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Koh L, Novera W, Lim SW, Chong YK, Pang QY, Low D, Ang BT, Tang C. Integrative multi-omics approach to targeted therapy for glioblastoma. Pharmacol Res 2022; 182:106308. [PMID: 35714825 DOI: 10.1016/j.phrs.2022.106308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
This review describes recent technological advances applied to glioblastoma (GBM), a brain tumor with dismal prognosis. International consortial efforts suggest the presence of molecular subtypes within histologically identical GBM tumors. This emphasizes that future treatment decisions should no longer be made based solely on morphological analyses, but must now take into consideration such molecular and cellular heterogeneity. The use of single-cell technologies has advanced our understanding and assignation of functional subtypes revealing therapeutic vulnerabilities. Our team has developed stratification approaches in the past few years, and we have been able to identify patient cohorts enriched for various signaling pathways. Importantly, our Glioportal brain tumor resource has been established under the National Neuroscience Institute Tissue Bank in 2021. This resource offers preclinical capability to validate working hypotheses established from patient clinical datasets. This review highlights recent developments with the ultimate goal of assigning functional meaning to molecular subtypes, revealing therapeutic vulnerabilities.
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Affiliation(s)
- Lynnette Koh
- Department of Research, National Neuroscience Institute, Singapore.
| | - Wisna Novera
- Department of Research, National Neuroscience Institute, Singapore
| | - See Wee Lim
- Department of Research, National Neuroscience Institute, Singapore
| | - Yuk Kien Chong
- Department of Research, National Neuroscience Institute, Singapore
| | - Qing You Pang
- Department of Research, National Neuroscience Institute, Singapore
| | - David Low
- Department of Neurosurgery, National Neuroscience Institute, Singapore; Duke-National University of Singapore, Singapore
| | - Beng Ti Ang
- Department of Neurosurgery, National Neuroscience Institute, Singapore; Duke-National University of Singapore, Singapore
| | - Carol Tang
- Department of Research, National Neuroscience Institute, Singapore; Duke-National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore.
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Hu Y, Jiang Y, Behnan J, Ribeiro MM, Kalantzi C, Zhang MD, Lou D, Häring M, Sharma N, Okawa S, Del Sol A, Adameyko I, Svensson M, Persson O, Ernfors P. Neural network learning defines glioblastoma features to be of neural crest perivascular or radial glia lineages. SCIENCE ADVANCES 2022; 8:eabm6340. [PMID: 35675414 PMCID: PMC9177076 DOI: 10.1126/sciadv.abm6340] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Glioblastoma is believed to originate from nervous system cells; however, a putative origin from vessel-associated progenitor cells has not been considered. We deeply single-cell RNA-sequenced glioblastoma progenitor cells of 18 patients and integrated 710 bulk tumors and 73,495 glioma single cells of 100 patients to determine the relation of glioblastoma cells to normal brain cell types. A novel neural network-based projection of the developmental trajectory of normal brain cells uncovered two principal cell-lineage features of glioblastoma, neural crest perivascular and radial glia, carrying defining methylation patterns and survival differences. Consistently, introducing tumorigenic alterations in naïve human brain perivascular cells resulted in brain tumors. Thus, our results suggest that glioblastoma can arise from the brains' vasculature, and patients with such glioblastoma have a significantly poorer outcome.
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Affiliation(s)
- Yizhou Hu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yiwen Jiang
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jinan Behnan
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Mariana Messias Ribeiro
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Chrysoula Kalantzi
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ming-Dong Zhang
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Daohua Lou
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Häring
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nilesh Sharma
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Satoshi Okawa
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
- CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Igor Adameyko
- Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Svensson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Oscar Persson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Patrik Ernfors
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Corresponding author.
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Varn FS, Johnson KC, Martinek J, Huse JT, Nasrallah MP, Wesseling P, Cooper LAD, Malta TM, Wade TE, Sabedot TS, Brat D, Gould PV, Wöehrer A, Aldape K, Ismail A, Sivajothi SK, Barthel FP, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon HE, Pollock S, Goldfarb C, Lee GH, Garofano L, Anderson KJ, Nehar-Belaid D, Barnholtz-Sloan JS, Bakas S, Byrne AT, D'Angelo F, Gan HK, Khasraw M, Migliozzi S, Ormond DR, Paek SH, Van Meir EG, Walenkamp AME, Watts C, Weiss T, Weller M, Palucka K, Stead LF, Poisson LM, Noushmehr H, Iavarone A, Verhaak RGW. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell 2022; 185:2184-2199.e16. [PMID: 35649412 PMCID: PMC9189056 DOI: 10.1016/j.cell.2022.04.038] [Citation(s) in RCA: 158] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 01/22/2022] [Accepted: 04/28/2022] [Indexed: 12/21/2022]
Abstract
The factors driving therapy resistance in diffuse glioma remain poorly understood. To identify treatment-associated cellular and genetic changes, we analyzed RNA and/or DNA sequencing data from the temporally separated tumor pairs of 304 adult patients with isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant glioma. Tumors recurred in distinct manners that were dependent on IDH mutation status and attributable to changes in histological feature composition, somatic alterations, and microenvironment interactions. Hypermutation and acquired CDKN2A deletions were associated with an increase in proliferating neoplastic cells at recurrence in both glioma subtypes, reflecting active tumor growth. IDH-wild-type tumors were more invasive at recurrence, and their neoplastic cells exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. Mesenchymal transition was associated with the presence of a myeloid cell state defined by specific ligand-receptor interactions with neoplastic cells. Collectively, these recurrence-associated phenotypes represent potential targets to alter disease progression.
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Affiliation(s)
- Frederick S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jan Martinek
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jason T Huse
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - MacLean P Nasrallah
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pieter Wesseling
- Amsterdam University Medical Centers/VUmc, Amsterdam, the Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Lee A D Cooper
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tathiane M Malta
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Brazil, Ribeirao Preto, São Paulo, Brazil
| | - Taylor E Wade
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Thais S Sabedot
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Daniel Brat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Peter V Gould
- service d'anatomopathologie, Hôpital de l'Enfant-Jésus du Centre hospitalier universitaire de Québec, Université Laval, Quebec City, QC, Canada
| | - Adelheid Wöehrer
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | | | - Azzam Ismail
- Department of Cellular and Molecular Pathology, Leeds Teaching Hospital NHS Trust, St James's University Hospital, Leeds, UK
| | | | - Floris P Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Cancer and Cell Biology Division, the Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Biopharmaceutical Convergence, Department of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeong gi-do, South Korea
| | - Emre Kocakavuk
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Hematology and Stem Cell Transplantation, West German Cancer Center, University Hospital Essen, Essen, Germany
| | | | - Kieron White
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Indrani Datta
- Department of Public Health Sciences, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Hyo-Eun Moon
- Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | | | | | - Ga-Hyun Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Luciano Garofano
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Kevin J Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Jill S Barnholtz-Sloan
- Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH, USA; Center for Biomedical Informatics and Information Technology & Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Spyridon Bakas
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Annette T Byrne
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Fulvio D'Angelo
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Hui K Gan
- Olivia Newton-John Cancer Research Institute, Austin Health, Melbourne, Australia
| | - Mustafa Khasraw
- Preston Robert Tisch Brain Tumor Center at Duke, Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Simona Migliozzi
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - D Ryan Ormond
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sun Ha Paek
- Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | - Erwin G Van Meir
- Department of Neurosurgery, School of Medicine and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Annemiek M E Walenkamp
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | - Colin Watts
- Academic Department of Neurosurgery, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Tobias Weiss
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zürich, Switzerland
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zürich, Switzerland
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Laila M Poisson
- Department of Public Health Sciences, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Houtan Noushmehr
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA; Department of Neurology, Columbia University Medical Center, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Neurosurgery, Amsterdam University Medical Centers/VUmc, Amsterdam, the Netherlands.
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54
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Xiao Y, Wang Z, Zhao M, Deng Y, Yang M, Su G, Yang K, Qian C, Hu X, Liu Y, Geng L, Xiao Y, Zou Y, Tang X, Liu H, Xiao H, Fan R. Single-Cell Transcriptomics Revealed Subtype-Specific Tumor Immune Microenvironments in Human Glioblastomas. Front Immunol 2022; 13:914236. [PMID: 35669791 PMCID: PMC9163377 DOI: 10.3389/fimmu.2022.914236] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
Human glioblastoma (GBM), the most aggressive brain tumor, comprises six major subtypes of malignant cells, giving rise to both inter-patient and intra-tumor heterogeneity. The interaction between different tumor subtypes and non-malignant cells to collectively shape a tumor microenvironment has not been systematically characterized. Herein, we sampled the cellular milieu of surgically resected primary tumors from 7 GBM patients using single-cell transcriptome sequencing. A lineage relationship analysis revealed that a neural-progenitor-2-like (NPC2-like) state with high metabolic activity was associated with the tumor cells of origin. Mesenchymal-1-like (MES1-like) and mesenchymal-2-like (MES2-like) tumor cells correlated strongly with immune infiltration and chronic hypoxia niche responses. We identified four subsets of tumor-associated macrophages/microglia (TAMs), among which TAM-1 co-opted both acute and chronic hypoxia-response signatures, implicated in tumor angiogenesis, invasion, and poor prognosis. MES-like GBM cells expressed the highest number of M2-promoting ligands compared to other cellular states while all six states were associated with TAM M2-type polarization and immunosuppression via a set of 10 ligand–receptor signaling pathways. Our results provide new insights into the differential roles of GBM cell subtypes in the tumor immune microenvironment that may be deployed for patient stratification and personalized treatment.
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Affiliation(s)
- Yong Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Zhen Wang
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Mengjie Zhao
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Mingyu Yang
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Kun Yang
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Chunfa Qian
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Xinhua Hu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yong Liu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Liangyuan Geng
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yang Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Yuanjie Zou
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Xianglong Tang
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Hongyi Liu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- *Correspondence: Hongyi Liu, ; Hong Xiao, ; Rong Fan,
| | - Hong Xiao
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- *Correspondence: Hongyi Liu, ; Hong Xiao, ; Rong Fan,
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, United States
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, United States
- *Correspondence: Hongyi Liu, ; Hong Xiao, ; Rong Fan,
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55
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Yuan F, Cai X, Cong Z, Wang Y, Geng Y, Aili Y, Du C, Zhu J, Yang J, Tang C, Zhang A, Zhao S, Ma C. Roles of the m 6A Modification of RNA in the Glioblastoma Microenvironment as Revealed by Single-Cell Analyses. Front Immunol 2022; 13:798583. [PMID: 35558067 PMCID: PMC9086907 DOI: 10.3389/fimmu.2022.798583] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
Purpose Glioblastoma multiforme (GBM) is a common and aggressive form of brain tumor. The N6-methyladenosine (m6A) mRNA modification plays multiple roles in many biological processes and disease states. However, the relationship between m6A modifications and the tumor microenvironment in GBM remains unclear, especially at the single-cell level. Experimental Design Single-cell and bulk RNA-sequencing data were acquired from the GEO and TCGA databases, respectively. We used bioinformatics and statistical tools to analyze associations between m6A regulators and multiple factors. Results HNRNPA2B1 and HNRNPC were extensively expressed in the GBM microenvironment. m6A regulators promoted the stemness state in GBM cancer cells. Immune-related BP terms were enriched in modules of m6A-related genes. Cell communication analysis identified genes in the GALECTIN signaling network in GBM samples, and expression of these genes (LGALS9, CD44, CD45, and HAVCR2) correlated with that of m6A regulators. Validation experiments revealed that MDK in MK signaling network promoted migration and immunosuppressive polarization of macrophage. Expression of m6A regulators correlated with ICPs in GBM cancer cells, M2 macrophages and T/NK cells. Bulk RNA-seq analysis identified two expression patterns (low m6A/high ICP and high m6A/low ICP) with different predicted immune infiltration and responses to ICP inhibitors. A predictive nomogram model to distinguish these 2 clusters was constructed and validated with excellent performance. Conclusion At the single-cell level, m6A modification facilitates the stemness state in GBM cancer cells and promotes an immunosuppressive microenvironment through ICPs and the GALECTIN signaling pathway network. And we also identified two m6A-ICP expression patterns. These findings could lead to novel treatment strategies for GBM patients.
