1
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Mondal S, Becskei A. Gene choice in cancer cells is exclusive in ion transport but concurrent in DNA replication. Comput Struct Biotechnol J 2024; 23:2534-2547. [PMID: 38974885 PMCID: PMC11226983 DOI: 10.1016/j.csbj.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024] Open
Abstract
Cancers share common cellular and physiological features. Little is known about whether distinctive gene expression patterns can be displayed at the single-cell level by gene families in cancer cells. The expression of gene homologs within a family can exhibit concurrence and exclusivity. Concurrence can promote all-or-none expression patterns of related genes and underlie alternative physiological states. Conversely, exclusive gene families express the same or similar number of homologs in each cell, allowing a broad repertoire of cell identities to be generated. We show that gene families involved in the cell-cycle and antigen presentation are expressed concurrently. Concurrence in the DNA replication complex MCM reflects the replicative status of cells, including cell lines and cancer-derived organoids. Exclusive expression requires precise regulatory mechanism, but cancer cells retain this form of control for ion homeostasis and extend it to gene families involved in cell migration. Thus, the cell adhesion-based identity of healthy cells is transformed to an identity based on migration in the population of cancer cells, reminiscent of epithelial-mesenchymal transition.
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Affiliation(s)
- Samuel Mondal
- Biozentrum, University of Basel, Spitalstrasse 41, Basel 4056, Switzerland
| | - Attila Becskei
- Biozentrum, University of Basel, Spitalstrasse 41, Basel 4056, Switzerland
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2
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Yuan D, Chen W, Jin S, Li W, Liu W, Liu L, Wu Y, Zhang Y, He X, Jiang J, Sun H, Liu X, Liu J. Co-expression of immune checkpoints in glioblastoma revealed by single-nucleus RNA sequencing and spatial transcriptomics. Comput Struct Biotechnol J 2024; 23:1534-1546. [PMID: 38633388 PMCID: PMC11021796 DOI: 10.1016/j.csbj.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Glioblastoma (GBM) is one of the most malignant tumors of the central nervous system. The pattern of immune checkpoint expression in GBM remains largely unknown. We performed snRNA-Seq and spatial transcriptomic (ST) analyses on untreated GBM samples. 8 major cell types were found in both tumor and adjacent normal tissues, with variations in infiltration grade. Neoplastic cells_6 was identified in malignant cells with high expression of invasion and proliferator-related genes, and analyzed its interactions with microglia, MDM cells and T cells. Significant alterations in ligand-receptor interactions were observed, particularly between Neoplastic cells_6 and microglia, and found prominent expression of VISTA/VSIG3, suggesting a potential mechanism for evading immune system attacks. High expression of TIM-3, VISTA, PSGL-1 and VSIG-3 with similar expression patterns in GBM, may have potential as therapeutic targets. The prognostic value of VISTA expression was cross-validated in 180 glioma patients, and it was observed that patients with high VISTA expression had a poorer prognosis. In addition, multimodal cross analysis integrated SnRNA-seq and ST, revealing complex intracellular communication and mapping the GBM tumor microenvironment. This study reveals novel molecular characteristics of GBM, co-expression of immune checkpoints, and potential therapeutic targets, contributing to improving the understanding and treatment of GBM.
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Affiliation(s)
- Dingyi Yuan
- New Drug Screening and Pharmacodynamics Evaluation Center, China Pharmaceutical University, Nanjing, China
| | - Wenting Chen
- New Drug Screening and Pharmacodynamics Evaluation Center, China Pharmaceutical University, Nanjing, China
| | - Shasha Jin
- New Drug Screening and Pharmacodynamics Evaluation Center, China Pharmaceutical University, Nanjing, China
| | - Wei Li
- Department of Neurosurgery, the Affiliated Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Wanmei Liu
- New Drug Screening and Pharmacodynamics Evaluation Center, China Pharmaceutical University, Nanjing, China
| | - Liu Liu
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing, China
| | - Yinhao Wu
- New Drug Screening and Pharmacodynamics Evaluation Center, China Pharmaceutical University, Nanjing, China
| | - Yuxin Zhang
- New Drug Screening and Pharmacodynamics Evaluation Center, China Pharmaceutical University, Nanjing, China
| | - Xiaoyu He
- New Drug Screening and Pharmacodynamics Evaluation Center, China Pharmaceutical University, Nanjing, China
| | - Jingwei Jiang
- New Drug Screening and Pharmacodynamics Evaluation Center, China Pharmaceutical University, Nanjing, China
| | - Hongbin Sun
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing, China
| | - Xiangyu Liu
- Department of Neurosurgery, the Affiliated Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Jun Liu
- New Drug Screening and Pharmacodynamics Evaluation Center, China Pharmaceutical University, Nanjing, China
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3
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van Solinge TS, Oh J, Abels E, Koch P, Breakefield XO, Weissleder R, Broekman MLD. Probing the glioma micro-environment: Analysis using biopsy in combination with ultra-fast cyclic immunolabeling. Neoplasia 2024; 57:101051. [PMID: 39270598 PMCID: PMC11415813 DOI: 10.1016/j.neo.2024.101051] [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: 06/27/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024]
Abstract
The interaction between gliomas and the immune system is poorly understood and thus hindering development of effective immunotherapies for glioma patients. The immune response is highly variable during tumor development, and affected by therapies such as surgery, radiation, and chemotherapy. Currently, analysis of these local changes is difficult due to poor accessibility of the tumor and high-morbidity of sampling. In this study, we developed a model for repeat-biopsy in mice to study these local immunological changes over time. Using fine needle biopsy we were able to safely and repeatedly collect cells from intracranial tumors in mice. Ultra-fast cycling technology (FAST) was used for multi-cycle immunofluorescence of retrieved cells, and provided insights in the changing immune response over time. The combination of these techniques can be utilized to study changes in the immune response in glioma or other intracranial diseases over time, and in response to treatment within the same animal.
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Affiliation(s)
- Thomas S van Solinge
- Departments of Neurology and Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Department of Neurosurgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Erik Abels
- Departments of Neurology and Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter Koch
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Xandra O Breakefield
- Departments of Neurology and Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Marike L D Broekman
- Departments of Neurology and Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Department of Neurosurgery, Leiden University Medical Center, Leiden, the Netherlands; Department of Neurosurgery, Haaglanden Medical Center, The Hague, the Netherlands.
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4
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Manoharan VT, Abdelkareem A, Gill G, Brown S, Gillmor A, Hall C, Seo H, Narta K, Grewal S, Dang NH, Ahn BY, Osz K, Lun X, Mah L, Zemp F, Mahoney D, Senger DL, Chan JA, Morrissy AS. Spatiotemporal modeling reveals high-resolution invasion states in glioblastoma. Genome Biol 2024; 25:264. [PMID: 39390467 DOI: 10.1186/s13059-024-03407-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 09/29/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Diffuse invasion of glioblastoma cells through normal brain tissue is a key contributor to tumor aggressiveness, resistance to conventional therapies, and dismal prognosis in patients. A deeper understanding of how components of the tumor microenvironment (TME) contribute to overall tumor organization and to programs of invasion may reveal opportunities for improved therapeutic strategies. RESULTS Towards this goal, we apply a novel computational workflow to a spatiotemporally profiled GBM xenograft cohort, leveraging the ability to distinguish human tumor from mouse TME to overcome previous limitations in the analysis of diffuse invasion. Our analytic approach, based on unsupervised deconvolution, performs reference-free discovery of cell types and cell activities within the complete GBM ecosystem. We present a comprehensive catalogue of 15 tumor cell programs set within the spatiotemporal context of 90 mouse brain and TME cell types, cell activities, and anatomic structures. Distinct tumor programs related to invasion align with routes of perivascular, white matter, and parenchymal invasion. Furthermore, sub-modules of genes serving as program network hubs are highly prognostic in GBM patients. CONCLUSION The compendium of programs presented here provides a basis for rational targeting of tumor and/or TME components. We anticipate that our approach will facilitate an ecosystem-level understanding of the immediate and long-term consequences of such perturbations, including the identification of compensatory programs that will inform improved combinatorial therapies.
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Affiliation(s)
- Varsha Thoppey Manoharan
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Aly Abdelkareem
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Gurveer Gill
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Samuel Brown
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Aaron Gillmor
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Courtney Hall
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Heewon Seo
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Kiran Narta
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Sean Grewal
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Ngoc Ha Dang
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Bo Young Ahn
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Kata Osz
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Xueqing Lun
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Laura Mah
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Franz Zemp
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Douglas Mahoney
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Donna L Senger
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.
| | - Jennifer A Chan
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada.
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| | - A Sorana Morrissy
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
- Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
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5
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Liu X, Fan H, Chen Z, Liu C. Exploring the significance and potential mechanisms of hippo pathway-associated genes in prognosis of glioma patients. Discov Oncol 2024; 15:536. [PMID: 39382606 DOI: 10.1007/s12672-024-01391-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024] Open
Abstract
PURPOSE Despite the efforts of countless researchers to develop glioma treatment strategies, the current therapeutic effect of glioma is still not ideal, and it is necessary to further explore the mechanism to guide treatment. Thus, this study aims to introduce a novel approach for predicting patient prognosis and guiding further treatment interventions. METHODS Initially, we conducted a differential gene expression analysis to identify Hippo pathway-associated genes overexpressed in tumors and determined genes correlated with prognosis. Subsequently, employing cluster analysis, we categorized samples into two groups and performed further analyses including prediction, immune cell infiltration abundance, and drug response rates. We utilized weighted gene co-expression analysis to reveal gene sets with high co-variation, delineate inter-sample gene correlation patterns, and conduct enrichment analysis. Prognostic models were built using ten machine learning algorithms combined in 101 different combinations, followed by evaluation and validation. Immune infiltration analysis, differential expression analysis of depleted T cell-related markers, drug sensitivity analysis, and exploration of pathway dysregulation were performed for different risk groups. Quality control and batch integration were performed, and single-cell data were analyzed using dimensionality reduction clustering algorithms and annotation tools to evaluate the activity of the prognostic model in malignant cells. RESULTS We conducted data filtering to identify genes overexpressed in tumors, intersecting these genes with Hippo pathway-related genes, identifying 62 genes correlated with prognosis, and performing cluster analysis to divide tumor tissues into two groups. Cluster 2 exhibited a poorer prognosis and demonstrated differences in immune cell infiltration. Utilizing weighted gene co-expression analysis on Cluster 2, we identified gene modules, conducted functional enrichment analysis, and delineated pathways. Employing a combined model based on ten machine learning algorithm combinations, we selected the optimal prognostic model system and validated the model's predictive ability within the dataset. Through immune-related analysis and drug sensitivity analysis, we uncovered differences in immune infiltration and varying sensitivities to chemotherapy drugs. Additionally, the enrichment analysis of gene set revealed discrepancies in upregulation within relevant pathways between the high and low-risk groups. Finally, annotation and evaluation of malignant cells via single-cell analysis showed increased activity of the prognostic model and variations in distribution across different prognostic levels in malignant cells. CONCLUSION This study introduces a novel approach utilizing the Hippo pathway and associated genes for glioma prognosis research, demonstrating the potential and significance of this method in evaluating the outcome for patients with glioma. These findings hold substantial clinical significance in guiding therapy and predicting outcomes for individuals diagnosed with glioma, offering significant clinical utility.
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Affiliation(s)
- XuKai Liu
- Department of Neurosurgery, Central Hospital of Zhuzhou, Zhuzhou, Hunan, China
| | - Hongjun Fan
- Department of Neurosurgery, Central Hospital of Zhuzhou, Zhuzhou, Hunan, China
| | - Zebo Chen
- Department of Neurosurgery, Central Hospital of Zhuzhou, Zhuzhou, Hunan, China
| | - Chao Liu
- Department of Neurosurgery, Central Hospital of Zhuzhou, Zhuzhou, Hunan, China.
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6
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Duan H, Xie Y, Wu S, Zhao G, Zeng Z, Hu H, Yu Y, Hu W, Yang Y, Chen Y, Xie H, Chen Z, Zhang G, Flaherty KT, Hu S, Xu H, Ma W, Mou Y. Effect of the mRNA decapping enzyme scavenger (DCPS) inhibitor RG3039 on glioblastoma. J Transl Med 2024; 22:880. [PMID: 39350123 PMCID: PMC11443721 DOI: 10.1186/s12967-024-05658-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 09/04/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Patients with glioblastoma (GBM) have a poor prognosis and limited treatment options. The mRNA decapping enzyme scavenger (DCPS) is a cap-hydrolyzing enzyme. The DCPS inhibitor RG3039 exhibited excellent central nervous system bioavailability in vivo and was safe and well tolerated in healthy volunteers in a phase 1 clinical trial. In this study, we investigated the expression of DCPS in GBM and the anti-tumor activity of RG3039 in various preclinical models of GBM. METHODS DCPS expression was examined in human GBM and paired peritumoral tissues. Its prognostic role was evaluated together with clinicopathological characteristics of patients. The anti-GBM effect of RG3039 was determined using GBM cell lines, patient-derived organoids, and orthotopic mouse models. The therapeutic mechanisms of DCPS inhibition were explored. RESULTS DCPS is overexpressed in GBM and is associated with poor survival of patients with GBM. The DCPS inhibitor RG3039 exhibited robust anti-GBM activities in GBM cell lines, patient-derived organoids and orthotopic mouse models, with drug exposure achievable in humans. Mechanistically, RG3039 downregulated STAT5B expression, thereby suppressing proliferation, survival and colony formation of GBM cells. CONCLUSIONS DCPS is a promising target for GBM. Inhibition of DCPS with RG3039 at doses achievable in humans downregulates STAT5B expression and reduces proliferation, survival and colony formation of GBM cells. Given the excellent anti-cancer activity and central nervous system bioavailability in vivo and good tolerance in humans, RG3039 warrants further study as a potential GBM therapy.
