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Broggi G, Mazzucchelli M, Salzano S, Barbagallo GMV, Certo F, Zanelli M, Palicelli A, Zizzo M, Koufopoulos N, Magro G, Caltabiano R. The emerging role of artificial intelligence in neuropathology: Where are we and where do we want to go? Pathol Res Pract 2024; 263:155671. [PMID: 39490225 DOI: 10.1016/j.prp.2024.155671] [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: 08/21/2024] [Revised: 09/11/2024] [Accepted: 10/20/2024] [Indexed: 11/05/2024]
Abstract
The field of neuropathology, a subspecialty of pathology which studies the diseases affecting the nervous system, is experiencing significant changes due to advancements in artificial intelligence (AI). Traditionally reliant on histological methods and clinical correlations, neuropathology is now experiencing a revolution due to the development of AI technologies like machine learning (ML) and deep learning (DL). These technologies enhance diagnostic accuracy, optimize workflows, and enable personalized treatment strategies. AI algorithms excel at analyzing histopathological images, often revealing subtle morphological changes missed by conventional methods. For example, deep learning models applied to digital pathology can effectively differentiate tumor grades and detect rare pathologies, leading to earlier and more precise diagnoses. Progress in neuroimaging is another helpful tool of AI, as enhanced analysis of MRI and CT scans supports early detection of neurodegenerative diseases. By identifying biomarkers and progression patterns, AI aids in timely therapeutic interventions, potentially slowing disease progression. In molecular pathology, AI's ability to analyze complex genomic data helps uncover the genetic and molecular basis of neuropathological conditions, facilitating personalized treatment plans. AI-driven automation streamlines routine diagnostic tasks, allowing pathologists to focus on complex cases, especially in settings with limited resources. This review explores AI's integration into neuropathology, highlighting its current applications, benefits, challenges, and future directions.
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Affiliation(s)
- Giuseppe Broggi
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Anatomic Pathology, University of Catania, Catania 95123, Italy.
| | - Manuel Mazzucchelli
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Anatomic Pathology, University of Catania, Catania 95123, Italy
| | - Serena Salzano
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Anatomic Pathology, University of Catania, Catania 95123, Italy
| | | | - Francesco Certo
- Department of Neurological Surgery, Policlinico "G. Rodolico-S. Marco" University Hospital, Catania 95121, Italy
| | - Magda Zanelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia 42123, Italy
| | - Andrea Palicelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia 42123, Italy
| | - Maurizio Zizzo
- Surgical Oncology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia 42123, Italy
| | - Nektarios Koufopoulos
- Second Department of Pathology, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens 15772, Greece
| | - Gaetano Magro
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Anatomic Pathology, University of Catania, Catania 95123, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Anatomic Pathology, University of Catania, Catania 95123, Italy
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De Luca C, Virtuoso A, Papa M, Cirillo G, La Rocca G, Corvino S, Barbarisi M, Altieri R. The Three Pillars of Glioblastoma: A Systematic Review and Novel Analysis of Multi-Omics and Clinical Data. Cells 2024; 13:1754. [PMID: 39513861 PMCID: PMC11544881 DOI: 10.3390/cells13211754] [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: 09/14/2024] [Revised: 10/11/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024] Open
Abstract
Glioblastoma is the most fatal and common malignant brain tumor, excluding metastasis and with a median survival of approximately one year. While solid tumors benefit from newly approved drugs, immunotherapy, and prevention, none of these scenarios are opening for glioblastoma. The key to unlocking the peculiar features of glioblastoma is observing its molecular and anatomical features tightly entangled with the host's central nervous system (CNS). In June 2024, we searched the PUBMED electronic database. Data collection and analysis were conducted independently by two reviewers. Results: A total of 215 articles were identified, and 192 were excluded based on inclusion and exclusion criteria. The remaining 23 were used for collecting divergent molecular pathways and anatomical features of glioblastoma. The analysis of the selected papers revealed a multifaced tumor with extreme variability and cellular reprogramming that are observable within the same patient. All the variability of glioblastoma could be clustered into three pillars to dissect the physiology of the tumor: 1. necrotic core; 2. vascular proliferation; 3. CNS infiltration. These three pillars support glioblastoma survival, with a pivotal role of the neurovascular unit, as supported by the most recent paper published by experts in the field.
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Affiliation(s)
- Ciro De Luca
- Laboratory of Neuronal Networks Morphology and System Biology, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.V.); (M.P.); (G.C.)
| | - Assunta Virtuoso
- Laboratory of Neuronal Networks Morphology and System Biology, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.V.); (M.P.); (G.C.)
| | - Michele Papa
- Laboratory of Neuronal Networks Morphology and System Biology, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.V.); (M.P.); (G.C.)
- ISBE Italy, SYSBIO Centre of Systems Biology, 20126 Milan, Italy
| | - Giovanni Cirillo
- Laboratory of Neuronal Networks Morphology and System Biology, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.V.); (M.P.); (G.C.)
| | - Giuseppe La Rocca
- Department of Neurosurgery, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Catholic University of Rome School of Medicine, 00153 Rome, Italy;
| | - Sergio Corvino
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Neurosurgical Clinic, University “Federico II” of Naples, 80131 Naples, Italy;
| | - Manlio Barbarisi
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania “Luigi Vanvitelli”, 80131 Naples, Italy (R.A.)
| | - Roberto Altieri
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania “Luigi Vanvitelli”, 80131 Naples, Italy (R.A.)
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103
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Yao J, Yao P, Li Y, He K, Ma X, Yang Q, Jia J, Chen Z, Yu S, Gu S, Chen K, Zhao Y, Li W, Wang G, Guo M. Integration of multi-omics data revealed the orphan CpG islands and enhancer-dominated c is-regulatory network in glioma. iScience 2024; 27:110946. [PMID: 39391717 PMCID: PMC11465130 DOI: 10.1016/j.isci.2024.110946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/12/2024] [Accepted: 09/10/2024] [Indexed: 10/12/2024] Open
Abstract
The complex transcriptional regulatory network leads to the poor prognosis of glioma. The role of orphan CpG islands (oCGIs) in the transcriptional regulatory network has been overlooked. We conducted a comprehensive exploration of the cis-regulatory roles of oCGIs and enhancers by integrating multi-omics data. Direct regulation of target genes by oCGIs or enhancers is of great importance in the cis-regulatory network. Furthermore, based on single-cell multi-omics data, we found that the highly activated cis-regulatory network in cluster 2 (C2) sustains the high proliferative potential of glioma cells. The upregulation of oCGIs and enhancers related genes in C2 results in glioma patients exhibiting resistance to radiotherapy and chemotherapy. These findings were further validated through glioma cell line related experiments. Our study offers insight into the pathogenesis of glioma and provides a strategy to treat this challenging disease.
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Affiliation(s)
- Jiawei Yao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Penglei Yao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yang Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Ke He
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Xinqi Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Qingsong Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Junming Jia
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Zeren Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Shan Yu
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Shuqing Gu
- Department of Neurosurgery, The First Hospital of Qiqihar, Qiqihar 161005, China
| | - Kunliang Chen
- Department of Neurosurgery, People’s Hospital of the Daxing’an Mountain Range, Daxing’an Mountain Range 165300, China
| | - Yan Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Weihua Li
- Medical Imaging Department, Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen 518035, China
| | - Guangzhi Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Mian Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
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Bartos LM, Quach S, Zenatti V, Kirchleitner SV, Blobner J, Wind-Mark K, Kolabas ZI, Ulukaya S, Holzgreve A, Ruf VC, Kunze LH, Kunte ST, Hoermann L, Härtel M, Park HE, Groß M, Franzmeier N, Zatcepin A, Zounek A, Kaiser L, Riemenschneider MJ, Perneczky R, Rauchmann BS, Stöcklein S, Ziegler S, Herms J, Ertürk A, Tonn JC, Thon N, von Baumgarten L, Prestel M, Tahirovic S, Albert NL, Brendel M. Remote Neuroinflammation in Newly Diagnosed Glioblastoma Correlates with Unfavorable Clinical Outcome. Clin Cancer Res 2024; 30:4618-4634. [PMID: 39150564 PMCID: PMC11474166 DOI: 10.1158/1078-0432.ccr-24-1563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/15/2024] [Accepted: 08/14/2024] [Indexed: 08/17/2024]
Abstract
PURPOSE Current therapy strategies still provide only limited success in the treatment of glioblastoma, the most frequent primary brain tumor in adults. In addition to the characterization of the tumor microenvironment, global changes in the brain of patients with glioblastoma have been described. However, the impact and molecular signature of neuroinflammation distant of the primary tumor site have not yet been thoroughly elucidated. EXPERIMENTAL DESIGN We performed translocator protein (TSPO)-PET in patients with newly diagnosed glioblastoma (n = 41), astrocytoma WHO grade 2 (n = 7), and healthy controls (n = 20) and compared TSPO-PET signals of the non-lesion (i.e., contralateral) hemisphere. Back-translation into syngeneic SB28 glioblastoma mice was used to characterize Pet alterations on a cellular level. Ultimately, multiplex gene expression analyses served to profile immune cells in remote brain. RESULTS Our study revealed elevated TSPO-PET signals in contralateral hemispheres of patients with newly diagnosed glioblastoma compared to healthy controls. Contralateral TSPO was associated with persisting epileptic seizures and shorter overall survival independent of the tumor phenotype. Back-translation into syngeneic glioblastoma mice pinpointed myeloid cells as the predominant source of contralateral TSPO-PET signal increases and identified a complex immune signature characterized by myeloid cell activation and immunosuppression in distant brain regions. CONCLUSIONS Neuroinflammation within the contralateral hemisphere can be detected with TSPO-PET imaging and associates with poor outcome in patients with newly diagnosed glioblastoma. The molecular signature of remote neuroinflammation promotes the evaluation of immunomodulatory strategies in patients with detrimental whole brain inflammation as reflected by high TSPO expression.
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Affiliation(s)
- Laura M. Bartos
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | - Stefanie Quach
- Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany.
| | - Valerio Zenatti
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany.
| | | | - Jens Blobner
- Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany.
| | - Karin Wind-Mark
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | - Zeynep Ilgin Kolabas
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Munich, Germany.
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
- Graduate School of Systemic Neurosciences (GSN), Munich, Germany.
| | - Selin Ulukaya
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Munich, Germany.
- Faculty of Biology, Master of Science Program in Molecular and Cellular Biology, Ludwig-Maximilians-Universität München, Planegg, Germany.
| | - Adrien Holzgreve
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | - Viktoria C. Ruf
- Center for Neuropathology and Prion Research, University Hospital, LMU Munich, Munich, Germany.
| | - Lea H. Kunze
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | - Sebastian T. Kunte
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | - Leonie Hoermann
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | - Marlies Härtel
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Ha Eun Park
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | - Mattes Groß
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
| | - Nicolai Franzmeier
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
| | - Artem Zatcepin
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany.
| | - Adrian Zounek
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | - Lena Kaiser
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | | | - Robert Perneczky
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), University of Munich, Munich, Germany.
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany.
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom.
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, United Kingdom.
| | | | - Sophia Stöcklein
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany.
| | - Sibylle Ziegler
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
| | - Jochen Herms
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany.
- Center for Neuropathology and Prion Research, University Hospital, LMU Munich, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), University of Munich, Munich, Germany.
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Munich, Germany.
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
- Graduate School of Systemic Neurosciences (GSN), Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), University of Munich, Munich, Germany.
| | - Joerg C. Tonn
- Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Cancer Research Center (BZKF), Erlangen, Germany.
| | - Niklas Thon
- Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Louisa von Baumgarten
- Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Cancer Research Center (BZKF), Erlangen, Germany.
| | - Matthias Prestel
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany.
| | - Sabina Tahirovic
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany.
| | - Nathalie L. Albert
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Cancer Research Center (BZKF), Erlangen, Germany.
| | - Matthias Brendel
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Munich Cluster for Systems Neurology (SyNergy), University of Munich, Munich, Germany.