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Affiliation(s)
- Feng Yuan
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xiangming Cai
- School of Medicine, Southeast University, Nanjing, China
| | - Zixiang Cong
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yingshuai Wang
- Department of Internal Medicine III, University Hospital Munich, Ludwig Maximilians-University Munich, Munich, Germany
| | - Yuanming Geng
- Department of Neurosurgery, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China
| | - Yiliyaer Aili
- Department of Neurosurgery, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China
| | - Chaonan Du
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Junhao Zhu
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jin Yang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Chao Tang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Aifeng Zhang
- School of Medicine, Southeast University, Nanjing, China.,Department of Pathology, School of Medicine, Southeast University, Nanjing, China
| | - Sheng Zhao
- School of Medicine, Southeast University, Nanjing, China.,Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, Nanjing, China.,The Key Laboratory of Developmental Genes and Human Disease, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Chiyuan Ma
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,School of Medicine, Southeast University, Nanjing, China.,Department of Neurosurgery, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China.,Department of Neurosurgery, Jinling Hospital, Nanjing, China.,Department of Neurosurgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
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56
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Wei M, Yang R, Ye M, Zhan Y, Liu B, Meng L, Xie L, Du M, Wang J, Gao R, Chen D, Dong R, Dong K. MYBL2 accelerates epithelial-mesenchymal transition and hepatoblastoma metastasis via the Smad/SNAI1 pathway. Am J Cancer Res 2022; 12:1960-1981. [PMID: 35693071 PMCID: PMC9185624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 03/19/2022] [Indexed: 06/15/2023] Open
Abstract
Hepatoblastoma (HB) accounts for the majority of hepatic malignancies in children. Although the prognosis of patients with HB has improved in past decades, metastasis is an indicator of poor overall survival. Herein, we applied single-cell RNA sequencing to explore the transcriptomic profiling of 25,264 metastatic cells isolated from the lungs of two patients with HB. The transcriptomes uncovered the heterogeneity of malignant cells after metastatic lung colonization, and these cells had varied expression signatures associated with the cell cycle, epithelial-mesenchymal plasticity, and hepatic differentiation. Single-cell regulatory network inference and clustering (SCENIC) was utilized to identify the co-expressed transcriptional factors which regulated and represented the different cell states. We further screened the key factor by bioinformatics analysis and found that MYBL2 upregulation was significantly associated with metastasis and poor prognosis. The relationship between ectopic MYBL2 and metastasis was subsequently proved by immunohistochemistry (IHC) of HB tissues, and the functions of MYBL2 in promoting proliferation, migration, and epithelial-to-mesenchymal transition (EMT) were verified by in vitro and in vivo assays. Importantly, the levels of Smad2/3 phosphorylation and SNAI1 expression were increased in MYBL2-transfected cells. Consequently, these results indicated that the MYBL2-controlled Smad/SNAI1 pathway induced EMT and promoted HB tumorigenesis and metastasis.
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Affiliation(s)
- Meng Wei
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Ran Yang
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Mujie Ye
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Yong Zhan
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Baihui Liu
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Lingdu Meng
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Lulu Xie
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Min Du
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
- Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of ChinaChengdu 610091, China
| | - Junfeng Wang
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Runnan Gao
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Deqian Chen
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Rui Dong
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children’s Hospital of Fudan University399 Wanyuan Road, Shanghai 201102, China
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57
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Zhang Z, Wang ZX, Chen YX, Wu HX, Yin L, Zhao Q, Luo HY, Zeng ZL, Qiu MZ, Xu RH. Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response. Genome Med 2022; 14:45. [PMID: 35488273 PMCID: PMC9052621 DOI: 10.1186/s13073-022-01050-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 04/19/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Although immune checkpoint inhibitor (ICI) is regarded as a breakthrough in cancer therapy, only a limited fraction of patients benefit from it. Cancer stemness can be the potential culprit in ICI resistance, but direct clinical evidence is lacking. METHODS Publicly available scRNA-Seq datasets derived from ICI-treated patients were collected and analyzed to elucidate the association between cancer stemness and ICI response. A novel stemness signature (Stem.Sig) was developed and validated using large-scale pan-cancer data, including 34 scRNA-Seq datasets, The Cancer Genome Atlas (TCGA) pan-cancer cohort, and 10 ICI transcriptomic cohorts. The therapeutic value of Stem.Sig genes was further explored using 17 CRISPR datasets that screened potential immunotherapy targets. RESULTS Cancer stemness, as evaluated by CytoTRACE, was found to be significantly associated with ICI resistance in melanoma and basal cell carcinoma (both P < 0.001). Significantly negative association was found between Stem.Sig and anti-tumor immunity, while positive correlations were detected between Stem.Sig and intra-tumoral heterogenicity (ITH) / total mutational burden (TMB). Based on this signature, machine learning model predicted ICI response with an AUC of 0.71 in both validation and testing set. Remarkably, compared with previous well-established signatures, Stem.Sig achieved better predictive performance across multiple cancers. Moreover, we generated a gene list ranked by the average effect of each gene to enhance tumor immune response after genetic knockout across different CRISPR datasets. Then we matched Stem.Sig to this gene list and found Stem.Sig significantly enriched 3% top-ranked genes from the list (P = 0.03), including EMC3, BECN1, VPS35, PCBP2, VPS29, PSMF1, GCLC, KXD1, SPRR1B, PTMA, YBX1, CYP27B1, NACA, PPP1CA, TCEB2, PIGC, NR0B2, PEX13, SERF2, and ZBTB43, which were potential therapeutic targets. CONCLUSIONS We revealed a robust link between cancer stemness and immunotherapy resistance and developed a promising signature, Stem.Sig, which showed increased performance in comparison to other signatures regarding ICI response prediction. This signature could serve as a competitive tool for patient selection of immunotherapy. Meanwhile, our study potentially paves the way for overcoming immune resistance by targeting stemness-associated genes.
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Affiliation(s)
- Zhen Zhang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Zi-Xian Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
- Laboratory of Artificial Intelligence and Data Science, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Yan-Xing Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Hao-Xiang Wu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Ling Yin
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Qi Zhao
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Hui-Yan Luo
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
- Laboratory of Artificial Intelligence and Data Science, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Zhao-Lei Zeng
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Miao-Zhen Qiu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China.
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China.
| | - Rui-Hua Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China.
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China.
- Laboratory of Artificial Intelligence and Data Science, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
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Chu T, Wang Z, Pe'er D, Danko CG. Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. NATURE CANCER 2022; 3:505-517. [PMID: 35469013 PMCID: PMC9046084 DOI: 10.1038/s43018-022-00356-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/03/2022] [Indexed: 12/14/2022]
Abstract
Inferring single-cell compositions and their contributions to global gene expression changes from bulk RNA sequencing (RNA-seq) datasets is a major challenge in oncology. Here we develop Bayesian cell proportion reconstruction inferred using statistical marginalization (BayesPrism), a Bayesian method to predict cellular composition and gene expression in individual cell types from bulk RNA-seq, using patient-derived, scRNA-seq as prior information. We conduct integrative analyses in primary glioblastoma, head and neck squamous cell carcinoma and skin cutaneous melanoma to correlate cell type composition with clinical outcomes across tumor types, and explore spatial heterogeneity in malignant and nonmalignant cell states. We refine current cancer subtypes using gene expression annotation after exclusion of confounding nonmalignant cells. Finally, we identify genes whose expression in malignant cells correlates with macrophage infiltration, T cells, fibroblasts and endothelial cells across multiple tumor types. Our work introduces a new lens to accurately infer cellular composition and expression in large cohorts of bulk RNA-seq data.
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Affiliation(s)
- Tinyi Chu
- 1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Graduate field of Computational Biology, Cornell University, Ithaca, NY, USA.
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Zhong Wang
- School of Software Technology, Dalian University of Technology, Dalian, China
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles G Danko
- 1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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59
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Association of Elevated Expression Levels of COL4A1 in Stromal Cells with an Immunosuppressive Tumor Microenvironment in Low-Grade Glioma, Pancreatic Adenocarcinoma, Skin Cutaneous Melanoma, and Stomach Adenocarcinoma. J Pers Med 2022; 12:jpm12040534. [PMID: 35455650 PMCID: PMC9029283 DOI: 10.3390/jpm12040534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Aberrant expression of collagen type IV alpha chain 1 (COL4A1) can influence tumor cell behavior. To examine the association of COL4A1 expression in the tumor microenvironment (TME) with tumor progression, we performed bioinformatics analyses of The Cancer Genome Atlas RNA sequencing and RNA microarray datasets available in public databases and identified upregulated COL4A1 expression in most examined tumor types compared to their normal counterparts. The elevated expression of COL4A1 was correlated with low survival rates of patients with low-grade glioma, pancreatic adenocarcinoma, skin cutaneous melanoma, and stomach adenocarcinoma, thus suggesting its potential use as a biomarker for the poor prognosis of these tumors. However, COL4A1 was mostly expressed in adjacent stromal cells, such as cancer-associated fibroblasts (CAFs) and endothelial cells. Additionally, COL4A1 expression was highly correlated with the signatures of CAFs and endothelial cells in all four tumor types. The expression of marker genes for the infiltration of pro-tumoral immune cells, such as Treg, M2, and TAM, and those of immunosuppressive cytokines exhibited very strong positive correlations with COL4A1 expression. Collectively, our data suggest that COL4A1 overexpression in stromal cells may be a potential regulator of tumor-supporting TME composition associated with poor prognosis.
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60
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The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective. Nat Commun 2022; 13:1613. [PMID: 35338126 PMCID: PMC8956718 DOI: 10.1038/s41467-022-29154-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/22/2022] [Indexed: 02/08/2023] Open
Abstract
Mining a large cohort of single-cell transcriptomics data, here we employ combinatorial optimization techniques to chart the landscape of optimal combination therapies in cancer. We assume that each individual therapy can target any one of 1269 genes encoding cell surface receptors, which may be targets of CAR-T, conjugated antibodies or coated nanoparticle therapies. We find that in most cancer types, personalized combinations composed of at most four targets are then sufficient for killing at least 80% of tumor cells while sparing at least 90% of nontumor cells in the tumor microenvironment. However, as more stringent and selective killing is required, the number of targets needed rises rapidly. Emerging individual targets include PTPRZ1 for brain and head and neck cancers and EGFR in multiple tumor types. In sum, this study provides a computational estimate of the identity and number of targets needed in combination to target cancers selectively and precisely. Intra-tumor heterogeneity is often associated with resistance to targeted therapy, requiring the design of combinatorial therapies. Here, based on tumor single-cell transcriptomic datasets, the authors develop a computational approach to identify optimal combinatorial treatments targeting membrane receptors for cancer therapy.
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61
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Xiao Y, Yang K, Wang Z, Zhao M, Deng Y, Ji W, Zou Y, Qian C, Liu Y, Xiao H, Liu H. CD44-Mediated Poor Prognosis in Glioma Is Associated With M2-Polarization of Tumor-Associated Macrophages and Immunosuppression. Front Surg 2022; 8:775194. [PMID: 35187044 PMCID: PMC8850306 DOI: 10.3389/fsurg.2021.775194] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/29/2021] [Indexed: 12/31/2022] Open
Abstract
Background Glioma is the most common primary brain tumor with a poor prognosis. Key genes that are negatively related to prognosis may provide the therapy targets to cure glioma. To clarify the role of CD44 in glioma, we explored its function at bulk-transcriptome, spatial and single-cell transcriptome levels. Methods In total, expression profiles with survival data of whole-grade glioma from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), RNA-seq data with anatomic information of glioblastoma (GBM) from the Ivy Glioblastoma Atlas Project, RNA-sequencing (RNA-seq) data from recurrent GBM receiving adjuvant anti-PD-1 immunotherapy accessed through GSE121810, and single-cell RNA-seq data of GBM under accession GSE103224 were enrolled in this study. CD44-specific findings were further analyzed by R language. Results CD44 is positively correlated with WHO grade of malignancy and is negatively related to prognosis in glioma. Meanwhile, CD44 predominantly expresses in GBM mesenchymal subtype, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses reveal that CD44 positively coexpressed genes are closely related to glioma immunity. Moreover, CD44+ cells mainly distribute in perinecrotic region with high expression of immune factors. At single-cell resolution, only malignant tumor cells, tumor-associated macrophages (TAMs), and T cells express CD44 in GBM. CD44+ malignant tumor cells are in mesenchymal-1-like (MES1-like) cellular state, and CD44+ TAMs are in M2 phenotype. CD44+ T cells have high expression of both PD-1 and PD-L1. CD44 and its directly interacted inhibitory immunomodulators are upregulated in patients with nonresponder recurrent GBM treated with PD-1 blockade therapy. Conclusion Our work demonstrates that CD44, a new M2 TAM biomarker, is involved in immune suppressor and promote glioma progression in glioma microenvironment. These results expand our understanding of CD44-specific clinical and immune features in glioma.
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Affiliation(s)
- Yong Xiao
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Kun Yang
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Zhen Wang
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Mengjie Zhao
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Wei Ji
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- Department of Neurosurgery, Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Yuanjie Zou
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Chunfa Qian
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yong Liu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Hong Xiao
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- *Correspondence: Hong Xiao
| | - Hongyi Liu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- Hongyi Liu
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62
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Single cell RNA sequencing reveals differentiation related genes with drawing implications in predicting prognosis and immunotherapy response in gliomas. Sci Rep 2022; 12:1872. [PMID: 35115572 PMCID: PMC8814011 DOI: 10.1038/s41598-022-05686-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/17/2022] [Indexed: 11/30/2022] Open
Abstract
Differentiation states of glioma cells correlated with prognosis and tumor-immune microenvironment (TIME) in patients with gliomas. We aimed to identify differentiation related genes (DRGs) for predicting the prognosis and immunotherapy response in patients with gliomas. We identified three differentiation states and the corresponding DRGs in glioma cells through single-cell transcriptomics analysis. Based on the DRGs, we separated glioma patients into three clusters with distinct clinicopathological features in combination with bulk RNA-seq data. Weighted correlation network analysis, univariate cox regression analysis and least absolute shrinkage and selection operator analysis were involved in the construction of the prognostic model based on DRGs. Distinct clinicopathological characteristics, TIME, immunogenomic patterns and immunotherapy responses were identified across three clusters. A DRG signature composing of 12 genes were identified for predicting the survival of glioma patients and nomogram model integrating the risk score and multi-clinicopathological factors were constructed for clinical practice. Patients in high-risk group tended to get shorter overall survival and better response to immune checkpoint blockage therapy. We obtained 9 candidate drugs through comprehensive analysis of the differentially expressed genes between the low and high-risk groups in the model. Our findings indicated that the risk score may not only contribute to the determination of prognosis but also facilitate in the prediction of immunotherapy response in glioma patients.