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Affiliation(s)
- Hao Duan
- Department of Neurosurgery/Neuro-Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuan Xie
- Department of Neurosurgery/Neuro-Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Suwen Wu
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guangyin Zhao
- Experimental Animal Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhen Zeng
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongrong Hu
- Department of Neurosurgery/Neuro-Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanjiao Yu
- Department of Neurosurgery/Neuro-Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wanming Hu
- Department of Pathology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuanzhong Yang
- Department of Pathology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yukun Chen
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Haoqun Xie
- Department of Neurosurgery/Neuro-Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zexin Chen
- Guangdong Research Center of Organoid Engineering and Technology, Guangzhou, China
| | - Gao Zhang
- Faculty of Dentistry, University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Keith T Flaherty
- Department of Medicine, Massachusetts General Hospital, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Shanshan Hu
- Department of Statistics, Rutgers University, New Brunswick, NJ, USA
| | - Haineng Xu
- Ovarian Cancer Research Center, Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Wenjuan Ma
- Intensive Care Unit, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Yonggao Mou
- Department of Neurosurgery/Neuro-Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China.
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7
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D'Uonnolo G, Isci D, Nosirov B, Kuppens A, Wantz M, Nazarov PV, Golebiewska A, Rogister B, Chevigné A, Neirinckx V, Szpakowska M. Patient-based multilevel transcriptome exploration highlights relevant chemokines and chemokine receptor axes in glioblastoma. Comput Biol Med 2024; 182:109197. [PMID: 39353298 DOI: 10.1016/j.compbiomed.2024.109197] [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: 06/21/2024] [Revised: 09/02/2024] [Accepted: 09/22/2024] [Indexed: 10/04/2024]
Abstract
Chemokines and their receptors form a complex interaction network, crucial for precise leukocyte positioning and trafficking. In cancer, they promote malignant cell proliferation and survival but are also critical for immune cell infiltration in the tumor microenvironment. Glioblastoma (GBM) is the most common and lethal brain tumor, characterized by an immunosuppressive TME, with restricted immune cell infiltration. A better understanding of chemokine-receptor interactions is therefore essential for improving tumor immunogenicity. In this study, we assessed the expression of all human chemokines in adult-type diffuse gliomas, with particular focus on GBM, based on patient-derived samples. Publicly available bulk RNA sequencing datasets allowed us to identify the chemokines most abundantly expressed in GBM, with regard to disease severity and across different tumor subregions. To gain insight into the chemokines-receptor network at the single cell resolution, we explored GBmap, a curated resource integrating multiple scRNAseq datasets from different published studies. Our study constitutes the first patient-based handbook highlighting the relevant chemokine-receptor crosstalks, which are of significant interest in the perspective of a therapeutic modulation of the TME in GBM.
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Affiliation(s)
- Giulia D'Uonnolo
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Damla Isci
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Belgium
| | - Bakhtiyor Nosirov
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg; Multiomics Data Science Research Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg
| | - Amandine Kuppens
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Belgium
| | - May Wantz
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg
| | - Petr V Nazarov
- Multiomics Data Science Research Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg
| | - Bernard Rogister
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Belgium; University Hospital, Neurology Department, University of Liège, Belgium
| | - Andy Chevigné
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg
| | - Virginie Neirinckx
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Belgium.
| | - Martyna Szpakowska
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg
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8
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Hofstätter Azambuja J, Yerneni SS, Maurer LM, Crentsil HE, Debom GN, Klei L, Smyers M, Sneiderman CT, Schwab KE, Acharya R, Lin Wu Y, Ekambaram P, Hu D, Gough PJ, Bertin J, Melnick A, Kohanbash G, Bao R, Lucas PC, McAllister-Lucas LM. MALT1 protease inhibition restrains glioblastoma progression by reversing tumor-associated macrophage-dependent immunosuppression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.614808. [PMID: 39386586 PMCID: PMC11463364 DOI: 10.1101/2024.09.26.614808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
MALT1 protease is an intracellular signaling molecule that promotes tumor progression via cancer cell-intrinsic and cancer cell-extrinsic mechanisms. MALT1 has been mostly studied in lymphocytes, and little is known about its role in tumor-associated macrophages. Here, we show that MALT1 plays a key role in glioblastoma (GBM)-associated macrophages. Mechanistically, GBM tumor cells induce a MALT1-NF-κB signaling axis within macrophages, leading to macrophage migration and polarization toward an immunosuppressive phenotype. Inactivation of MALT1 protease promotes transcriptional reprogramming that reduces migration and restores a macrophage "M1-like" phenotype. Preclinical in vivo analysis shows that MALT1 inhibitor treatment results in increased immuno-reactivity of GBM-associated macrophages and reduced GBM tumor growth. Further, the addition of MALT1 inhibitor to temozolomide reduces immunosuppression in the tumor microenvironment, which may enhance the efficacy of this standard-of-care chemotherapeutic. Together, our findings suggest that MALT1 protease inhibition represents a promising macrophage-targeted immunotherapeutic strategy for the treatment of GBM. Graphical abstract
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9
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Zhao Y, Zhang D, Meng B, Zhang Y, Ma S, Zeng J, Wang X, Peng T, Gong X, Zhai R, Dong L, Jiang Y, Dai X, Fang X, Jia W. Integrated proteomic and glycoproteomic analysis reveals heterogeneity and molecular signatures of brain metastases from lung adenocarcinomas. Cancer Lett 2024; 605:217262. [PMID: 39341452 DOI: 10.1016/j.canlet.2024.217262] [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: 05/09/2024] [Revised: 07/26/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024]
Abstract
Brain metastasis is a major cause of poor prognosis and death in lung adenocarcinoma (LUAD); however, the understanding of therapeutic strategies and mechanisms for brain metastases from LUAD (BM-LUAD) remains notably limited, especially at the proteomics levels. To address this issue, we conducted integrated proteomic and glycoproteomic analyses on 49 BM-LUAD tumors, revealing two distinct subtypes of the disease: BM-S1 and BM-S2. Whole exome sequencing analysis revealed that somatic mutations in STK11 and KEAP1, as well as copy number deletions on chr19p13.3, such as STK11, UQCR11, and SLC25A23, were more frequently detected in BM-S2. In BM-S1 tumors, we observed significant infiltration of GFAP + astrocytes, as evidenced by elevated levels of GFAP, GABRA2, GABRG1 and GAP43 proteins and an enrichment of astrocytic signatures in both our proteomic data and external spatial transcriptomic data. Conversely, BM-S2 tumors demonstrated higher levels of PD-1 immune cell infiltration, supported by the upregulation of PD-1 and LAG-3 genes. These findings suggest distinct microenvironmental adaptations required by the different BM-LUAD subtypes. Additionally, we observed unique glycosylation patterns between the subtypes, with increased fucosylation in BM-S1 and enhanced sialylation in BM-S2, primarily affected by glycosylation enzymes such as FUT9, B4GALT1, and ST6GAL1. Specifically, in BM-S2, these sialylation modifications are predominantly localized to the lysosomes, underscoring the critical role of N-glycosylation in the tumor progression of BM-LUAD. Overall, our study not only provides a comprehensive multi-omic data resource but also offers valuable biological insights into BM-LUAD, highlighting potential mechanisms and therapeutic targets for further investigation.
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Affiliation(s)
- Yang Zhao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Dainan Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China; Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Bo Meng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Yong Zhang
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shunchang Ma
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China; Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Jiaming Zeng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Xi Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China; Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Tao Peng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Rui Zhai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Lianhua Dong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China.
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China.
| | - Wang Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China; Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China.
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10
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Budhiraja S, Baisiwala S, Cho S, Chojak R, Kazi HA, Stepniak A, Perrault EN, Chen L, Park CH, Dmello C, Lin P, Sonabend AM, Ahmed AU. THOC1 complexes with SIN3A to regulate R-loops and promote glioblastoma progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614748. [PMID: 39386597 PMCID: PMC11463517 DOI: 10.1101/2024.09.24.614748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Glioblastoma (GBM), the most common and aggressive malignant brain tumor in adults, has a median survival of 21 months. To identify drivers of GBM proliferation, we conducted a CRISPR-knockout screen, which revealed THO Complex 1 (THOC1) as a key driver. Knocking down THOC1 significantly reduced GBM cell viability across patient-derived xenograft (PDX) lines, enhancing survival (p<0.01) in primary PDX models. Conversely, overexpressing THOC1 in non-cancerous cells bolstered viability, decreasing survival and causing tumor engraftment in vivo (p<0.01). Further investigation revealed THOC1's robust interaction with SIN3A, a histone deacetylase complex. Histone deacetylation has been previously shown to prevent the buildup of R-loops, structures that form normally during transcription but can be lethal in excess. We found that THOC1-knockdown leads to elevated R-loop levels and reduced histone deacetylation levels. Next, to understand the networks specifically regulated by THOC1-mediated R-loop prevention, we conducted unbiased RNA-sequencing on control and THOC1-knockdown GBM cells. We found that THOC1's role in R-loop prevention primarily affects telomeres, critical regions for cell replication. We further show that THOC1-knockdown results in significantly increased telomeric R-loop levels and shortened telomeres. Ultimately, this study suggests that targeting THOC1 shows promise as a therapeutic strategy to disrupt the delicate R-loop landscape and undermine GBM's replicative potential.
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11
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Snacel-Fazy E, Soubéran A, Grange M, Joseph K, Colin C, Morando P, Luche H, Pagano A, Brustlein S, Debarbieux F, Toutain S, Siret C, van de Pavert SA, Rougon G, Figarella-Branger D, Ravi VM, Tabouret E, Tchoghandjian A. SMAC mimetic drives microglia phenotype and glioblastoma immune microenvironment. Cell Death Dis 2024; 15:676. [PMID: 39278921 PMCID: PMC11402972 DOI: 10.1038/s41419-024-07056-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 09/02/2024] [Accepted: 09/04/2024] [Indexed: 09/18/2024]
Abstract
Tumor-associated macrophages/microglia (TAMs) are highly plastic and heterogeneous immune cells that can be immune-supportive or tumor-supportive depending of the microenvironment. TAMs are the most abundant immune cells in glioblastoma (GB), and play a key role in immunosuppression. Therefore, TAMs reprogramming toward immune-supportive cells is a promising strategy to overcome immunosuppression. By leveraging scRNAseq human GB databases, we identified that Inhibitor of Apoptosis Proteins (IAP) were expressed by TAMs. To investigate their role in TAMs-related immunosuppression, we antagonized IAP using the central nervous system permeant SMAC mimetic GDC-0152 (SMg). On explants and cultured immune cells isolated from human GB samples, SMg modified TAMs activity. We showed that SMg treatment promoted microglia pro-apoptotic and anti-tumoral function via caspase-3 pro-inflammatory cleavage and the inhibition of tumoroids growth. Then we designed a relevant immunogenic mouse GB model to decipher the spatio-temporal densities, distribution, phenotypes and function of TAMs with or without SMg treatment. We used 3D imaging techniques, a transgenic mouse with fluorescent TAM subsets and mass cytometry. We confirmed that SMg promoted microglia activation, antigen-presenting function and tumor infiltration. In addition, we observed a remodeling of blood vessels, a decrease in anti-inflammatory macrophages and an increased level of monocytes and their mo-DC progeny. This remodeling of the TAM landscape is associated with an increase in CD8 T cell density and activation. Altogether, these results demonstrated that SMg drives the immunosuppressive basal microglia toward an active phenotype with pro-apoptotic and anti-tumoral function and modifies the GB immune landscape. This identifies IAP as targets of choice for a potential mechanism-based therapeutic strategy and SMg as a promising molecule for this application.
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Affiliation(s)
- Emmanuel Snacel-Fazy
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
| | - Aurélie Soubéran
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
- APHM, CHU Timone, Service de Neurooncologie, Marseille, France
| | - Magali Grange
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, Inserm, CNRS, Marseille, France
| | - Kevin Joseph
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- 3D-Brain Models for Neurodegenerative Diseases, Medical Center, University of Freiburg, Freiburg, Germany
- Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carole Colin
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
| | - Philippe Morando
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
| | - Hervé Luche
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, Inserm, CNRS, Marseille, France
| | - Alessandra Pagano
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
| | - Sophie Brustlein
- Aix-Marseille Univ, INSERM, INMED, Turing Center for Living System, Marseille, France
| | - Franck Debarbieux
- Aix-Marseille Univ, CNRS, INT, Institut de Neurosciences de la Timone, Marseille, France
| | - Soline Toutain
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
| | - Carole Siret
- Aix-Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Serge A van de Pavert
- Aix-Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Geneviève Rougon
- Aix-Marseille Univ, CNRS, INT, Institut de Neurosciences de la Timone, Marseille, France
| | | | - Vidhya Madapusi Ravi
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- 3D-Brain Models for Neurodegenerative Diseases, Medical Center, University of Freiburg, Freiburg, Germany
- Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Emeline Tabouret
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- APHM, CHU Timone, Service de Neurooncologie, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PE"TRANSLA", Marseille, France
| | - Aurélie Tchoghandjian
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France.
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France.