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105
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Gong D, Arbesfeld-Qiu JM, Perrault E, Bae JW, Hwang WL. Spatial oncology: Translating contextual biology to the clinic. Cancer Cell 2024; 42:1653-1675. [PMID: 39366372 PMCID: PMC12051486 DOI: 10.1016/j.ccell.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/01/2024] [Accepted: 09/06/2024] [Indexed: 10/06/2024]
Abstract
Microscopic examination of cells in their tissue context has been the driving force behind diagnostic histopathology over the past two centuries. Recently, the rise of advanced molecular biomarkers identified through single cell profiling has increased our understanding of cellular heterogeneity in cancer but have yet to significantly impact clinical care. Spatial technologies integrating molecular profiling with microenvironmental features are poised to bridge this translational gap by providing critical in situ context for understanding cellular interactions and organization. Here, we review how spatial tools have been used to study tumor ecosystems and their clinical applications. We detail findings in cell-cell interactions, microenvironment composition, and tissue remodeling for immune evasion and therapeutic resistance. Additionally, we highlight the emerging role of multi-omic spatial profiling for characterizing clinically relevant features including perineural invasion, tertiary lymphoid structures, and the tumor-stroma interface. Finally, we explore strategies for clinical integration and their augmentation of therapeutic and diagnostic approaches.
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Affiliation(s)
- Dennis Gong
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeanna M Arbesfeld-Qiu
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard University, Graduate School of Arts and Sciences, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ella Perrault
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard University, Graduate School of Arts and Sciences, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Jung Woo Bae
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William L Hwang
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard University, Graduate School of Arts and Sciences, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
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106
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Jiang C, Wu W, Jiang X, Qian K. Integrative multi-omics analysis unveils the connection between transcriptomic characteristics associated with mitochondria and the tumor immune microenvironment in lower-grade gliomas. Sci Rep 2024; 14:23675. [PMID: 39390013 PMCID: PMC11467307 DOI: 10.1038/s41598-024-74281-z] [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: 03/26/2024] [Accepted: 09/24/2024] [Indexed: 10/12/2024] Open
Abstract
Lower-grade gliomas (LGGs) exhibit diverse clinical behaviors and varying immune infiltration levels. Mitochondria have been implicated in numerous cancer pathogenesis and development, including LGGs. However, the precise biological functions of mitochondrial genes in shaping the immune landscape and the prognostic significance of LGGs remain elusive. Utilizing the Mito-Carta3.0 database, we curated a total of 1136 genes implicated in mitochondrial functions. By leveraging the expression profiles of 1136 genes related to mitochondria, we successfully categorized LGGs into four distinctive mitochondria-related transcriptome (MRT) subtypes. Our thorough analysis conclusively demonstrated that these subtypes exhibited marked disparities. To enable a personalized and integrated evaluation of LGG patients, we developed a prognostic signature known as MRT-related prognostic signature (MTRS). MTRS demonstrated correlation with mitochondria-related transcriptome (MRT) subtypes, allowing the assessment of patients' prognosis and immune microenvironment. We conducted a detailed exploration of the single-cell distribution of MTRS in lower-grade gliomas and verified the core genes of MTRS within the spatial transcriptome of these tumors. Furthermore, our study pinpointed MGME1 as the pivotal gene in the model, functioning as an oncogene that exerts influence on cell proliferation and migration capabilities. Our research highlights the importance of mitochondrial transcriptomic features in LGGs, offering paths for tailored therapies.
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Affiliation(s)
- Cheng Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Wenjie Wu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China.
| | - Kang Qian
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China.
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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 PMCID: PMC11465563 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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Chokshi CR, Shaikh MV, Brakel B, Rossotti MA, Tieu D, Maich W, Anand A, Chafe SC, Zhai K, Suk Y, Kieliszek AM, Miletic P, Mikolajewicz N, Chen D, McNicol JD, Chan K, Tong AHY, Kuhlmann L, Liu L, Alizada Z, Mobilio D, Tatari N, Savage N, Aghaei N, Grewal S, Puri A, Subapanditha M, McKenna D, Ignatchenko V, Salamoun JM, Kwiecien JM, Wipf P, Sharlow ER, Provias JP, Lu JQ, Lazo JS, Kislinger T, Lu Y, Brown KR, Venugopal C, Henry KA, Moffat J, Singh SK. Targeting axonal guidance dependencies in glioblastoma with ROBO1 CAR T cells. Nat Med 2024; 30:2936-2946. [PMID: 39095594 DOI: 10.1038/s41591-024-03138-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/18/2024] [Indexed: 08/04/2024]
Abstract
Resistance to genotoxic therapies and tumor recurrence are hallmarks of glioblastoma (GBM), an aggressive brain tumor. In this study, we investigated functional drivers of post-treatment recurrent GBM through integrative genomic analyses, genome-wide genetic perturbation screens in patient-derived GBM models and independent lines of validation. Specific genetic dependencies were found consistent across recurrent tumor models, accompanied by increased mutational burden and differential transcript and protein expression compared to its primary GBM predecessor. Our observations suggest a multi-layered genetic response to drive tumor recurrence and implicate PTP4A2 (protein tyrosine phosphatase 4A2) as a modulator of self-renewal, proliferation and tumorigenicity in recurrent GBM. Genetic perturbation or small-molecule inhibition of PTP4A2 acts through a dephosphorylation axis with roundabout guidance receptor 1 (ROBO1) and its downstream molecular players, exploiting a functional dependency on ROBO signaling. Because a pan-PTP4A inhibitor was limited by poor penetrance across the blood-brain barrier in vivo, we engineered a second-generation chimeric antigen receptor (CAR) T cell therapy against ROBO1, a cell surface receptor enriched across recurrent GBM specimens. A single dose of ROBO1-targeted CAR T cells doubled median survival in cell-line-derived xenograft (CDX) models of recurrent GBM. Moreover, in CDX models of adult lung-to-brain metastases and pediatric relapsed medulloblastoma, ROBO1 CAR T cells eradicated tumors in 50-100% of mice. Our study identifies a promising multi-targetable PTP4A-ROBO1 signaling axis that drives tumorigenicity in recurrent GBM, with potential in other malignant brain tumors.
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Affiliation(s)
- Chirayu R Chokshi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Muhammad Vaseem Shaikh
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
- Department of Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Benjamin Brakel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Martin A Rossotti
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - David Tieu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - William Maich
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Alisha Anand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Shawn C Chafe
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
- Department of Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Kui Zhai
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
- Department of Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Yujin Suk
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Agata M Kieliszek
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Petar Miletic
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
- Department of Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Nicholas Mikolajewicz
- Program for Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research & Learning, Toronto, ON, Canada
| | - David Chen
- Program for Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research & Learning, Toronto, ON, Canada
| | - Jamie D McNicol
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Katherine Chan
- Program for Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research & Learning, Toronto, ON, Canada
| | - Amy H Y Tong
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Laura Kuhlmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lina Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Zahra Alizada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
- Department of Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Daniel Mobilio
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Nazanin Tatari
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Neil Savage
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Nikoo Aghaei
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Shan Grewal
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Anish Puri
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | | | - Dillon McKenna
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
- Department of Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | | | - Joseph M Salamoun
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jacek M Kwiecien
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elizabeth R Sharlow
- Department of Pharmacology, Fiske Drug Discovery Laboratory, University of Virginia, Charlottesville, VA, USA
| | - John P Provias
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Jian-Qiang Lu
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - John S Lazo
- Department of Pharmacology, Fiske Drug Discovery Laboratory, University of Virginia, Charlottesville, VA, USA
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Yu Lu
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
| | - Kevin R Brown
- Program for Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research & Learning, Toronto, ON, Canada
| | - Chitra Venugopal
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada
- Department of Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Kevin A Henry
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Program for Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research & Learning, Toronto, ON, Canada.
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
| | - Sheila K Singh
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
- Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON, Canada.
- Department of Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
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109
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Cheng X, Cao Y, Liu X, Li Y, Li Q, Gao D, Yu Q. Single-cell and spatial omics unravel the spatiotemporal biology of tumour border invasion and haematogenous metastasis. Clin Transl Med 2024; 14:e70036. [PMID: 39350478 PMCID: PMC11442492 DOI: 10.1002/ctm2.70036] [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: 05/05/2024] [Revised: 08/14/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
Solid tumours exhibit a well-defined architecture, comprising a differentiated core and a dynamic border that interfaces with the surrounding tissue. This border, characterised by distinct cellular morphology and molecular composition, serves as a critical determinant of the tumour's invasive behaviour. Notably, the invasive border of the primary tumour represents the principal site for intravasation of metastatic cells. These cells, known as circulating tumour cells (CTCs), function as 'seeds' for distant dissemination and display remarkable heterogeneity. Advancements in spatial sequencing technology are progressively unveiling the spatial biological features of tumours. However, systematic investigations specifically targeting the characteristics of the tumour border remain scarce. In this comprehensive review, we illuminate key biological insights along the tumour body-border-haematogenous metastasis axis over the past five years. We delineate the distinctive landscape of tumour invasion boundaries and delve into the intricate heterogeneity and phenotype of CTCs, which orchestrate haematogenous metastasis. These insights have the potential to explain the basis of tumour invasion and distant metastasis, offering new perspectives for the development of more complex and precise clinical interventions and treatments.
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Affiliation(s)
- Xifu Cheng
- Department of Gastroenterology and Hepatologythe Second Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangChina
- Department of Pathogen Biology and ImmunologySchool of Basic Medical SciencesJiangxi Medical CollegeNanchang UniversityNanchangChina
| | - Yuke Cao
- Department of Gastroenterology and Hepatologythe Second Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangChina
| | - Xiangyi Liu
- Queen Mary SchoolJiangxi Medical CollegeNanchang UniversityNanchangChina
| | - Yuanheng Li
- Queen Mary SchoolJiangxi Medical CollegeNanchang UniversityNanchangChina
| | - Qing Li
- Department of Oncologythe Second Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangChina
| | - Dian Gao
- Department of Gastroenterology and Hepatologythe Second Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangChina
- Department of Pathogen Biology and ImmunologySchool of Basic Medical SciencesJiangxi Medical CollegeNanchang UniversityNanchangChina
| | - Qiongfang Yu
- Department of Gastroenterology and Hepatologythe Second Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangChina
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110
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Bareham B, Dibble M, Parsons M. Defining and modeling dynamic spatial heterogeneity within tumor microenvironments. Curr Opin Cell Biol 2024; 90:102422. [PMID: 39216233 PMCID: PMC11846781 DOI: 10.1016/j.ceb.2024.102422] [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: 05/08/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Many solid tumors exhibit significant genetic, cellular, and biophysical heterogeneity which dynamically evolves during disease progression and after treatment. This constant flux in cell composition, phenotype, spatial relationships, and tissue properties poses significant challenges in accurately diagnosing and treating patients. Much of the complexity lies in unraveling the molecular changes in different tumor compartments, how they influence one another in space and time and where vulnerabilities exist that might be appropriate to target therapeutically. Recent advances in spatial profiling tools and technologies are enabling new insight into the underlying biology of complex tumors, creating a greater understanding of the intricate relationship between cell types, states, and the microenvironment. Here we reflect on some recent discoveries in this area, where the key knowledge and technology gaps lie, and the advancements in spatial measurements and in vitro models for the study of spatial intratumoral heterogeneity.
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Affiliation(s)
- Bethany Bareham
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Matthew Dibble
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK.