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63
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Xie XP, Laks DR, Sun D, Ganbold M, Wang Z, Pedraza AM, Bale T, Tabar V, Brennan C, Zhou X, Parada LF. Quiescent human glioblastoma cancer stem cells drive tumor initiation, expansion, and recurrence following chemotherapy. Dev Cell 2022; 57:32-46.e8. [PMID: 35016005 PMCID: PMC8820651 DOI: 10.1016/j.devcel.2021.12.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/01/2021] [Accepted: 12/03/2021] [Indexed: 01/12/2023]
Abstract
We test the hypothesis that glioblastoma harbors quiescent cancer stem cells that evade anti-proliferative therapies. Functional characterization of spontaneous glioblastomas from genetically engineered mice reveals essential quiescent stem-like cells that can be directly isolated from tumors. A derived quiescent cancer-stem-cell-specific gene expression signature is enriched in pre-formed patient GBM xenograft single-cell clusters that lack proliferative gene expression. A refined human 118-gene signature is preserved in quiescent single-cell populations from primary and recurrent human glioblastomas. The F3 cell-surface receptor mRNA, expressed in the conserved signature, identifies quiescent tumor cells by antibody immunohistochemistry. F3-antibody-sorted glioblastoma cells exhibit stem cell gene expression, enhance self-renewal in culture, drive tumor initiation and serial transplantation, and reconstitute tumor heterogeneity. Upon chemotherapy, the spared cancer stem cell pool becomes activated and accelerates transition to proliferation. These results help explain conventional treatment failure and lay a conceptual framework for alternative therapies.
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Affiliation(s)
- Xuanhua P. Xie
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,These authors contributed equally,Correspondence: ,
| | - Dan R. Laks
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,These authors contributed equally,Present address: Voyager Therapeutics, Cambridge, MA 02139, USA
| | - Daochun Sun
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Present address: Medical College of Wisconsin, Wauwatosa, WI 53226, USA
| | - Mungunsarnai Ganbold
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Zilai Wang
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Present address: Chicago Biosolutions, Inc, Chicago, IL 60612, USA
| | - Alicia M. Pedraza
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Tejus Bale
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Viviane Tabar
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Cameron Brennan
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Xiuping Zhou
- Institute of Nervous System Diseases, Xuzhou Medical University, Jiangsu 221002, PR China
| | - Luis F. Parada
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA,Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Lead Contact,Correspondence: ,
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Arrieta VA, Najem H, Petrosyan E, Lee-Chang C, Chen P, Sonabend AM, Heimberger AB. The Eclectic Nature of Glioma-Infiltrating Macrophages and Microglia. Int J Mol Sci 2021; 22:13382. [PMID: 34948178 PMCID: PMC8705822 DOI: 10.3390/ijms222413382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/23/2022] Open
Abstract
Glioblastomas (GBMs) are complex ecosystems composed of highly multifaceted tumor and myeloid cells capable of responding to different environmental pressures, including therapies. Recent studies have uncovered the diverse phenotypical identities of brain-populating myeloid cells. Differences in the immune proportions and phenotypes within tumors seem to be dictated by molecular features of glioma cells. Furthermore, increasing evidence underscores the significance of interactions between myeloid cells and glioma cells that allow them to evolve in a synergistic fashion to sustain tumor growth. In this review, we revisit the current understanding of glioma-infiltrating myeloid cells and their dialogue with tumor cells in consideration of their increasing recognition in response and resistance to immunotherapies as well as the immune impact of the current chemoradiotherapy used to treat gliomas.
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Affiliation(s)
- Víctor A. Arrieta
- Department of Neurosurgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (V.A.A.); (H.N.); (E.P.); (C.L.-C.); (P.C.)
- PECEM, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04360, Mexico
| | - Hinda Najem
- Department of Neurosurgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (V.A.A.); (H.N.); (E.P.); (C.L.-C.); (P.C.)
| | - Edgar Petrosyan
- Department of Neurosurgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (V.A.A.); (H.N.); (E.P.); (C.L.-C.); (P.C.)
| | - Catalina Lee-Chang
- Department of Neurosurgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (V.A.A.); (H.N.); (E.P.); (C.L.-C.); (P.C.)
| | - Peiwen Chen
- Department of Neurosurgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (V.A.A.); (H.N.); (E.P.); (C.L.-C.); (P.C.)
| | - Adam M. Sonabend
- Department of Neurosurgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (V.A.A.); (H.N.); (E.P.); (C.L.-C.); (P.C.)
| | - Amy B. Heimberger
- Department of Neurosurgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (V.A.A.); (H.N.); (E.P.); (C.L.-C.); (P.C.)
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65
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Unravelling glioblastoma heterogeneity by means of single-cell RNA sequencing. Cancer Lett 2021; 527:66-79. [PMID: 34902524 DOI: 10.1016/j.canlet.2021.12.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/11/2022]
Abstract
Glioblastoma (GBM) is the most invasive and deadliest brain cancer in adults. Its inherent heterogeneity has been designated as the main cause of treatment failure. Thus, a deeper understanding of the diversity that shapes GBM pathobiology is of utmost importance. Single-cell RNA sequencing (scRNA-seq) technologies have begun to uncover the hidden composition of complex tumor ecosystems. Herein, a semi-systematic search of reference literature databases provided all existing publications using scRNA-seq for the investigation of human GBM. We compared and discussed findings from these works to build a more robust and unified knowledge base. All aspects ranging from inter-patient heterogeneity to intra-tumoral organization, cancer stem cell diversity, clonal mosaicism, and the tumor microenvironment (TME) are comprehensively covered in this report. Tumor composition not only differs across patients but also involves a great extent of heterogeneity within itself. Spatial and cellular heterogeneity can reveal tumor evolution dynamics. In addition, the discovery of distinct cell phenotypes might lead to the development of targeted treatment approaches. In conclusion, scRNA-seq expands our knowledge of GBM heterogeneity and helps to unravel putative therapeutic targets.
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66
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ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma. NATURE CANCER 2021; 2:1372-1386. [PMID: 35121903 PMCID: PMC8818262 DOI: 10.1038/s43018-021-00260-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/20/2021] [Indexed: 12/16/2022]
Abstract
Only a subset of recurrent glioblastoma (rGBM) responds to anti-PD-1 immunotherapy. Previously, we reported enrichment of BRAF/PTPN11 mutations in 30% of rGBM that responded to PD-1 blockade. Given that BRAF and PTPN11 promote MAPK/ERK signaling, we investigated whether activation of this pathway is associated with response to PD-1 inhibitors in rGBM, including patients that do not harbor BRAF/PTPN11 mutations. Here we show that immunohistochemistry for ERK1/2 phosphorylation (p-ERK), a marker of MAPK/ERK pathway activation, is predictive of overall survival following adjuvant PD-1 blockade in two independent rGBM patient cohorts. Single-cell RNA-sequencing and multiplex immunofluorescence analyses revealed that p-ERK was mainly localized in tumor cells and that high-p-ERK GBMs contained tumor-infiltrating myeloid cells and microglia with elevated expression of MHC class II and associated genes. These findings indicate that ERK1/2 activation in rGBM is predictive of response to PD-1 blockade and is associated with a distinct myeloid cell phenotype.
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67
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Nagarajan PP, Tora MS, Neill SG, Federici T, Texakalidis P, Donsante A, Canoll P, Lei K, Boulis NM. Lentiviral-Induced Spinal Cord Gliomas in Rat Model. Int J Mol Sci 2021; 22:12943. [PMID: 34884748 PMCID: PMC8657985 DOI: 10.3390/ijms222312943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022] Open
Abstract
Intramedullary spinal cord tumors are a rare and understudied cancer with poor treatment options and prognosis. Our prior study used a combination of PDGF-B, HRAS, and p53 knockdown to induce the development of high-grade glioma in the spinal cords of minipigs. In this study, we evaluate the ability of each vector alone and combinations of vectors to produce high-grade spinal cord gliomas. Eight groups of rats (n = 8/group) underwent thoracolumbar laminectomy and injection of lentiviral vector in the lateral white matter of the spinal cord. Each group received a different combination of lentiviral vectors expressing PDGF-B, a constitutively active HRAS mutant, or shRNA targeting p53, or a control vector. All animals were monitored once per week for clinical deficits for 98 days. Tissues were harvested and analyzed using hematoxylin and eosin (H&E) and immunohistochemical (IHC) staining. Rats injected with PDGF-B+HRAS+sh-p53 (triple cocktail) exhibited statistically significant declines in all behavioral measures (Basso Beattie Bresnahan scoring, Tarlov scoring, weight, and survival rate) over time when compared to the control. Histologically, all groups except the control and those injected with sh-p53 displayed the development of tumors at the injection site, although there were differences in the rate of tumor growth and the histopathological features of the lesions between groups. Examination of immunohistochemistry revealed rats receiving triple cocktail displayed the largest and most significant increase in the Ki67 proliferation index and GFAP positivity than any other group. PDGF-B+HRAS also displayed a significant increase in the Ki67 proliferation index. Rats receiving PDGF-B alone and PDGF-B+ sh-p53 displayed more a significant increase in SOX2-positive staining than in any other group. We found that different vector combinations produced differing high-grade glioma models in rodents. The combination of all three vectors produced a model of high-grade glioma more efficiently and aggressively with respect to behavioral, physiological, and histological characteristics than the rest of the vector combinations. Thus, the present rat model of spinal cord glioma may potentially be used to evaluate therapeutic strategies in the future.
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Affiliation(s)
- Purva P. Nagarajan
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Muhibullah S. Tora
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Stewart G. Neill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Thais Federici
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Pavlos Texakalidis
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Anthony Donsante
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA;
| | - Kecheng Lei
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Nicholas M. Boulis
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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68
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Kenchappa RS, Liu Y, Argenziano MG, Banu MA, Mladek AC, West R, Luu A, Quiñones-Hinojosa A, Hambardzumyan D, Justilien V, Leitges M, Sarkaria JN, Sims PA, Canoll P, Murray NR, Fields AP, Rosenfeld SS. Protein kinase C ι and SRC signaling define reciprocally related subgroups of glioblastoma with distinct therapeutic vulnerabilities. Cell Rep 2021; 37:110054. [PMID: 34818553 PMCID: PMC9845019 DOI: 10.1016/j.celrep.2021.110054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/17/2021] [Accepted: 11/03/2021] [Indexed: 01/19/2023] Open
Abstract
We report that atypical protein kinase Cι (PKCι) is an oncogenic driver of glioblastoma (GBM). Deletion or inhibition of PKCι significantly impairs tumor growth and prolongs survival in murine GBM models. GBM cells expressing elevated PKCι signaling are sensitive to PKCι inhibitors, whereas those expressing low PKCι signaling exhibit active SRC signaling and sensitivity to SRC inhibitors. Resistance to the PKCι inhibitor auranofin is associated with activated SRC signaling and response to a SRC inhibitor, whereas resistance to a SRC inhibitor is associated with activated PKCι signaling and sensitivity to auranofin. Interestingly, PKCι- and SRC-dependent cells often co-exist in individual GBM tumors, and treatment of GBM-bearing mice with combined auranofin and SRC inhibitor prolongs survival beyond either drug alone. Thus, we identify PKCι and SRC signaling as distinct therapeutic vulnerabilities that are directly translatable into an improved treatment for GBM.
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Affiliation(s)
- Rajappa S. Kenchappa
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA,These authors contributed equally,Correspondence: (R.S.K.), (N.R.M.), (A.P.F.), (S.S.R.)
| | - Yi Liu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA,These authors contributed equally
| | - Michael G. Argenziano
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Matei A. Banu
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ann C. Mladek
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Rita West
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Amanda Luu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Dolores Hambardzumyan
- Departments of Neurosurgery and Oncological Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Verline Justilien
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Jann N. Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Peter A. Sims
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Nicole R. Murray
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA,Correspondence: (R.S.K.), (N.R.M.), (A.P.F.), (S.S.R.)
| | - Alan P. Fields
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA,Correspondence: (R.S.K.), (N.R.M.), (A.P.F.), (S.S.R.)
| | - Steven S. Rosenfeld
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA,Lead contact,Correspondence: (R.S.K.), (N.R.M.), (A.P.F.), (S.S.R.)
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69
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Mahlokozera T, Patel B, Chen H, Desouza P, Qu X, Mao DD, Hafez D, Yang W, Taiwo R, Paturu M, Salehi A, Gujar AD, Dunn GP, Mosammaparast N, Petti AA, Yano H, Kim AH. Competitive binding of E3 ligases TRIM26 and WWP2 controls SOX2 in glioblastoma. Nat Commun 2021; 12:6321. [PMID: 34732716 PMCID: PMC8566473 DOI: 10.1038/s41467-021-26653-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
The pluripotency transcription factor SOX2 is essential for the maintenance of glioblastoma stem cells (GSC), which are thought to underlie tumor growth, treatment resistance, and recurrence. To understand how SOX2 is regulated in GSCs, we utilized a proteomic approach and identified the E3 ubiquitin ligase TRIM26 as a direct SOX2-interacting protein. Unexpectedly, we found TRIM26 depletion decreased SOX2 protein levels and increased SOX2 polyubiquitination in patient-derived GSCs, suggesting TRIM26 promotes SOX2 protein stability. Accordingly, TRIM26 knockdown disrupted the SOX2 gene network and inhibited both self-renewal capacity as well as in vivo tumorigenicity in multiple GSC lines. Mechanistically, we found TRIM26, via its C-terminal PRYSPRY domain, but independent of its RING domain, stabilizes SOX2 protein by directly inhibiting the interaction of SOX2 with WWP2, which we identify as a bona fide SOX2 E3 ligase in GSCs. Our work identifies E3 ligase competition as a critical mechanism of SOX2 regulation, with functional consequences for GSC identity and maintenance. SOX2 is required for the maintenance of glioblastoma stem cells (GSCs). Here the authors identify that the RING family E3 ubiquitin ligase TRIM26 promotes SOX2 stability in a non-canonical ligase-independent manner and thus, increases the tumorigenicity of GSCs.