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12
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Gan S, Macalinao DG, Shahoei SH, Tian L, Jin X, Basnet H, Bibby C, Muller JT, Atri P, Seffar E, Chatila W, Karacay A, Chanda P, Hadjantonakis AK, Schultz N, Brogi E, Bale TA, Moss NS, Murali R, Pe'er D, Massagué J. Distinct tumor architectures and microenvironments for the initiation of breast cancer metastasis in the brain. Cancer Cell 2024:S1535-6108(24)00314-3. [PMID: 39270646 DOI: 10.1016/j.ccell.2024.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 12/15/2023] [Accepted: 08/20/2024] [Indexed: 09/15/2024]
Abstract
Brain metastasis, a serious complication of cancer, hinges on the initial survival, microenvironment adaptation, and outgrowth of disseminated cancer cells. To understand the early stages of brain colonization, we investigated two prevalent sources of cerebral relapse, triple-negative (TNBC) and HER2+ (HER2BC) breast cancers. Using mouse models and human tissue samples, we found that these tumor types colonize the brain, with a preference for distinctive tumor architectures, stromal interfaces, and autocrine programs. TNBC models tend to form perivascular sheaths with diffusive contact with astrocytes and microglia. In contrast, HER2BC models tend to form compact spheroids driven by autonomous tenascin C production, segregating stromal cells to the periphery. Single-cell transcriptomics of the tumor microenvironment revealed that these architectures evoke differential Alzheimer's disease-associated microglia (DAM) responses and engagement of the GAS6 receptor AXL. The spatial features of the two modes of brain colonization have relevance for leveraging the stroma to treat brain metastasis.
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Affiliation(s)
- Siting Gan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Danilo G Macalinao
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sayyed Hamed Shahoei
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lin Tian
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xin Jin
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310024, China; Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Harihar Basnet
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Catherine Bibby
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James T Muller
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pranita Atri
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Evan Seffar
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Walid Chatila
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ali Karacay
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pharto Chanda
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nikolaus Schultz
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tejus A Bale
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nelson S Moss
- Department of Neurological Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rajmohan Murali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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13
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Harwood DSL, Pedersen V, Bager NS, Schmidt AY, Stannius TO, Areškevičiūtė A, Josefsen K, Nørøxe DS, Scheie D, Rostalski H, Lü MJS, Locallo A, Lassen U, Bagger FO, Weischenfeldt J, Heiland DH, Vitting-Seerup K, Michaelsen SR, Kristensen BW. Glioblastoma cells increase expression of notch signaling and synaptic genes within infiltrated brain tissue. Nat Commun 2024; 15:7857. [PMID: 39251578 PMCID: PMC11385527 DOI: 10.1038/s41467-024-52167-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 08/28/2024] [Indexed: 09/11/2024] Open
Abstract
Glioblastoma remains one of the deadliest brain malignancies. First-line therapy consists of maximal surgical tumor resection, accompanied by chemotherapy and radiotherapy. Malignant cells escape surgical resection by migrating into the surrounding healthy brain tissue, where they give rise to the recurrent tumor. Based on gene expression, tumor cores can be subtyped into mesenchymal, proneural, and classical tumors, each being associated with differences in genetic alterations and cellular composition. In contrast, the adjacent brain parenchyma where infiltrating malignant cells escape surgical resection is less characterized in patients. Using spatial transcriptomics (n = 11), we show that malignant cells within proneural or mesenchymal tumor cores display spatially organized differences in gene expression, although such differences decrease within the infiltrated brain tissue. Malignant cells residing in infiltrated brain tissue have increased expression of genes related to neurodevelopmental pathways and glial cell differentiation. Our findings provide an updated view of the spatial landscape of glioblastomas and further our understanding of the malignant cells that infiltrate the healthy brain, providing new avenues for the targeted therapy of these cells after surgical resection.
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Affiliation(s)
- Dylan Scott Lykke Harwood
- Department of Clinical Medicine and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
| | - Vilde Pedersen
- Department of Clinical Medicine and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Nicolai Schou Bager
- Department of Clinical Medicine and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ane Yde Schmidt
- Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Aušrinė Areškevičiūtė
- Danish Reference Center for Prion Diseases, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Knud Josefsen
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Dorte Schou Nørøxe
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hannah Rostalski
- Department of Clinical Medicine and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maya Jeje Schuang Lü
- Department of Clinical Medicine and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Alessio Locallo
- Department of Clinical Medicine and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Lassen
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Frederik Otzen Bagger
- Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Joachim Weischenfeldt
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Dieter Henrik Heiland
- Department of Neurosurgery, Medical Center-University of Freiburg, Freiburg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center-University of Freiburg, Freiburg, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, USA
- German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany
| | - Kristoffer Vitting-Seerup
- Section for Bioinformatics, Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Signe Regner Michaelsen
- Department of Clinical Medicine and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bjarne Winther Kristensen
- Department of Clinical Medicine and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
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14
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Deng Y, Mao J, Choi J, Lê Cao KA. StableMate: a statistical method to select stable predictors in omics data. NAR Genom Bioinform 2024; 6:lqae130. [PMID: 39345755 PMCID: PMC11437361 DOI: 10.1093/nargab/lqae130] [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: 02/01/2024] [Revised: 06/16/2024] [Accepted: 09/13/2024] [Indexed: 10/01/2024] Open
Abstract
Identifying statistical associations between biological variables is crucial to understanding molecular mechanisms. Most association studies are based on correlation or linear regression analyses, but the identified associations often lack reproducibility and interpretability due to the complexity and variability of omics datasets, making it difficult to translate associations into meaningful biological hypotheses. We developed StableMate, a regression framework, to address these challenges through a process of variable selection across heterogeneous datasets. Given datasets from different environments, such as experimental batches, StableMate selects environment-agnostic (stable) and environment-specific predictors in predicting the response of interest. Stable predictors represent robust functional dependencies with the response, and can be used to build regression models that make generalizable predictions in unseen environments. We applied StableMate to (i) RNA sequencing data of breast cancer to discover genes that consistently predict estrogen receptor expression across disease status; (ii) metagenomics data to identify microbial signatures that show persistent association with colon cancer across study cohorts; and (iii) single-cell RNA sequencing data of glioblastoma to discern signature genes associated with the development of pro-tumour microglia regardless of cell location. Our case studies demonstrate that StableMate is adaptable to regression and classification analyses and achieves comprehensive characterization of biological systems for different omics data types.
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Affiliation(s)
- Yidi Deng
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Royal Parade, Melbourne, 3052, Australia
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Grattan Street, Melbourne, 3010, Australia
| | - Jiadong Mao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Royal Parade, Melbourne, 3052, Australia
| | - Jarny Choi
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Grattan Street, Melbourne, 3010, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Royal Parade, Melbourne, 3052, Australia
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15
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Li L, Zhang T, Xiao M, Lu Y, Gao L. Brain macrophage senescence in glioma. Semin Cancer Biol 2024; 104-105:46-60. [PMID: 39098625 DOI: 10.1016/j.semcancer.2024.07.005] [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: 06/07/2024] [Revised: 07/20/2024] [Accepted: 07/29/2024] [Indexed: 08/06/2024]
Abstract
Gliomas are a diverse group of primary central nervous system neoplasms with no curative therapies available. Brain macrophages comprise microglia in the brain parenchyma, border-associated macrophages in the meningeal-choroid plexus-perivascular space and monocyte-derived macrophages infiltrating the brain. With the great improvement of our recognition of brain macrophages, diverse macrophage populations have been found in the context of glioma, which exhibit functional and phenotypic heterogeneity. We have long thought that brain macrophage senescence is detrimental, manifested by specialized forms of persistent cell cycle arrest and chronic low-grade inflammation. Persistent senescence of macrophages may result in immune dysfunction, potentially contributing to glioma initiation and development. Given the crucial roles played by brain macrophages in glioma, we unravel how brain macrophages undergo reprogramming and their contribution to glioma. We outline general molecular alterations and specific biomarkers in senescent brain macrophages, as well as functional changes (such as metabolism, autophagy, phagocytosis, antigen presentation, and infiltration and recruitment). In addition, recent advances in genetic regulation and mechanisms linked to senescent brain macrophages are discussed. In particular, this review emphasizes the contribution of senescent brain macrophages to glioma, which may drive translational efforts to utilize brain macrophages as a prognostic marker or/and treatment target in glioma. An in-depth comprehending of how brain macrophage senescence functionally influences the tumor microenvironment will be key to our development of innovative therapeutics for glioma.
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Affiliation(s)
- Lu Li
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Tianhe Zhang
- Department of Neurosurgery, The People's Hospital of China Medical University, The People's Hospital of Liaoning Province, Shenyang, Liaoning 110016, China
| | - Meiling Xiao
- Department of Rehabilitation, The Central Hospital of Shenyang Medical College, Shenyang, Liaoning 110024, China
| | - Yu Lu
- Rehabilitation Medicine Department, The People's Hospital of China Medical University, The People's Hospital of Liaoning Province, Shenyang, Liaoning 110016, China.
| | - Lin Gao
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
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16
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Pirrotta S, Masatti L, Bortolato A, Corrà A, Pedrini F, Aere M, Esposito G, Martini P, Risso D, Romualdi C, Calura E. Exploring public cancer gene expression signatures across bulk, single-cell and spatial transcriptomics data with signifinder Bioconductor package. NAR Genom Bioinform 2024; 6:lqae138. [PMID: 39363890 PMCID: PMC11447528 DOI: 10.1093/nargab/lqae138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 09/01/2024] [Accepted: 09/24/2024] [Indexed: 10/05/2024] Open
Abstract
Understanding cancer mechanisms, defining subtypes, predicting prognosis and assessing therapy efficacy are crucial aspects of cancer research. Gene-expression signatures derived from bulk gene expression data have played a significant role in these endeavors over the past decade. However, recent advancements in high-resolution transcriptomic technologies, such as single-cell RNA sequencing and spatial transcriptomics, have revealed the complex cellular heterogeneity within tumors, necessitating the development of computational tools to characterize tumor mass heterogeneity accurately. Thus we implemented signifinder, a novel R Bioconductor package designed to streamline the collection and use of cancer transcriptional signatures across bulk, single-cell, and spatial transcriptomics data. Leveraging publicly available signatures curated by signifinder, users can assess a wide range of tumor characteristics, including hallmark processes, therapy responses, and tumor microenvironment peculiarities. Through three case studies, we demonstrate the utility of transcriptional signatures in bulk, single-cell, and spatial transcriptomic data analyses, providing insights into cell-resolution transcriptional signatures in oncology. Signifinder represents a significant advancement in cancer transcriptomic data analysis, offering a comprehensive framework for interpreting high-resolution data and addressing tumor complexity.
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Affiliation(s)
| | - Laura Masatti
- Department of Biology, University of Padua, Padua 35121, Italy
| | - Anna Bortolato
- Department of Biology, University of Padua, Padua 35121, Italy
| | - Anna Corrà
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua 35127, Italy
| | - Fabiola Pedrini
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Martina Aere
- Department of Biology, University of Padua, Padua 35121, Italy
| | - Giovanni Esposito
- Immunology and Molecular Oncology Diagnostic Unit of The Veneto Institute of Oncology IOV – IRCCS, Padua 35128, Italy
| | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy
| | - Davide Risso
- Department of Statistical Sciences, University of Padua, Padua 35121, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padua, Padua 35121, Italy
| | - Enrica Calura
- Department of Biology, University of Padua, Padua 35121, Italy
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17
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de Dios O, Ramírez-González MA, Gómez-Soria I, Segura-Collar B, Manosalva J, Megías D, De Andrea CE, Fernández-Rubio L, Hernández-Laín A, Sepúlveda-Sánchez JM, Rodriguez-Ruiz ME, Pérez-Núñez Á, Wainwright DA, Gargini R, Sánchez-Gómez P. NKG2C/ KLRC2 tumor cell expression enhances immunotherapeutic efficacy against glioblastoma. J Immunother Cancer 2024; 12:e009210. [PMID: 39214651 PMCID: PMC11367385 DOI: 10.1136/jitc-2024-009210] [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] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Activating and inhibitory receptors of natural killer (NK) cells such as NKp, NKG2, or CLEC are highly relevant to cold tumors including glioblastoma (GBM). Here, we aimed to characterize the expression of these receptors in GBM to gain insight into their potential role as modulators of the intratumoral microenvironment. METHODS We performed a transcriptomic analysis of several NK receptors with a focus on the activating receptor encoded by KLRC2, NKG2C, among bulk and single-cell RNA sequencing GBM data sets. We also evaluated the effects of KLRC2-overexpressing GL261 cells in mice treated with or without programmed cell death protein-1 (PD-1) monoclonal antibody (mAb). Finally, we analyzed samples from two clinical trials evaluating PD-1 mAb effects in patients with GBM to determine the potential of NKG2C to serve as a biomarker of response. RESULTS We observed significant expression of several inhibitory NK receptors on GBM-infiltrating NK and T cells, which contrasts with the strong expression of KLRC2 on tumor cells, mainly at the infiltrative margin. Neoplastic KLRC2 expression was associated with a reduction in the number of myeloid-derived suppressor cells and with a higher level of tumor-resident lymphocytes. A stronger antitumor activity after PD-1 mAb treatment was observed in NKG2Chigh-expressing tumors both in mouse models and patients with GBM whereas the expression of inhibitory NK receptors showed an inverse association. CONCLUSIONS This study explored the role of neoplastic NKG2C/KLRC2 expression in shaping the immune profile of GBM and suggests that it is a predictive biomarker for positive responses to immune checkpoint inhibitor treatment in patients with GBM. Future studies could further validate this finding in prospective trials.