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111
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Wang J, Alhaskawi A, Dong Y, Tian T, Abdalbary SA, Lu H. Advances in spatial multi-omics in tumors. TUMORI JOURNAL 2024; 110:327-339. [PMID: 39185632 DOI: 10.1177/03008916241271458] [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: 08/27/2024]
Abstract
Single-cell techniques have convincingly demonstrated that tumor tissue usually contains multiple genetically defined cell subclones with different gene mutation sets as well as various transcriptional profiles, but the spatial heterogeneity of the microenvironment and the macrobiological characteristics of the tumor ecosystem have not been described. For the past few years, spatial multi-omics technologies have revealed the cellular interactions, microenvironment, and even systemic tumor-host interactions in the tumor ecosystem at the spatial level, which can not only improve classical therapies such as surgery, radiotherapy, and chemotherapy but also promote the development of emerging targeted therapies in immunotherapy. Here, we review some emerging spatial omics techniques in cancer research and therapeutic applications and propose prospects for their future development.
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Affiliation(s)
- Junyan Wang
- The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ahmad Alhaskawi
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yanzhao Dong
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Tu Tian
- Department of Plastic Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Sahar Ahmed Abdalbary
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Department of Orthopedic Physical Therapy, Faculty of Physical Therapy, Nahda University in Beni Suef, Beni Suef, Egypt
| | - Hui Lu
- The First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
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112
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Lv W, Wang Y. Neural Influences on Tumor Progression Within the Central Nervous System. CNS Neurosci Ther 2024; 30:e70097. [PMID: 39469896 PMCID: PMC11519750 DOI: 10.1111/cns.70097] [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: 07/08/2024] [Revised: 09/21/2024] [Accepted: 10/13/2024] [Indexed: 10/30/2024] Open
Abstract
For decades, researchers have studied how brain tumors, the immune system, and drugs interact. With the advances in cancer neuroscience, which centers on defining and therapeutically targeting nervous system-cancer interactions, both within the local tumor microenvironment (TME) and on a systemic level, the subtle relationship between neurons and tumors in the central nervous system (CNS) has been deeply studied. Neurons, as the executors of brain functional activities, have been shown to significantly influence the emergence and development of brain tumors, including both primary and metastatic tumors. They engage with tumor cells via chemical or electrical synapses, directly regulating tumors or via intricate coupling networks, and also contribute to the TME through paracrine signaling, secreting proteins that exert regulatory effects. For instance, in a study involving a mouse model of glioblastoma, the authors observed a 42% increase in tumor volume when neuronal activity was stimulated, compared to controls (p < 0.01), indicating a direct correlation between neural activity and tumor growth. These thought-provoking results offer promising new strategies for brain tumor therapies, highlighting the potential of neuronal modulation to curb tumor progression. Future strategies may focus on developing drugs to inhibit or neutralize proteins and other bioactive substances secreted by neurons, break synaptic connections and interactions between infiltrating cells and tumor cells, as well as disrupt electrical coupling within glioma cell networks. By harnessing the insights gained from this research, we aspire to usher in a new era of brain tumor therapies that are both more potent and precise.
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Affiliation(s)
- Wenhao Lv
- Affiliated Hospital of Hangzhou Normal UniversityHangzhou Normal UniversityHangzhouZhejiangChina
- School of PharmacyHangzhou Normal UniversityHangzhouZhejiangChina
| | - Yongjie Wang
- School of PharmacyHangzhou Normal UniversityHangzhouZhejiangChina
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113
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Bao Y, Qiao J, Gong W, Zhang R, Zhou Y, Xie Y, Xie Y, He J, Yin T. Spatial metabolomics highlights metabolic reprogramming in acute myeloid leukemia mice through creatine pathway. Acta Pharm Sin B 2024; 14:4461-4477. [PMID: 39525575 PMCID: PMC11544190 DOI: 10.1016/j.apsb.2024.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/13/2024] [Accepted: 07/02/2024] [Indexed: 11/16/2024] Open
Abstract
Acute myeloid leukemia (AML) is recognized as an aggressive cancer that is characterized by significant metabolic reprogramming. Here, we applied spatial metabolomics to achieve high-throughput, in situ identification of metabolites within the liver metastases of AML mice. Alterations at metabolite and protein levels were further mapped out and validated by integrating untargeted metabolomics and proteomics. This study showed a downregulation in arginine's contribution to polyamine biosynthesis and urea cycle, coupled with an upregulation of the creatine metabolism. The upregulation of creatine synthetases Gatm and Gamt, as well as the creatine transporter Slc6a8, resulted in a marked accumulation of creatine within tumor foci. This process further enhances oxidative phosphorylation and glycolysis of leukemia cells, thereby boosting ATP production to foster proliferation and infiltration. Importantly, we discovered that inhibiting Slc6a8 can counter these detrimental effects, offering a new strategy for treating AML by targeting metabolic pathways.
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Affiliation(s)
- Yucheng Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jing Qiao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wenjie Gong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ruihong Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yanting Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yinyin Xie
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuan Xie
- College of Osteopathic Medicine, Kansas City University, Kansas City, MO 64106, USA
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing 100050, China
| | - Tong Yin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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114
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Du Y, Ding X, Ye Y. The spatial multi-omics revolution in cancer therapy: Precision redefined. Cell Rep Med 2024; 5:101740. [PMID: 39293393 PMCID: PMC11525011 DOI: 10.1016/j.xcrm.2024.101740] [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: 04/06/2024] [Revised: 07/11/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024]
Abstract
Spatially resolved multi-omics revolutionizes cancer therapy by decoding the cellular and molecular heterogeneity of the tumor microenvironment through spatial coordinates. This commentary discusses the roles of spatial multi-omics in identifying precise therapeutic targets and predicting treatment responses while also highlighting the challenges that impede its integration into precision medicine.
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Affiliation(s)
- Yanhua Du
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinyu Ding
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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115
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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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Liang W, Zhu Z, Xu D, Wang P, Guo F, Xiao H, Hou C, Xue J, Zhi X, Ran R. The burgeoning spatial multi-omics in human gastrointestinal cancers. PeerJ 2024; 12:e17860. [PMID: 39285924 PMCID: PMC11404479 DOI: 10.7717/peerj.17860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/14/2024] [Indexed: 09/19/2024] Open
Abstract
The development and progression of diseases in multicellular organisms unfold within the intricate three-dimensional body environment. Thus, to comprehensively understand the molecular mechanisms governing individual development and disease progression, precise acquisition of biological data, including genome, transcriptome, proteome, metabolome, and epigenome, with single-cell resolution and spatial information within the body's three-dimensional context, is essential. This foundational information serves as the basis for deciphering cellular and molecular mechanisms. Although single-cell multi-omics technology can provide biological information such as genome, transcriptome, proteome, metabolome, and epigenome with single-cell resolution, the sample preparation process leads to the loss of spatial information. Spatial multi-omics technology, however, facilitates the characterization of biological data, such as genome, transcriptome, proteome, metabolome, and epigenome in tissue samples, while retaining their spatial context. Consequently, these techniques significantly enhance our understanding of individual development and disease pathology. Currently, spatial multi-omics technology has played a vital role in elucidating various processes in tumor biology, including tumor occurrence, development, and metastasis, particularly in the realms of tumor immunity and the heterogeneity of the tumor microenvironment. Therefore, this article provides a comprehensive overview of spatial transcriptomics, spatial proteomics, and spatial metabolomics-related technologies and their application in research concerning esophageal cancer, gastric cancer, and colorectal cancer. The objective is to foster the research and implementation of spatial multi-omics technology in digestive tumor diseases. This review will provide new technical insights for molecular biology researchers.
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Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
| | - Zhenpeng Zhu
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Dandan Xu
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
| | - Peng Wang
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Fei Guo
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
| | - Haoshan Xiao
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Chenyang Hou
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Jun Xue
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
| | - Xuejun Zhi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
| | - Rensen Ran
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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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] [Key Words] [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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118
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Sevenich L. Lipid recycling by macrophage cells drives the growth of brain cancer. Nature 2024; 633:777-778. [PMID: 39261694 DOI: 10.1038/d41586-024-02868-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
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119
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Jimenez-Macias JL, Vaughn-Beaucaire P, Bharati A, Xu Z, Forrest M, Hong J, Sun M, Schmidt A, Clark J, Hawkins W, Mercado N, Real J, Huntington K, Zdioruk M, Nowicki MO, Cho CF, Wu B, Li W, Logan T, Manz KE, Pennell KD, Fedeles BI, Brodsky AS, Lawler SE. Modulation of blood-tumor barrier transcriptional programs improves intra-tumoral drug delivery and potentiates chemotherapy in GBM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609797. [PMID: 39253453 PMCID: PMC11382996 DOI: 10.1101/2024.08.26.609797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Glioblastoma (GBM) is the most common malignant primary brain tumor. GBM has an extremely poor prognosis and new treatments are badly needed. Efficient drug delivery to GBM is a major obstacle as the blood-brain barrier (BBB) prevents passage of the majority of cancer drugs into the brain. It is also recognized that the blood-brain tumor barrier (BTB) in the growing tumor represents a challenge. The BTB is heterogeneous and poorly characterized, but similar to the BBB it can prevent therapeutics from reaching effective intra-tumoral doses, dramatically hindering their potential. Here, we identified a 12-gene signature associated with the BTB, with functions related to vasculature development, morphogenesis and cell migration. We identified CDH5 as a core molecule in this set and confirmed its over-expression in GBM vasculature using spatial transcriptomics of GBM patient specimens. We found that the indirubin-derivative, 6-bromoindirubin acetoxime (BIA), could downregulate CDH5 and other BTB signature genes, causing endothelial barrier disruption in endothelial monolayers and BBB 3D spheroids in vitro. Treatment of tumor-bearing mice with BIA enabled increased intra-tumoral accumulation of the BBB non-penetrant chemotherapeutic drug cisplatin and potentiated cisplatin-mediated DNA damage by targeting DNA repair pathways. Finally, using an injectable BIA nanoparticle formulation, PPRX-1701, we significantly improved the efficacy of cisplatin in patient-derived GBM xenograms and prolonged their survival. Overall, our work reveals potential targets at the BTB for improved chemotherapy delivery and the bifunctional properties of BIA as a BTB modulator and potentiator of chemotherapy, supporting its further development.
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Affiliation(s)
- Jorge L. Jimenez-Macias
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Philippa Vaughn-Beaucaire
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ayush Bharati
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Zheyun Xu
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Megan Forrest
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Jason Hong
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Michael Sun
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Andrea Schmidt
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Jasmine Clark
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - William Hawkins
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Noe Mercado
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Jacqueline Real
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Kelsey Huntington
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Mykola Zdioruk
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michal O. Nowicki
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Choi-Fong Cho
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02115, USA
| | - Bin Wu
- Cytodigm, Inc, Natick, MA 01760, USA
| | - Weiyi Li
- Phosphorex, Inc, Hopkinton, MA 01748, USA
| | | | | | - Kurt D. Pennell
- School of Engineering, Brown University, Providence, RI 02912, USA
| | - Bogdan I. Fedeles
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexander S. Brodsky
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
| | - Sean E. Lawler
- Legorreta Cancer Center, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
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Liu X, Peng T, Xu M, Lin S, Hu B, Chu T, Liu B, Xu Y, Ding W, Li L, Cao C, Wu P. Spatial multi-omics: deciphering technological landscape of integration of multi-omics and its applications. J Hematol Oncol 2024; 17:72. [PMID: 39182134 PMCID: PMC11344930 DOI: 10.1186/s13045-024-01596-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/09/2024] [Indexed: 08/27/2024] Open
Abstract
The emergence of spatial multi-omics has helped address the limitations of single-cell sequencing, which often leads to the loss of spatial context among cell populations. Integrated analysis of the genome, transcriptome, proteome, metabolome, and epigenome has enhanced our understanding of cell biology and the molecular basis of human diseases. Moreover, this approach offers profound insights into the interactions between intracellular and intercellular molecular mechanisms involved in the development, physiology, and pathogenesis of human diseases. In this comprehensive review, we examine current advancements in multi-omics technologies, focusing on their evolution and refinement over the past decade, including improvements in throughput and resolution, modality integration, and accuracy. We also discuss the pivotal contributions of spatial multi-omics in revealing spatial heterogeneity, constructing detailed spatial atlases, deciphering spatial crosstalk in tumor immunology, and advancing translational research and cancer therapy through precise spatial mapping.