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Affiliation(s)
- Tatenda Mahlokozera
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Bhuvic Patel
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Hao Chen
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Desouza
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Xuan Qu
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Diane D Mao
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel Hafez
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Yang
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rukayat Taiwo
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Mounica Paturu
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Afshin Salehi
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Amit D Gujar
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Allegra A Petti
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA.,The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA. .,The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA. .,The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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70
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Parekh U, McDonald D, Dailamy A, Wu Y, Cordes T, Zhang K, Tipps A, Metallo C, Mali P. Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas. iScience 2021; 24:103149. [PMID: 34646987 PMCID: PMC8496177 DOI: 10.1016/j.isci.2021.103149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/27/2021] [Accepted: 09/15/2021] [Indexed: 11/22/2022] Open
Abstract
Deconstructing tissue-specific effects of genes and variants on proliferation is critical to understanding cellular transformation and systematically selecting cancer therapeutics. This requires scalable methods for multiplexed genetic screens tracking fitness across time, across lineages, and in a suitable niche, since physiological cues influence functional differences. Towards this, we present an approach, coupling single-cell cancer driver screens in teratomas with hit enrichment by serial teratoma reinjection, to simultaneously screen drivers across multiple lineages in vivo. Using this system, we analyzed population shifts and lineage-specific enrichment for 51 cancer associated genes and variants, profiling over 100,000 cells spanning over 20 lineages, across two rounds of serial reinjection. We confirmed that c-MYC alone or combined with myristoylated AKT1 potently drives proliferation in progenitor neural lineages, demonstrating signatures of malignancy. Additionally, mutant MEK1 S218D/S222D provides a proliferative advantage in mesenchymal lineages like fibroblasts. Our method provides a powerful platform for multi-lineage longitudinal study of oncogenesis.
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Affiliation(s)
- Udit Parekh
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, USA
| | - Daniella McDonald
- Department of Bioengineering, University of California San Diego, San Diego, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, USA
| | - Amir Dailamy
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Yan Wu
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Thekla Cordes
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Ann Tipps
- School of Medicine, University of California San Diego, San Diego, USA
| | - Christian Metallo
- Department of Bioengineering, University of California San Diego, San Diego, USA
- Salk Institute of Biological Studies, La Jolla, USA
| | - Prashant Mali
- Department of Bioengineering, University of California San Diego, San Diego, USA
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71
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Zeng J, Zhang Y, Shang Y, Mai J, Shi S, Lu M, Bu C, Zhang Z, Zhang Z, Li Y, Du Z, Xiao J. CancerSCEM: a database of single-cell expression map across various human cancers. Nucleic Acids Res 2021; 50:D1147-D1155. [PMID: 34643725 PMCID: PMC8728207 DOI: 10.1093/nar/gkab905] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/15/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
With the proliferating studies of human cancers by single-cell RNA sequencing technique (scRNA-seq), cellular heterogeneity, immune landscape and pathogenesis within diverse cancers have been uncovered successively. The exponential explosion of massive cancer scRNA-seq datasets in the past decade are calling for a burning demand to be integrated and processed for essential investigations in tumor microenvironment of various cancer types. To fill this gap, we developed a database of Cancer Single-cell Expression Map (CancerSCEM, https://ngdc.cncb.ac.cn/cancerscem), particularly focusing on a variety of human cancers. To date, CancerSCE version 1.0 consists of 208 cancer samples across 28 studies and 20 human cancer types. A series of uniformly and multiscale analyses for each sample were performed, including accurate cell type annotation, functional gene expressions, cell interaction network, survival analysis and etc. Plus, we visualized CancerSCEM as a user-friendly web interface for users to browse, search, online analyze and download all the metadata as well as analytical results. More importantly and unprecedentedly, the newly-constructed comprehensive online analyzing platform in CancerSCEM integrates seven analyze functions, where investigators can interactively perform cancer scRNA-seq analyses. In all, CancerSCEM paves an informative and practical way to facilitate human cancer studies, and also provides insights into clinical therapy assessments.
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Affiliation(s)
- Jingyao Zeng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yadong Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunfei Shang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jialin Mai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo Shi
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Lu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congfan Bu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhewen Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zaichao Zhang
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Yang Li
- Beijing Tongren Eye Center, Beijing key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Zhenglin Du
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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72
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Xiao Z, Zhang W, Li G, Li W, Li L, Sun T, He Y, Liu G, Wang L, Han X, Wen H, Liu Y, Chen Y, Wang H, Li J, Fan Y, Zhang J. Multiomics Analysis Reveals the Prognostic Non-tumor Cell Landscape in Glioblastoma Niches. Front Genet 2021; 12:741325. [PMID: 34603399 PMCID: PMC8481948 DOI: 10.3389/fgene.2021.741325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/11/2021] [Indexed: 11/21/2022] Open
Abstract
A comprehensive characterization of non-tumor cells in the niches of primary glioblastoma is not fully established yet. This study aims to present an overview of non-malignant cells in the complex microenvironment of glioblastoma with detailed characterizations of their prognostic effects. We curate 540 gene signatures covering a total of 64 non-tumor cell types. Cell type-specific expression patterns are interrogated by normalized enrichment score across four large gene expression profiling cohorts of glioblastoma with a total number of 967 cases. The glioblastoma multiforms (GBMs) in each cohort are hierarchically clustered into negative or positive immune response classes with significantly different overall survival. Our results show that astrocytes, macrophages, monocytes, NKTs, and MSC are risk factors, while CD8 T cells, CD8 naive T cells, and plasma cells are protective factors. Moreover, we find that the immune system and organogenesis are uniformly enriched in negative immune response clusters, in contrast to the enrichment of nervous system in positive immune response clusters. Mesenchymal differentiation is also observed in the negative immune response clusters. High enrichment status of macrophages in negative immune response clusters is independently validated by analyzing scRNA-seq data from eight high-grade gliomas, revealing that negative immune response samples comprised 46.63 to 55.12% of macrophages, whereas positive immune response samples comprised only 1.70 to 8.12%, with IHC staining of samples from six short-term and six long-term survivors of GBMs confirming the results.
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Affiliation(s)
- Zixuan Xiao
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Wei Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guanzhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wendong Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Lin Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Ting Sun
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Yufei He
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Guang Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Lu Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Xiaohan Han
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Hao Wen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Yong Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Yifan Chen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Haoyu Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Jing Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Jing Zhang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
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73
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Maas RR, Soukup K, Klemm F, Kornete M, Bowman RL, Bedel R, Marie DN, Álvarez-Prado ÁF, Labes D, Wilson A, Brouland JP, Daniel RT, Hegi ME, Joyce JA. An integrated pipeline for comprehensive analysis of immune cells in human brain tumor clinical samples. Nat Protoc 2021; 16:4692-4721. [PMID: 34462595 DOI: 10.1038/s41596-021-00594-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/21/2021] [Indexed: 11/08/2022]
Abstract
Human tissue samples represent an invaluable source of information for the analysis of disease-specific cellular alterations and their variation between different pathologies. In cancer research, advancing a comprehensive understanding of the unique characteristics of individual tumor types and their microenvironment is of considerable importance for clinical translation. However, investigating human brain tumor tissue is challenging due to the often-limited availability of surgical specimens. Here we describe a multimodule integrated pipeline for the processing of freshly resected human brain tumor tissue and matched blood that enables analysis of the tumor microenvironment, with a particular focus on the tumor immune microenvironment (TIME). The protocol maximizes the information yield from limited tissue and includes both the preservation of bulk tissue, which can be performed within 1 h following surgical resection, as well as tissue dissociation for an in-depth characterization of individual TIME cell populations, which typically takes several hours depending on tissue quantity and further downstream processing. We also describe integrated modules for immunofluorescent staining of sectioned tissue, bulk tissue genomic analysis and fluorescence- or magnetic-activated cell sorting of digested tissue for subsequent culture or transcriptomic analysis by RNA sequencing. Applying this pipeline, we have previously described the overall TIME landscape across different human brain malignancies, and were able to delineate disease-specific alterations of tissue-resident versus recruited macrophage populations. This protocol will enable researchers to use this pipeline to address further research questions regarding the tumor microenvironment.
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Affiliation(s)
- Roeltje R Maas
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Klara Soukup
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Florian Klemm
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Mara Kornete
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | | | - Romain Bedel
- Flow Cytometry Facility, Department of Formation and Research, University of Lausanne, Epalinges, Switzerland
| | - Damien N Marie
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Ángel F Álvarez-Prado
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Danny Labes
- Flow Cytometry Facility, Department of Formation and Research, University of Lausanne, Epalinges, Switzerland
| | - Anne Wilson
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Flow Cytometry Facility, Department of Formation and Research, University of Lausanne, Epalinges, Switzerland
| | - Jean-Philippe Brouland
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Roy T Daniel
- Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Monika E Hegi
- Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Johanna A Joyce
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.
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74
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Johnson KC, Anderson KJ, Courtois ET, Gujar AD, Barthel FP, Varn FS, Luo D, Seignon M, Yi E, Kim H, Estecio MRH, Zhao D, Tang M, Navin NE, Maurya R, Ngan CY, Verburg N, de Witt Hamer PC, Bulsara K, Samuels ML, Das S, Robson P, Verhaak RGW. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nat Genet 2021; 53:1456-1468. [PMID: 34594038 PMCID: PMC8570135 DOI: 10.1038/s41588-021-00926-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
Glioma intratumoral heterogeneity enables adaptation to challenging microenvironments and contributes to therapeutic resistance. We integrated 914 single-cell DNA methylomes, 55,284 single-cell transcriptomes and bulk multi-omic profiles across 11 adult IDH mutant or IDH wild-type gliomas to delineate sources of intratumoral heterogeneity. We showed that local DNA methylation disorder is associated with cell-cell DNA methylation differences, is elevated in more aggressive tumors, links with transcriptional disruption and is altered during the environmental stress response. Glioma cells under in vitro hypoxic and irradiation stress increased local DNA methylation disorder and shifted cell states. We identified a positive association between genetic and epigenetic instability that was supported in bulk longitudinally collected DNA methylation data. Increased DNA methylation disorder associated with accelerated disease progression and recurrently selected DNA methylation changes were enriched for environmental stress response pathways. Our work identified an epigenetically facilitated adaptive stress response process and highlights the importance of epigenetic heterogeneity in shaping therapeutic outcomes.
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Affiliation(s)
- Kevin C. Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,These authors contributed equally,Co-corresponding authors: and
| | - Kevin J. Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,These authors contributed equally
| | - Elise T. Courtois
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Amit D. Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Floris P. Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Brain Tumor Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Frederick S. Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Diane Luo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Martine Seignon
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Marcos RH Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, US
| | - Dacheng Zhao
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, US
| | - Nicholas E. Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, US
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Niels Verburg
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurosurgery, Brain Tumor Center Amsterdam, de Boelelaan 1117, Amsterdam, The Netherlands
| | - Philip C de Witt Hamer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurosurgery, Brain Tumor Center Amsterdam, de Boelelaan 1117, Amsterdam, The Netherlands
| | - Ketan Bulsara
- Division of Neurosurgery, The University of Connecticut Health Center, Farmington, CT, US
| | | | - Sunit Das
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for SickKids, University of Toronto.,Institute of Medical Science, University of Toronto.,Division of Neurosurgery, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, University of Toronto
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Genetics and Genome Sciences, University of Connecticut School of Medicine
| | - Roel GW Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Co-corresponding authors: and
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75
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Rao R, Han R, Ogurek S, Xue C, Wu LM, Zhang L, Zhang L, Hu J, Phoenix TN, Waggoner SN, Lu QR. Glioblastoma Genetic Drivers Dictate the Function of Tumor-Associated Macrophages/Microglia and Responses to CSF1R Inhibition. Neuro Oncol 2021; 24:584-597. [PMID: 34562087 PMCID: PMC8972285 DOI: 10.1093/neuonc/noab228] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tumor-associated macrophages/microglia (TAMs) are prominent microenvironment components in human glioblastoma (GBM) that are potential targets for anti-tumor therapy. However, TAM depletion by CSF1R inhibition showed mixed results in clinical trials. We hypothesized that GBM subtype-specific tumor microenvironment convey distinct sensitivities to TAM targeting. METHODS We generated syngeneic PDGFB-driven and RAS-driven GBM models that resemble proneural-like and mesenchymal-like gliomas, and determined the effect of TAM targeting by CSF1R inhibitor PLX3397 on glioma growth. We also investigated the co-targeting of TAMs and angiogenesis on PLX3397-resistant RAS-driven GBM. Using single-cell transcriptomic profiling, we further explored differences in tumor microenvironment cellular compositions and functions in PDGFB- and RAS-driven gliomas. RESULTS We found that growth of PDGFB-driven tumors was markedly inhibited by PLX3397. In contrast, depletion of TAMs at the early phase accelerated RAS-driven tumor growth and had no effects on other proneural and mesenchymal GBM models. In addition, PLX3397-resistant RAS-driven tumors did not respond to PI3K signaling inhibition. Single-cell transcriptomic profiling revealed that PDGFB-driven gliomas induced expansion and activation of pro-tumor microglia, whereas TAMs in mesenchymal RAS-driven GBM were enriched in pro-inflammatory and angiogenic signaling. Co-targeting of TAMs and angiogenesis decreased cell proliferation and changed the morphology of RAS-driven gliomas. CONCLUSIONS Our work identify functionally distinct TAM subpopulations in the growth of different glioma subtypes. Notably, we uncover a potential responsiveness of resistant mesenchymal-like gliomas to combined anti-angiogenic therapy and CSF1R inhibition. These data highlight the importance of characterization of the microenvironment landscape in order to optimally stratify patients for TAM-targeted therapy.
