e16. [PMID: 38242087 PMCID: PMC10832360 DOI: 10.1016/j.cell.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/03/2023] [Accepted: 12/06/2023] [Indexed: 01/21/2024]
Abstract
Treatment failure for the lethal brain tumor glioblastoma (GBM) is attributed to intratumoral heterogeneity and tumor evolution. We utilized 3D neuronavigation during surgical resection to acquire samples representing the whole tumor mapped by 3D spatial coordinates. Integrative tissue and single-cell analysis revealed sources of genomic, epigenomic, and microenvironmental intratumoral heterogeneity and their spatial patterning. By distinguishing tumor-wide molecular features from those with regional specificity, we inferred GBM evolutionary trajectories from neurodevelopmental lineage origins and initiating events such as chromothripsis to emergence of genetic subclones and spatially restricted activation of differential tumor and microenvironmental programs in the core, periphery, and contrast-enhancing regions. Our work depicts GBM evolution and heterogeneity from a 3D whole-tumor perspective, highlights potential therapeutic targets that might circumvent heterogeneity-related failures, and establishes an interactive platform enabling 360° visualization and analysis of 3D spatial patterns for user-selected genes, programs, and other features across whole GBM tumors.
Collapse
Affiliation(s)
- Radhika Mathur
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Qixuan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Patrick G Schupp
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ana Nikolic
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nadia R Grishanina
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Darwin Kwok
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mark W Youngblood
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lena Ann Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ye Hou
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Juan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California, Los Angeles, Los Angees, CA, USA
| | - Marisa Lafontaine
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ivan V Smirnov
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David A Solomon
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Janine M Lupo
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Hideho Okada
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angees, CA, USA
| | - Marco Gallo
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB; Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Michael C Oldham
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
9
|
Sarkari A, Korenfeld S, Deniz K, Ladner K, Wong P, Padmanabhan S, Vogel RI, Sherer LA, Courtemanche N, Steer C, Wainer-Katsir K, Lou E. Treatment with tumor-treating fields (TTFields) suppresses intercellular tunneling nanotube formation in vitro and upregulates immuno-oncologic biomarkers in vivo in malignant mesothelioma. eLife 2023; 12:e85383. [PMID: 37955637 PMCID: PMC10642963 DOI: 10.7554/elife.85383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Disruption of intercellular communication within tumors is emerging as a novel potential strategy for cancer-directed therapy. Tumor-Treating Fields (TTFields) therapy is a treatment modality that has itself emerged over the past decade in active clinical use for patients with glioblastoma and malignant mesothelioma, based on the principle of using low-intensity alternating electric fields to disrupt microtubules in cancer cells undergoing mitosis. There is a need to identify other cellular and molecular effects of this treatment approach that could explain reported increased overall survival when TTFields are added to standard systemic agents. Tunneling nanotube (TNTs) are cell-contact-dependent filamentous-actin-based cellular protrusions that can connect two or more cells at long-range. They are upregulated in cancer, facilitating cell growth, differentiation, and in the case of invasive cancer phenotypes, a more chemoresistant phenotype. To determine whether TNTs present a potential therapeutic target for TTFields, we applied TTFields to malignant pleural mesothelioma (MPM) cells forming TNTs in vitro. TTFields at 1.0 V/cm significantly suppressed TNT formation in biphasic subtype MPM, but not sarcomatoid MPM, independent of effects on cell number. TTFields did not significantly affect function of TNTs assessed by measuring intercellular transport of mitochondrial cargo via intact TNTs. We further leveraged a spatial transcriptomic approach to characterize TTFields-induced changes to molecular profiles in vivo using an animal model of MPM. We discovered TTFields induced upregulation of immuno-oncologic biomarkers with simultaneous downregulation of pathways associated with cell hyperproliferation, invasion, and other critical regulators of oncogenic growth. Several molecular classes and pathways coincide with markers that we and others have found to be differentially expressed in cancer cell TNTs, including MPM specifically. We visualized short TNTs in the dense stromatous tumor material selected as regions of interest for spatial genomic assessment. Superimposing these regions of interest from spatial genomics over the plane of TNT clusters imaged in intact tissue is a new method that we designate Spatial Profiling of Tunneling nanoTubes (SPOTT). In sum, these results position TNTs as potential therapeutic targets for TTFields-directed cancer treatment strategies. We also identified the ability of TTFields to remodel the tumor microenvironment landscape at the molecular level, thereby presenting a potential novel strategy for converting tumors at the cellular level from 'cold' to 'hot' for potential response to immunotherapeutic drugs.