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Affiliation(s)
- Xiaojie Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ting Peng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Miaochun Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shitong Lin
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bai Hu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tian Chu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Binghan Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yashi Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wencheng Ding
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Canhui Cao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Peng Wu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Kueckelhaus J, Frerich S, Kada-Benotmane J, Koupourtidou C, Ninkovic J, Dichgans M, Beck J, Schnell O, Heiland DH. Inferring histology-associated gene expression gradients in spatial transcriptomic studies. Nat Commun 2024; 15:7280. [PMID: 39179527 PMCID: PMC11343836 DOI: 10.1038/s41467-024-50904-x] [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: 05/29/2023] [Accepted: 07/24/2024] [Indexed: 08/26/2024] Open
Abstract
Spatially resolved transcriptomics has revolutionized RNA studies by aligning RNA abundance with tissue structure, enabling direct comparisons between histology and gene expression. Traditional approaches to identifying signature genes often involve preliminary data grouping, which can overlook subtle expression patterns in complex tissues. We present Spatial Gradient Screening, an algorithm which facilitates the supervised detection of histology-associated gene expression patterns without prior data grouping. Utilizing spatial transcriptomic data along with single-cell deconvolution from injured mouse cortex, and TCR-seq data from brain tumors, we compare our methodology to standard differential gene expression analysis. Our findings illustrate both the advantages and limitations of cluster-free detection of gene expression, offering more profound insights into the spatial architecture of transcriptomes. The algorithm is embedded in SPATA2, an open-source framework written in R, which provides a comprehensive set of tools for investigating gene expression within tissue.
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Affiliation(s)
- Jan Kueckelhaus
- Microenvironment and Immunology Research Laboratory, Medical Center, Faculty of Medicine, Freiburg University, Freiburg, Germany.
- Department of Neurosurgery, Medical Center, Faculty of Medicine, Erlangen University, Erlangen, Germany.
| | - Simon Frerich
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU Munich, Munich, Germany
| | - Jasim Kada-Benotmane
- Microenvironment and Immunology Research Laboratory, Medical Center, Faculty of Medicine, Freiburg University, Freiburg, Germany
- Department of Neurosurgery, Medical Center, Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Christina Koupourtidou
- Department of Cell Biology and Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Jovica Ninkovic
- Department of Cell Biology and Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Juergen Beck
- Department of Neurosurgery, Medical Center, Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Oliver Schnell
- Department of Neurosurgery, Medical Center, Faculty of Medicine, Erlangen University, Erlangen, Germany
| | - Dieter Henrik Heiland
- Microenvironment and Immunology Research Laboratory, Medical Center, Faculty of Medicine, Freiburg University, Freiburg, Germany.
- Department of Neurosurgery, Medical Center, Faculty of Medicine, Erlangen University, Erlangen, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, University of Freiburg, Freiburg, Germany.
- German Cancer Consortium (DKTK) partner site Freiburg, Freiburg, Germany.
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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122
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Rosberg R, Smolag KI, Sjölund J, Johansson E, Bergelin C, Wahldén J, Pantazopoulou V, Ceberg C, Pietras K, Blom AM, Pietras A. Hypoxia-induced complement component 3 promotes aggressive tumor growth in the glioblastoma microenvironment. JCI Insight 2024; 9:e179854. [PMID: 39172519 PMCID: PMC11466187 DOI: 10.1172/jci.insight.179854] [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: 01/29/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024] Open
Abstract
Glioblastoma (GBM) is the most aggressive form of glioma with a high rate of relapse despite intensive treatment. Tumor recurrence is tightly linked to radio-resistance, which in turn is associated with hypoxia. Here, we discovered a strong link between hypoxia and local complement signaling using publicly available bulk, single-cell, and spatially resolved transcriptomic data from patients with GBM. Complement component 3 (C3) and the receptor C3AR1 were both associated with aggressive disease and shorter survival in human glioma. In a genetically engineered mouse model of GBM, we found C3 specifically in hypoxic tumor areas. In vitro, we found an oxygen level-dependent increase in C3 and C3AR1 expression in response to hypoxia in several GBM and stromal cell types. C3a induced M2 polarization of cultured microglia and macrophages in a C3aR-dependent fashion. Targeting C3aR using the antagonist SB290157 prolonged survival of glioma-bearing mice both alone and in combination with radiotherapy while reducing the number of M2-polarized macrophages. Our findings establish a strong link between hypoxia and complement pathways in GBM and support a role of hypoxia-induced C3a/C3aR signaling as a contributor to glioma aggressiveness by regulating macrophage polarization.
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Affiliation(s)
- Rebecca Rosberg
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Karolina I. Smolag
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
- Section of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Jonas Sjölund
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Elinn Johansson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Christina Bergelin
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Julia Wahldén
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Vasiliki Pantazopoulou
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Crister Ceberg
- Division of Medical Radiation Physics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Kristian Pietras
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Anna M. Blom
- Section of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Alexander Pietras
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
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Carrillo-Perez F, Cramer EM, Pizurica M, Andor N, Gevaert O. Towards Digital Quantification of Ploidy from Pan-Cancer Digital Pathology Slides using Deep Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608555. [PMID: 39229200 PMCID: PMC11370345 DOI: 10.1101/2024.08.19.608555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Abnormal DNA ploidy, found in numerous cancers, is increasingly being recognized as a contributor in driving chromosomal instability, genome evolution, and the heterogeneity that fuels cancer cell progression. Furthermore, it has been linked with poor prognosis of cancer patients. While next-generation sequencing can be used to approximate tumor ploidy, it has a high error rate for near-euploid states, a high cost and is time consuming, motivating alternative rapid quantification methods. We introduce PloiViT, a transformer-based model for tumor ploidy quantification that outperforms traditional machine learning models, enabling rapid and cost-effective quantification directly from pathology slides. We trained PloiViT on a dataset of fifteen cancer types from The Cancer Genome Atlas and validated its performance in multiple independent cohorts. Additionally, we explored the impact of self-supervised feature extraction on performance. PloiViT, using self-supervised features, achieved the lowest prediction error in multiple independent cohorts, exhibiting better generalization capabilities. Our findings demonstrate that PloiViT predicts higher ploidy values in aggressive cancer groups and patients with specific mutations, validating PloiViT potential as complementary for ploidy assessment to next-generation sequencing data. To further promote its use, we release our models as a user-friendly inference application and a Python package for easy adoption and use.
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Affiliation(s)
- Francisco Carrillo-Perez
- Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94304, CA, USA
| | - Eric M. Cramer
- Department of Biomedical Engineering, Oregon Health & Science University (OHSU), Portland, 97239, OR, USA
| | - Marija Pizurica
- Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94304, CA, USA
- Internet technology and Data science Lab (IDLab), Ghent University, Ghent, 9052, Ghent, Belgium
| | - Noemi Andor
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, 33612, FL, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94304, CA, USA
- Department of Biomedical Data Science (DBDS), Stanford University, Palo Alto, 94305, CA, USA
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Motevasseli M, Darvishi M, Khoshnevisan A, Zeinalizadeh M, Saffar H, Bayat S, Najafi A, Abbaspour MJ, Mamivand A, Olson SB, Tabrizi M. Distinct tumor-TAM interactions in IDH-stratified glioma microenvironments unveiled by single-cell and spatial transcriptomics. Acta Neuropathol Commun 2024; 12:133. [PMID: 39148129 PMCID: PMC11328419 DOI: 10.1186/s40478-024-01837-5] [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: 06/01/2024] [Accepted: 07/02/2024] [Indexed: 08/17/2024] Open
Abstract
Tumor-associated macrophages (TAMs) residing in the tumor microenvironment (TME) are characterized by their pivotal roles in tumor progression, antitumor immunity, and TME remodeling. However, a thorough comparative characterization of tumor-TAM crosstalk across IDH-defined categories of glioma remains elusive, likely contributing to mixed outcomes in clinical trials. We delineated the phenotypic heterogeneity of TAMs across IDH-stratified gliomas. Notably, two TAM subsets with a mesenchymal phenotype were enriched in IDH-WT glioblastoma (GBM) and correlated with poorer patient survival and reduced response to anti-PD-1 immune checkpoint inhibitor (ICI). We proposed SLAMF9 receptor as a potential therapeutic target. Inference of gene regulatory networks identified PPARG, ELK1, and MXI1 as master transcription factors of mesenchymal BMD-TAMs. Our analyses of reciprocal tumor-TAM interactions revealed distinct crosstalk in IDH-WT tumors, including ANXA1-FPR1/3, FN1-ITGAVB1, VEGFA-NRP1, and TNFSF12-TNFRSF12A with known contribution to immunosuppression, tumor proliferation, invasion and TAM recruitment. Spatially resolved transcriptomics further elucidated the architectural organization of highlighted communications. Furthermore, we demonstrated significant upregulation of ANXA1, FN1, NRP1, and TNFRSF12A genes in IDH-WT tumors using bulk RNA-seq and RT-qPCR. Longitudinal expression analysis of candidate genes revealed no difference between primary and recurrent tumors indicating that the interactive network of malignant states with TAMs does not drastically change upon recurrence. Collectively, our study offers insights into the unique cellular composition and communication of TAMs in glioma TME, revealing novel vulnerabilities for therapeutic interventions in IDH-WT GBM.
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Affiliation(s)
- Meysam Motevasseli
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Darvishi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Khoshnevisan
- Department of Neurosurgery, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Zeinalizadeh
- Department of Neurosurgery, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Hiva Saffar
- Department of Pathology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Shiva Bayat
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Abbaspour
- Department of Neurosurgery, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Mamivand
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Susan B Olson
- Molecular and Medical Genetics, Knight Diagnostics Laboratories, Oregon Health and Science University, Portland, OR, USA
| | - Mina Tabrizi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Molecular and Medical Genetics, Knight Diagnostics Laboratories, Oregon Health and Science University, Portland, OR, USA.
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Norton ES, Whaley LA, Jones VK, Brooks MM, Russo MN, Morderer D, Jessen E, Schiapparelli P, Ramos-Fresnedo A, Zarco N, Carrano A, Rossoll W, Asmann YW, Lam TT, Chaichana KL, Anastasiadis PZ, Quiñones-Hinojosa A, Guerrero-Cázares H. Cell-specific cross-talk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone. SCIENCE ADVANCES 2024; 10:eadn1607. [PMID: 39110807 PMCID: PMC11305394 DOI: 10.1126/sciadv.adn1607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Glioblastoma (GBM) is the most prevalent and aggressive malignant primary brain tumor. GBM proximal to the lateral ventricles (LVs) is more aggressive, potentially because of subventricular zone contact. Despite this, cross-talk between GBM and neural stem/progenitor cells (NSC/NPCs) is not well understood. Using cell-specific proteomics, we show that LV-proximal GBM prevents neuronal maturation of NSCs through induction of senescence. In addition, GBM brain tumor-initiating cells (BTICs) increase expression of cathepsin B (CTSB) upon interaction with NPCs. Lentiviral knockdown and recombinant protein experiments reveal that both cell-intrinsic and soluble CTSB promote malignancy-associated phenotypes in BTICs. Soluble CTSB stalls neuronal maturation in NPCs while promoting senescence, providing a link between LV-tumor proximity and neurogenesis disruption. Last, we show LV-proximal CTSB up-regulation in patients, showing the relevance of this cross-talk in human GBM biology. These results demonstrate the value of proteomic analysis in tumor microenvironment research and provide direction for new therapeutic strategies in GBM.