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Affiliation(s)
- Rohit Rao
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Rong Han
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sean Ogurek
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chengbin Xue
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lai Man Wu
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Liguo Zhang
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Li Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH
| | - Jian Hu
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
| | - Stephen N Waggoner
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Q Richard Lu
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
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76
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Liu H, Sun Y, Zhang Q, Jin W, Gordon RE, Zhang Y, Wang J, Sun C, Wang ZJ, Qi X, Zhang J, Huang B, Gui Q, Yuan H, Chen L, Ma X, Fang C, Liu YQ, Yu X, Feng S. Pro-inflammatory and proliferative microglia drive progression of glioblastoma. Cell Rep 2021; 36:109718. [PMID: 34525361 DOI: 10.1016/j.celrep.2021.109718] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 04/01/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
Scant understanding of the glioblastoma microenvironment and molecular bases hampers development of efficient treatment strategies. Analyses of gene signatures of human gliomas demonstrate that the SETD2 mutation is correlated with poor prognosis of IDH1/2 wild-type (IDH-WT) adult glioblastoma patients. To better understand the crosstalk between SETD2 mutant (SETD2-mut) glioblastoma cells and the tumor microenvironment, we leverage single-cell transcriptomics to comprehensively map cellular populations in glioblastoma. In this study, we identify a specific subtype of high-grade glioma-associated microglia (HGG-AM). Further analysis shows that transforming growth factor (TGF)-β1 derived from SETD2-mut/IDH-WT tumor cells activates HGG-AM, exhibiting pro-inflammation and proliferation signatures. Particularly, HGG-AM secretes interleukin (IL)-1β via the apolipoprotein E (ApoE)-mediated NLRP1 inflammasome, thereby promoting tumor progression. HGG-AM present extensive proliferation and infiltration to supplement the activated microglia pool. Notably, TGF-β1/TβRI depletion dramatically reduces HGG-AM density and suppresses tumor growth. Altogether, our studies identify a specific microglia subpopulation and establish the cellular basis of interactions between HGG-AM and glioblastoma cells.
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Affiliation(s)
- Hailong Liu
- Department of Neurosurgery, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China; Department of Radiotherapy, Beijing Tiantan Hospital, Capital Medical University, Beijing 10070, P.R. China
| | - Youliang Sun
- School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Qian Zhang
- Medical Laboratory Center, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, P.R. China; Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518000, P.R. China
| | - Wei Jin
- Department of Pathology, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | | | - Yanyang Zhang
- Department of Neurosurgery, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Jian Wang
- Department of Neurosurgery, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Caihong Sun
- Department of Neurosurgery, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Zeyuan John Wang
- School of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, USA
| | - Xueling Qi
- Department of Neuro-Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P. R. China
| | - Junping Zhang
- Department of Neuro-Oncology, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P.R. China
| | - Boyuan Huang
- Department of Neurosurgery, Beijing Electric Power Hospital, Beijing 100073, P.R. China
| | - Qiuping Gui
- Department of Pathology, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Hongyu Yuan
- State Key Laboratory of Molecular Oncology, Chinese Academy of Medical Science Cancer Hospital/National Cancer Center, Beijing 100021, P.R. China
| | - Ling Chen
- Department of Neurosurgery, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Xiaodong Ma
- Department of Neurosurgery, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Chuan Fang
- Department of Neurosurgery, The Affiliated Hospital of Hebei University, Baoding 122311, P.R. China
| | - Yong-Qiang Liu
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China.
| | - Xinguang Yu
- Department of Neurosurgery, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China.
| | - Shiyu Feng
- Department of Neurosurgery, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China.
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77
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Cui X, Wang Q, Zhou J, Wang Y, Xu C, Tong F, Wang H, Kang C. Single-Cell Transcriptomics of Glioblastoma Reveals a Unique Tumor Microenvironment and Potential Immunotherapeutic Target Against Tumor-Associated Macrophage. Front Oncol 2021; 11:710695. [PMID: 34434898 PMCID: PMC8382282 DOI: 10.3389/fonc.2021.710695] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
Background The main immune cells in GBM are tumor-associated macrophages (TAMs). Thus far, the studies investigating the activation status of TAM in GBM are mainly limited to bulk RNA analyses of individual tumor biopsies. The activation states and transcriptional signatures of TAMs in GBM remain poorly characterized. Methods We comprehensively analyzed single-cell RNA-sequencing data, covering a total of 16,201 cells, to clarify the relative proportions of the immune cells infiltrating GBMs. The origin and TAM states in GBM were characterized using the expression profiles of differential marker genes. The vital transcription factors were examined by SCENIC analysis. By comparing the variable gene expression patterns in different clusters and cell types, we identified components and characteristics of TAMs unique to each GBM subtype. Meanwhile, we interrogated the correlation between SPI1 expression and macrophage infiltration in the TCGA-GBM dataset. Results The expression patterns of TMEM119 and MHC-II can be utilized to distinguish the origin and activation states of TAMs. In TCGA-Mixed tumors, almost all TAMs were bone marrow-derived macrophages. The TAMs in TCGA-proneural tumors were characterized by primed microglia. A different composition was observed in TCGA-classical tumors, which were infiltrated by repressed microglia. Our results further identified SPI1 as a crucial regulon and potential immunotherapeutic target important for TAM maturation and polarization in GBM. Conclusions We describe the immune landscape of human GBM at a single-cell level and define a novel categorization scheme for TAMs in GBM. The immunotherapy against SPI1 would reprogram the immune environment of GBM and enhance the treatment effect of conventional chemotherapy drugs.
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Affiliation(s)
- Xiaoteng Cui
- Lab of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Qixue Wang
- Lab of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Junhu Zhou
- Lab of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yunfei Wang
- Lab of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Can Xu
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Fei Tong
- Lab of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongjun Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chunsheng Kang
- Lab of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
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78
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Zhou D, Feng H, Yang Y, Huang T, Qiu P, Zhang C, Olsen T, Zhang J, Chen YE, Mizrak D, Yang B. hiPSC Modeling of Lineage-Specific Smooth Muscle Cell Defects Caused by TGFBR1A230T Variant, and its Therapeutic Implications for Loeys-Dietz Syndrome. Circulation 2021; 144:1145-1159. [PMID: 34346740 DOI: 10.1161/circulationaha.121.054744] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Loeys-Dietz Syndrome (LDS) is an inherited disorder predisposing individuals to thoracic aortic aneurysm and dissection (TAAD). Currently, there are no medical treatments except surgical resection. Although the genetic basis of LDS is well-understood, molecular mechanisms underlying the disease remain elusive impeding the development of a therapeutic strategy. In addition, aortic smooth muscle cells (SMC) have heterogenous embryonic origins depending on their spatial location, and lineage-specific effects of pathogenic variants on SMC function, likely causing regionally constrained LDS manifestations, have been unexplored. Methods: We identified an LDS family with a dominant pathogenic variant in TGFBR1 gene (TGFBR1A230T) causing aortic root aneurysm and dissection. To accurately model the molecular defects caused by this mutation, we used human-induced pluripotent stem cells (hiPSC) from subject with normal aorta to generate hiPSC carrying TGFBR1A230T, and corrected the mutation in patient-derived hiPSC using CRISPR-Cas9 gene editing. Following their lineage-specific SMC differentiation through cardiovascular progenitor cell (CPC) and neural crest stem cell (NCSC) lineages, we employed conventional molecular techniques and single-cell RNA-sequencing (scRNA-seq) to characterize the molecular defects. The resulting data led to subsequent molecular and functional rescue experiments employing Activin A and rapamycin. Results: Our results indicate the TGFBR1A230T mutation impairs contractile transcript and protein levels, and function in CPC-SMC, but not in NCSC-SMC. ScRNA-seq results implicate defective differentiation even in TGFBR1A230T/+ CPC-SMC including disruption of SMC contraction, and extracellular matrix formation. Comparison of patient-derived and mutation-corrected cells supported the contractile phenotype observed in the mutant CPC-SMC. TGFBR1A230T selectively disrupted SMAD3 and AKT activation in CPC-SMC, and led to increased cell proliferation. Consistently, scRNA-seq revealed molecular similarities between a loss-of-function SMAD3 mutation (SMAD3c.652delA/+) and TGFBR1A230T/+. Lastly, combination treatment with Activin A and rapamycin during or after SMC differentiation significantly improved the mutant CPC-SMC contractile gene expression, and function; and rescued the mechanical properties of mutant CPC-SMC tissue constructs. Conclusions: This study reveals that a pathogenic TGFBR1 variant causes lineage-specific SMC defects informing the etiology of LDS-associated aortic root aneurysm. As a potential pharmacological strategy, our results highlight a combination treatment with Activin A and rapamycin that can rescue the SMC defects caused by the variant.
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Affiliation(s)
- Dong Zhou
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI; Xiangya School of Medicine, Central South University, Changsha, PRC
| | - Hao Feng
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI; Xiangya School of Medicine, Central South University, Changsha, PRC
| | - Ying Yang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI
| | - Tingting Huang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI; Xiangya School of Medicine, Central South University, Changsha, PRC
| | - Ping Qiu
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Timothy Olsen
- Department of Systems Biology, Columbia University, New York, NY
| | - Jifeng Zhang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Y Eugene Chen
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI; Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Dogukan Mizrak
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI
| | - Bo Yang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI
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Zadeh Shirazi A, McDonnell MD, Fornaciari E, Bagherian NS, Scheer KG, Samuel MS, Yaghoobi M, Ormsby RJ, Poonnoose S, Tumes DJ, Gomez GA. A deep convolutional neural network for segmentation of whole-slide pathology images identifies novel tumour cell-perivascular niche interactions that are associated with poor survival in glioblastoma. Br J Cancer 2021; 125:337-350. [PMID: 33927352 PMCID: PMC8329064 DOI: 10.1038/s41416-021-01394-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/16/2021] [Accepted: 04/08/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Glioblastoma is the most aggressive type of brain cancer with high-levels of intra- and inter-tumour heterogeneity that contribute to its rapid growth and invasion within the brain. However, a spatial characterisation of gene signatures and the cell types expressing these in different tumour locations is still lacking. METHODS We have used a deep convolutional neural network (DCNN) as a semantic segmentation model to segment seven different tumour regions including leading edge (LE), infiltrating tumour (IT), cellular tumour (CT), cellular tumour microvascular proliferation (CTmvp), cellular tumour pseudopalisading region around necrosis (CTpan), cellular tumour perinecrotic zones (CTpnz) and cellular tumour necrosis (CTne) in digitised glioblastoma histopathological slides from The Cancer Genome Atlas (TCGA). Correlation analysis between segmentation results from tumour images together with matched RNA expression data was performed to identify genetic signatures that are specific to different tumour regions. RESULTS We found that spatially resolved gene signatures were strongly correlated with survival in patients with defined genetic mutations. Further in silico cell ontology analysis along with single-cell RNA sequencing data from resected glioblastoma tissue samples showed that these tumour regions had different gene signatures, whose expression was driven by different cell types in the regional tumour microenvironment. Our results further pointed to a key role for interactions between microglia/pericytes/monocytes and tumour cells that occur in the IT and CTmvp regions, which may contribute to poor patient survival. CONCLUSIONS This work identified key histopathological features that correlate with patient survival and detected spatially associated genetic signatures that contribute to tumour-stroma interactions and which should be investigated as new targets in glioblastoma. The source codes and datasets used are available in GitHub: https://github.com/amin20/GBM_WSSM .
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Affiliation(s)
- Amin Zadeh Shirazi
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Computational Learning Systems Laboratory, UniSA STEM, University of South Australia, Mawson Lakes, SA, Australia
| | - Mark D McDonnell
- Computational Learning Systems Laboratory, UniSA STEM, University of South Australia, Mawson Lakes, SA, Australia
| | - Eric Fornaciari
- Department of Mathematics of Computation, University of California, Los Angeles (UCLA), CA, USA
| | | | - Kaitlin G Scheer
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Michael S Samuel
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Mahdi Yaghoobi
- Electrical and Computer Engineering Department, Department of Artificial Intelligence, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Rebecca J Ormsby
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
| | - Santosh Poonnoose
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
- Department of Neurosurgery, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Damon J Tumes
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Guillermo A Gomez
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia.