Collapse
Affiliation(s)
- Akshat Sarkari
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of MinnesotaMinneapolisUnited States
| | - Sophie Korenfeld
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of MinnesotaMinneapolisUnited States
| | - Karina Deniz
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of MinnesotaMinneapolisUnited States
| | - Katherine Ladner
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of MinnesotaMinneapolisUnited States
| | - Phillip Wong
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of MinnesotaMinneapolisUnited States
| | - Sanyukta Padmanabhan
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of MinnesotaMinneapolisUnited States
| | - Rachel I Vogel
- Department of Obstetrics, Gynecology and Women's Health, University of MinnesotaMinneapolisUnited States
| | - Laura A Sherer
- Department of Genetics, Cell Biology and Development, University of MinnesotaMinneapolisUnited States
| | - Naomi Courtemanche
- Department of Genetics, Cell Biology and Development, University of MinnesotaMinneapolisUnited States
| | - Clifford Steer
- Department of Genetics, Cell Biology and Development, University of MinnesotaMinneapolisUnited States
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of MinnesotaMinneapolisUnited States
| | | | - Emil Lou
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of MinnesotaMinneapolisUnited States
- Graduate Faculty, Integrative Biology and Physiology Department, University of MinnesotaMinneapolisUnited States
| |
Collapse
|
10
|
Premachandran S, Haldavnekar R, Ganesh S, Das S, Venkatakrishnan K, Tan B. Self-Functionalized Superlattice Nanosensor Enables Glioblastoma Diagnosis Using Liquid Biopsy. ACS NANO 2023; 17:19832-19852. [PMID: 37824714 DOI: 10.1021/acsnano.3c04118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Glioblastoma (GBM), the most aggressive and lethal brain cancer, is detected only in the advanced stage, resulting in a median survival rate of 15 months. Therefore, there is an urgent need to establish GBM diagnosis tools to identify the tumor accurately. The clinical relevance of the current liquid biopsy techniques for GBM diagnosis remains mostly undetermined, owing to the challenges posed by the blood-brain barrier (BBB) that restricts biomarkers entering the circulation, resulting in the unavailability of clinically validated circulating GBM markers. GBM-specific liquid biopsy for diagnosis and prognosis of GBM has not yet been developed. Here, we introduce extracellular vesicles of GBM cancer stem cells (GBM CSC-EVs) as a previously unattempted, stand-alone GBM diagnosis modality. As GBM CSCs are fundamental building blocks of tumor initiation and recurrence, it is desirable to investigate these reliable signals of malignancy in circulation for accurate GBM diagnosis. So far, there are no clinically validated circulating biomarkers available for GBM. Therefore, a marker-free approach was essential since conventional liquid biopsy relying on isolation methodology was not viable. Additionally, a mechanism capable of trace-level detection was crucial to detecting the rare GBM CSC-EVs from the complex environment in circulation. To break these barriers, we applied an ultrasensitive superlattice sensor, self-functionalized for surface-enhanced Raman scattering (SERS), to obtain holistic molecular profiling of GBM CSC-EVs with a marker-free approach. The superlattice sensor exhibited substantial SERS enhancement and ultralow limit of detection (LOD of attomolar 10-18 M concentration) essential for trace-level detection of invisible GBM CSC-EVs directly from patient serum (without isolation). We detected as low as 5 EVs in 5 μL of solution, achieving the lowest LOD compared to existing SERS-based studies. We have experimentally demonstrated the crucial role of the signals of GBM CSC-EVs in the precise detection of glioblastoma. This was evident from the unique molecular profiles of GBM CSC-EVs demonstrating significant variation compared to noncancer EVs and EVs of GBM cancer cells, thus adding more clarity to the current understanding of GBM CSC-EVs. Preliminary validation of our approach was undertaken with a small amount of peripheral blood (5 μL) derived from GBM patients with 100% sensitivity and 97% specificity. Identification of the signals of GBM CSC-EV in clinical sera specimens demonstrated that our technology could be used for accurate GBM detection. Our technology has the potential to improve GBM liquid biopsy, including real-time surveillance of GBM evolution in patients upon clinical validation. This demonstration of liquid biopsy with GBM CSC-EV provides an opportunity to introduce a paradigm potentially impacting the current landscape of GBM diagnosis.
Collapse
Affiliation(s)
- Srilakshmi Premachandran
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University (formerly Ryerson University) and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano Characterization Laboratory, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Rupa Haldavnekar
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University (formerly Ryerson University) and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano Characterization Laboratory, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Swarna Ganesh
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University (formerly Ryerson University) and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano Characterization Laboratory, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Sunit Das
- Scientist, St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Institute of Medical Sciences, Neurosurgery, University of Toronto, Toronto, Ontario M5T 1P5, Canada
| | - Krishnan Venkatakrishnan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University (formerly Ryerson University) and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Bo Tan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University (formerly Ryerson University) and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Nano Characterization Laboratory, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| |
Collapse
|
11
|
Faisal SM, Castro MG, Lowenstein PR. Combined cytotoxic and immune-stimulatory gene therapy using Ad-TK and Ad-Flt3L: Translational developments from rodents to glioma patients. Mol Ther 2023; 31:2839-2860. [PMID: 37574780 PMCID: PMC10556227 DOI: 10.1016/j.ymthe.2023.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/14/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023] Open
Abstract
Gliomas are the most prevalent and devastating primary malignant brain tumors in adults. Despite substantial advances in understanding glioma biology, there have been no regulatory drug approvals in the US since bevacizumab in 2009 and tumor treating fields in 2011. Recent phase III clinical trials have failed to meet their prespecified therapeutic primary endpoints, highlighting the need for novel therapies. The poor prognosis of glioma patients, resistance to chemo-radiotherapy, and the immunosuppressive tumor microenvironment underscore the need for the development of novel therapies. Gene therapy-based immunotherapeutic strategies that couple the ability of the host immune system to specifically kill glioma cells and develop immunological memory have shown remarkable progress. Two adenoviral vectors expressing Ad-HSV1-TK/GCV and Ad-Flt3L have shown promising preclinical data, leading to FDA approval of a non-randomized, phase I open-label, first in human trial to test safety, cytotoxicity, and immune-stimulatory efficiency in high-grade glioma patients (NCT01811992). This review provides a thorough overview of immune-stimulatory gene therapy highlighting recent advancements, potential drawbacks, future directions, and recommendations for future implementation of clinical trials.