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Affiliation(s)
- Olaya de Dios
- Neurooncology Unit, Chronic Disease Deparment (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - M Angeles Ramírez-González
- Neurooncology Unit, Chronic Disease Deparment (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Irene Gómez-Soria
- Neurooncology Unit, Chronic Disease Deparment (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Berta Segura-Collar
- Neurooncology Unit, Instituto de Investigaciones Biomédicas I+12, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Anatomical Pathology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Juliana Manosalva
- Advanced Microscopy Unit, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Diego Megías
- Advanced Microscopy Unit, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Carlos E De Andrea
- Department of Anatomy, Physiology and Pathology, Universidad de Navarra, Pamplona, Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Leticia Fernández-Rubio
- Division of Immunology and Immunotherapy, Clínica Universidad de Navarra, Centro de Investigación Médica Aplicada (CIMA), Pamplona, Navarra, Spain
| | - Aurelio Hernández-Laín
- Neurooncology Unit, Instituto de Investigaciones Biomédicas I+12, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Neuropathology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Juan M Sepúlveda-Sánchez
- Neurooncology Unit, Instituto de Investigaciones Biomédicas I+12, Hospital Universitario 12 de Octubre, Madrid, Spain
- Hospital HM Sanchinarro, Centro Integral Oncologico Clara Campal, Madrid, Spain
| | - Maria E Rodriguez-Ruiz
- Division of Immunology and Immunotherapy, Clínica Universidad de Navarra, Centro de Investigación Médica Aplicada (CIMA), Pamplona, Navarra, Spain
- Department of Radiation Oncology, Clinica Universidad de Navarra, Pamplona, Navarra, Spain
| | - Ángel Pérez-Núñez
- Department of Neurosurgery, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Surgery, Universidad Complutense de Madrid, Facultad de Medicina, Madrid, Spain
| | - Derek A Wainwright
- Department of Neurological Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, USA
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, USA
| | - Ricardo Gargini
- Neurooncology Unit, Instituto de Investigaciones Biomédicas I+12, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Anatomical Pathology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Pilar Sánchez-Gómez
- Neurooncology Unit, Chronic Disease Deparment (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Zhang J, Li J, Qi R, Li S, Geng X, Shi H, Yu H. The microenvironmental factors induced invasive tumor cells in glioblastoma. Heliyon 2024; 10:e35770. [PMID: 39253204 PMCID: PMC11381606 DOI: 10.1016/j.heliyon.2024.e35770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/07/2024] [Accepted: 08/02/2024] [Indexed: 09/11/2024] Open
Abstract
Glioblastoma (GBM) cells have the potential to switch from being "proliferative cells" to peritumoral "invasive cells". Peritumoral GBM cells have highly invasive properties that allow them to survive surgery, leading to recurrence. The mechanisms underlying the manner in which the tumor microenvironment (TME) regulates the invasiveness of GBM remain unclear. Single-cell RNA sequencing analysis revealed heterogeneity in GBM cells, microglia and macrophages. In this study, the Oncostatin M receptor (OSMR) and leukemia inhibitory factor receptor (LIFR) expression indicated higher invasiveness in core GBM cells. Under environmental stress, the expression of OSMR and LIFR were up-regulated with the effect of hypoxic, acidic, and low-glucose conditions in vitro. Functional experiments revealed that TME stress significantly influences the proliferation, migration and invasion of GBM cells. The differences in core/peripheral TMEs in GBM affected the invasive properties, indicating the significant role of OSMR expression within the TME in tumor progression and postoperative therapy.
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Affiliation(s)
- Jianyu Zhang
- Second Department of Neurosurgery, Kunming Medical University First Affiliated Hospital, Kunming, Yunnan, China
| | - Jinghui Li
- Second Department of Neurosurgery, Kunming Medical University First Affiliated Hospital, Kunming, Yunnan, China
| | - Renli Qi
- Second Department of Neurosurgery, Kunming Medical University First Affiliated Hospital, Kunming, Yunnan, China
| | - Shipeng Li
- Second Department of Neurosurgery, Kunming Medical University First Affiliated Hospital, Kunming, Yunnan, China
| | - Xin Geng
- Second Department of Neurosurgery, Kunming Medical University First Affiliated Hospital, Kunming, Yunnan, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hualin Yu
- Second Department of Neurosurgery, Kunming Medical University First Affiliated Hospital, Kunming, Yunnan, China
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19
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Tang W, Chen B, Leung GKK, Kiang KM. Sirtuin 5 (SIRT5) Suppresses Tumor Growth by Regulating Mitochondrial Metabolism and Synaptic Remodeling in Gliomas. Int J Mol Sci 2024; 25:9125. [PMID: 39201811 PMCID: PMC11354685 DOI: 10.3390/ijms25169125] [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: 07/26/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/03/2024] Open
Abstract
Sirtuin 5 (SIRT5) is increasingly recognized as a key regulator of cellular metabolism, which is commonly dysregulated in cancer cells, resulting in enhanced proliferation and tumor progression. To investigate the clinicopathologic implications of SIRT5 dysregulation in glioblastoma, we performed comprehensive analyses of transcriptomic data and functional verifications using in vitro and in vivo glioblastoma models. We found that higher SIRT5 expression levels were associated with a favorable prognosis in glioma patients. Knockdown of SIRT5 significantly enhanced glioblastoma cell growth. Our data suggest its potential role in regulating mitochondrial metabolism in gliomas. Furthermore, SIRT5 is also significantly correlated with synaptic remodeling pathways. Our findings indicate a tumor-suppressive role for SIRT5 that extends beyond regulating cancer metabolism, by which it may function through modulating neuroplasticity. Understanding these cellular interactions provides nuanced insights into the multifaceted role of SIRT5 and the broader therapeutic implications of this for the development of novel treatment strategies.
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Affiliation(s)
- Wanjun Tang
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Bo Chen
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Gilberto Ka-Kit Leung
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong
| | - Karrie M. Kiang
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
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20
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Tsuji S, Kudo U, Takahashi K, Nakamura S, Shimazawa M. The role of progranulin in macrophages of a glioblastoma model. J Neurooncol 2024:10.1007/s11060-024-04793-1. [PMID: 39141257 DOI: 10.1007/s11060-024-04793-1] [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: 06/04/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024]
Abstract
PURPOSE Glioblastoma (GBM), characterized by astrocytic tumorigenesis, remains one of the most prognostically challenging tumor types. Targeting entire GBM microenvironment using novel therapeutic factors is currently desired investigation approach. In this study, we focused on progranulin (PGRN), a regulator of diverse cellular functions. Recent studies implicated PGRN in the poor prognostics of GBM patients. However, the specific role of PGRN in the GBM microenvironment remains elusive. METHODS We utilized public databases of GBM patient and previous single-cell RNA sequence to examine association between PGRN expression and patient survival/grade, and expression levels of PGRN in each cell constituting the tumor microenvironment. To clarify the role of PGRN in Tumor-associated macrophage (TAM), we examined cell proliferation and expression of some proteins in murine GBM cells when cell supernatants derived from TAM of PGRN knockout (Grn-/-) or wild type mice were treated with murine GBM cells. RESULTS Our results reveal significant PGRN expression in macrophages within the GBM environment, suggesting an association between increased PGRN expression in macrophages and tumor malignancy. TAM induction led to PGRN expression enhancement. Treatment with Grn-/- mouse -derived bone marrow-derived macrophage (BMDM) supernatant resulted in diminished GBM cell proliferation and cell cycle- and mesenchymal GBM subtype-associated reduced protein expression. Furthermore, the Grn-/- mouse-derived BMDM supernatant treatment reduced the phosphorylated STAT3 expression in GBM cells, while the expression of IL-6 and IL-10, known STAT3 pathway activators, diminished in Grn-/- mouse-derived BMDMs. CONCLUSION Our results suggest that macrophage-derived PGRN is pivotal for fostering malignant transformations within the tumor microenvironment.
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Affiliation(s)
- Shohei Tsuji
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501- 1196, Japan
| | - Urara Kudo
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501- 1196, Japan
| | - Kei Takahashi
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501- 1196, Japan
| | - Shinsuke Nakamura
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501- 1196, Japan
| | - Masamitsu Shimazawa
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501- 1196, Japan.
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21
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Budhiraja S, McManus G, Baisiwala S, Perrault EN, Cho S, Saathoff M, Chen L, Park CH, Kazi HA, Dmello C, Lin P, James CD, Sonabend AM, Heiland DH, Ahmed AU. ARF4-mediated retrograde trafficking as a driver of chemoresistance in glioblastoma. Neuro Oncol 2024; 26:1421-1437. [PMID: 38506351 PMCID: PMC11300013 DOI: 10.1093/neuonc/noae059] [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: 10/17/2023] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Cellular functions hinge on the meticulous orchestration of protein transport, both spatially and temporally. Central to this process is retrograde trafficking, responsible for targeting proteins to the nucleus. Despite its link to many diseases, the implications of retrograde trafficking in glioblastoma (GBM) are still unclear. METHODS To identify genetic drivers of TMZ resistance, we conducted comprehensive CRISPR-knockout screening, revealing ADP-ribosylation factor 4 (ARF4), a regulator of retrograde trafficking, as a major contributor. RESULTS Suppressing ARF4 significantly enhanced TMZ sensitivity in GBM patient-derived xenograft (PDX) models, leading to improved survival rates (P < .01) in both primary and recurrent lines. We also observed that TMZ exposure stimulates ARF4-mediated retrograde trafficking. Proteomics analysis of GBM cells with varying levels of ARF4 unveiled the influence of this pathway on EGFR signaling, with increased nuclear trafficking of EGFR observed in cells with ARF4 overexpression and TMZ treatment. Additionally, spatially resolved RNA-sequencing of GBM patient tissues revealed substantial correlations between ARF4 and crucial nuclear EGFR (nEGFR) downstream targets, such as MYC, STAT1, and DNA-PK. Decreased activity of DNA-PK, a DNA repair protein downstream of nEGFR signaling that contributes to TMZ resistance, was observed in cells with suppressed ARF4 levels. Notably, treatment with DNA-PK inhibitor, KU-57788, in mice with a recurrent PDX line resulted in prolonged survival (P < .01), highlighting the promising therapeutic implications of targeting proteins reliant on ARF4-mediated retrograde trafficking. CONCLUSIONS Our findings demonstrate that ARF4-mediated retrograde trafficking contributes to the development of TMZ resistance, cementing this pathway as a viable strategy to overcome chemoresistance in GBM.
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Affiliation(s)
- Shreya Budhiraja
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Graysen McManus
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | - Ella N Perrault
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Sia Cho
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Miranda Saathoff
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Li Chen
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Cheol H Park
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hasaan A Kazi
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Crismita Dmello
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Peiyu Lin
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - C David James
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Adam M Sonabend
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Dieter H Heiland
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Microenvironment and Immunology Research Laboratory, Medical Center - University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
| | - Atique U Ahmed
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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22
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Škarková A, Pelantová M, Tolde O, Legátová A, Mateu R, Bušek P, Garcia-Borja E, Šedo A, Etienne-Manneville S, Rösel D, Brábek J. Microtubule-associated NAV3 regulates invasive phenotypes in glioblastoma cells. Brain Pathol 2024:e13294. [PMID: 39097525 DOI: 10.1111/bpa.13294] [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: 03/11/2024] [Accepted: 07/17/2024] [Indexed: 08/05/2024] Open
Abstract
Glioblastomas are aggressive brain tumors for which effective therapy is still lacking, resulting in dismal survival rates. These tumors display significant phenotypic plasticity, harboring diverse cell populations ranging from tumor core cells to dispersed, highly invasive cells. Neuron navigator 3 (NAV3), a microtubule-associated protein affecting microtubule growth and dynamics, is downregulated in various cancers, including glioblastoma, and has thus been considered a tumor suppressor. In this study, we challenge this designation and unveil distinct expression patterns of NAV3 across different invasion phenotypes. Using glioblastoma cell lines and patient-derived glioma stem-like cell cultures, we disclose an upregulation of NAV3 in invading glioblastoma cells, contrasting with its lower expression in cells residing in tumor spheroid cores. Furthermore, we establish an association between low and high NAV3 expression and the amoeboid and mesenchymal invasive phenotype, respectively, and demonstrate that overexpression of NAV3 directly stimulates glioblastoma invasive behavior in both 2D and 3D environments. Consistently, we observed increased NAV3 expression in cells migrating along blood vessels in mouse xenografts. Overall, our results shed light on the role of NAV3 in glioblastoma invasion, providing insights into this lethal aspect of glioblastoma behavior.