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Affiliation(s)
- Emily S. Norton
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL 32224, USA
- Regenerative Sciences Training Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Lauren A. Whaley
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Vanessa K. Jones
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Mieu M. Brooks
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Marissa N. Russo
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dmytro Morderer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Erik Jessen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | | | - Natanael Zarco
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Anna Carrano
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Yan W. Asmann
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - TuKiet T. Lam
- Keck MS and Proteomics Resource, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06510, USA
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Huang R, Huang X, Tong Y, Yan HYN, Leung SY, Stegle O, Huang Y. Robust analysis of allele-specific copy number alterations from scRNA-seq data with XClone. Nat Commun 2024; 15:6684. [PMID: 39107346 PMCID: PMC11303794 DOI: 10.1038/s41467-024-51026-0] [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: 07/20/2023] [Accepted: 07/27/2024] [Indexed: 08/10/2024] Open
Abstract
Somatic copy number alterations (CNAs) are major mutations that contribute to the development and progression of various cancers. Despite a few computational methods proposed to detect CNAs from single-cell transcriptomic data, the technical sparsity of such data makes it challenging to identify allele-specific CNAs, particularly in complex clonal structures. In this study, we present a statistical method, XClone, that strengthens the signals of read depth and allelic imbalance by effective smoothing on cell neighborhood and gene coordinate graphs to detect haplotype-aware CNAs from scRNA-seq data. By applying XClone to multiple datasets with challenging compositions, we demonstrated its ability to robustly detect different types of allele-specific CNAs and potentially indicate whole genome duplication, therefore enabling the discovery of corresponding subclones and the dissection of their phenotypic impacts.
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Affiliation(s)
- Rongting Huang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Xianjie Huang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
- Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Yin Tong
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Helen Y N Yan
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
- The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Oliver Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yuanhua Huang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China.
- Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China.
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong SAR, China.
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127
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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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128
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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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129
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Zhang H, Lu KH, Ebbini M, Huang P, Lu H, Li L. Mass spectrometry imaging for spatially resolved multi-omics molecular mapping. NPJ IMAGING 2024; 2:20. [PMID: 39036554 PMCID: PMC11254763 DOI: 10.1038/s44303-024-00025-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
The recent upswing in the integration of spatial multi-omics for conducting multidimensional information measurements is opening a new chapter in biological research. Mapping the landscape of various biomolecules including metabolites, proteins, nucleic acids, etc., and even deciphering their functional interactions and pathways is believed to provide a more holistic and nuanced exploration of the molecular intricacies within living systems. Mass spectrometry imaging (MSI) stands as a forefront technique for spatially mapping the metabolome, lipidome, and proteome within diverse tissue and cell samples. In this review, we offer a systematic survey delineating different MSI techniques for spatially resolved multi-omics analysis, elucidating their principles, capabilities, and limitations. Particularly, we focus on the advancements in methodologies aimed at augmenting the molecular sensitivity and specificity of MSI; and depict the burgeoning integration of MSI-based spatial metabolomics, lipidomics, and proteomics, encompassing the synergy with other imaging modalities. Furthermore, we offer speculative insights into the potential trajectory of MSI technology in the future.
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Affiliation(s)
- Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - Kelly H. Lu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Malik Ebbini
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - Penghsuan Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
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130
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Yalamandala B, Chen YJ, Lin YH, Huynh TMH, Chiang WH, Chou TC, Liu HW, Huang CC, Lu YJ, Chiang CS, Chu LA, Hu SH. A Self-Cascade Penetrating Brain Tumor Immunotherapy Mediated by Near-Infrared II Cell Membrane-Disrupting Nanoflakes via Detained Dendritic Cells. ACS NANO 2024; 18:18712-18728. [PMID: 38952208 PMCID: PMC11256899 DOI: 10.1021/acsnano.4c06183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024]
Abstract
Immunotherapy can potentially suppress the highly aggressive glioblastoma (GBM) by promoting T lymphocyte infiltration. Nevertheless, the immune privilege phenomenon, coupled with the generally low immunogenicity of vaccines, frequently hampers the presence of lymphocytes within brain tumors, particularly in brain tumors. In this study, the membrane-disrupted polymer-wrapped CuS nanoflakes that can penetrate delivery to deep brain tumors via releasing the cell-cell interactions, facilitating the near-infrared II (NIR II) photothermal therapy, and detaining dendritic cells for a self-cascading immunotherapy are developed. By convection-enhanced delivery, membrane-disrupted amphiphilic polymer micelles (poly(methoxypoly(ethylene glycol)-benzoic imine-octadecane, mPEG-b-C18) with CuS nanoflakes enhances tumor permeability and resides in deep brain tumors. Under low-power NIR II irradiation (0.8 W/cm2), the intense heat generated by well-distributed CuS nanoflakes actuates the thermolytic efficacy, facilitating cell apoptosis and the subsequent antigen release. Then, the positively charged polymer after hydrolysis of the benzoic-imine bond serves as an antigen depot, detaining autologous tumor-associated antigens and presenting them to dendritic cells, ensuring sustained immune stimulation. This self-cascading penetrative immunotherapy amplifies the immune response to postoperative brain tumors but also enhances survival outcomes through effective brain immunotherapy.
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Affiliation(s)
- Bhanu
Nirosha Yalamandala
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Yu-Jen Chen
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Ya-Hui Lin
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
- Brain
Research Center, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Thi My Hue Huynh
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Wen-Hsuan Chiang
- Department
of Chemical Engineering, National Chung
Hsing University, Taichung 402, Taiwan
| | - Tsu-Chin Chou
- Institute
of Analytical and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Heng-Wei Liu
- Department
of Neurosurgery, Shuang Ho Hospital, Taipei
Medical University, New Taipei
City 23561, Taiwan
- Taipei Neuroscience
Institute, Taipei Medical University, Taipei 11031, Taiwan
- Department
of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Chieh-Cheng Huang
- Institute
of Biomedical Engineering, National Tsing
Hua University, Hsinchu 300044, Taiwan
| | - Yu-Jen Lu
- Department
of Neurosurgery, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan 33305, Taiwan
- College
of Medicine, Chang Gung University, Kwei-San, Taoyuan 33302, Taiwan
| | - Chi-Shiun Chiang
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Li-An Chu
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
- Brain
Research Center, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Shang-Hsiu Hu
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
- Institute
of Analytical and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
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131
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Di Mauro F, Arbore G. Spatial Dissection of the Immune Landscape of Solid Tumors to Advance Precision Medicine. Cancer Immunol Res 2024; 12:800-813. [PMID: 38657223 PMCID: PMC11217735 DOI: 10.1158/2326-6066.cir-23-0699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Chemotherapeutics, radiation, targeted therapeutics, and immunotherapeutics each demonstrate clinical benefits for a small subset of patients with solid malignancies. Immune cells infiltrating the tumor and the surrounding stroma play a critical role in shaping cancer progression and modulating therapy response. They do this by interacting with the other cellular and molecular components of the tumor microenvironment. Spatial multi-omics technologies are rapidly evolving. Currently, such technologies allow high-throughput RNA and protein profiling and retain geographical information about the tumor microenvironment cellular architecture and the functional phenotype of tumor, immune, and stromal cells. An in-depth spatial characterization of the heterogeneous tumor immune landscape can improve not only the prognosis but also the prediction of therapy response, directing cancer patients to more tailored and efficacious treatments. This review highlights recent advancements in spatial transcriptomics and proteomics profiling technologies and the ways these technologies are being applied for the dissection of the immune cell composition in solid malignancies in order to further both basic research in oncology and the implementation of precision treatments in the clinic.
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Affiliation(s)
- Francesco Di Mauro
- Vita-Salute San Raffaele University, Milan, Italy.
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Giuseppina Arbore
- Vita-Salute San Raffaele University, Milan, Italy.
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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132
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Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR, Ma Z. Integration of spatial and single-cell data across modalities with weakly linked features. Nat Biotechnol 2024; 42:1096-1106. [PMID: 37679544 PMCID: PMC11638971 DOI: 10.1038/s41587-023-01935-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integration methods, the feasibility of cross-modal integration relies on the existence of highly correlated, a priori 'linked' features. We describe matching X-modality via fuzzy smoothed embedding (MaxFuse), a cross-modal data integration method that, through iterative coembedding, data smoothing and cell matching, uses all information in each modality to obtain high-quality integration even when features are weakly linked. MaxFuse is modality-agnostic and demonstrates high robustness and accuracy in the weak linkage scenario, achieving 20~70% relative improvement over existing methods under key evaluation metrics on benchmarking datasets. A prototypical example of weak linkage is the integration of spatial proteomic data with single-cell sequencing data. On two example analyses of this type, MaxFuse enabled the spatial consolidation of proteomic, transcriptomic and epigenomic information at single-cell resolution on the same tissue section.
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Affiliation(s)
- Shuxiao Chen
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Bokai Zhu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sijia Huang
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - John W Hickey
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kevin Z Lin
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Nancy R Zhang
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA.
| | - Zongming Ma
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA.
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133
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Villa G, Delev D, Heiland DH. Mapping myeloid cell function: Spatial diversity in tumor and neuronal microenvironment. Cancer Cell 2024; 42:934-936. [PMID: 38861929 DOI: 10.1016/j.ccell.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
In this issue of Cancer Cell, Zhong et al. explore the dual role of TREM2 in glioblastoma-associated myeloid cells, demonstrating its function in promoting inflammation at the tumor-neural interface and suppression within the tumor core, influenced by the local microenvironment. These findings open up promising prospects for advancements in neuro-oncological immunotherapy.
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Affiliation(s)
- Giulia Villa
- Department of Translational Neurosurgery, Alexander-Friedrich-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Daniel Delev
- Department of Neurosurgery, University Hospital Erlangen, Friedrich-Alexander University, Erlangen Nürnberg, Erlangen, Germany
| | - Dieter Henrik Heiland
- Department of Translational Neurosurgery, Alexander-Friedrich-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Neurosurgery, University Hospital Erlangen, Friedrich-Alexander University, Erlangen Nürnberg, Erlangen, Germany; Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany; Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany.
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134
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Steiner D, Sultan L, Sullivan T, Liu H, Zhang S, LeClerc A, Alekseyev YO, Liu G, Mazzilli SA, Zhang J, Rieger-Christ K, Burks EJ, Beane J, Lenburg ME. Identification of a gene expression signature of vascular invasion and recurrence in stage I lung adenocarcinoma via bulk and spatial transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597993. [PMID: 38915565 PMCID: PMC11195124 DOI: 10.1101/2024.06.07.597993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Microscopic vascular invasion (VI) is predictive of recurrence and benefit from lobectomy in stage I lung adenocarcinoma (LUAD) but is difficult to assess in resection specimens and cannot be accurately predicted prior to surgery. Thus, new biomarkers are needed to identify this aggressive subset of stage I LUAD tumors. To assess molecular and microenvironment features associated with angioinvasive LUAD we profiled 162 resected stage I tumors with and without VI by RNA-seq and explored spatial patterns of gene expression in a subset of 15 samples by high-resolution spatial transcriptomics (stRNA-seq). Despite the small size of invaded blood vessels, we identified a gene expression signature of VI from the bulk RNA-seq discovery cohort (n=103) and found that it was associated with VI foci, desmoplastic stroma, and high-grade patterns in our stRNA-seq data. We observed a stronger association with high-grade patterns from VI+ compared with VI- tumors. Using the discovery cohort, we developed a transcriptomic predictor of VI, that in an independent validation cohort (n=60) was associated with VI (AUROC=0.86; p=5.42×10-6) and predictive of recurrence-free survival (HR=1.98; p=0.024), even in VI- LUAD (HR=2.76; p=0.003). To determine our VI predictor's robustness to intra-tumor heterogeneity we used RNA-seq data from multi-region sampling of stage I LUAD cases in TRACERx, where the predictor scores showed high correlation (R=0.87, p<2.2×10-16) between two randomly sampled regions of the same tumor. Our study suggests that VI-associated gene expression changes are detectable beyond the site of intravasation and can be used to predict the presence of VI. This may enable the prediction of angioinvasive LUAD from biopsy specimens, allowing for more tailored medical and surgical management of stage I LUAD.