Collapse
Affiliation(s)
- Syed M Faisal
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48108, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48108, USA; Rogel Cancer Centre, University of Michigan Medical School, Ann Arbor, MI 48108, USA
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48108, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48108, USA; Rogel Cancer Centre, University of Michigan Medical School, Ann Arbor, MI 48108, USA
| | - Pedro R Lowenstein
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48108, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48108, USA; Rogel Cancer Centre, University of Michigan Medical School, Ann Arbor, MI 48108, USA; Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48108, USA.
| |
Collapse
|
12
|
Linares CA, Varghese A, Ghose A, Shinde SD, Adeleke S, Sanchez E, Sheriff M, Chargari C, Rassy E, Boussios S. Hallmarks of the Tumour Microenvironment of Gliomas and Its Interaction with Emerging Immunotherapy Modalities. Int J Mol Sci 2023; 24:13215. [PMID: 37686020 PMCID: PMC10487469 DOI: 10.3390/ijms241713215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Gliomas are aggressive, primary central nervous system tumours arising from glial cells. Glioblastomas are the most malignant. They are known for their poor prognosis or median overall survival. The current standard of care is overwhelmed by the heterogeneous, immunosuppressive tumour microenvironment promoting immune evasion and tumour proliferation. The advent of immunotherapy with its various modalities-immune checkpoint inhibitors, cancer vaccines, oncolytic viruses and chimeric antigen receptor T cells and NK cells-has shown promise. Clinical trials incorporating combination immunotherapies have overcome the microenvironment resistance and yielded promising survival and prognostic benefits. Rolling these new therapies out in the real-world scenario in a low-cost, high-throughput manner is the unmet need of the hour. These will have practice-changing implications to the glioma treatment landscape. Here, we review the immunobiological hallmarks of the TME of gliomas, how the TME evades immunotherapies and the work that is being conducted to overcome this interplay.
Collapse
Affiliation(s)
- Christian A. Linares
- Guy’s Cancer Centre, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 9RT, UK; (C.A.L.); (S.A.)
| | - Anjana Varghese
- Kent Oncology Centre, Maidstone and Tunbridge Wells NHS Trust, Hermitage Lane, Maidstone, Kent ME16 9QQ, UK;
| | - Aruni Ghose
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham ME7 5NY, UK; (A.G.); (E.S.); (M.S.)
- Barts Cancer Centre, Barts Health NHS Trust, London EC1A 7BE, UK
- Mount Vernon Cancer Centre, East and North Hertfordshire NHS Trust, Northwood HA6 2RN, UK
- Immuno-Oncology Clinical Network, UK
| | - Sayali D. Shinde
- Centre for Tumour Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, London EC1M 6BQ, UK;
| | - Sola Adeleke
- Guy’s Cancer Centre, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 9RT, UK; (C.A.L.); (S.A.)
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, Strand, London WC2R 2LS, UK
| | - Elisabet Sanchez
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham ME7 5NY, UK; (A.G.); (E.S.); (M.S.)
| | - Matin Sheriff
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham ME7 5NY, UK; (A.G.); (E.S.); (M.S.)
| | - Cyrus Chargari
- Department of Radiation Oncology, Pitié-Salpêtrière University Hospital, 75013 Paris, France;
| | - Elie Rassy
- Department of Medical Oncology, Institut Gustave Roussy, 94805 Villejuif, France;
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham ME7 5NY, UK; (A.G.); (E.S.); (M.S.)
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, Strand, London WC2R 2LS, UK
- Kent and Medway Medical School, University of Kent, Canterbury CT2 7LX, UK
- AELIA Organization, 9th Km Thessaloniki–Thermi, 57001 Thessaloniki, Greece
| |
Collapse
|
13
|
García-Montaño LA, Licón-Muñoz Y, Martinez FJ, Keddari YR, Ziemke MK, Chohan MO, Piccirillo SG. Dissecting Intra-tumor Heterogeneity in the Glioblastoma Microenvironment Using Fluorescence-Guided Multiple Sampling. Mol Cancer Res 2023; 21:755-767. [PMID: 37255362 PMCID: PMC10390891 DOI: 10.1158/1541-7786.mcr-23-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/25/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
The treatment of the most aggressive primary brain tumor in adults, glioblastoma (GBM), is challenging due to its heterogeneous nature, invasive potential, and poor response to chemo- and radiotherapy. As a result, GBM inevitably recurs and only a few patients survive 5 years post-diagnosis. GBM is characterized by extensive phenotypic and genetic heterogeneity, creating a diversified genetic landscape and a network of biological interactions between subclones, ultimately promoting tumor growth and therapeutic resistance. This includes spatial and temporal changes in the tumor microenvironment, which influence cellular and molecular programs in GBM and therapeutic responses. However, dissecting phenotypic and genetic heterogeneity at spatial and temporal levels is extremely challenging, and the dynamics of the GBM microenvironment cannot be captured by analysis of a single tumor sample. In this review, we discuss the current research on GBM heterogeneity, in particular, the utility and potential applications of fluorescence-guided multiple sampling to dissect phenotypic and genetic intra-tumor heterogeneity in the GBM microenvironment, identify tumor and non-tumor cell interactions and novel therapeutic targets in areas that are key for tumor growth and recurrence, and improve the molecular classification of GBM.