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Affiliation(s)
- Aneta Škarková
- Laboratory of Cancer Cell Invasion, Department of Cell Biology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Markéta Pelantová
- Laboratory of Cancer Cell Invasion, Department of Cell Biology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Ondřej Tolde
- Laboratory of Cancer Cell Invasion, Department of Cell Biology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Anna Legátová
- Laboratory of Cancer Cell Invasion, Department of Cell Biology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Rosana Mateu
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Bušek
- 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
| | - Aleksi Šedo
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Université Paris Cité, UMR3691 CNRS, Institut Pasteur, Paris, France
| | - Daniel Rösel
- Laboratory of Cancer Cell Invasion, Department of Cell Biology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Jan Brábek
- Laboratory of Cancer Cell Invasion, Department of Cell Biology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
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23
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Arbatskiy M, Balandin D, Churov A, Varachev V, Nikolaeva E, Mitrofanov A, Bekyashev A, Tkacheva O, Susova O, Nasedkina T. Intratumoral Cell Heterogeneity in Patient-Derived Glioblastoma Cell Lines Revealed by Single-Cell RNA-Sequencing. Int J Mol Sci 2024; 25:8472. [PMID: 39126040 PMCID: PMC11313325 DOI: 10.3390/ijms25158472] [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: 06/30/2024] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
Glioblastoma cell lines derived from different patients are widely used in tumor biology research and drug screening. A key feature of glioblastoma is the high level of inter- and intratumor heterogeneity that accounts for treatment resistance. Our aim was to investigate whether intratumor heterogeneity is maintained in cell models. Single-cell RNA sequencing was used to investigate the cellular composition of a tumor sample and six patient-derived glioblastoma cell lines. Three cell lines preserved the mutational profile of the original tumor, whereas three others differed from their precursors. Copy-number variation analysis showed significantly rearranged genomes in all the cell lines and in the tumor sample. The tumor had the most complex cell composition, including cancer cells and microenvironmental cells. Cell lines with a conserved genome had less diverse cellularity, and during cultivation, a relative increase in the stem-cell-derived progenitors was noticed. Cell lines with genomes different from those of the primary tumors mainly contained neural progenitor cells and microenvironmental cells. The establishment of cell lines without the driver mutations that are intrinsic to the original tumors may be related to the selection of clones or cell populations during cultivation. Thus, patient-derived glioblastoma cell lines differ substantially in their cellular profile, which should be taken into account in translational studies.
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Affiliation(s)
- Mikhail Arbatskiy
- Russian Clinical Research Center of Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 129226 Moscow, Russia (A.C.); (O.T.)
| | - Dmitriy Balandin
- Russian Clinical Research Center of Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 129226 Moscow, Russia (A.C.); (O.T.)
| | - Alexey Churov
- Russian Clinical Research Center of Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 129226 Moscow, Russia (A.C.); (O.T.)
| | - Vyacheslav Varachev
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (V.V.); (T.N.)
| | - Eugenia Nikolaeva
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (E.N.); (A.M.); (A.B.); (O.S.)
| | - Alexei Mitrofanov
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (E.N.); (A.M.); (A.B.); (O.S.)
| | - Ali Bekyashev
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (E.N.); (A.M.); (A.B.); (O.S.)
| | - Olga Tkacheva
- Russian Clinical Research Center of Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 129226 Moscow, Russia (A.C.); (O.T.)
| | - Olga Susova
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (E.N.); (A.M.); (A.B.); (O.S.)
| | - Tatiana Nasedkina
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (V.V.); (T.N.)
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24
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Weiss A, D'Amata C, Pearson BJ, Hayes MN. A syngeneic spontaneous zebrafish model of tp53-deficient, EGFR vIII, and PI3KCA H1047R-driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapse in vivo. eLife 2024; 13:RP93077. [PMID: 39052000 PMCID: PMC11272161 DOI: 10.7554/elife.93077] [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] [Indexed: 07/27/2024] Open
Abstract
High-throughput vertebrate animal model systems for the study of patient-specific biology and new therapeutic approaches for aggressive brain tumors are currently lacking, and new approaches are urgently needed. Therefore, to build a patient-relevant in vivo model of human glioblastoma, we expressed common oncogenic variants including activated human EGFRvIII and PI3KCAH1047R under the control of the radial glial-specific promoter her4.1 in syngeneic tp53 loss-of-function mutant zebrafish. Robust tumor formation was observed prior to 45 days of life, and tumors had a gene expression signature similar to human glioblastoma of the mesenchymal subtype, with a strong inflammatory component. Within early stage tumor lesions, and in an in vivo and endogenous tumor microenvironment, we visualized infiltration of phagocytic cells, as well as internalization of tumor cells by mpeg1.1:EGFP+ microglia/macrophages, suggesting negative regulatory pressure by pro-inflammatory cell types on tumor growth at early stages of glioblastoma initiation. Furthermore, CRISPR/Cas9-mediated gene targeting of master inflammatory transcription factors irf7 or irf8 led to increased tumor formation in the primary context, while suppression of phagocyte activity led to enhanced tumor cell engraftment following transplantation into otherwise immune-competent zebrafish hosts. Altogether, we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging, high-throughput genetic and chemical manipulations to highlight important tumor-suppressive roles for the innate immune system on glioblastoma initiation, with important future opportunities for therapeutic discovery and optimizations.
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Affiliation(s)
- Alex Weiss
- Developmental and Stem Cell Biology Program, The Hospital for Sick ChildrenTorontoCanada
| | - Cassandra D'Amata
- Developmental and Stem Cell Biology Program, The Hospital for Sick ChildrenTorontoCanada
| | - Bret J Pearson
- Department of Molecular Genetics, University of TorontoTorontoCanada
- Knight Cancer Institute, Oregon Health & Science UniversityPortlandUnited States
- Department of Pediatrics, Papé Research Institute, Oregon Health & Science UniversityPortlandUnited States
| | - Madeline N Hayes
- Developmental and Stem Cell Biology Program, The Hospital for Sick ChildrenTorontoCanada
- Department of Molecular Genetics, University of TorontoTorontoCanada
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25
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Fazzari E, Azizad DJ, Yu K, Ge W, Li MX, Nano PR, Kan RL, Tum HA, Tse C, Bayley NA, Haka V, Cadet D, Perryman T, Soto JA, Wick B, Raleigh DR, Crouch EE, Patel KS, Liau LM, Deneen B, Nathanson DA, Bhaduri A. Glioblastoma Neurovascular Progenitor Orchestrates Tumor Cell Type Diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604840. [PMID: 39091877 PMCID: PMC11291138 DOI: 10.1101/2024.07.24.604840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Glioblastoma (GBM) is the deadliest form of primary brain tumor with limited treatment options. Recent studies have profiled GBM tumor heterogeneity, revealing numerous axes of variation that explain the molecular and spatial features of the tumor. Here, we seek to bridge descriptive characterization of GBM cell type heterogeneity with the functional role of individual populations within the tumor. Our lens leverages a gene program-centric meta-atlas of published transcriptomic studies to identify commonalities between diverse tumors and cell types in order to decipher the mechanisms that drive them. This approach led to the discovery of a tumor-derived stem cell population with mixed vascular and neural stem cell features, termed a neurovascular progenitor (NVP). Following in situ validation and molecular characterization of NVP cells in GBM patient samples, we characterized their function in vivo. Genetic depletion of NVP cells resulted in altered tumor cell composition, fewer cycling cells, and extended survival, underscoring their critical functional role. Clonal analysis of primary patient tumors in a human organoid tumor transplantation system demonstrated that the NVP has dual potency, generating both neuronal and vascular tumor cells. Although NVP cells comprise a small fraction of the tumor, these clonal analyses demonstrated that they strongly contribute to the total number of cycling cells in the tumor and generate a defined subset of the whole tumor. This study represents a paradigm by which cell type-specific interrogation of tumor populations can be used to study functional heterogeneity and therapeutically targetable vulnerabilities of GBM.
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Affiliation(s)
- Elisa Fazzari
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Daria J Azizad
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Kwanha Yu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Weihong Ge
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Matthew X Li
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Patricia R Nano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Ryan L Kan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Hong A Tum
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher Tse
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nicholas A Bayley
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Vjola Haka
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dimitri Cadet
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Travis Perryman
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Jose A Soto
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Brittney Wick
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Elizabeth E Crouch
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Kunal S Patel
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - David A Nathanson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
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Vázquez-Cabrera G, Škandík M, Roncier N, Real Oualit F, Cruz De Los Santos M, Baleviciute A, Cheray M, Joseph B. ID2-ETS2 axis regulates the transcriptional acquisition of pro-tumoral microglia phenotype in glioma. Cell Death Dis 2024; 15:512. [PMID: 39019900 PMCID: PMC11255298 DOI: 10.1038/s41419-024-06903-3] [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: 02/18/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
Glioblastoma is a highly aggressive brain tumour that creates an immunosuppressive microenvironment. Microglia, the brain's resident immune cells, play a crucial role in this environment. Glioblastoma cells can reprogramme microglia to create a supportive niche that promotes tumour growth. However, the mechanisms controlling the acquisition of a transcriptome associated with a tumour-supportive microglial reactive state are not fully understood. In this study, we investigated changes in the transcriptional profile of BV2 microglia exposed to C6 glioma cells. RNA-sequencing analysis revealed a significant upregulation of microglial inhibitor of DNA binding 1 (Id1) and Id2, helix-loop-helix negative transcription regulatory factors. The concomitant regulation of microglial ETS proto-oncogene 2, transcription factor (ETS2)-target genes, i.e., Dusp6, Fli1, Jun, Hmox1, and Stab1, led us to hypothesize that ETS2 could be regulated by ID proteins. In fact, ID2-ETS2 protein interactions increased in microglia exposed to glioma cells. In addition, perturbation of the ID2-ETS2 transcriptional axis influenced the acquisition of a microglial tumour-supportive phenotype. ID2 and ETS2 genes were found to be expressed by the tumour-associated microglia isolated from human glioblastoma tumour biopsies. Furthermore, ID2 and ETS2 gene expressions exhibited inverse prognostic values in patients with glioma in cohorts from The Cancer Genome Atlas. Collectively, our findings indicate that the regulation of ETS2 by ID2 plays a role in the transcriptional regulation of microglia in response to stimuli originating from glioblastoma cells, information that could lead to developing therapeutic strategies to manipulate microglial tumour-trophic functions.
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Affiliation(s)
| | - Martin Škandík
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Noémie Roncier
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Farah Real Oualit
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Austeja Baleviciute
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mathilde Cheray
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bertrand Joseph
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
- Center for Neuromusculoskeletal Restorative Medicine, Shui On Centre, Wan Chai, Hong Kong.
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27
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Liang B, Ding X, Yang S, Feng E. Endothelial cell ferroptosis influences IDH wild-type glioblastoma growth in recurrent glioblastoma multiforme patients. Braz J Med Biol Res 2024; 57:e13961. [PMID: 38985083 PMCID: PMC11249198 DOI: 10.1590/1414-431x2024e13961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/22/2024] [Indexed: 07/11/2024] Open
Abstract
Glioblastomas are known for their poor clinical prognosis, with recurrent tumors often exhibiting greater invasiveness and faster growth rates compared to primary tumors. To understand the intratumoral changes driving this phenomenon, we employed single-cell sequencing to analyze the differences between two pairs of primary and recurrent glioblastomas. Our findings revealed an upregulation of ferroptosis in endothelial cells within recurrent tumors, identified by the significant overexpression of the NOX4 gene. Further analysis indicated that knocking down NOX4 in endothelial cells reduced the activity of the ferroptosis pathway. Utilizing conditioned media from endothelial cells with lower ferroptosis activity, we observed a decrease in the growth rate of glioblastoma cells. These results highlighted the complex role of ferroptosis within tumors and suggested that targeting ferroptosis in the treatment of glioblastomas requires careful consideration of its effects on endothelial cells, as it may otherwise produce counterproductive outcomes.
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Affiliation(s)
- Bo Liang
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xinghuan Ding
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Siyuan Yang
- Laboratory of Infectious Diseases Center, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Enshan Feng
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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28
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Oh E, Lee H. DeepPIG: deep neural network architecture with pairwise connected layers and stochastic gates using knockoff frameworks for feature selection. Sci Rep 2024; 14:15582. [PMID: 38971807 PMCID: PMC11227546 DOI: 10.1038/s41598-024-66061-6] [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: 03/28/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
Selecting relevant feature subsets is essential for machine learning applications. Among the feature selection techniques, the knockoff filter procedure proposes a unique framework that minimizes false discovery rates (FDR). However, employing a deep neural network architecture for a knockoff filter framework requires higher detection power. Using the knockoff filter framework, we present a Deep neural network with PaIrwise connected layers integrated with stochastic Gates (DeepPIG) for the feature selection model. DeepPIG exhibited better detection power in synthetic data than the baseline and recent models such as Deep feature selection using Paired-Input Nonlinear Knockoffs (DeepPINK), Stochastic Gates (STG), and SHapley Additive exPlanations (SHAP) while not violating the preselected FDR level, especially when the signal of the features were weak. The selected features determined by DeepPIG demonstrated superior classification performance compared with the baseline model in real-world data analyses, including the prediction of certain cancer prognosis and classification tasks using microbiome and single-cell datasets. In conclusion, DeepPIG is a robust feature selection approach even when the signals of features are weak. Source code is available at https://github.com/DMCB-GIST/DeepPIG .
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Affiliation(s)
- Euiyoung Oh
- Gwangju Institute of Science and Technology, School of Electrical Engineering and Computer Science, Gwangju, 61005, South Korea
| | - Hyunju Lee
- Gwangju Institute of Science and Technology, School of Electrical Engineering and Computer Science, Gwangju, 61005, South Korea.
- Gwangju Institute of Science and Technology, Artificial Intelligence Graduate School, Gwangju, 61005, South Korea.