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80
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Li Y, Wang X, Qi S, Gao L, Huang G, Ren Z, Li K, Peng Y, Yi G, Guo J, Yang R, Wang H, Zhang X, Liu Y. Spliceosome-regulated RSRP1-dependent NF-κB activation promotes the glioblastoma mesenchymal phenotype. Neuro Oncol 2021; 23:1693-1708. [PMID: 34042961 DOI: 10.1093/neuonc/noab126] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The glioblastoma (GBM) mesenchymal (MES) phenotype, induced by NF-κB activation, is characterized by aggressive tumour progression and poor clinical outcomes. Our previous analysis indicated that MES GBM has a unique alternative splicing (AS) pattern; however, the underlying mechanism remains obscure. We aimed to reveal how splicing regulation contributes to MES phenotype promotion in GBM. METHODS We screened novel candidate splicing factors that participate in NF-κB activation and MES phenotype promotion in GBM. In vitro and in vivo assays were used to explore the function of RSRP1 in MES GBM. RESULTS Here, we identified that arginine/serine-rich protein 1 (RSRP1) promotes the MES phenotype by facilitating GBM cell invasion and apoptosis resistance. Proteomic, transcriptomic and functional analyses confirmed that RSRP1 regulates AS in MES GBM through mediating spliceosome assembly. One RSRP1-regulated AS event resulted in skipping PARP6 exon 18 to form truncated, oncogenic PARP6-s. This isoform was unable to effectively suppress NF-κB. Co-treatment of cultured GBM cells and GBM tumour-bearing mice with spliceosome and NF-κB inhibitors exerted a synergistic effect on MES GBM growth. CONCLUSION We identified a novel mechanism through which RSRP1-dependent splicing promotes the GBM MES phenotype. Targeting AS via RSRP1-related spliceosomal factors might constitute a promising treatment for GBM.
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Affiliation(s)
- Yaomin Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiran Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lei Gao
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Guanglong Huang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhonglu Ren
- College of Medical Information Engineering, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Kaishu Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuping Peng
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Guozhong Yi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jinglin Guo
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Runwei Yang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Hai Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xian Zhang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yawei Liu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
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81
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Chen AX, Gartrell RD, Zhao J, Upadhyayula PS, Zhao W, Yuan J, Minns HE, Dovas A, Bruce JN, Lasorella A, Iavarone A, Canoll P, Sims PA, Rabadan R. Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker. Genome Med 2021; 13:88. [PMID: 34011400 PMCID: PMC8136167 DOI: 10.1186/s13073-021-00906-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 05/07/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Macrophages are the most common infiltrating immune cells in gliomas and play a wide variety of pro-tumor and anti-tumor roles. However, the different subpopulations of macrophages and their effects on the tumor microenvironment remain poorly understood. METHODS We combined new and previously published single-cell RNA-seq data from 98,015 single cells from a total of 66 gliomas to profile 19,331 individual macrophages. RESULTS Unsupervised clustering revealed a pro-tumor subpopulation of bone marrow-derived macrophages characterized by the scavenger receptor MARCO, which is almost exclusively found in IDH1-wild-type glioblastomas. Previous studies have implicated MARCO as an unfavorable marker in melanoma and non-small cell lung cancer; here, we find that bulk MARCO expression is associated with worse prognosis and mesenchymal subtype. Furthermore, MARCO expression is significantly altered over the course of treatment with anti-PD1 checkpoint inhibitors in a response-dependent manner, which we validate with immunofluorescence imaging. CONCLUSIONS These findings illustrate a novel macrophage subpopulation that drives tumor progression in glioblastomas and suggest potential therapeutic targets to prevent their recruitment.
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Affiliation(s)
- Andrew X Chen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY, USA
| | - Robyn D Gartrell
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Junfei Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Pavan S Upadhyayula
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenting Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jinzhou Yuan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hanna E Minns
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Athanassios Dovas
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jeffrey N Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Anna Lasorella
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
| | - Antonio Iavarone
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter Canoll
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
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82
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Zhao W, Dovas A, Spinazzi EF, Levitin HM, Banu MA, Upadhyayula P, Sudhakar T, Marie T, Otten ML, Sisti MB, Bruce JN, Canoll P, Sims PA. Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq. Genome Med 2021; 13:82. [PMID: 33975634 PMCID: PMC8114529 DOI: 10.1186/s13073-021-00894-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Preclinical studies require models that recapitulate the cellular diversity of human tumors and provide insight into the drug sensitivities of specific cellular populations. The ideal platform would enable rapid screening of cell type-specific drug sensitivities directly in patient tumor tissue and reveal strategies to overcome intratumoral heterogeneity. METHODS We combine multiplexed drug perturbation in acute slice culture from freshly resected tumors with single-cell RNA sequencing (scRNA-seq) to profile transcriptome-wide drug responses in individual patients. We applied this approach to drug perturbations on slices derived from six glioblastoma (GBM) resections to identify conserved drug responses and to one additional GBM resection to identify patient-specific responses. RESULTS We used scRNA-seq to demonstrate that acute slice cultures recapitulate the cellular and molecular features of the originating tumor tissue and the feasibility of drug screening from an individual tumor. Detailed investigation of etoposide, a topoisomerase poison, and the histone deacetylase (HDAC) inhibitor panobinostat in acute slice cultures revealed cell type-specific responses across multiple patients. Etoposide has a conserved impact on proliferating tumor cells, while panobinostat treatment affects both tumor and non-tumor populations, including unexpected effects on the immune microenvironment. CONCLUSIONS Acute slice cultures recapitulate the major cellular and molecular features of GBM at the single-cell level. In combination with scRNA-seq, this approach enables cell type-specific analysis of sensitivity to multiple drugs in individual tumors. We anticipate that this approach will facilitate pre-clinical studies that identify effective therapies for solid tumors.
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Affiliation(s)
- Wenting Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Athanassios Dovas
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - Hanna Mendes Levitin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Matei Alexandru Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Pavan Upadhyayula
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Tejaswi Sudhakar
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Tamara Marie
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Marc L Otten
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Michael B Sisti
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jeffrey N Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter Canoll
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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83
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Li L, Xiong F, Wang Y, Zhang S, Gong Z, Li X, He Y, Shi L, Wang F, Liao Q, Xiang B, Zhou M, Li X, Li Y, Li G, Zeng Z, Xiong W, Guo C. What are the applications of single-cell RNA sequencing in cancer research: a systematic review. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:163. [PMID: 33975628 PMCID: PMC8111731 DOI: 10.1186/s13046-021-01955-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a tool for studying gene expression at the single-cell level that has been widely used due to its unprecedented high resolution. In the present review, we outline the preparation process and sequencing platforms for the scRNA-seq analysis of solid tumor specimens and discuss the main steps and methods used during data analysis, including quality control, batch-effect correction, normalization, cell cycle phase assignment, clustering, cell trajectory and pseudo-time reconstruction, differential expression analysis and gene set enrichment analysis, as well as gene regulatory network inference. Traditional bulk RNA sequencing does not address the heterogeneity within and between tumors, and since the development of the first scRNA-seq technique, this approach has been widely used in cancer research to better understand cancer cell biology and pathogenetic mechanisms. ScRNA-seq has been of great significance for the development of targeted therapy and immunotherapy. In the second part of this review, we focus on the application of scRNA-seq in solid tumors, and summarize the findings and achievements in tumor research afforded by its use. ScRNA-seq holds promise for improving our understanding of the molecular characteristics of cancer, and potentially contributing to improved diagnosis, prognosis, and therapeutics.
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Affiliation(s)
- Lvyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Fang Xiong
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Shanshan Zhang
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yi He
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Lei Shi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yong Li
- Department of Medicine, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
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84
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Lenin S, Ponthier E, Scheer KG, Yeo ECF, Tea MN, Ebert LM, Oksdath Mansilla M, Poonnoose S, Baumgartner U, Day BW, Ormsby RJ, Pitson SM, Gomez GA. A Drug Screening Pipeline Using 2D and 3D Patient-Derived In Vitro Models for Pre-Clinical Analysis of Therapy Response in Glioblastoma. Int J Mol Sci 2021; 22:4322. [PMID: 33919246 PMCID: PMC8122466 DOI: 10.3390/ijms22094322] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma is one of the most common and lethal types of primary brain tumor. Despite aggressive treatment with chemotherapy and radiotherapy, tumor recurrence within 6-9 months is common. To overcome this, more effective therapies targeting cancer cell stemness, invasion, metabolism, cell death resistance and the interactions of tumor cells with their surrounding microenvironment are required. In this study, we performed a systematic review of the molecular mechanisms that drive glioblastoma progression, which led to the identification of 65 drugs/inhibitors that we screened for their efficacy to kill patient-derived glioma stem cells in two dimensional (2D) cultures and patient-derived three dimensional (3D) glioblastoma explant organoids (GBOs). From the screening, we found a group of drugs that presented different selectivity on different patient-derived in vitro models. Moreover, we found that Costunolide, a TERT inhibitor, was effective in reducing the cell viability in vitro of both primary tumor models as well as tumor models pre-treated with chemotherapy and radiotherapy. These results present a novel workflow for screening a relatively large groups of drugs, whose results could lead to the identification of more personalized and effective treatment for recurrent glioblastoma.
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Affiliation(s)
- Sakthi Lenin
- Centre for Cancer Biology, SA Pathology and the University of South of Australia, Adelaide, SA 5000, Australia; (S.L.); (E.P.); (K.G.S.); (E.C.F.Y.); (M.N.T.); (L.M.E.); (M.O.M.); (S.M.P.)
| | - Elise Ponthier
- Centre for Cancer Biology, SA Pathology and the University of South of Australia, Adelaide, SA 5000, Australia; (S.L.); (E.P.); (K.G.S.); (E.C.F.Y.); (M.N.T.); (L.M.E.); (M.O.M.); (S.M.P.)
| | - Kaitlin G. Scheer
- Centre for Cancer Biology, SA Pathology and the University of South of Australia, Adelaide, SA 5000, Australia; (S.L.); (E.P.); (K.G.S.); (E.C.F.Y.); (M.N.T.); (L.M.E.); (M.O.M.); (S.M.P.)
| | - Erica C. F. Yeo
- Centre for Cancer Biology, SA Pathology and the University of South of Australia, Adelaide, SA 5000, Australia; (S.L.); (E.P.); (K.G.S.); (E.C.F.Y.); (M.N.T.); (L.M.E.); (M.O.M.); (S.M.P.)
| | - Melinda N. Tea
- Centre for Cancer Biology, SA Pathology and the University of South of Australia, Adelaide, SA 5000, Australia; (S.L.); (E.P.); (K.G.S.); (E.C.F.Y.); (M.N.T.); (L.M.E.); (M.O.M.); (S.M.P.)
| | - Lisa M. Ebert
- Centre for Cancer Biology, SA Pathology and the University of South of Australia, Adelaide, SA 5000, Australia; (S.L.); (E.P.); (K.G.S.); (E.C.F.Y.); (M.N.T.); (L.M.E.); (M.O.M.); (S.M.P.)
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Mariana Oksdath Mansilla
- Centre for Cancer Biology, SA Pathology and the University of South of Australia, Adelaide, SA 5000, Australia; (S.L.); (E.P.); (K.G.S.); (E.C.F.Y.); (M.N.T.); (L.M.E.); (M.O.M.); (S.M.P.)
| | - Santosh Poonnoose
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Adelaide, SA 5042, Australia; (S.P.); (R.J.O.)
- Department of Neurosurgery, Flinders Medical Centre, Adelaide, SA 5042, Australia
| | - Ulrich Baumgartner
- Cell and Molecular Biology Department, Sid Faithfull Brain Cancer Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (U.B.); (B.W.D.)
- Faculty of Health, Queensland University of Technology, Brisbane, QLD 4006, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Bryan W. Day
- Cell and Molecular Biology Department, Sid Faithfull Brain Cancer Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (U.B.); (B.W.D.)
- Faculty of Health, Queensland University of Technology, Brisbane, QLD 4006, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Rebecca J. Ormsby
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Adelaide, SA 5042, Australia; (S.P.); (R.J.O.)
| | - Stuart M. Pitson
- Centre for Cancer Biology, SA Pathology and the University of South of Australia, Adelaide, SA 5000, Australia; (S.L.); (E.P.); (K.G.S.); (E.C.F.Y.); (M.N.T.); (L.M.E.); (M.O.M.); (S.M.P.)
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Guillermo A. Gomez
- Centre for Cancer Biology, SA Pathology and the University of South of Australia, Adelaide, SA 5000, Australia; (S.L.); (E.P.); (K.G.S.); (E.C.F.Y.); (M.N.T.); (L.M.E.); (M.O.M.); (S.M.P.)
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85
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Xu L, Chen Y, Huang Y, Sandanaraj E, Yu JS, Lin RYT, Dakle P, Ke XY, Chong YK, Koh L, Mayakonda A, Nacro K, Hill J, Huang ML, Gery S, Lim SW, Huang Z, Xu Y, Chen J, Bai L, Wang S, Wakimoto H, Yeo TT, Ang BT, Müschen M, Tang C, Tan TZ, Koeffler HP. Topography of transcriptionally active chromatin in glioblastoma. SCIENCE ADVANCES 2021; 7:7/18/eabd4676. [PMID: 33931443 PMCID: PMC8087410 DOI: 10.1126/sciadv.abd4676] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 03/08/2021] [Indexed: 05/07/2023]
Abstract
Molecular profiling of the most aggressive brain tumor glioblastoma (GBM) on the basis of gene expression, DNA methylation, and genomic variations advances both cancer research and clinical diagnosis. The enhancer architectures and regulatory circuitries governing tumor-intrinsic transcriptional diversity and subtype identity are still elusive. Here, by mapping H3K27ac deposition, we analyze the active regulatory landscapes across 95 GBM biopsies, 12 normal brain tissues, and 38 cell line counterparts. Analyses of differentially regulated enhancers and super-enhancers uncovered previously unrecognized layers of intertumor heterogeneity. Integrative analysis of variant enhancer loci and transcriptome identified topographies of transcriptional enhancers and core regulatory circuitries in four molecular subtypes of primary tumors: AC1-mesenchymal, AC1-classical, AC2-proneural, and AC3-proneural. Moreover, this study reveals core oncogenic dependency on super-enhancer-driven transcriptional factors, long noncoding RNAs, and druggable targets in GBM. Through profiling of transcriptional enhancers, we provide clinically relevant insights into molecular classification, pathogenesis, and therapeutic intervention of GBM.