Collapse
Affiliation(s)
- Leopoldo A. García-Montaño
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
- University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico
| | - Yamhilette Licón-Muñoz
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
- University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico
| | - Frank J. Martinez
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
- University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico
| | - Yasine R. Keddari
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
- University of California, Merced, California
| | - Michael K. Ziemke
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, Mississippi
| | - Muhammad O. Chohan
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, Mississippi
| | - Sara G.M. Piccirillo
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
- University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico
| |
Collapse
|
14
|
Guo KS, Brodsky AS. Tumor collagens predict genetic features and patient outcomes. NPJ Genom Med 2023; 8:15. [PMID: 37414817 DOI: 10.1038/s41525-023-00358-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023] Open
Abstract
The extracellular matrix (ECM) is a critical determinant of tumor fate that reflects the output from myriad cell types in the tumor. Collagens constitute the principal components of the tumor ECM. The changing collagen composition in tumors along with their impact on patient outcomes and possible biomarkers remains largely unknown. The RNA expression of the 43 collagen genes from solid tumors in The Cancer Genome Atlas (TCGA) was clustered to classify tumors. PanCancer analysis revealed how collagens by themselves can identify the tissue of origin. Clustering by collagens in each cancer type demonstrated strong associations with survival, specific immunoenvironments, somatic gene mutations, copy number variations, and aneuploidy. We developed a machine learning classifier that predicts aneuploidy, and chromosome arm copy number alteration (CNA) status based on collagen expression alone with high accuracy in many cancer types with somatic mutations, suggesting a strong relationship between the collagen ECM context and specific molecular alterations. These findings have broad implications in defining the relationship between cancer-related genetic defects and the tumor microenvironment to improve prognosis and therapeutic targeting for patient care, opening new avenues of investigation to define tumor ecosystems.
Collapse
Affiliation(s)
- Kevin S Guo
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Alexander S Brodsky
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA.
| |
Collapse
|
15
|
Vadla R, Miki S, Taylor B, Kawauchi D, Jones BM, Nathwani N, Pham P, Tsang J, Nathanson DA, Furnari FB. Glioblastoma Mesenchymal Transition and Invasion are Dependent on a NF-κB/BRD2 Chromatin Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.546613. [PMID: 37461511 PMCID: PMC10349949 DOI: 10.1101/2023.07.03.546613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Glioblastoma (GBM) represents the most aggressive subtype of glioma, noted for its profound invasiveness and molecular heterogeneity. The mesenchymal (MES) transcriptomic subtype is frequently associated with therapy resistance, rapid recurrence, and increased tumor-associated macrophages. Notably, activation of the NF-κB pathway and alterations in the PTEN gene are both associated with this malignant transition. Although PTEN aberrations have been shown to be associated with enhanced NF-κB signaling, the relationships between PTEN, NF-κB and MES transition are poorly understood in GBM. Here, we show that PTEN regulates the chromatin binding of bromodomain and extraterminal (BET) family proteins, BRD2 and BRD4, mediated by p65/RelA localization to the chromatin. By utilizing patient-derived glioblastoma stem cells and CRISPR gene editing of the RELA gene, we demonstrate a crucial role for RelA lysine 310 acetylation in recruiting BET proteins to chromatin for MES gene expression and GBM cell invasion upon PTEN loss. Remarkably, we found that BRD2 is dependent on chromatin associated acetylated RelA for its recruitment to MES gene promoters and their expression. Furthermore, loss of BRD2 results in the loss of MES signature, accompanied by an enrichment of proneural signature and enhanced therapy responsiveness. Finally, we demonstrate that disrupting the NFκB/BRD2 interaction with a brain penetrant BET-BD2 inhibitor reduces mesenchymal gene expression, GBM invasion, and therapy resistance in GBM models. This study uncovers the role of hitherto unexplored PTEN-NF-κB-BRD2 pathway in promoting MES transition and suggests inhibiting this complex with BET-BD2 specific inhibitors as a therapeutic approach to target the MES phenotype in GBM.