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29
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Loginova N, Aniskin D, Timashev P, Ulasov I, Kharwar RK. GBM Immunotherapy: Macrophage Impacts. Immunol Invest 2024; 53:730-751. [PMID: 38634572 DOI: 10.1080/08820139.2024.2337022] [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] [Indexed: 04/19/2024]
Abstract
BACKGROUND Glioblastoma (GBM) is an extremely aggressive form of brain tumor with low survival rates. Current treatments such as chemotherapy, radiation, and surgery are problematic due to tumor growth, invasion, and tumor microenvironment. GBM cells are resistant to these standard treatments, and the heterogeneity of the tumor makes it difficult to find a universal approach. Progression of GBM and acquisition of resistance to therapy are due to the complex interplay between tumor cells and the TME. A significant portion of the TME consists of an inflammatory infiltrate, with microglia and macrophages being the predominant cells. METHODS Analysis of the literature data over a course of 5 years suggest that the tumor-associated macrophages (TAMs) are capable of releasing cytokines and growth factors that promote tumor proliferation, survival, and metastasis while inhibiting immune cell function at the same time. RESULTS Thus, immunosuppressive state, provided with this intensively studied kind of TME cells, is supposed to promote GBM development through TAMs modulation of tumor treatment-resistance and aggressiveness. Therefore, TAMs are an attractive therapeutic target in the treatment of glioblastoma. CONCLUSION This review provides a comprehensive overview of the latest research on the nature of TAMs and the development of therapeutic strategies targeting TAMs, focusing on the variety of macrophage properties, being modulated, as well as molecular targets.
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Affiliation(s)
- Nina Loginova
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Denis Aniskin
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Peter Timashev
- World-Class Research Centre "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
| | - Ilya Ulasov
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Rajesh Kumar Kharwar
- Endocrine Research Laboratory, Department of Zoology, University of Lucknow, Lucknow, India
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30
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Read RD, Tapp ZM, Rajappa P, Hambardzumyan D. Glioblastoma microenvironment-from biology to therapy. Genes Dev 2024; 38:360-379. [PMID: 38811170 PMCID: PMC11216181 DOI: 10.1101/gad.351427.123] [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] [Indexed: 05/31/2024]
Abstract
Glioblastoma (GBM) is the most aggressive primary brain cancer. These tumors exhibit high intertumoral and intratumoral heterogeneity in neoplastic and nonneoplastic compartments, low lymphocyte infiltration, and high abundance of myeloid subsets that together create a highly protumorigenic immunosuppressive microenvironment. Moreover, heterogeneous GBM cells infiltrate adjacent brain tissue, remodeling the neural microenvironment to foster tumor electrochemical coupling with neurons and metabolic coupling with nonneoplastic astrocytes, thereby driving growth. Here, we review heterogeneity in the GBM microenvironment and its role in low-to-high-grade glioma transition, concluding with a discussion of the challenges of therapeutically targeting the tumor microenvironment and outlining future research opportunities.
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Affiliation(s)
- Renee D Read
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA;
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Zoe M Tapp
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Prajwal Rajappa
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA;
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43215, USA
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio 43215, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA;
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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31
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Chang C, Chavarro VS, Gerstl JVE, Blitz SE, Spanehl L, Dubinski D, Valdes PA, Tran LN, Gupta S, Esposito L, Mazzetti D, Gessler FA, Arnaout O, Smith TR, Friedman GK, Peruzzi P, Bernstock JD. Recurrent Glioblastoma-Molecular Underpinnings and Evolving Treatment Paradigms. Int J Mol Sci 2024; 25:6733. [PMID: 38928445 PMCID: PMC11203521 DOI: 10.3390/ijms25126733] [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: 05/14/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Glioblastoma is the most common and lethal central nervous system malignancy with a median survival after progression of only 6-9 months. Major biochemical mechanisms implicated in glioblastoma recurrence include aberrant molecular pathways, a recurrence-inducing tumor microenvironment, and epigenetic modifications. Contemporary standard-of-care (surgery, radiation, chemotherapy, and tumor treating fields) helps to control the primary tumor but rarely prevents relapse. Cytoreductive treatment such as surgery has shown benefits in recurrent glioblastoma; however, its use remains controversial. Several innovative treatments are emerging for recurrent glioblastoma, including checkpoint inhibitors, chimeric antigen receptor T cell therapy, oncolytic virotherapy, nanoparticle delivery, laser interstitial thermal therapy, and photodynamic therapy. This review seeks to provide readers with an overview of (1) recent discoveries in the molecular basis of recurrence; (2) the role of surgery in treating recurrence; and (3) novel treatment paradigms emerging for recurrent glioblastoma.
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Affiliation(s)
- Christopher Chang
- Warren Alpert Medical School, Brown University, Providence, RI 02912, USA;
| | - Velina S. Chavarro
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
| | - Jakob V. E. Gerstl
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
| | - Sarah E. Blitz
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Lennard Spanehl
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
- Department of Neurosurgery, University of Rostock, 18055 Rostock, Germany; (D.D.); (F.A.G.)
| | - Daniel Dubinski
- Department of Neurosurgery, University of Rostock, 18055 Rostock, Germany; (D.D.); (F.A.G.)
| | - Pablo A. Valdes
- Department of Neurosurgery, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Lily N. Tran
- Division of Biology and Medicine, Brown University, Providence, RI 02912, USA;
| | - Saksham Gupta
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Luisa Esposito
- Department of Medicine and Surgery, Unicamillus University, 00131 Rome, Italy;
| | - Debora Mazzetti
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
| | - Florian A. Gessler
- Department of Neurosurgery, University of Rostock, 18055 Rostock, Germany; (D.D.); (F.A.G.)
| | - Omar Arnaout
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Timothy R. Smith
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Gregory K. Friedman
- Division of Pediatrics, Neuro-Oncology Section, MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Pierpaolo Peruzzi
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA; (V.S.C.); (J.V.E.G.); (S.E.B.); (L.S.); (S.G.); (D.M.); (O.A.); (T.R.S.); (J.D.B.)
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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32
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Pollack IF, Felker J, Frederico SC, Raphael I, Kohanbash G. Immunotherapy for pediatric low-grade gliomas. Childs Nerv Syst 2024:10.1007/s00381-024-06491-9. [PMID: 38884777 DOI: 10.1007/s00381-024-06491-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/01/2024] [Indexed: 06/18/2024]
Abstract
Pediatric low-grade gliomas (pLGGs) are the most common brain tumor types affecting children. Although gross-total resection remains the treatment of choice, many tumors are not amenable to complete removal, because they either involve midline structures, such as the optic chiasm or hypothalamus, and are not conducive to aggressive resection, or have diffuse biological features and blend with the surrounding brain. Historically, radiation therapy was used as the second-line option for disease control, but with the recognition that this often led to adverse long-term sequelae, particularly in young children, conventional chemotherapy assumed a greater role in initial therapy for unresectable tumors. A variety of agents demonstrated activity, but long-term disease control was suboptimal, with more than 50% of tumors exhibiting disease progression within 5 years. More recently, it has been recognized that a high percentage of these tumors in children exhibit constitutive activation of the mitogen-activated protein kinase (MAPK) pathway because of BRAF translocations or mutations, NFI mutations, or a host of other anomalies that converged on MAPK. This led to phase 1, 2, and 3 trials that explored the activity of blocking this signaling pathway, and the efficacy of this approach compared to conventional chemotherapy. Despite initial promise of these strategies, not all children tolerate this therapy, and many tumors resume growth once MAPK inhibition is stopped, raising concern that long-term and potentially life-long treatment will be required to maintain tumor control, even among responders. This observation has led to interest in other treatments, such as immunotherapy, that may delay or avoid the need for additional treatments. This chapter will summarize the place of immunotherapy in the current armamentarium for these tumors and discuss prior results and future options to improve disease control, with a focus on our prior efforts and experience in this field.
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Affiliation(s)
- Ian F Pollack
- Department of Neurosurgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Neurosurgery, UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA.
| | - James Felker
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Neurosurgery, UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Stephen C Frederico
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Neurosurgery, UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Itay Raphael
- Department of Neurosurgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Neurosurgery, UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Gary Kohanbash
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Neurosurgery, UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
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33
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van Solinge TS, Oh J, Abels E, Koch P, Breakefield XO, Weissleder R, Broekman MLD. Probing the glioma micro-environment: analysis using biopsy in combination with ultra-fast cyclic immunolabeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599078. [PMID: 38948851 PMCID: PMC11212862 DOI: 10.1101/2024.06.15.599078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The interaction between gliomas and the immune system is poorly understood and thus hindering development of effective immunotherapies for glioma patients. The immune response is highly variable during tumor development, and affected by therapies such as surgery, radiation, and chemotherapy. Currently, analysis of these local changes is difficult due to poor accessibility of the tumor and high-morbidity of sampling. In this study, we developed a model for repeat-biopsy in mice to study these local immunological changes over time. Using fine needle biopsy we were able to safely and repeatedly collect cells from intracranial tumors in mice. Ultra-fast cycling technology (FAST) was used for multi-cycle immunofluorescence of retrieved cells, and provided insights in the changing immune response over time. The combination of these techniques can be utilized to study changes in the immune response in glioma or other intracranial diseases over time, and in response to treatment within the same animal.
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Affiliation(s)
- Thomas S van Solinge
- Departments of Neurology and Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurosurgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Juhyun Oh
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Center for Systems Biology, Massachusetts General Hospital, Boston , Massachusetts, USA
| | - Erik Abels
- Departments of Neurology and Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Koch
- Center for Systems Biology, Massachusetts General Hospital, Boston , Massachusetts, USA
| | - Xandra O Breakefield
- Departments of Neurology and Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston , Massachusetts, USA
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marike L D Broekman
- Departments of Neurology and Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurosurgery, Leiden University Medical Center, Leiden, The Netherlands
- Department of Neurosurgery, Haaglanden Medical Center, The Hague, The Netherlands
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Wang Y, Ran T, Li Y, Tian L, Yang L, Liu Z, Yao B. Identification of JUN gene and cellular microenvironment in response to PD-1 blockade treatment in lung cancer patients via single-cell RNA sequencing. Aging (Albany NY) 2024; 16:10348-10365. [PMID: 38874497 PMCID: PMC11236306 DOI: 10.18632/aging.205932] [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: 12/07/2023] [Accepted: 05/03/2024] [Indexed: 06/15/2024]
Abstract
Exploring the molecular mechanisms of PD-1/PDL-1 blockade for non-small cell lung cancer (NSCLC) would facilitate understanding for tumor microenvironment (TME) and development of individualized medicine. To date, biomarkers of response to PD-1 blockade therapy were still limited. In this study, we hypothesize that cell type in the tumor microenvironment can influence the effect of PD-1 blockade immunotherapy through specific genes. Therefore, we re-analyze the single-cell RNA sequencing data and validation in tissue from lung adenocarcinoma patients. Dynamic changes of cellular subpopulation were observed after anti-PD-1 immunotherapy among TMEs between primary/metastasis or good/poor response patients. Non-exhausted CD8 T cells and dysregulated genes were observed in responsing patients from PD-1 blockade therapy. Among all changed genes, JUN, involved in PD-1 blockade immunotherapy pathway, and could be considered as a PD-1 responsing biomarker.
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Affiliation(s)
- Yuxuan Wang
- No.2 Department of Thoracic Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Tao Ran
- Department of Oncology, Tongren People’s Hospital, Tongren, Guizhou, China
| | - Yunke Li
- Beijing Digitf Biotechnology Co., Ltd, Beijing, China
| | - Lei Tian
- Department of Oncology, Tongren People’s Hospital, Tongren, Guizhou, China
| | - Lifeng Yang
- Department of Oncology, Tongren People’s Hospital, Tongren, Guizhou, China
| | - Zhidong Liu
- No.2 Department of Thoracic Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Biao Yao
- Department of Oncology, Tongren People’s Hospital, Tongren, Guizhou, China
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35
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Sadowski K, Jażdżewska A, Kozłowski J, Zacny A, Lorenc T, Olejarz W. Revolutionizing Glioblastoma Treatment: A Comprehensive Overview of Modern Therapeutic Approaches. Int J Mol Sci 2024; 25:5774. [PMID: 38891962 PMCID: PMC11172387 DOI: 10.3390/ijms25115774] [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: 05/05/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Glioblastoma is the most common malignant primary brain tumor in the adult population, with an average survival of 12.1 to 14.6 months. The standard treatment, combining surgery, radiotherapy, and chemotherapy, is not as efficient as we would like. However, the current possibilities are no longer limited to the standard therapies due to rapid advancements in biotechnology. New methods enable a more precise approach by targeting individual cells and antigens to overcome cancer. For the treatment of glioblastoma, these are gamma knife therapy, proton beam therapy, tumor-treating fields, EGFR and VEGF inhibitors, multiple RTKs inhibitors, and PI3K pathway inhibitors. In addition, the increasing understanding of the role of the immune system in tumorigenesis and the ability to identify tumor-specific antigens helped to develop immunotherapies targeting GBM and immune cells, including CAR-T, CAR-NK cells, dendritic cells, and immune checkpoint inhibitors. Each of the described methods has its advantages and disadvantages and faces problems, such as the inefficient crossing of the blood-brain barrier, various neurological and systemic side effects, and the escape mechanism of the tumor. This work aims to present the current modern treatments of glioblastoma.
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Affiliation(s)
- Karol Sadowski
- The Department of Histology and Embryology, Medical University of Warsaw, Chalubinskiego 5, 02-004 Warsaw, Poland; (K.S.)