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Affiliation(s)
- Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ye Chen
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
| | - Yulun Huang
- Department of Neurosurgery, Dushu Lake Hospital Affiliated of Soochow University, Suzhou, 215124, China
- Department of Neurosurgery, Medical Center of Soochow University, Suzhou, 215124, China
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Edwin Sandanaraj
- Department of Research, National Neuroscience Institute, 308433, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology, and Research, 117609, Singapore
| | - John S Yu
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ruby Yu-Tong Lin
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Xin-Yu Ke
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Yuk Kien Chong
- Department of Research, National Neuroscience Institute, 308433, Singapore
| | - Lynnette Koh
- Department of Research, National Neuroscience Institute, 308433, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Kassoum Nacro
- Experimental Drug Development Centre, Agency for Science, Technology and Research, 138670, Singapore
| | - Jeffrey Hill
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Mo-Li Huang
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Sigal Gery
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - See Wee Lim
- Department of Research, National Neuroscience Institute, 308433, Singapore
| | - Zhengyun Huang
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, 215123, China
| | - Ying Xu
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, 215123, China
| | - Jianxiang Chen
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, China
- Department of Hepatology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310015, China
| | - Longchuan Bai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tseng Tsai Yeo
- National University Cancer Institute, National University Hospital, 119074, Singapore
| | - Beng Ti Ang
- Department of Neurosurgery, National Neuroscience Institute, 308433, Singapore
- Duke-National University of Singapore Medical School, 169857, Singapore
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA
- Department of Immunobiology, Yale University, New Haven, CT 06511, USA
| | - Carol Tang
- Department of Research, National Neuroscience Institute, 308433, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
- Cancer and Stem Cell Biology Program, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- National University Cancer Institute, National University Hospital, 119074, Singapore
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86
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Sutcliffe MD, Galvao RP, Wang L, Kim J, Rosenfeld LK, Singh S, Zong H, Janes KA. Premalignant Oligodendrocyte Precursor Cells Stall in a Heterogeneous State of Replication Stress Prior to Gliomagenesis. Cancer Res 2021; 81:1868-1882. [PMID: 33531372 PMCID: PMC8137536 DOI: 10.1158/0008-5472.can-20-1037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 12/02/2020] [Accepted: 01/28/2021] [Indexed: 11/16/2022]
Abstract
Cancer evolves from premalignant clones that adopt unusual cell states to achieve transformation. We previously pinpointed the oligodendrocyte precursor cell (OPC) as a cell of origin for glioma, but the early changes of mutant OPCs during premalignancy remained unknown. Using mice engineered for inducible Nf1-Trp53 loss in OPCs, we acutely isolated labeled mutant OPCs by laser-capture microdissection, determined global gene-expression changes by bulk RNA sequencing, and compared with cell-state fluctuations at the single-cell level by stochastic profiling, which uses RNA-sequencing measurements from random pools of 10 mutant cells. At 12 days after Nf1-Trp53 deletion, bulk differences were mostly limited to mitotic hallmarks and genes for ribosome biosynthesis, and stochastic profiling revealed a spectrum of stem-progenitor (Axl, Aldh1a1), proneural, and mesenchymal states as potential starting points for gliomagenesis. At 90 days, bulk sequencing detected few differentially expressed transcripts, whereas stochastic profiling revealed cell states for neurons and mural cells that do not give rise to glial tumors, suggesting cellular dead-ends for gliomagenesis. Importantly, mutant OPCs that strongly expressed key effectors of nonsense-mediated decay (Upf3b) and homology-dependent DNA repair (Rad51c, Slx1b, Ercc4) were identified along with DNA-damage markers, suggesting transcription-associated replication stress. Analysis of 10-cell transcriptomes at 90 days identified a locus of elevated gene expression containing an additional repair endonuclease (Mus81) and Rin1, a Ras-Raf antagonist and possible counterbalance to Nf1 loss, which was microdeleted or downregulated in gliomas at 150 days. These hidden cell-state variations uncover replication stress as a potential bottleneck that must be resolved for glioma initiation. SIGNIFICANCE: Profiling premalignant cell states in a mouse model of glioma uncovers regulatory heterogeneity in glioma cells-of-origin and defines a state of replication stress that precedes tumor initiation.See related articles by Singh and colleagues, p. 1840 and Schaff and colleagues, p. 1853.
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Affiliation(s)
- Matthew D Sutcliffe
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Rui P Galvao
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, Virginia
| | - Lixin Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Jungeun Kim
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, Virginia
| | - Lauren K Rosenfeld
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, Virginia
| | - Shambhavi Singh
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Hui Zong
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, Virginia.
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia.
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, Virginia
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87
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Oksdath Mansilla M, Salazar-Hernandez C, Perrin SL, Scheer KG, Cildir G, Toubia J, Sedivakova K, Tea MN, Lenin S, Ponthier E, Yeo ECF, Tergaonkar V, Poonnoose S, Ormsby RJ, Pitson SM, Brown MP, Ebert LM, Gomez GA. 3D-printed microplate inserts for long term high-resolution imaging of live brain organoids. BMC Biomed Eng 2021; 3:6. [PMID: 33789767 PMCID: PMC8015192 DOI: 10.1186/s42490-021-00049-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Organoids are a reliable model used in the study of human brain development and under pathological conditions. However, current methods for brain organoid culture generate tissues that range from 0.5 to 2 mm of size, which need to be constantly agitated to allow proper oxygenation. The culture conditions are, therefore, not suitable for whole-brain organoid live imaging, required to study developmental processes and disease progression within physiologically relevant time frames (i.e. days, weeks, months). RESULTS Here we designed 3D-printed microplate inserts adaptable to standard 24 multi-well plates, which allow the growth of multiple organoids in pre-defined and fixed XYZ coordinates. This innovation facilitates high-resolution imaging of whole-cerebral organoids, allowing precise assessment of organoid growth and morphology, as well as cell tracking within the organoids, over long periods. We applied this technology to track neocortex development through neuronal progenitors in brain organoids, as well as the movement of patient-derived glioblastoma stem cells within healthy brain organoids. CONCLUSIONS This new bioengineering platform constitutes a significant advance that permits long term detailed analysis of whole-brain organoids using multimodal inverted fluorescence microscopy.
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Affiliation(s)
- Mariana Oksdath Mansilla
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.
| | - Camilo Salazar-Hernandez
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Sally L Perrin
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Kaitlin G Scheer
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Gökhan Cildir
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - John Toubia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Frome Road, Adelaide, SA, 5000, Australia
| | - Kristyna Sedivakova
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Melinda N Tea
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Sakthi Lenin
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Elise Ponthier
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Erica C F Yeo
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Vinay Tergaonkar
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Santosh Poonnoose
- Department of Neurosurgery, Flinders Medical Centre, Adelaide, SA, 5042, Australia
- Flinders Health & Medical Research Institute, College of Medicine & Public Health, Flinders University, Adelaide, SA, 5042, Australia
| | - Rebecca J Ormsby
- Flinders Health & Medical Research Institute, College of Medicine & Public Health, Flinders University, Adelaide, SA, 5042, Australia
| | - Stuart M Pitson
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Michael P Brown
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, 5000, Australia
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Lisa M Ebert
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, 5000, Australia
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Guillermo A Gomez
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.
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88
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Kim Y, Varn FS, Park SH, Yoon BW, Park HR, Lee C, Verhaak RGW, Paek SH. Perspective of mesenchymal transformation in glioblastoma. Acta Neuropathol Commun 2021; 9:50. [PMID: 33762019 PMCID: PMC7992784 DOI: 10.1186/s40478-021-01151-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/06/2021] [Indexed: 12/20/2022] Open
Abstract
Despite aggressive multimodal treatment, glioblastoma (GBM), a grade IV primary brain tumor, still portends a poor prognosis with a median overall survival of 12–16 months. The complexity of GBM treatment mainly lies in the inter- and intra-tumoral heterogeneity, which largely contributes to the treatment-refractory and recurrent nature of GBM. By paving the road towards the development of personalized medicine for GBM patients, the cancer genome atlas classification scheme of GBM into distinct transcriptional subtypes has been considered an invaluable approach to overcoming this heterogeneity. Among the identified transcriptional subtypes, the mesenchymal subtype has been found associated with more aggressive, invasive, angiogenic, hypoxic, necrotic, inflammatory, and multitherapy-resistant features than other transcriptional subtypes. Accordingly, mesenchymal GBM patients were found to exhibit worse prognosis than other subtypes when patients with high transcriptional heterogeneity were excluded. Furthermore, identification of the master mesenchymal regulators and their downstream signaling pathways has not only increased our understanding of the complex regulatory transcriptional networks of mesenchymal GBM, but also has generated a list of potent inhibitors for clinical trials. Importantly, the mesenchymal transition of GBM has been found to be tightly associated with treatment-induced phenotypic changes in recurrence. Together, these findings indicate that elucidating the governing and plastic transcriptomic natures of mesenchymal GBM is critical in order to develop novel and selective therapeutic strategies that can improve both patient care and clinical outcomes. Thus, the focus of our review will be on the recent advances in the understanding of the transcriptome of mesenchymal GBM and discuss microenvironmental, metabolic, and treatment-related factors as critical components through which the mesenchymal signature may be acquired. We also take into consideration the transcriptomic plasticity of GBM to discuss the future perspectives in employing selective therapeutic strategies against mesenchymal GBM.
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89
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Caponegro MD, Oh K, Madeira MM, Radin D, Sterge N, Tayyab M, Moffitt RA, Tsirka SE. A distinct microglial subset at the tumor-stroma interface of glioma. Glia 2021; 69:1767-1781. [PMID: 33704822 DOI: 10.1002/glia.23991] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/09/2021] [Accepted: 03/02/2021] [Indexed: 02/01/2023]
Abstract
The characterization of the tumor microenvironment (TME) in high grade gliomas (HGG) has generated significant interest in an effort to understand how neoplastic lesions in the central nervous system (CNS) are supported and to devise novel therapeutic targets. The TME of the CNS contains unique and specialized cells, including the resident myeloid cells, microglia. Myeloid involvement in HGG, such as glioblastoma, is associated with poor outcomes. Glioma-associated microglia and infiltrating monocytes/macrophages (GAM) accumulate within the neoplastic lesion where they facilitate tumor growth and drive immunosuppression. However, it has been difficult to differentiate whether microglia and macrophages have similar or distinct roles in pathology, and if the spatial organization of these cells informs outcomes. Here, we characterize the tumor-stroma border and identify peritumoral GAM (PGAM) as a unique subpopulation of GAM. Using data mining and analyses of samples derived from both murine and human sources we show that PGAM exhibit a pro-inflammatory and chemotactic phenotype that is associated with peripheral monocyte recruitment, and decreased overall survival. PGAM act as a unique subset of GAM at the tumor-stroma interface. We define a novel gene signature to identify these cells and suggest that PGAM constitute a cellular target of the TME.
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Affiliation(s)
- Michael D Caponegro
- Program in Molecular and Cellular Pharmacology, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA.,Department of Pharmacological Sciences, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA
| | - Ki Oh
- Medical Scientist Training Program, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA.,Department of Biomedical Informatics, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA
| | - Miguel M Madeira
- Program in Molecular and Cellular Pharmacology, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA.,Department of Pharmacological Sciences, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA
| | - Daniel Radin
- Program in Molecular and Cellular Pharmacology, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA.,Department of Pharmacological Sciences, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA.,Medical Scientist Training Program, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA
| | - Nicholas Sterge
- Department of Pharmacological Sciences, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA
| | - Maryam Tayyab
- Department of Pharmacological Sciences, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA
| | - Richard A Moffitt
- Department of Pharmacological Sciences, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA.,Department of Biomedical Informatics, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA.,Department of Pathology, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA.,Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA
| | - Stella E Tsirka
- Program in Molecular and Cellular Pharmacology, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA.,Department of Pharmacological Sciences, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, USA
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90
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Involvement of the Catecholamine Pathway in Glioblastoma Development. Cells 2021; 10:cells10030549. [PMID: 33806345 PMCID: PMC7998903 DOI: 10.3390/cells10030549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive tumor of the central nervous system (CNS). The standard of care improves the overall survival of patients only by a few months. Explorations of new therapeutic targets related to molecular properties of the tumor are under way. Even though neurotransmitters and their receptors normally function as mediators of interneuronal communication, growing data suggest that these molecules are also involved in modulating the development and growth of GBM by acting on neuronal and glioblastoma stem cells. In our previous DNA CpG methylation studies, gene ontology analyses revealed the involvement of the monoamine pathway in sequential GBM. In this follow-up study, we quantitated the expression levels of four selected catecholamine pathway markers (alpha 1D adrenergic receptor-ADRA1D; adrenergic beta receptor kinase 1 or G protein-coupled receptor kinase 2-ADRBK1/GRK2; dopamine receptor D2-DRD2; and synaptic vesicle monoamine transporter-SLC18A2) by immunohistochemistry, and compared the histological scores with the methylation levels within the promoters + genes of these markers in 21 pairs of sequential GBM and in controls. Subsequently, we also determined the promoter and gene methylation levels of the same markers in an independent database cohort of sequential GBM pairs. These analyses revealed partial inverse correlations between the catecholamine protein expression and promoter + gene methylation levels, when the tumor and control samples were compared. However, we found no differences in the promoter + gene methylation levels of these markers in either our own or in the database primary-recurrent GBM pairs, despite the higher protein expression of all markers in the primary samples. This observation suggests that regulation of catecholamine expression is only partially related to CpG methylation within the promoter + gene regions, and additional mechanisms may also influence the expression of these markers in progressive GBM. These analyses underscore the involvement of certain catecholamine pathway markers in GBM development and suggest that these molecules mediating or modulating tumor growth merit further exploration.