Collapse
Affiliation(s)
- Raghavendra Vadla
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Shunichiro Miki
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Brett Taylor
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Daisuke Kawauchi
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Brandon M Jones
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nidhi Nathwani
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Philip Pham
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jonathan Tsang
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, California 90095, United States
| | - David A Nathanson
- Departments of Molecular and Medical Pharmacology, University of California, Los Angeles, California 90095, United States
| | - Frank B Furnari
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
16
|
Wood KB, Comba A, Motsch S, Grigera TS, Lowenstein PR. Scale-free correlations and potential criticality in weakly ordered populations of brain cancer cells. SCIENCE ADVANCES 2023; 9:eadf7170. [PMID: 37379380 PMCID: PMC10306295 DOI: 10.1126/sciadv.adf7170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/24/2023] [Indexed: 06/30/2023]
Abstract
Collective behavior spans several orders of magnitude of biological organization, from cell colonies to flocks of birds. We used time-resolved tracking of individual glioblastoma cells to investigate collective motion in an ex vivo model of glioblastoma. At the population level, glioblastoma cells display weakly polarized motion in the (directional) velocities of single cells. Unexpectedly, fluctuations in velocities are correlated over distances many times the size of a cell. Correlation lengths scale linearly with the maximum end-to-end length of the population, indicating that they are scale-free and lack a characteristic decay scale other than the size of the system. Last, a data-driven maximum entropy model captures statistical features of the experimental data with only two free parameters: the effective length scale (nc) and strength (J) of local pairwise interactions between tumor cells. These results show that glioblastoma assemblies exhibit scale-free correlations in the absence of polarization, suggesting that they may be poised near a critical point.
Collapse
Affiliation(s)
- Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Department of Physics, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Comba
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sebastien Motsch
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
| | - Tomás S. Grigera
- Instituto de Física de Líquidos y Sistemas Biológicos (IFLySiB), Buenos Aires, Argentina
- Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- CONICET, Godoy Cruz, Buenos Aires, Argentina
- Departamento de Física, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Pedro R. Lowenstein
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
17
|
Yuile A, Wei JQ, Mohan AA, Hotchkiss KM, Khasraw M. Interdependencies of the Neuronal, Immune and Tumor Microenvironment in Gliomas. Cancers (Basel) 2023; 15:2856. [PMID: 37345193 DOI: 10.3390/cancers15102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
Gliomas are the most common primary brain malignancy and are universally fatal. Despite significant breakthrough in understanding tumor biology, treatment breakthroughs have been limited. There is a growing appreciation that major limitations on effective treatment are related to the unique and highly complex glioma tumor microenvironment (TME). The TME consists of multiple different cell types, broadly categorized into tumoral, immune and non-tumoral, non-immune cells. Each group provides significant influence on the others, generating a pro-tumor dynamic with significant immunosuppression. In addition, glioma cells are highly heterogenous with various molecular distinctions on the cellular level. These variations, in turn, lead to their own unique influence on the TME. To develop future treatments, an understanding of this complex TME interplay is needed. To this end, we describe the TME in adult gliomas through interactions between its various components and through various glioma molecular phenotypes.
Collapse
Affiliation(s)
- Alexander Yuile
- Department of Medical Oncology, Royal North Shore Hospital, Reserve Road, St Leonards, NSW 2065, Australia
- The Brain Cancer Group, North Shore Private Hospital, 3 Westbourne Street, St Leonards, NSW 2065, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Joe Q Wei
- Department of Medical Oncology, Royal North Shore Hospital, Reserve Road, St Leonards, NSW 2065, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Aditya A Mohan
- The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC 27710, USA
| | - Kelly M Hotchkiss
- The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC 27710, USA
| | - Mustafa Khasraw
- The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC 27710, USA
| |
Collapse
|
18
|
Xia M, Jiao L, Wang XH, Tong M, Yao MD, Li XM, Yao J, Li D, Zhao PQ, Yan B. Single-cell RNA sequencing reveals a unique pericyte type associated with capillary dysfunction. Theranostics 2023; 13:2515-2530. [PMID: 37215579 PMCID: PMC10196835 DOI: 10.7150/thno.83532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/10/2023] [Indexed: 05/24/2023] Open
Abstract
Background: Capillary dysfunction has been implicated in a series of life- threatening vascular diseases characterized by pericyte and endothelial cell (EC) degeneration. However, the molecular profiles that govern the heterogeneity of pericytes have not been fully elucidated. Methods: Single-cell RNA sequencing was conducted on oxygen-induced proliferative retinopathy (OIR) model. Bioinformatics analysis was conducted to identify specific pericytes involved in capillary dysfunction. qRT-PCRs and western blots were conducted to detect Col1a1 expression pattern during capillary dysfunction. Matrigel co-culture assays, PI staining, and JC-1 staining was conducted to determine the role of Col1a1 in pericyte biology. IB4 and NG2 staining was conducted to determine the role of Col1a1 in capillary dysfunction. Results: We constructed an atlas of > 76,000 single-cell transcriptomes from 4 mouse retinas, which could be annotated to 10 distinct retinal cell types. Using the sub-clustering analysis, we further characterized retinal pericytes into 3 different subpopulations. Notably, GO and KEGG pathway analysis demonstrated that pericyte sub-population 2 was identified to be vulnerable to retinal capillary dysfunction. Based on the single-cell sequencing results, Col1a1 was identified as a marker gene of pericyte sub-population 2 and a promising therapeutic target for capillary dysfunction. Col1a1 was abundantly expressed in pericytes and its expression was obviously upregulated in OIR retinas. Col1a1 silencing could retard the recruitment of pericytes toward endothelial cells and aggravated hypoxia-induced pericyte apoptosis in vitro. Col1a1 silencing could reduce the size of neovascular area and avascular area in OIR retinas and suppressed pericyte-myofibroblast transition and endothelial-mesenchymal transition. Moreover, Col1a1 expression was up-regulated in the aqueous humor of the patients with proliferative diabetic retinopathy (PDR) or retinopathy of prematurity (ROP) and up-regulated in the proliferative membranes of PDR patients. Conclusions: These findings enhance the understanding of the complexity and heterogeneity of retinal cells and have important implications for future treatment of capillary dysfunction.