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, 02-091 Warsaw, Poland;
- Centre for Preclinical Research, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Adrianna Jażdżewska
- The Department of Anatomy and Neurobiology, Medical University of Gdansk, Dębinki 1, 80-211 Gdansk, Poland;
| | - Jan Kozłowski
- The Department of Histology and Embryology, Medical University of Warsaw, Chalubinskiego 5, 02-004 Warsaw, Poland; (K.S.)
| | - Aleksandra Zacny
- The Department of Histology and Embryology, Medical University of Warsaw, Chalubinskiego 5, 02-004 Warsaw, Poland; (K.S.)
| | - Tomasz Lorenc
- Department of Radiology I, The Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - Wioletta Olejarz
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, 02-091 Warsaw, Poland;
- Centre for Preclinical Research, Medical University of Warsaw, 02-091 Warsaw, Poland
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36
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Alorfi NM, Ashour AM, Alharbi AS, Alshehri FS. Targeting inflammation in glioblastoma: An updated review from pathophysiology to novel therapeutic approaches. Medicine (Baltimore) 2024; 103:e38245. [PMID: 38788009 PMCID: PMC11124608 DOI: 10.1097/md.0000000000038245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Glioblastoma (GBM) is a highly aggressive primary malignant brain tumor with a dismal prognosis despite current treatment strategies. Inflammation plays an essential role in GBM pathophysiology, contributing to tumor growth, invasion, immunosuppression, and angiogenesis. As a result, pharmacological intervention with anti-inflammatory drugs has been used as a potential approach for the management of GBM. To provide an overview of the current understanding of GBM pathophysiology, potential therapeutic applications of anti-inflammatory drugs in GBM, conventional treatments of glioblastoma and emerging therapeutic approaches currently under investigation. A narrative review was carried out, scanning publications from 2000 to 2023 on PubMed and Google Scholar. The search was not guided by a set research question or a specific search method but rather focused on the area of interest. Conventional treatments such as surgery, radiotherapy, and chemotherapy have shown some benefits, but their effectiveness is limited by various factors such as tumor heterogeneity and resistance.
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Affiliation(s)
- Nasser M. Alorfi
- Pharmacology and Toxicology Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ahmed M. Ashour
- Pharmacology and Toxicology Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Adnan S. Alharbi
- Pharmacy Practice Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Fahad S. Alshehri
- Pharmacology and Toxicology Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
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37
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Douglas C, Lomeli N, Vu T, Pham J, Bota DA. WITHDRAWN: LonP1 Drives Proneural Mesenchymal Transition in IDH1-R132H Diffuse Glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.13.536817. [PMID: 37131765 PMCID: PMC10153221 DOI: 10.1101/2023.04.13.536817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The authors have withdrawn their manuscript owing to massive revision and data validation. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
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38
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Nusraty S, Boddeti U, Zaghloul KA, Brown DA. Microglia in Glioblastomas: Molecular Insight and Immunotherapeutic Potential. Cancers (Basel) 2024; 16:1972. [PMID: 38893093 PMCID: PMC11171200 DOI: 10.3390/cancers16111972] [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: 04/03/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Glioblastoma (GBM) is one of the most aggressive and devastating primary brain tumors, with a median survival of 15 months following diagnosis. Despite the intense treatment regimen which routinely includes maximal safe neurosurgical resection followed by adjuvant radio- and chemotherapy, the disease remains uniformly fatal. The poor prognosis associated with GBM is multifactorial owing to factors such as increased proliferation, angiogenesis, and metabolic switching to glycolytic pathways. Critically, GBM-mediated local and systemic immunosuppression result in inadequate immune surveillance and ultimately, tumor-immune escape. Microglia-the resident macrophages of the central nervous system (CNS)-play crucial roles in mediating the local immune response in the brain. Depending on the specific pathological cues, microglia are activated into either a pro-inflammatory, neurotoxic phenotype, known as M1, or an anti-inflammatory, regenerative phenotype, known as M2. In either case, microglia secrete corresponding pro- or anti-inflammatory cytokines and chemokines that either promote or hinder tumor growth. Herein, we review the interplay between GBM cells and resident microglia with a focus on contemporary studies highlighting the effect of GBM on the subtypes of microglia expressed, the associated cytokines/chemokines secreted, and ultimately, their impact on tumor pathogenesis. Finally, we explore how understanding the intricacies of the tumor-immune landscape can inform novel immunotherapeutic strategies against this devastating disease.
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Affiliation(s)
| | | | | | - Desmond A. Brown
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; (S.N.); (U.B.); (K.A.Z.)
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39
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Bumbaca B, Birtwistle MR, Gallo JM. Network Analyses of Brain Tumor Patients' Multiomic Data Reveals Pharmacological Opportunities to Alter Cell State Transitions. RESEARCH SQUARE 2024:rs.3.rs-4391296. [PMID: 38826227 PMCID: PMC11142360 DOI: 10.21203/rs.3.rs-4391296/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Glioblastoma Multiforme (GBM) remains a particularly difficult cancer to treat, and survival outcomes remain poor. In addition to the lack of dedicated drug discovery programs for GBM, extensive intratumor heterogeneity and epigenetic plasticity related to cell-state transitions are major roadblocks to successful drug therapy in GBM. To study these phenomenon, publicly available snRNAseq and bulk RNAseq data from patient samples were used to categorize cells from patients into four cell states (i.e. phenotypes), namely: (i) neural progenitor-like (NPC-like), (ii) oligodendrocyte progenitor-like (OPC-like), (iii) astrocyte- like (AC-like), and (iv) mesenchymal-like (MES-like). Patients were subsequently grouped into subpopulations based on which cell-state was the most dominant in their respective tumor. By incorporating phosphoproteomic measurements from the same patients, a protein-protein interaction network (PPIN) was constructed for each cell state. These four-cell state PPINs were pooled to form a single Boolean network that was used for in silico protein knockout simulations to investigate mechanisms that either promote or prevent cell state transitions. Simulation results were input into a boosted tree machine learning model which predicted the cell states or phenotypes of GBM patients from an independent public data source, the Glioma Longitudinal Analysis (GLASS) Consortium. Combining the simulation results and the machine learning predictions, we generated hypotheses for clinically relevant causal mechanisms of cell state transitions. For example, the transcription factor TFAP2A can be seen to promote a transition from the NPC-like to the MES-like state. Such protein nodes and the associated signaling pathways provide potential drug targets that can be further tested in vitro and support cell state-directed (CSD) therapy.
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Affiliation(s)
- Brandon Bumbaca
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
| | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC, USA
- Department of Bioengineering, Clemson University, Clemson SC, USA
| | - James M Gallo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
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Haley MJ, Bere L, Minshull J, Georgaka S, Garcia-Martin N, Howell G, Coope DJ, Roncaroli F, King A, Wedge DC, Allan SM, Pathmanaban ON, Brough D, Couper KN. Hypoxia coordinates the spatial landscape of myeloid cells within glioblastoma to affect survival. SCIENCE ADVANCES 2024; 10:eadj3301. [PMID: 38758780 PMCID: PMC11100569 DOI: 10.1126/sciadv.adj3301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
Myeloid cells are highly prevalent in glioblastoma (GBM), existing in a spectrum of phenotypic and activation states. We now have limited knowledge of the tumor microenvironment (TME) determinants that influence the localization and the functions of the diverse myeloid cell populations in GBM. Here, we have utilized orthogonal imaging mass cytometry with single-cell and spatial transcriptomic approaches to identify and map the various myeloid populations in the human GBM tumor microenvironment (TME). Our results show that different myeloid populations have distinct and reproducible compartmentalization patterns in the GBM TME that is driven by tissue hypoxia, regional chemokine signaling, and varied homotypic and heterotypic cellular interactions. We subsequently identified specific tumor subregions in GBM, based on composition of identified myeloid cell populations, that were linked to patient survival. Our results provide insight into the spatial organization of myeloid cell subpopulations in GBM, and how this is predictive of clinical outcome.
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Affiliation(s)
- Michael J. Haley
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Inflammation and Immunology, University of Manchester, Manchester, UK
| | - Leoma Bere
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Inflammation and Immunology, University of Manchester, Manchester, UK
| | - James Minshull
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
| | - Sokratia Georgaka
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, UK
| | | | - Gareth Howell
- Flow Cytometry Core Research Facility, University of Manchester, Manchester, UK
| | - David J. Coope
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
- Manchester Centre for Clinical Neurosciences, Manchester, UK
| | - Federico Roncaroli
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
- Manchester Centre for Clinical Neurosciences, Manchester, UK
| | - Andrew King
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Manchester Centre for Clinical Neurosciences, Manchester, UK
- Division of Cardiovascular Sciences, University of Manchester, Manchester, UK
| | - David C. Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Stuart M. Allan
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
| | - Omar N. Pathmanaban
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
- Manchester Centre for Clinical Neurosciences, Manchester, UK
| | - David Brough
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Inflammation and Immunology, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
| | - Kevin N. Couper
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Inflammation and Immunology, University of Manchester, Manchester, UK
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41
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Bumbaca B, Birtwistle MR, Gallo JM. Network Analyses of Brain Tumor Patients' Multiomic Data Reveals Pharmacological Opportunities to Alter Cell State Transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593202. [PMID: 38766170 PMCID: PMC11100715 DOI: 10.1101/2024.05.08.593202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Glioblastoma Multiforme (GBM) remains a particularly difficult cancer to treat, and survival outcomes remain poor. In addition to the lack of dedicated drug discovery programs for GBM, extensive intratumor heterogeneity and epigenetic plasticity related to cell-state transitions are major roadblocks to successful drug therapy in GBM. To study these phenomenon, publicly available snRNAseq and bulk RNAseq data from patient samples were used to categorize cells from patients into four cell states (i.e. phenotypes), namely: (i) neural progenitor-like (NPC-like), (ii) oligodendrocyte progenitor-like (OPC-like), (iii) astrocyte-like (AC-like), and (iv) mesenchymal-like (MES-like). Patients were subsequently grouped into subpopulations based on which cell-state was the most dominant in their respective tumor. By incorporating phosphoproteomic measurements from the same patients, a protein-protein interaction network (PPIN) was constructed for each cell state. These four-cell state PPINs were pooled to form a single Boolean network that was used for in silico protein knockout simulations to investigate mechanisms that either promote or prevent cell state transitions. Simulation results were input into a boosted tree machine learning model which predicted the cell states or phenotypes of GBM patients from an independent public data source, the Glioma Longitudinal Analysis (GLASS) Consortium. Combining the simulation results and the machine learning predictions, we generated hypotheses for clinically relevant causal mechanisms of cell state transitions. For example, the transcription factor TFAP2A can be seen to promote a transition from the NPC-like to the MES-like state. Such protein nodes and the associated signaling pathways provide potential drug targets that can be further tested in vitro and support cell state-directed (CSD) therapy.
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Affiliation(s)
- Brandon Bumbaca
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
| | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC, USA
- Department of Bioengineering, Clemson University, Clemson SC, USA
| | - James M Gallo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
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42
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Sun C, Wang S, Ma Z, Zhou J, Ding Z, Yuan G, Pan Y. Neutrophils in glioma microenvironment: from immune function to immunotherapy. Front Immunol 2024; 15:1393173. [PMID: 38779679 PMCID: PMC11109384 DOI: 10.3389/fimmu.2024.1393173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Glioma is a malignant tumor of the central nervous system (CNS). Currently, effective treatment options for gliomas are still lacking. Neutrophils, as an important member of the tumor microenvironment (TME), are widely distributed in circulation. Recently, the discovery of cranial-meningeal channels and intracranial lymphatic vessels has provided new insights into the origins of neutrophils in the CNS. Neutrophils in the brain may originate more from the skull and adjacent vertebral bone marrow. They cross the blood-brain barrier (BBB) under the action of chemokines and enter the brain parenchyma, subsequently migrating to the glioma TME and undergoing phenotypic changes upon contact with tumor cells. Under glycolytic metabolism model, neutrophils show complex and dual functions in different stages of cancer progression, including participation in the malignant progression, immune suppression, and anti-tumor effects of gliomas. Additionally, neutrophils in the TME interact with other immune cells, playing a crucial role in cancer immunotherapy. Targeting neutrophils may be a novel generation of immunotherapy and improve the efficacy of cancer treatments. This article reviews the molecular mechanisms of neutrophils infiltrating the central nervous system from the external environment, detailing the origin, functions, classifications, and targeted therapies of neutrophils in the context of glioma.
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Affiliation(s)
- Chao Sun
- The Second Clinical Medical School, Lanzhou University, Lanzhou, China
- Department of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Neurology of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Siwen Wang
- The Second Clinical Medical School, Lanzhou University, Lanzhou, China
| | - Zhen Ma
- The Second Clinical Medical School, Lanzhou University, Lanzhou, China
- Department of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Neurology of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Jinghuan Zhou
- The Second Clinical Medical School, Lanzhou University, Lanzhou, China
- Department of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Neurology of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Zilin Ding
- The Second Clinical Medical School, Lanzhou University, Lanzhou, China
- Department of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Neurology of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Guoqiang Yuan
- The Second Clinical Medical School, Lanzhou University, Lanzhou, China
- Department of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Neurology of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Yawen Pan
- The Second Clinical Medical School, Lanzhou University, Lanzhou, China
- Department of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Neurology of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
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43
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Solomou G, Young AMH, Bulstrode HJCJ. Microglia and macrophages in glioblastoma: landscapes and treatment directions. Mol Oncol 2024. [PMID: 38712663 DOI: 10.1002/1878-0261.13657] [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: 11/28/2023] [Revised: 02/29/2024] [Accepted: 04/19/2024] [Indexed: 05/08/2024] Open
Abstract
Glioblastoma is the most common primary malignant tumour of the central nervous system and remains uniformly and rapidly fatal. The tumour-associated macrophage (TAM) compartment comprises brain-resident microglia and bone marrow-derived macrophages (BMDMs) recruited from the periphery. Immune-suppressive and tumour-supportive TAM cell states predominate in glioblastoma, and immunotherapies, which have achieved striking success in other solid tumours have consistently failed to improve survival in this 'immune-cold' niche context. Hypoxic and necrotic regions in the tumour core are found to enrich, especially in anti-inflammatory and immune-suppressive TAM cell states. Microglia predominate at the invasive tumour margin and express pro-inflammatory and interferon TAM cell signatures. Depletion of TAMs, or repolarisation towards a pro-inflammatory state, are appealing therapeutic strategies and will depend on effective understanding and classification of TAM cell ontogeny and state based on new single-cell and spatial multi-omic in situ profiling. Here, we explore the application of these datasets to expand and refine TAM characterisation, to inform improved modelling approaches, and ultimately underpin the effective manipulation of function.