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Affiliation(s)
- Dylan Steiner
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Lila Sultan
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Travis Sullivan
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA, USA
| | - Hanqiao Liu
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Sherry Zhang
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Ashley LeClerc
- Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA
| | - Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Gang Liu
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Sarah A Mazzilli
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Jiarui Zhang
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Kimberly Rieger-Christ
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA, USA
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Jennifer Beane
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Marc E Lenburg
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA, Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
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135
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Cilento MA, Sweeney CJ, Butler LM. Spatial transcriptomics in cancer research and potential clinical impact: a narrative review. J Cancer Res Clin Oncol 2024; 150:296. [PMID: 38850363 PMCID: PMC11162383 DOI: 10.1007/s00432-024-05816-0] [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: 03/19/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024]
Abstract
Spatial transcriptomics (ST) provides novel insights into the tumor microenvironment (TME). ST allows the quantification and illustration of gene expression profiles in the spatial context of tissues, including both the cancer cells and the microenvironment in which they are found. In cancer research, ST has already provided novel insights into cancer metastasis, prognosis, and immunotherapy responsiveness. The clinical precision oncology application of next-generation sequencing (NGS) and RNA profiling of tumors relies on bulk methods that lack spatial context. The ability to preserve spatial information is now possible, as it allows us to capture tumor heterogeneity and multifocality. In this narrative review, we summarize precision oncology, discuss tumor sequencing in the clinic, and review the available ST research methods, including seqFISH, MERFISH (Vizgen), CosMx SMI (NanoString), Xenium (10x), Visium (10x), Stereo-seq (STOmics), and GeoMx DSP (NanoString). We then review the current ST literature with a focus on solid tumors organized by tumor type. Finally, we conclude by addressing an important question: how will spatial transcriptomics ultimately help patients with cancer?
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Affiliation(s)
- Michael A Cilento
- South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia.
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
- The Queen Elizabeth Hospital, Woodville South, SA, Australia.
| | - Christopher J Sweeney
- South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Lisa M Butler
- South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
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136
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Lucas CHG, Mirchia K, Seo K, Najem H, Chen WC, Zakimi N, Foster K, Eaton CD, Cady MA, Choudhury A, Liu SJ, Phillips JJ, Magill ST, Horbinski CM, Solomon DA, Perry A, Vasudevan HN, Heimberger AB, Raleigh DR. Spatial genomic, biochemical and cellular mechanisms underlying meningioma heterogeneity and evolution. Nat Genet 2024; 56:1121-1133. [PMID: 38760638 PMCID: PMC11239374 DOI: 10.1038/s41588-024-01747-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 04/08/2024] [Indexed: 05/19/2024]
Abstract
Intratumor heterogeneity underlies cancer evolution and treatment resistance, but targetable mechanisms driving intratumor heterogeneity are poorly understood. Meningiomas are the most common primary intracranial tumors and are resistant to all medical therapies, and high-grade meningiomas have significant intratumor heterogeneity. Here we use spatial approaches to identify genomic, biochemical and cellular mechanisms linking intratumor heterogeneity to the molecular, temporal and spatial evolution of high-grade meningiomas. We show that divergent intratumor gene and protein expression programs distinguish high-grade meningiomas that are otherwise grouped together by current classification systems. Analyses of matched pairs of primary and recurrent meningiomas reveal spatial expansion of subclonal copy number variants associated with treatment resistance. Multiplexed sequential immunofluorescence and deconvolution of meningioma spatial transcriptomes using cell types from single-cell RNA sequencing show decreased immune infiltration, decreased MAPK signaling, increased PI3K-AKT signaling and increased cell proliferation, which are associated with meningioma recurrence. To translate these findings to preclinical models, we use CRISPR interference and lineage tracing approaches to identify combination therapies that target intratumor heterogeneity in meningioma cell co-cultures.
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Affiliation(s)
- Calixto-Hope G Lucas
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
| | - Kanish Mirchia
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Kyounghee Seo
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Hinda Najem
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - William C Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Naomi Zakimi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Kyla Foster
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Charlotte D Eaton
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Martha A Cady
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Abrar Choudhury
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - S John Liu
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Stephen T Magill
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Craig M Horbinski
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University, Chicago, IL, USA
| | - David A Solomon
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Amy B Heimberger
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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137
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Nasir-Moin M, Wadiura LI, Sacalean V, Juros D, Movahed-Ezazi M, Lock EK, Smith A, Lee M, Weiss H, Müther M, Alber D, Ratna S, Fang C, Suero-Molina E, Hellwig S, Stummer W, Rössler K, Hainfellner JA, Widhalm G, Kiesel B, Reichert D, Mischkulnig M, Jain R, Straehle J, Neidert N, Schnell O, Beck J, Trautman J, Pastore S, Pacione D, Placantonakis D, Oermann EK, Golfinos JG, Hollon TC, Snuderl M, Freudiger CW, Heiland DH, Orringer DA. Localization of protoporphyrin IX during glioma-resection surgery via paired stimulated Raman histology and fluorescence microscopy. Nat Biomed Eng 2024; 8:672-688. [PMID: 38987630 DOI: 10.1038/s41551-024-01217-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/20/2024] [Indexed: 07/12/2024]
Abstract
The most widely used fluorophore in glioma-resection surgery, 5-aminolevulinic acid (5-ALA), is thought to cause the selective accumulation of fluorescent protoporphyrin IX (PpIX) in tumour cells. Here we show that the clinical detection of PpIX can be improved via a microscope that performs paired stimulated Raman histology and two-photon excitation fluorescence microscopy (TPEF). We validated the technique in fresh tumour specimens from 115 patients with high-grade gliomas across four medical institutions. We found a weak negative correlation between tissue cellularity and the fluorescence intensity of PpIX across all imaged specimens. Semi-supervised clustering of the TPEF images revealed five distinct patterns of PpIX fluorescence, and spatial transcriptomic analyses of the imaged tissue showed that myeloid cells predominate in areas where PpIX accumulates in the intracellular space. Further analysis of external spatially resolved metabolomics, transcriptomics and RNA-sequencing datasets from glioblastoma specimens confirmed that myeloid cells preferentially accumulate and metabolize PpIX. Our findings question 5-ALA-induced fluorescence in glioma cells and show how 5-ALA and TPEF imaging can provide a window into the immune microenvironment of gliomas.
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Affiliation(s)
- Mustafa Nasir-Moin
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Vlad Sacalean
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center - University of Freiburg, Freiburg, Germany
| | - Devin Juros
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Emily K Lock
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Andrew Smith
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Matthew Lee
- Department of Radiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Hannah Weiss
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Michael Müther
- Department of Neurosurgery, Münster University Hospital, Münster, Germany
| | - Daniel Alber
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Camila Fang
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Eric Suero-Molina
- Department of Neurosurgery, Münster University Hospital, Münster, Germany
| | - Sönke Hellwig
- Department of Neurosurgery, Münster University Hospital, Münster, Germany
| | - Walter Stummer
- Department of Neurosurgery, Münster University Hospital, Münster, Germany
| | - Karl Rössler
- Department of Neurosurgery, Medical University Vienna, Vienna, Austria
| | - Johannes A Hainfellner
- Division of Neuropathology and Neurochemistry (Obersteiner Institute), Department of Neurology, Medical University Vienna, Vienna, Austria
| | - Georg Widhalm
- Department of Neurosurgery, Medical University Vienna, Vienna, Austria
| | - Barbara Kiesel
- Department of Neurosurgery, Medical University Vienna, Vienna, Austria
| | - David Reichert
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Mario Mischkulnig
- Department of Neurosurgery, Medical University Vienna, Vienna, Austria
| | - Rajan Jain
- Department of Radiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jakob Straehle
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Berta-Ottenstein Clinician Scientist Program, Faculty of Medicine, University Freiburg, Freiburg, Germany
| | - Nicolas Neidert
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Berta-Ottenstein Clinician Scientist Program, Faculty of Medicine, University Freiburg, Freiburg, Germany
| | - Oliver Schnell
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Translational NeuroOncology Research Group, Medical Center - University of Freiburg, Freiburg, Germany
| | - Jürgen Beck
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for NeuroModulation (NeuroModul), University of Freiburg, Freiburg, Germany
| | | | | | - Donato Pacione
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Eric Karl Oermann
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA
- Center for Data Science, New York University, New York, USA
| | - John G Golfinos
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Todd C Hollon
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Dieter Henrik Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Microenvironment and Immunology Research Laboratory, Medical Center - University of Freiburg, Freiburg, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center - University of Freiburg, Freiburg, Germany.
- German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany.
| | - Daniel A Orringer
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.
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138
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Iwahashi N, Umakoshi H, Fujita M, Fukumoto T, Ogasawara T, Yokomoto-Umakoshi M, Kaneko H, Nakao H, Kawamura N, Uchida N, Matsuda Y, Sakamoto R, Seki M, Suzuki Y, Nakatani K, Izumi Y, Bamba T, Oda Y, Ogawa Y. Single-cell and spatial transcriptomics analysis of human adrenal aging. Mol Metab 2024; 84:101954. [PMID: 38718896 PMCID: PMC11101872 DOI: 10.1016/j.molmet.2024.101954] [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] [Revised: 03/30/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
OBJECTIVE The human adrenal cortex comprises three functionally and structurally distinct layers that produce layer-specific steroid hormones. With aging, the human adrenal cortex undergoes functional and structural alteration or "adrenal aging", leading to the unbalanced production of steroid hormones. Given the marked species differences in adrenal biology, the underlying mechanisms of human adrenal aging have not been sufficiently studied. This study was designed to elucidate the mechanisms linking the functional and structural alterations of the human adrenal cortex. METHODS We conducted single-cell RNA sequencing and spatial transcriptomics analysis of the aged human adrenal cortex. RESULTS The data of this study suggest that the layer-specific alterations of multiple signaling pathways underlie the abnormal layered structure and layer-specific changes in steroidogenic cells. We also highlighted that macrophages mediate age-related adrenocortical cell inflammation and senescence. CONCLUSIONS This study is the first detailed analysis of the aged human adrenal cortex at single-cell resolution and helps to elucidate the mechanism of human adrenal aging, thereby leading to a better understanding of the pathophysiology of age-related disorders associated with adrenal aging.
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Affiliation(s)
- Norifusa Iwahashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hironobu Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Masamichi Fujita
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tazuru Fukumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuki Ogasawara
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Maki Yokomoto-Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Kaneko
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Nakao
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Namiko Kawamura
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naohiro Uchida
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yayoi Matsuda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryuichi Sakamoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kohta Nakatani
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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139
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Hu H, Wang C, Tao R, Liu B, Peng D, Chen Y, Zhang W. Evidences of neurological injury caused by COVID-19 from glioma tissues and glioma organoids. CNS Neurosci Ther 2024; 30:e14822. [PMID: 38923860 PMCID: PMC11199819 DOI: 10.1111/cns.14822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
INTRODUCTION Despite the extensive neurological symptoms induced by COVID-19 and the identification of SARS-CoV-2 in post-mortem brain samples from COVID-19 patients months after death, the precise mechanisms of SARS-CoV-2 invasion into the central nervous system remain unclear due to the lack of research models. METHODS We collected glioma tissue samples from glioma patients who had a recent history of COVID-19 and examined the presence of the SARS-CoV-2 spike protein. Subsequently, spatial transcriptomic analyses were conducted on normal brain tissues, glioma tissues, and glioma tissues from glioma patients with recent COVID-19 history. Additionally, single-cell sequencing data from both glioma tissues and glioma organoids were collected and analyzed. Glioma organoids were utilized to evaluate the efficacy of potential COVID-19 blocking agents. RESULTS Glioma tissues from glioma patients with recent COVID-19 history exhibited the presence of the SARS-CoV-2 spike protein. Differences between glioma tissues from glioma patients who had a recent history of COVID-19 and healthy brain tissues primarily manifested in neuronal cells. Notably, neuronal cells within glioma tissues of COVID-19 history demonstrated heightened susceptibility to Alzheimer's disease, depression, and synaptic dysfunction, indicative of neuronal aberrations. Expressions of SARS-CoV-2 entry factors were confirmed in both glioma tissues and glioma organoids. Moreover, glioma organoids were susceptible to pseudo-SARS-CoV-2 infection and the infections could be partly blocked by the potential COVID-19 drugs. CONCLUSIONS Gliomas had inherent traits that render them susceptible to SARS-CoV-2 infection, leading to their representability of COVID-19 neurological symptoms. This established a biological foundation for the rationality and feasibility of utilization of glioma organoids as research and blocking drug testing model in SARS-CoV-2 infection within the central nervous system.