Collapse
Affiliation(s)
- Min Xia
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing 210000, China
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing 210000, China
| | - Lyu Jiao
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Xiao-Han Wang
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Min Tong
- Eye Institute, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200030, China
| | - Mu-Di Yao
- Eye Institute, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200030, China
| | - Xiu-Miao Li
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing 210000, China
| | - Jin Yao
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing 210000, China
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing 210000, China
| | - Dan Li
- Eye Institute, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200030, China
| | - Pei-Quan Zhao
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Biao Yan
- Eye Institute, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200030, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration (Fudan University), Shanghai 200030, China
| |
Collapse
|
19
|
Ghannoum S, Fantini D, Zahoor M, Reiterer V, Phuyal S, Leoncio Netto W, Sørensen Ø, Iyer A, Sengupta D, Prasmickaite L, Mælandsmo GM, Köhn-Luque A, Farhan H. A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression. PLoS Comput Biol 2023; 19:e1010995. [PMID: 37068117 PMCID: PMC10159355 DOI: 10.1371/journal.pcbi.1010995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 05/04/2023] [Accepted: 03/04/2023] [Indexed: 04/18/2023] Open
Abstract
Our understanding of how speed and persistence of cell migration affects the growth rate and size of tumors remains incomplete. To address this, we developed a mathematical model wherein cells migrate in two-dimensional space, divide, die or intravasate into the vasculature. Exploring a wide range of speed and persistence combinations, we find that tumor growth positively correlates with increasing speed and higher persistence. As a biologically relevant example, we focused on Golgi fragmentation, a phenomenon often linked to alterations of cell migration. Golgi fragmentation was induced by depletion of Giantin, a Golgi matrix protein, the downregulation of which correlates with poor patient survival. Applying the experimentally obtained migration and invasion traits of Giantin depleted breast cancer cells to our mathematical model, we predict that loss of Giantin increases the number of intravasating cells. This prediction was validated, by showing that circulating tumor cells express significantly less Giantin than primary tumor cells. Altogether, our computational model identifies cell migration traits that regulate tumor progression and uncovers a role of Giantin in breast cancer progression.
Collapse
Affiliation(s)
- Salim Ghannoum
- Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - Damiano Fantini
- Department of Urology, Northwestern University, Chicago, Illinois, United States of America
| | - Muhammad Zahoor
- Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - Veronika Reiterer
- Institute of Pathophysiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Santosh Phuyal
- Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - Waldir Leoncio Netto
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Øystein Sørensen
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Arvind Iyer
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Debarka Sengupta
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
- Centre for Artificial Intelligence, Indraprastha Institute of Information Technology, Delhi, India
| | - Lina Prasmickaite
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Gunhild Mari Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Medical Biology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Alvaro Köhn-Luque
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hesso Farhan
- Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Oslo, Norway
- Institute of Pathophysiology, Medical University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
20
|
Mao XG, Xue XY, Lv R, Ji A, Shi TY, Chen XY, Jiang XF, Zhang X. CEBPD is a master transcriptional factor for hypoxia regulated proteins in glioblastoma and augments hypoxia induced invasion through extracellular matrix-integrin mediated EGFR/PI3K pathway. Cell Death Dis 2023; 14:269. [PMID: 37059730 PMCID: PMC10104878 DOI: 10.1038/s41419-023-05788-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/16/2023]
Abstract
Hypoxia contributes to the initiation and progression of glioblastoma by regulating a cohort of genes called hypoxia-regulated genes (HRGs) which form a complex molecular interacting network (HRG-MINW). Transcription factors (TFs) often play central roles for MINW. The key TFs for hypoxia induced reactions were explored using proteomic analysis to identify a set of hypoxia-regulated proteins (HRPs) in GBM cells. Next, systematic TF analysis identified CEBPD as a top TF that regulates the greatest number of HRPs and HRGs. Clinical sample and public database analysis revealed that CEBPD is significantly up-regulated in GBM, high levels of CEBPD predict poor prognosis. In addition, CEBPD is highly expressed in hypoxic condition both in GBM tissue and cell lines. For molecular mechanisms, HIF1α and HIF2α can activate the CEBPD promotor. In vitro and in vivo experiments demonstrated that CEBPD knockdown impaired the invasion and growth capacity of GBM cells, especially in hypoxia condition. Next, proteomic analysis identified that CEBPD target proteins are mainly involved in the EGFR/PI3K pathway and extracellular matrix (ECM) functions. WB assays revealed that CEBPD significantly positively regulated EGFR/PI3K pathway. Chromatin immunoprecipitation (ChIP) qPCR/Seq analysis and Luciferase reporter assay demonstrated that CEBPD binds and activates the promotor of a key ECM protein FN1 (fibronectin). In addition, the interactions of FN1 and its integrin receptors are necessary for CEBPD-induced EGFR/PI3K activation by promoting EGFR phosphorylation. Furthermore, GBM sample analysis in the database corroborated that CEBPD is positively correlated with the pathway activities of EGFR/PI3K and HIF1α, especially in highly hypoxic samples. At last, HRPs are also enriched in ECM proteins, indicating that ECM activities are important components of hypoxia induced responses in GBM. In conclusion, CEPBD plays important regulatory roles in the GBM HRG-MINW as a key TF, which activates the EGFR/PI3K pathway through ECM, especially FN1, mediated EGFR phosphorylation.