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Affiliation(s)
- Georgios Solomou
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, UK
- Department of Neurosurgery, Addenbrooke's Hospital, Cambridge, UK
| | - Adam M H Young
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, UK
- Department of Neurosurgery, Addenbrooke's Hospital, Cambridge, UK
| | - Harry J C J Bulstrode
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, UK
- Department of Neurosurgery, Addenbrooke's Hospital, Cambridge, UK
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44
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Yabo YA, Heiland DH. Understanding glioblastoma at the single-cell level: Recent advances and future challenges. PLoS Biol 2024; 22:e3002640. [PMID: 38814900 PMCID: PMC11139343 DOI: 10.1371/journal.pbio.3002640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Abstract
Glioblastoma, the most aggressive and prevalent form of primary brain tumor, is characterized by rapid growth, diffuse infiltration, and resistance to therapies. Intrinsic heterogeneity and cellular plasticity contribute to its rapid progression under therapy; therefore, there is a need to fully understand these tumors at a single-cell level. Over the past decade, single-cell transcriptomics has enabled the molecular characterization of individual cells within glioblastomas, providing previously unattainable insights into the genetic and molecular features that drive tumorigenesis, disease progression, and therapy resistance. However, despite advances in single-cell technologies, challenges such as high costs, complex data analysis and interpretation, and difficulties in translating findings into clinical practice persist. As single-cell technologies are developed further, more insights into the cellular and molecular heterogeneity of glioblastomas are expected, which will help guide the development of personalized and effective therapies, thereby improving prognosis and quality of life for patients.
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Affiliation(s)
- Yahaya A Yabo
- Translational Neurosurgery, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Microenvironment and Immunology Research Laboratory, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Dieter Henrik Heiland
- Translational Neurosurgery, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Microenvironment and Immunology Research Laboratory, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurosurgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurosurgery, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- German Cancer Consortium (DKTK) partner site, Freiburg, Germany
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45
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Junior MGV, Côrtes AMDA, Carneiro FRG, Carels N, da Silva FAB. Unveiling the Dynamics behind Glioblastoma Multiforme Single-Cell Data Heterogeneity. Int J Mol Sci 2024; 25:4894. [PMID: 38732140 PMCID: PMC11084314 DOI: 10.3390/ijms25094894] [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: 03/08/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 05/13/2024] Open
Abstract
Glioblastoma Multiforme is a brain tumor distinguished by its aggressiveness. We suggested that this aggressiveness leads single-cell RNA-sequence data (scRNA-seq) to span a representative portion of the cancer attractors domain. This conjecture allowed us to interpret the scRNA-seq heterogeneity as reflecting a representative trajectory within the attractor's domain. We considered factors such as genomic instability to characterize the cancer dynamics through stochastic fixed points. The fixed points were derived from centroids obtained through various clustering methods to verify our method sensitivity. This methodological foundation is based upon sample and time average equivalence, assigning an interpretative value to the data cluster centroids and supporting parameters estimation. We used stochastic simulations to reproduce the dynamics, and our results showed an alignment between experimental and simulated dataset centroids. We also computed the Waddington landscape, which provided a visual framework for validating the centroids and standard deviations as characterizations of cancer attractors. Additionally, we examined the stability and transitions between attractors and revealed a potential interplay between subtypes. These transitions might be related to cancer recurrence and progression, connecting the molecular mechanisms of cancer heterogeneity with statistical properties of gene expression dynamics. Our work advances the modeling of gene expression dynamics and paves the way for personalized therapeutic interventions.
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Affiliation(s)
- Marcos Guilherme Vieira Junior
- Graduate Program in Computational and Systems Biology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil;
| | - Adriano Maurício de Almeida Côrtes
- Department of Applied Mathematics, Institute of Mathematics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil;
- Systems Engineering and Computer Science Program, Coordination of Postgraduate Programs in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-972, Brazil
| | - Flávia Raquel Gonçalves Carneiro
- Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-361, Brazil;
- Laboratório Interdisciplinar de Pesquisas Médicas, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rio de Janeiro 20231-050, Brazil
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-361, Brazil
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46
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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.
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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
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Choi SH, Jang J, Kim Y, Park CG, Lee SY, Kim H, Kim H. ID1 high/activin A high glioblastoma cells contribute to resistance to anti-angiogenesis therapy through malformed vasculature. Cell Death Dis 2024; 15:292. [PMID: 38658527 PMCID: PMC11043395 DOI: 10.1038/s41419-024-06678-7] [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: 06/26/2023] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
Although bevacizumab (BVZ), a representative drug for anti-angiogenesis therapy (AAT), is used as a first-line treatment for patients with glioblastoma (GBM), its efficacy is notably limited. Whereas several mechanisms have been proposed to explain the acquisition of AAT resistance, the specific underlying mechanisms have yet to be sufficiently ascertained. Here, we established that inhibitor of differentiation 1 (ID1)high/activin Ahigh glioblastoma cell confers resistance to BVZ. The bipotent effect of activin A during its active phase was demonstrated to reduce vasculature dependence in tumorigenesis. In response to a temporary exposure to activin A, this cytokine was found to induce endothelial-to-mesenchymal transition via the Smad3/Slug axis, whereas prolonged exposure led to endothelial apoptosis. ID1 tumors showing resistance to BVZ were established to be characterized by a hypovascular structure, hyperpermeability, and scattered hypoxic regions. Using a GBM mouse model, we demonstrated that AAT resistance can be overcome by administering therapy based on a combination of BVZ and SB431542, a Smad2/3 inhibitor, which contributed to enhancing survival. These findings offer valuable insights that could contribute to the development of new strategies for treating AAT-resistant GBM.
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Affiliation(s)
- Sang-Hun Choi
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Junseok Jang
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Yoonji Kim
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Cheol Gyu Park
- MEDIFIC Inc, Hwaseong-si, Gyeonggi-do, 18469, Republic of Korea
| | - Seon Yong Lee
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Hyojin Kim
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunggee Kim
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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48
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Smith CM, Catchpoole D, Hutvagner G. MiRNAs from the Dlk1-Dio3 locus and miR-224/452 cluster contribute to glioblastoma tumor heterogeneity. Sci Rep 2024; 14:8570. [PMID: 38609422 PMCID: PMC11014907 DOI: 10.1038/s41598-024-58870-6] [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: 10/30/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Glioblastoma is one of the most common and aggressive brain tumors and has seen few improvements in patient outcomes. Inter-tumor heterogeneity between tumors of different patients as well as intra-tumor heterogeneity of cells within the same tumor challenge the development of effective drugs. MiRNAs play an essential role throughout the developing brain and regulate many key genes involved in oncogenesis, yet their role in driving many of the processes underlying tumor heterogeneity remains unclear. In this study, we highlight miRNAs from the Dlk1-Dio3 and miR-224/452 clusters which may be expressed cell autonomously and have expression that is associated with cell state genes in glioblastoma, most prominently in neural progenitor-like and mesenchymal-like states respectively. These findings implicate these miRNA clusters as potential regulators of glioblastoma intra-tumoral heterogeneity and may serve as valuable biomarkers for cell state identification.
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Affiliation(s)
- Christopher M Smith
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Sydney, Australia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Daniel Catchpoole
- School of Computer Sciences, Faculty of Engineering and IT, University of Technology Sydney, Sydney, NSW, Australia
- The Tumour Bank, The Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Gyorgy Hutvagner
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Sydney, Australia.
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49
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Pallarés-Moratalla C, Bergers G. The ins and outs of microglial cells in brain health and disease. Front Immunol 2024; 15:1305087. [PMID: 38665919 PMCID: PMC11043497 DOI: 10.3389/fimmu.2024.1305087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Microglia are the brain's resident macrophages that play pivotal roles in immune surveillance and maintaining homeostasis of the Central Nervous System (CNS). Microglia are functionally implicated in various cerebrovascular diseases, including stroke, aneurysm, and tumorigenesis as they regulate neuroinflammatory responses and tissue repair processes. Here, we review the manifold functions of microglia in the brain under physiological and pathological conditions, primarily focusing on the implication of microglia in glioma propagation and progression. We further review the current status of therapies targeting microglial cells, including their re-education, depletion, and re-population approaches as therapeutic options to improve patient outcomes for various neurological and neuroinflammatory disorders, including cancer.
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50
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Yabo YA, Moreno-Sanchez PM, Pires-Afonso Y, Kaoma T, Nosirov B, Scafidi A, Ermini L, Lipsa A, Oudin A, Kyriakis D, Grzyb K, Poovathingal SK, Poli A, Muller A, Toth R, Klink B, Berchem G, Berthold C, Hertel F, Mittelbronn M, Heiland DH, Skupin A, Nazarov PV, Niclou SP, Michelucci A, Golebiewska A. Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts. Genome Med 2024; 16:51. [PMID: 38566128 PMCID: PMC10988817 DOI: 10.1186/s13073-024-01321-8] [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: 12/14/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND A major contributing factor to glioblastoma (GBM) development and progression is its ability to evade the immune system by creating an immune-suppressive environment, where GBM-associated myeloid cells, including resident microglia and peripheral monocyte-derived macrophages, play critical pro-tumoral roles. However, it is unclear whether recruited myeloid cells are phenotypically and functionally identical in GBM patients and whether this heterogeneity is recapitulated in patient-derived orthotopic xenografts (PDOXs). A thorough understanding of the GBM ecosystem and its recapitulation in preclinical models is currently missing, leading to inaccurate results and failures of clinical trials. METHODS Here, we report systematic characterization of the tumor microenvironment (TME) in GBM PDOXs and patient tumors at the single-cell and spatial levels. We applied single-cell RNA sequencing, spatial transcriptomics, multicolor flow cytometry, immunohistochemistry, and functional studies to examine the heterogeneous TME instructed by GBM cells. GBM PDOXs representing different tumor phenotypes were compared to glioma mouse GL261 syngeneic model and patient tumors. RESULTS We show that GBM tumor cells reciprocally interact with host cells to create a GBM patient-specific TME in PDOXs. We detected the most prominent transcriptomic adaptations in myeloid cells, with brain-resident microglia representing the main population in the cellular tumor, while peripheral-derived myeloid cells infiltrated the brain at sites of blood-brain barrier disruption. More specifically, we show that GBM-educated microglia undergo transition to diverse phenotypic states across distinct GBM landscapes and tumor niches. GBM-educated microglia subsets display phagocytic and dendritic cell-like gene expression programs. Additionally, we found novel microglial states expressing cell cycle programs, astrocytic or endothelial markers. Lastly, we show that temozolomide treatment leads to transcriptomic plasticity and altered crosstalk between GBM tumor cells and adjacent TME components. CONCLUSIONS Our data provide novel insights into the phenotypic adaptation of the heterogeneous TME instructed by GBM tumors. We show the key role of microglial phenotypic states in supporting GBM tumor growth and response to treatment. Our data place PDOXs as relevant models to assess the functionality of the TME and changes in the GBM ecosystem upon treatment.
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Affiliation(s)
- Yahaya A Yabo
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Pilar M Moreno-Sanchez
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Yolanda Pires-Afonso
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Bakhtiyor Nosirov
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Andrea Scafidi
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
| | - Luca Ermini
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
| | - Anuja Lipsa
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
| | - Anaïs Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
| | - Dimitrios Kyriakis
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Suresh K Poovathingal
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
- Single Cell Analytics & Microfluidics Core, Vlaams Instituut Voor Biotechnologie-KU Leuven, 3000, Louvain, Belgium
| | - Aurélie Poli
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
| | - Arnaud Muller
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Reka Toth
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, L-3555, Dudelange, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
- German Cancer Consortium (DKTK): Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC), Cancer Consortium (DKTK) Partner Site Dresden, and German Cancer Research Center (DKFZ), Dresden, Heidelberg, 01307, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Guy Berchem
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
- Centre Hospitalier Luxembourg, L-1210, Luxembourg, Luxembourg
| | | | - Frank Hertel
- Centre Hospitalier Luxembourg, L-1210, Luxembourg, Luxembourg
| | - Michel Mittelbronn
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), L-3555, Dudelange, Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé, L-3555, Dudelange, Luxembourg
| | - Dieter H Heiland
- Translational Neurosurgery, Friedrich-Alexander University Erlangen Nuremberg, 91054, Erlangen, Germany
- Department of Neurosurgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen Nuremberg, 91054, Erlangen, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Neurosurgery, Medical Center, University of Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79106, Freiburg, Germany
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
- Department of Physics and Material Science, University Luxembourg, L-4367, Belvaux, Luxembourg
- Department of Neuroscience, University of California San Diego, La Jolla, CA, 92093, USA
| | - Petr V Nazarov
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Alessandro Michelucci
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg.
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg.
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg.
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg.
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