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Affiliation(s)
- Huimin Hu
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Chen Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Rui Tao
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Bohan Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Dazhao Peng
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Yankun Chen
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Wei Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
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Matchett KP, Wilson-Kanamori JR, Portman JR, Kapourani CA, Fercoq F, May S, Zajdel E, Beltran M, Sutherland EF, Mackey JBG, Brice M, Wilson GC, Wallace SJ, Kitto L, Younger NT, Dobie R, Mole DJ, Oniscu GC, Wigmore SJ, Ramachandran P, Vallejos CA, Carragher NO, Saeidinejad MM, Quaglia A, Jalan R, Simpson KJ, Kendall TJ, Rule JA, Lee WM, Hoare M, Weston CJ, Marioni JC, Teichmann SA, Bird TG, Carlin LM, Henderson NC. Multimodal decoding of human liver regeneration. Nature 2024; 630:158-165. [PMID: 38693268 PMCID: PMC11153152 DOI: 10.1038/s41586-024-07376-2] [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: 02/08/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
The liver has a unique ability to regenerate1,2; however, in the setting of acute liver failure (ALF), this regenerative capacity is often overwhelmed, leaving emergency liver transplantation as the only curative option3-5. Here, to advance understanding of human liver regeneration, we use paired single-nucleus RNA sequencing combined with spatial profiling of healthy and ALF explant human livers to generate a single-cell, pan-lineage atlas of human liver regeneration. We uncover a novel ANXA2+ migratory hepatocyte subpopulation, which emerges during human liver regeneration, and a corollary subpopulation in a mouse model of acetaminophen (APAP)-induced liver regeneration. Interrogation of necrotic wound closure and hepatocyte proliferation across multiple timepoints following APAP-induced liver injury in mice demonstrates that wound closure precedes hepatocyte proliferation. Four-dimensional intravital imaging of APAP-induced mouse liver injury identifies motile hepatocytes at the edge of the necrotic area, enabling collective migration of the hepatocyte sheet to effect wound closure. Depletion of hepatocyte ANXA2 reduces hepatocyte growth factor-induced human and mouse hepatocyte migration in vitro, and abrogates necrotic wound closure following APAP-induced mouse liver injury. Together, our work dissects unanticipated aspects of liver regeneration, demonstrating an uncoupling of wound closure and hepatocyte proliferation and uncovering a novel migratory hepatocyte subpopulation that mediates wound closure following liver injury. Therapies designed to promote rapid reconstitution of normal hepatic microarchitecture and reparation of the gut-liver barrier may advance new areas of therapeutic discovery in regenerative medicine.
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Affiliation(s)
- K P Matchett
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J R Wilson-Kanamori
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J R Portman
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - C A Kapourani
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - F Fercoq
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - S May
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - E Zajdel
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - M Beltran
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - E F Sutherland
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J B G Mackey
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - M Brice
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - G C Wilson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - S J Wallace
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - L Kitto
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - N T Younger
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - R Dobie
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - D J Mole
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- University Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - G C Oniscu
- Edinburgh Transplant Centre, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Transplant Surgery, CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - S J Wigmore
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- University Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - P Ramachandran
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - C A Vallejos
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- The Alan Turing Institute, London, UK
| | - N O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - M M Saeidinejad
- Institute for Liver and Digestive Health, University College London, London, UK
| | - A Quaglia
- Department of Cellular Pathology, Royal Free London NHS Foundation Trust, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - R Jalan
- Institute for Liver and Digestive Health, University College London, London, UK
- European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain
| | - K J Simpson
- Department of Hepatology, University of Edinburgh and Scottish Liver Transplant Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - T J Kendall
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J A Rule
- Department of Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - W M Lee
- Department of Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - M Hoare
- Early Cancer Institute, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - C J Weston
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - J C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, UK
| | - S A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, UK
- Department of Physics, Cavendish Laboratory, Cambridge, UK
| | - T G Bird
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - L M Carlin
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - N C Henderson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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141
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Zhang L, Xiong Z, Xiao M. A Review of the Application of Spatial Transcriptomics in Neuroscience. Interdiscip Sci 2024; 16:243-260. [PMID: 38374297 DOI: 10.1007/s12539-024-00603-4] [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: 10/10/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Since spatial transcriptomics can locate and distinguish the gene expression of functional genes in special regions and tissue, it is important for us to investigate the brain development, the development mechanism of brain diseases, and the relationship between brain structure and function in Neuroscience (or Brain science). While previous studies have introduced the crucial spatial transcriptomic techniques and data analysis methods, there are few studies to comprehensively overview the key methods, data resources, and technological applications of spatial transcriptomics in Neuroscience. For these reasons, we first investigate several common spatial transcriptomic data analysis approaches and data resources. Second, we introduce the applications of the spatial transcriptomic data analysis approaches in Neuroscience. Third, we summarize the integrating spatial transcriptomics with other technologies in Neuroscience. Finally, we discuss the challenges and future research directions of spatial transcriptomics in Neuroscience.
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Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Zhenqi Xiong
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Ming Xiao
- College of Computer Science, Sichuan University, Chengdu, 610065, China.
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142
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Drexler R, Khatri R, Sauvigny T, Mohme M, Maire CL, Ryba A, Zghaibeh Y, Dührsen L, Salviano-Silva A, Lamszus K, Westphal M, Gempt J, Wefers AK, Neumann JE, Bode H, Hausmann F, Huber TB, Bonn S, Jütten K, Delev D, Weber KJ, Harter PN, Onken J, Vajkoczy P, Capper D, Wiestler B, Weller M, Snijder B, Buck A, Weiss T, Göller PC, Sahm F, Menstel JA, Zimmer DN, Keough MB, Ni L, Monje M, Silverbush D, Hovestadt V, Suvà ML, Krishna S, Hervey-Jumper SL, Schüller U, Heiland DH, Hänzelmann S, Ricklefs FL. A prognostic neural epigenetic signature in high-grade glioma. Nat Med 2024; 30:1622-1635. [PMID: 38760585 PMCID: PMC11186787 DOI: 10.1038/s41591-024-02969-w] [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: 08/07/2023] [Accepted: 04/03/2024] [Indexed: 05/19/2024]
Abstract
Neural-tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is limited. We present an epigenetically defined neural signature of glioblastoma that independently predicts patients' survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals a high abundance of malignant stemcell-like cells in high-neural glioblastoma, primarily of the neural lineage. These cells are further classified as neural-progenitor-cell-like, astrocyte-like and oligodendrocyte-progenitor-like, alongside oligodendrocytes and excitatory neurons. In line with these findings, high-neural glioblastoma cells engender neuron-to-glioma synapse formation in vitro and in vivo and show an unfavorable survival after xenografting. In patients, a high-neural signature is associated with decreased overall and progression-free survival. High-neural tumors also exhibit increased functional connectivity in magnetencephalography and resting-state magnet resonance imaging and can be detected via DNA analytes and brain-derived neurotrophic factor in patients' plasma. The prognostic importance of the neural signature was further validated in patients diagnosed with diffuse midline glioma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant. High-neural gliomas likely require a maximized surgical resection approach for improved outcomes.
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Affiliation(s)
- Richard Drexler
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Sauvigny
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cecile L Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alice Ryba
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yahya Zghaibeh
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Amanda Salviano-Silva
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jens Gempt
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia E Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology Hamburg (ZMNH), University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Helena Bode
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Jütten
- Department of Neurosurgery, University Hospital Aachen, Aachen, Germany
| | - Daniel Delev
- Department of Neurosurgery, University Hospital Aachen, Aachen, Germany
- Department of Neurosurgery, University Clinic Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Katharina J Weber
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
- University Cancer Center (UCT) Frankfurt, Frankfurt am Main, Germany
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- Institute of Neuropathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Julia Onken
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Benedikt Wiestler
- Department of Neuroradiology, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Munich, Germany
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zürich, Zurich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Alicia Buck
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zürich, Zurich, Switzerland
| | - Tobias Weiss
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zürich, Zurich, Switzerland
| | - Pauline C Göller
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Joelle Aline Menstel
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | - David Niklas Zimmer
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | | | - Lijun Ni
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Michelle Monje
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Dana Silverbush
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Saritha Krishna
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, Research Institute Children's Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, University Clinic Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
- Translational Neurosurgery, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Wu Q, Berglund AE, Macaulay RJ, Etame AB. The Role of Mesenchymal Reprogramming in Malignant Clonal Evolution and Intra-Tumoral Heterogeneity in Glioblastoma. Cells 2024; 13:942. [PMID: 38891074 PMCID: PMC11171993 DOI: 10.3390/cells13110942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Glioblastoma (GBM) is the most common yet uniformly fatal adult brain cancer. Intra-tumoral molecular and cellular heterogeneities are major contributory factors to therapeutic refractoriness and futility in GBM. Molecular heterogeneity is represented through molecular subtype clusters whereby the proneural (PN) subtype is associated with significantly increased long-term survival compared to the highly resistant mesenchymal (MES) subtype. Furthermore, it is universally recognized that a small subset of GBM cells known as GBM stem cells (GSCs) serve as reservoirs for tumor recurrence and progression. The clonal evolution of GSC molecular subtypes in response to therapy drives intra-tumoral heterogeneity and remains a critical determinant of GBM outcomes. In particular, the intra-tumoral MES reprogramming of GSCs using current GBM therapies has emerged as a leading hypothesis for therapeutic refractoriness. Preventing the intra-tumoral divergent evolution of GBM toward the MES subtype via new treatments would dramatically improve long-term survival for GBM patients and have a significant impact on GBM outcomes. In this review, we examine the challenges of the role of MES reprogramming in the malignant clonal evolution of glioblastoma and provide future perspectives for addressing the unmet therapeutic need to overcome resistance in GBM.