Collapse
Affiliation(s)
- Xing-Gang Mao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, People's Republic of China.
| | - Xiao-Yan Xue
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi Province, People's Republic of China
| | - Rui Lv
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, People's Republic of China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, People's Republic of China
| | - Ang Ji
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, People's Republic of China
| | - Ting-Yu Shi
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, People's Republic of China
| | - Xiao-Yan Chen
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, People's Republic of China
| | - Xiao-Fan Jiang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, People's Republic of China.
| | - Xiang Zhang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, People's Republic of China.
| |
Collapse
|
21
|
Comba A, Varela ML, Faisal SM, Abel CC, Argento AE, Al-Holou WN, Hollon TC, Perelman JD, Dunn PJ, Motsch S, Castro MG, Lowenstein PR. Generation of 3D ex vivo mouse- and patient-derived glioma explant slice model for integration of confocal time-lapse imaging and spatial analysis. STAR Protoc 2023; 4:102174. [PMID: 36930648 PMCID: PMC10036861 DOI: 10.1016/j.xpro.2023.102174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/12/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
Development of spatial-integrative pre-clinical models is needed for glioblastoma, which are heterogenous tumors with poor prognosis. Here, we present an optimized protocol to generate three-dimensional ex vivo explant slice glioma model from orthotopic tumors, genetically engineered mouse models, and fresh patient-derived specimens. We describe a step-by-step workflow for tissue acquisition, dissection, and sectioning of 300-μm tumor slices maintaining cell viability. The explant slice model allows the integration of confocal time-lapse imaging with spatial analysis for studying migration, invasion, and tumor microenvironment, making it a valuable platform for testing effective treatment modalities. For complete details on the use and execution of this protocol, please refer to Comba et al. (2022).1.
Collapse
Affiliation(s)
- Andrea Comba
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Maria Luisa Varela
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Syed M Faisal
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Clifford C Abel
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anna E Argento
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wajd N Al-Holou
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Todd C Hollon
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jacqueline D Perelman
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Patrick J Dunn
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sebastien Motsch
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pedro R Lowenstein
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
22
|
Cell signaling activation and extracellular matrix remodeling underpin glioma tumor microenvironment heterogeneity and organization. Cell Oncol 2022; 46:589-602. [PMID: 36567397 DOI: 10.1007/s13402-022-00763-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2022] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Tumor cells thrive by adapting to the signals in their microenvironment. To adapt, cancer cells activate signaling and transcriptional programs and migrate to establish micro-niches, in response to signals from neighboring cells and non-cellular stromal factors. Understanding how the tumor microenvironment evolves during disease progression is crucial to deciphering the mechanisms underlying the functional behavior of cancer cells. METHODS Multiplex immunohistochemistry, spatial analysis and histological dyes were used to identify and measure immune cell infiltration, cell signal activation and extracellular matrix deposition in low-grade, high-grade astrocytoma and glioblastoma. RESULTS We show that lower grade astrocytoma tissue is largely devoid of infiltrating immune cells and extracellular matrix proteins, while high-grade astrocytoma exhibits abundant immune cell infiltration, activation, and extensive tissue remodeling. Spatial analysis shows that most T-cells are restricted to perivascular regions, but bone marrow-derived macrophages penetrate deep into neoplastic cell-rich regions. The tumor microenvironment is characterized by heterogeneous PI3K, MAPK and CREB signaling, with specific signaling profiles correlating with distinct pathological hallmarks, including angiogenesis, tumor cell density and regions where neoplastic cells border the extracellular matrix. Our results also show that tissue remodeling is important in regulating the architecture of the tumor microenvironment during tumor progression. CONCLUSION The tumor microenvironment in malignant astrocytoma, exhibits changes in cell composition, cell signaling activation and extracellular matrix deposition during disease development and that targeting the extracellular matrix, as well as cell signaling activation will be critical to designing personalized therapy.