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Affiliation(s)
- Qiong Wu
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Anders E. Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Robert J. Macaulay
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Arnold B. Etame
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
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144
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Faisal SM, Ravi VM, Miska JM. Editorial: Spatiotemporal heterogeneity in CNS tumors. Front Immunol 2024; 15:1430227. [PMID: 38868775 PMCID: PMC11167105 DOI: 10.3389/fimmu.2024.1430227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Affiliation(s)
- Syed M. Faisal
- Department of Pediatrics, Division of Hematology/Oncology, Children’s Mercy Research Institute, Kansas City, MO, United States
| | - Vidhya M. Ravi
- Department of Neurosurgery, Medical Center – University of Freiburg, Freiburg, Germany
| | - Jason M. Miska
- Lou and Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, United States
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Dong M, Zhang X, Peng P, Chen Z, Zhang Y, Wan L, Xiang W, Liu G, Guo Y, Xiao Q, Wang B, Guo D, Zhu M, Yu X, Wan F. Hypoxia-induced TREM1 promotes mesenchymal-like states of glioma stem cells via alternatively activating tumor-associated macrophages. Cancer Lett 2024; 590:216801. [PMID: 38479552 DOI: 10.1016/j.canlet.2024.216801] [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: 10/17/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/19/2024]
Abstract
The mesenchymal subtype of glioblastoma (GBM) cells characterized by aggressive invasion and therapeutic resistance is thought to be dependent on cell-intrinsic alteration and extrinsic cellular crosstalk. Tumor-associated macrophages (TAMs) are pivotal in tumor progression, chemo-resistance, angiogenesis, and stemness maintenance. However, the impact of TAMs on the shifts in glioma stem cells (GSCs) states remains largely uncovered. Herein, we showed that the triggering receptor expressed on myeloid cells-1 (TREM1) preferentially expressed by M2-like TAMs and induced GSCs into mesenchymal-like states by modulating the secretion of TGFβ2, which activated the TGFβR/SMAD2/3 signaling in GSCs. Furthermore, we demonstrated that TREM1 was transcriptionally regulated by HIF1a under the hypoxic environment and thus promoted an immunosuppressive type of TAMs via activating the TLR2/AKT/mTOR/c-MYC axis. Collectively, this study reveals that cellular communication between TAMs and GSCs through the TREM1-mediated TGFβ2/TGFβR axis is involved in the mesenchymal-like transitions of GSCs. Our study provides valuable insights into the regulatory mechanisms between the tumor immune microenvironment and the malignant characteristics of GBM, which can lead to potential novel strategies targeting TAMs for tumor control.
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Affiliation(s)
- Minhai Dong
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaolin Zhang
- Department of Neurosurgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Peng Peng
- Department of Neurosurgery, Xiangyang Central Hospital, Affiliated Hospital to Hubei University of Arts and Science, Xiangyang, 441021, China
| | - Zirong Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yang Zhang
- Department of Histology and Embryology, College of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lijun Wan
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wang Xiang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Guohao Liu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yang Guo
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qungen Xiao
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Baofeng Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dongsheng Guo
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Min Zhu
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Xingjiang Yu
- Department of Histology and Embryology, College of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Feng Wan
- Department of Neurosurgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
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146
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Onubogu U, Gatenbee CD, Prabhakaran S, Wolfe KL, Oakes B, Salatino R, Vaubel R, Szentirmai O, Anderson AR, Janiszewska M. Spatial analysis of recurrent glioblastoma reveals perivascular niche organization. JCI Insight 2024; 9:e179853. [PMID: 38805346 PMCID: PMC11383164 DOI: 10.1172/jci.insight.179853] [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: 05/30/2024] Open
Abstract
Tumor evolution is driven by genetic variation; however, it is the tumor microenvironment (TME) that provides the selective pressure contributing to evolution in cancer. Despite high histopathological heterogeneity within glioblastoma (GBM), the most aggressive brain tumor, the interactions between the genetically distinct GBM cells and the surrounding TME are not fully understood. To address this, we analyzed matched primary and recurrent GBM archival tumor tissues with imaging-based techniques aimed to simultaneously evaluate tumor tissues for the presence of hypoxic, angiogenic, and inflammatory niches, extracellular matrix (ECM) organization, TERT promoter mutational status, and several oncogenic amplifications on the same slide and location. We found that the relationships between genetic and TME diversity are different in primary and matched recurrent tumors. Interestingly, the texture of the ECM, identified by label-free reflectance imaging, was predictive of single-cell genetic traits present in the tissue. Moreover, reflectance of ECM revealed structured organization of the perivascular niche in recurrent GBM, enriched in immunosuppressive macrophages. Single-cell spatial transcriptomics further confirmed the presence of the niche-specific macrophage populations and identified interactions between endothelial cells, perivascular fibroblasts, and immunosuppressive macrophages. Our results underscore the importance of GBM tissue organization in tumor evolution and highlight genetic and spatial dependencies.
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Affiliation(s)
- Ugoma Onubogu
- The Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Chandler D Gatenbee
- Department of Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Sandhya Prabhakaran
- Department of Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Kelsey L Wolfe
- The Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Benjamin Oakes
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Roberto Salatino
- The Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Rachael Vaubel
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Oszkar Szentirmai
- Center for Neurological Surgery and Neuroscience, Cleveland Clinic Martin Health, Port St. Lucie, Florida, USA
| | - Alexander Ra Anderson
- Department of Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Michalina Janiszewska
- The Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
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147
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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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148
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Ospina OE, Soupir AC, Manjarres-Betancur R, Gonzalez-Calderon G, Yu X, Fridley BL. Differential gene expression analysis of spatial transcriptomic experiments using spatial mixed models. Sci Rep 2024; 14:10967. [PMID: 38744956 PMCID: PMC11094014 DOI: 10.1038/s41598-024-61758-0] [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: 02/01/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
Spatial transcriptomics (ST) assays represent a revolution in how the architecture of tissues is studied by allowing for the exploration of cells in their spatial context. A common element in the analysis is delineating tissue domains or "niches" followed by detecting differentially expressed genes to infer the biological identity of the tissue domains or cell types. However, many studies approach differential expression analysis by using statistical approaches often applied in the analysis of non-spatial scRNA data (e.g., two-sample t-tests, Wilcoxon's rank sum test), hence neglecting the spatial dependency observed in ST data. In this study, we show that applying linear mixed models with spatial correlation structures using spatial random effects effectively accounts for the spatial autocorrelation and reduces inflation of type-I error rate observed in non-spatial based differential expression testing. We also show that spatial linear models with an exponential correlation structure provide a better fit to the ST data as compared to non-spatial models, particularly for spatially resolved technologies that quantify expression at finer scales (i.e., single-cell resolution).
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Affiliation(s)
- Oscar E Ospina
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alex C Soupir
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | | | - Xiaoqing Yu
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
- Biostatistics and Epidemiology Core, Division of Health Services & Outcomes Research, Children's Mercy, Kansas City, MO, USA.
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149
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Wang W, Li T, Cheng Y, Li F, Qi S, Mao M, Wu J, Liu Q, Zhang X, Li X, Zhang L, Qi H, Yang L, Yang K, He Z, Ding S, Qin Z, Yang Y, Yang X, Luo C, Guo Y, Wang C, Liu X, Zhou L, Liu Y, Kong W, Miao J, Ye S, Luo M, An L, Wang L, Che L, Niu Q, Ma Q, Zhang X, Zhang Z, Hu R, Feng H, Ping YF, Bian XW, Shi Y. Identification of hypoxic macrophages in glioblastoma with therapeutic potential for vasculature normalization. Cancer Cell 2024; 42:815-832.e12. [PMID: 38640932 DOI: 10.1016/j.ccell.2024.03.013] [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: 08/01/2023] [Revised: 01/21/2024] [Accepted: 03/25/2024] [Indexed: 04/21/2024]
Abstract
Monocyte-derived tumor-associated macrophages (Mo-TAMs) intensively infiltrate diffuse gliomas with remarkable heterogeneity. Using single-cell transcriptomics, we chart a spatially resolved transcriptional landscape of Mo-TAMs across 51 patients with isocitrate dehydrogenase (IDH)-wild-type glioblastomas or IDH-mutant gliomas. We characterize a Mo-TAM subset that is localized to the peri-necrotic niche and skewed by hypoxic niche cues to acquire a hypoxia response signature. Hypoxia-TAM destabilizes endothelial adherens junctions by activating adrenomedullin paracrine signaling, thereby stimulating a hyperpermeable neovasculature that hampers drug delivery in glioblastoma xenografts. Accordingly, genetic ablation or pharmacological blockade of adrenomedullin produced by Hypoxia-TAM restores vascular integrity, improves intratumoral concentration of the anti-tumor agent dabrafenib, and achieves combinatorial therapeutic benefits. Increased proportion of Hypoxia-TAM or adrenomedullin expression is predictive of tumor vessel hyperpermeability and a worse prognosis of glioblastoma. Our findings highlight Mo-TAM diversity and spatial niche-steered Mo-TAM reprogramming in diffuse gliomas and indicate potential therapeutics targeting Hypoxia-TAM to normalize tumor vasculature.
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Affiliation(s)
- Wenying Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Tianran Li
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Yue Cheng
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Fei Li
- Department of Neurosurgery and Glioma Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Shuhong Qi
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P.R. China
| | - Min Mao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Jingjing Wu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Qing Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xiaoning Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xuegang Li
- Department of Neurosurgery and Glioma Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Lu Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Haoyue Qi
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Lan Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Kaidi Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Zhicheng He
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Shuaishuai Ding
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Zhongyi Qin
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China; Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Ying Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xi Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Chunhua Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Ying Guo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Chao Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xindong Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Lei Zhou
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Yuqi Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Weikai Kong
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Jingya Miao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Shuanghui Ye
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Min Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Lele An
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Lujing Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Linrong Che
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Qin Niu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Qinghua Ma
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xia Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Zhihong Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P.R. China
| | - Rong Hu
- Department of Neurosurgery and Glioma Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Hua Feng
- Department of Neurosurgery and Glioma Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Yi-Fang Ping
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China; Chongqing Advanced Pathology Research Institute, Jinfeng Laboratory, Chongqing 400039, P. R. China; Yu-Yue Scientific Research Center for Pathology, Jinfeng Laboratory, Chongqing 400039, P.R. China.
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China; Chongqing Advanced Pathology Research Institute, Jinfeng Laboratory, Chongqing 400039, P. R. China; Yu-Yue Scientific Research Center for Pathology, Jinfeng Laboratory, Chongqing 400039, P.R. China.
| | - Yu Shi
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China; Chongqing Advanced Pathology Research Institute, Jinfeng Laboratory, Chongqing 400039, P. R. China; Yu-Yue Scientific Research Center for Pathology, Jinfeng Laboratory, Chongqing 400039, P.R. China.
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150
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Greenwald AC, Darnell NG, Hoefflin R, Simkin D, Mount CW, Gonzalez Castro LN, Harnik Y, Dumont S, Hirsch D, Nomura M, Talpir T, Kedmi M, Goliand I, Medici G, Laffy J, Li B, Mangena V, Keren-Shaul H, Weller M, Addadi Y, Neidert MC, Suvà ML, Tirosh I. Integrative spatial analysis reveals a multi-layered organization of glioblastoma. Cell 2024; 187:2485-2501.e26. [PMID: 38653236 PMCID: PMC11088502 DOI: 10.1016/j.cell.2024.03.029] [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: 06/16/2023] [Revised: 01/11/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Glioma contains malignant cells in diverse states. Here, we combine spatial transcriptomics, spatial proteomics, and computational approaches to define glioma cellular states and uncover their organization. We find three prominent modes of organization. First, gliomas are composed of small local environments, each typically enriched with one major cellular state. Second, specific pairs of states preferentially reside in proximity across multiple scales. This pairing of states is consistent across tumors. Third, these pairwise interactions collectively define a global architecture composed of five layers. Hypoxia appears to drive the layers, as it is associated with a long-range organization that includes all cancer cell states. Accordingly, tumor regions distant from any hypoxic/necrotic foci and tumors that lack hypoxia such as low-grade IDH-mutant glioma are less organized. In summary, we provide a conceptual framework for the organization of cellular states in glioma, highlighting hypoxia as a long-range tissue organizer.
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Affiliation(s)
- Alissa C Greenwald
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Galili Darnell
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rouven Hoefflin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dor Simkin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Christopher W Mount
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - L Nicolas Gonzalez Castro
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sydney Dumont
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dana Hirsch
- Immunohistochemistry Unit, Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Masashi Nomura
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tom Talpir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Goliand
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Gioele Medici
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julie Laffy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Baoguo Li
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Vamsi Mangena
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hadas Keren-Shaul
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Weller
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Marian C Neidert
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Neurosurgery, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Mario L Suvà
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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