Collapse
|
23
|
Role of nerves in neurofibromatosis type 1-related nervous system tumors. Cell Oncol (Dordr) 2022; 45:1137-1153. [PMID: 36327093 DOI: 10.1007/s13402-022-00723-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disorder that affects nearly 1 in 3000 infants. Neurofibromin inactivation and NF1 gene mutations are involved in various aspects of neuronal function regulation, including neuronal development induction, electrophysiological activity elevation, growth factor expression, and neurotransmitter release. NF1 patients often exhibit a predisposition to tumor development, especially in the nervous system, resulting in the frequent occurrence of peripheral nerve sheath tumors and gliomas. Recent evidence suggests that nerves play a role in the development of multiple tumor types, prompting researchers to investigate the nerve as a vital component in and regulator of the initiation and progression of NF1-related nervous system tumors. CONCLUSION In this review, we summarize existing evidence about the specific effects of NF1 mutation on neurons and emerging research on the role of nerves in neurological tumor development, promising a new set of selective and targeted therapies for NF1-related tumors.
Collapse
|
24
|
Faisal SM, Comba A, Varela ML, Argento AE, Brumley E, Abel C, Castro MG, Lowenstein PR. The complex interactions between the cellular and non-cellular components of the brain tumor microenvironmental landscape and their therapeutic implications. Front Oncol 2022; 12:1005069. [PMID: 36276147 PMCID: PMC9583158 DOI: 10.3389/fonc.2022.1005069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
Glioblastoma (GBM), an aggressive high-grade glial tumor, is resistant to therapy and has a poor prognosis due to its universal recurrence rate. GBM cells interact with the non-cellular components in the tumor microenvironment (TME), facilitating their rapid growth, evolution, and invasion into the normal brain. Herein we discuss the complexity of the interactions between the cellular and non-cellular components of the TME and advances in the field as a whole. While the stroma of non-central nervous system (CNS) tissues is abundant in fibrillary collagens, laminins, and fibronectin, the normal brain extracellular matrix (ECM) predominantly includes proteoglycans, glycoproteins, and glycosaminoglycans, with fibrillary components typically found only in association with the vasculature. However, recent studies have found that in GBMs, the microenvironment evolves into a more complex array of components, with upregulated collagen gene expression and aligned fibrillary ECM networks. The interactions of glioma cells with the ECM and the degradation of matrix barriers are crucial for both single-cell and collective invasion into neighboring brain tissue. ECM-regulated mechanisms also contribute to immune exclusion, resulting in a major challenge to immunotherapy delivery and efficacy. Glioma cells chemically and physically control the function of their environment, co-opting complex signaling networks for their own benefit, resulting in radio- and chemo-resistance, tumor recurrence, and cancer progression. Targeting these interactions is an attractive strategy for overcoming therapy resistance, and we will discuss recent advances in preclinical studies, current clinical trials, and potential future clinical applications. In this review, we also provide a comprehensive discussion of the complexities of the interconnected cellular and non-cellular components of the microenvironmental landscape of brain tumors to guide the development of safe and effective therapeutic strategies against brain cancer.
Collapse
Affiliation(s)
- Syed M. Faisal
- Dept. of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, United States
- Dept. of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Andrea Comba
- Dept. of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, United States
- Dept. of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Maria L. Varela
- Dept. of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, United States
- Dept. of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Anna E. Argento
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Emily Brumley
- Dept. of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, United States
- Dept. of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Clifford Abel
- Dept. of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, United States
- Dept. of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Maria G. Castro
- Dept. of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, United States
- Dept. of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Pedro R. Lowenstein
- Dept. of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, United States
- Dept. of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Pedro R. Lowenstein,
| |
Collapse
|
25
|
Yang Y, Schubert MC, Kuner T, Wick W, Winkler F, Venkataramani V. Brain Tumor Networks in Diffuse Glioma. Neurotherapeutics 2022; 19:1832-1843. [PMID: 36357661 PMCID: PMC9723066 DOI: 10.1007/s13311-022-01320-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
Diffuse gliomas are primary brain tumors associated with a poor prognosis. Cellular and molecular mechanisms driving the invasive growth patterns and therapeutic resistance are incompletely understood. The emerging field of cancer neuroscience offers a novel approach to study these brain tumors in the context of their intricate interactions with the nervous system employing and combining methodological toolsets from neuroscience and oncology. Increasing evidence has shown how neurodevelopmental and neuronal-like mechanisms are hijacked leading to the discovery of multicellular brain tumor networks. Here, we review how gap junction-coupled tumor-tumor-astrocyte networks, as well as synaptic and paracrine neuron-tumor networks drive glioma progression. Molecular mechanisms of these malignant, homo- and heterotypic networks, and their complex interplay are reviewed. Lastly, potential clinical-translational implications and resulting therapeutic strategies are discussed.
Collapse
Affiliation(s)
- Yvonne Yang
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), INF 280, 69120, Heidelberg, Germany
| | - Marc C Schubert
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), INF 280, 69120, Heidelberg, Germany
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, INF 307, 69120, Heidelberg, Germany
| | - Thomas Kuner
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, INF 307, 69120, Heidelberg, Germany
| | - Wolfgang Wick
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), INF 280, 69120, Heidelberg, Germany
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), INF 280, 69120, Heidelberg, Germany
| | - Varun Venkataramani
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany.
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), INF 280, 69120, Heidelberg, Germany.
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, INF 307, 69120, Heidelberg, Germany.
| |
Collapse
|