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91
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Ren X, Zhang L, Zhang Y, Li Z, Siemers N, Zhang Z. Insights Gained from Single-Cell Analysis of Immune Cells in the Tumor Microenvironment. Annu Rev Immunol 2021; 39:583-609. [PMID: 33637019 DOI: 10.1146/annurev-immunol-110519-071134] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding tumor immune microenvironments is critical for identifying immune modifiers of cancer progression and developing cancer immunotherapies. Recent applications of single-cell RNA sequencing (scRNA-seq) in dissecting tumor microenvironments have brought important insights into the biology of tumor-infiltrating immune cells, including their heterogeneity, dynamics, and potential roles in both disease progression and response to immune checkpoint inhibitors and other immunotherapies. This review focuses on the advances in knowledge of tumor immune microenvironments acquired from scRNA-seq studies across multiple types of human tumors, with a particular emphasis on the study of phenotypic plasticity and lineage dynamics of immune cells in the tumor environment. We also discuss several imminent questions emerging from scRNA-seq observations and their potential solutions on the horizon.
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Affiliation(s)
- Xianwen Ren
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China;
| | - Lei Zhang
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China; .,Current affiliation: Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Yuanyuan Zhang
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China;
| | - Ziyi Li
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China;
| | - Nathan Siemers
- Abiosciences, South San Francisco, California 94080, USA
| | - Zemin Zhang
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China;
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92
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Bernstein MN, Ni Z, Collins M, Burkard ME, Kendziorski C, Stewart R. CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets. BMC Bioinformatics 2021; 22:83. [PMID: 33622236 PMCID: PMC7903756 DOI: 10.1186/s12859-021-04021-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single-cell RNA-seq (scRNA-seq) enables the profiling of genome-wide gene expression at the single-cell level and in so doing facilitates insight into and information about cellular heterogeneity within a tissue. This is especially important in cancer, where tumor and tumor microenvironment heterogeneity directly impact development, maintenance, and progression of disease. While publicly available scRNA-seq cancer data sets offer unprecedented opportunity to better understand the mechanisms underlying tumor progression, metastasis, drug resistance, and immune evasion, much of the available information has been underutilized, in part, due to the lack of tools available for aggregating and analysing these data. RESULTS We present CHARacterizing Tumor Subpopulations (CHARTS), a web application for exploring publicly available scRNA-seq cancer data sets in the NCBI's Gene Expression Omnibus. More specifically, CHARTS enables the exploration of individual gene expression, cell type, malignancy-status, differentially expressed genes, and gene set enrichment results in subpopulations of cells across tumors and data sets. Along with the web application, we also make available the backend computational pipeline that was used to produce the analyses that are available for exploration in the web application. CONCLUSION CHARTS is an easy to use, comprehensive platform for exploring single-cell subpopulations within tumors across the ever-growing collection of public scRNA-seq cancer data sets. CHARTS is freely available at charts.morgridge.org.
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Affiliation(s)
| | - Zijian Ni
- Department of Statistics, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | | | - Mark E Burkard
- Department of Medicine, Hematology/Oncology, University of Wisconsin - Madison, Madison, WI, 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, WI, 53705, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53792, USA.
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, 53715, USA.
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93
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Garofano L, Migliozzi S, Oh YT, D'Angelo F, Najac RD, Ko A, Frangaj B, Caruso FP, Yu K, Yuan J, Zhao W, Di Stefano AL, Bielle F, Jiang T, Sims P, Suvà ML, Tang F, Su XD, Ceccarelli M, Sanson M, Lasorella A, Iavarone A. Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities. NATURE CANCER 2021; 2:141-156. [PMID: 33681822 PMCID: PMC7935068 DOI: 10.1038/s43018-020-00159-4] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/25/2020] [Indexed: 12/28/2022]
Abstract
The transcriptomic classification of glioblastoma (GBM) has failed to predict survival and therapeutic vulnerabilities. A computational approach for unbiased identification of core biological traits of single cells and bulk tumors uncovered four tumor cell states and GBM subtypes distributed along neurodevelopmental and metabolic axes, classified as proliferative/progenitor, neuronal, mitochondrial and glycolytic/plurimetabolic. Each subtype was enriched with biologically coherent multiomic features. Mitochondrial GBM was associated with the most favorable clinical outcome. It relied exclusively on oxidative phosphorylation for energy production, whereas the glycolytic/plurimetabolic subtype was sustained by aerobic glycolysis and amino acid and lipid metabolism. Deletion of the glucose-proton symporter SLC45A1 was the truncal alteration most significantly associated with mitochondrial GBM, and the reintroduction of SLC45A1 in mitochondrial glioma cells induced acidification and loss of fitness. Mitochondrial, but not glycolytic/plurimetabolic, GBM exhibited marked vulnerability to inhibitors of oxidative phosphorylation. The pathway-based classification of GBM informs survival and enables precision targeting of cancer metabolism.
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Affiliation(s)
- Luciano Garofano
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
| | - Simona Migliozzi
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Young Taek Oh
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Fulvio D'Angelo
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
- Bioinformatics Lab, BIOGEM, Ariano Irpino, Italy
| | - Ryan D Najac
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Aram Ko
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Brulinda Frangaj
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Francesca Pia Caruso
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
| | - Kai Yu
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
| | - Jinzhou Yuan
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Wenting Zhao
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Anna Luisa Di Stefano
- Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Institut du Cerveau et de la Moelle épinière, Paris, France
- AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
- Department of Neurology, Foch Hospital, Suresnes, Paris, France
| | - Franck Bielle
- Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Institut du Cerveau et de la Moelle épinière, Paris, France
- AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Service de Neuropathologie Raymond Escourolle, Paris, France
- Brain and Spine Institute, Paris, France
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Peter Sims
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
| | - Xiao-Dong Su
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
- Bioinformatics Lab, BIOGEM, Ariano Irpino, Italy
| | - Marc Sanson
- Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Institut du Cerveau et de la Moelle épinière, Paris, France
- Onconeurotek Tumor Bank, Institut du Cerveau et de la Moelle épinère, Paris, France
- Department of Neurology 2, GH Pitié-Salpêtrière, Paris, France
| | - Anna Lasorella
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
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94
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Miska J, Rashidi A, Lee-Chang C, Gao P, Lopez-Rosas A, Zhang P, Burga R, Castro B, Xiao T, Han Y, Hou D, Sampat S, Cordero A, Stoolman JS, Horbinski CM, Burns M, Reshetnyak YK, Chandel NS, Lesniak MS. Polyamines drive myeloid cell survival by buffering intracellular pH to promote immunosuppression in glioblastoma. SCIENCE ADVANCES 2021; 7:eabc8929. [PMID: 33597238 PMCID: PMC7888943 DOI: 10.1126/sciadv.abc8929] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Glioblastoma is characterized by the robust infiltration of immunosuppressive tumor-associated myeloid cells (TAMCs). It is not fully understood how TAMCs survive in the acidic tumor microenvironment to cause immunosuppression in glioblastoma. Metabolic and RNA-seq analysis of TAMCs revealed that the arginine-ornithine-polyamine axis is up-regulated in glioblastoma TAMCs but not in tumor-infiltrating CD8+ T cells. Active de novo synthesis of highly basic polyamines within TAMCs efficiently buffered low intracellular pH to support the survival of these immunosuppressive cells in the harsh acidic environment of solid tumors. Administration of difluoromethylornithine (DFMO), a clinically approved inhibitor of polyamine generation, enhanced animal survival in immunocompetent mice by causing a tumor-specific reduction of polyamines and decreased intracellular pH in TAMCs. DFMO combination with immunotherapy or radiotherapy further enhanced animal survival. These findings indicate that polyamines are used by glioblastoma TAMCs to maintain normal intracellular pH and cell survival and thus promote immunosuppression during tumor evolution.
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Affiliation(s)
- Jason Miska
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA.
| | - Aida Rashidi
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Catalina Lee-Chang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Peng Gao
- Metabolomics Core Facility, Feinberg School of Medicine, Northwestern University, 710 N Fairbanks Court, Chicago, IL 60611, USA
| | - Aurora Lopez-Rosas
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Peng Zhang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Rachel Burga
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Brandyn Castro
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Ting Xiao
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Yu Han
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - David Hou
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Samay Sampat
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Alex Cordero
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Joshua S Stoolman
- Department of Medicine, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2330, Chicago, IL 60611, USA
| | - Craig M Horbinski
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
| | - Mark Burns
- Aminex Therapeutics Inc., Epsom, NH 03234, USA
| | - Yana K Reshetnyak
- Physics Department, University of Rhode Island, Kingston, RI 02881, USA
| | - Navdeep S Chandel
- Department of Medicine, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2330, Chicago, IL 60611, USA
| | - Maciej S Lesniak
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 2210, Chicago, IL 60611, USA
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95
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Yu G, Butler MK, Abdelmaksoud A, Pang Y, Su YT, Rae Z, Dadkhah K, Kelly MC, Song YK, Wei JS, Terabe M, Atony R, Mentges K, Theeler BJ, Penas-Prado M, Butman J, Camphausen K, Zaghloul KA, Nduom E, Quezado M, Aldape K, Armstrong TS, Gilbert MR, Gulley JL, Khan J, Wu J. Case Report: Single-Cell Transcriptomic Analysis of an Anaplastic Oligodendroglioma Post Immunotherapy. Front Oncol 2021; 10:601452. [PMID: 33520712 PMCID: PMC7841290 DOI: 10.3389/fonc.2020.601452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/20/2020] [Indexed: 11/13/2022] Open
Abstract
Glioma is the most common primary malignant brain tumor with a poor prognosis. Immune checkpoint inhibitors have been of great interest in investigation of glioma treatments. Here, we report single-cell transcriptomic analyses of two tumor areas from an oligodendroglioma taken from a patient who had multiple tumor recurrences, following several chemotherapies and radiation treatments. The patient subsequently received nivolumab and was considered have disease progression based on conventional diagnostic imaging after two cycles of treatment. He underwent a debulking surgical resection and pathological diagnosis was recurrent disease. During the surgery, tumor tissues were also collected from the enhancing and non-enhancing areas for a scRNAseq analysis to investigate the tumor microenvironment of these radiographically divergent areas. The scRNAseq analysis reveals a plethora of immune cells, suggesting that the increased mass observed on MRI may be partially a result of immune cell infiltration. The patient continued to receive immunotherapy after a short course of palliative radiation and remained free of disease progression for at least 12 months after the last surgery, suggesting a sustained response to immunotherapy. The scRNAseq analysis indicated that the radiological progression was in large part due to immune cell infiltrate and continued immunotherapy led to a positive clinical outcome in a patient who would have otherwise been admitted to hospice care with halting of immunotherapy. Our study demonstrates the potential of scRNAseq analyses in understanding the tumor microenvironment, which may assist the clinical decision-making process for challenging glioma cases following immunotherapy.
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Affiliation(s)
- Guangyang Yu
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Madison K. Butler
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Abdalla Abdelmaksoud
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ying Pang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yu-Ting Su
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Zachary Rae
- Single Cell Analysis Facility, Center for Cancer Research, National Institutes of Health, Bethesda, MD, United States
| | - Kimia Dadkhah
- Single Cell Analysis Facility, Center for Cancer Research, National Institutes of Health, Bethesda, MD, United States
| | - Michael C. Kelly
- Single Cell Analysis Facility, Center for Cancer Research, National Institutes of Health, Bethesda, MD, United States
| | - Young K. Song
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jun S. Wei
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Masaki Terabe
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ramya Atony
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kelly Mentges
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Brett J. Theeler
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Marta Penas-Prado
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - John Butman
- Diagnostic Radiology Department, The Clinical Center of the National Institutes of Health, Bethesda, MD, United States
| | - Kevin Camphausen
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kareem A. Zaghloul
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Edjah Nduom
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Terri S. Armstrong
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mark R. Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - James L. Gulley
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jing Wu
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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96
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Pang B, Quan F, Ping Y, Hu J, Lan Y, Pang L. Dissecting the Invasion-Associated Long Non-coding RNAs Using Single-Cell RNA-Seq Data of Glioblastoma. Front Genet 2021; 11:633455. [PMID: 33505440 PMCID: PMC7831882 DOI: 10.3389/fgene.2020.633455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/14/2020] [Indexed: 12/25/2022] Open
Abstract
Glioblastoma (GBM) is characterized by rapid and lethal infiltration of brain tissue, which is the primary cause of treatment failure and deaths for GBM. Therefore, understanding the molecular mechanisms of tumor cell invasion is crucial for the treatment of GBM. In this study, we dissected the single-cell RNA-seq data of 3345 cells from four patients and identified dysregulated genes including long non-coding RNAs (lncRNAs), which were involved in the development and progression of GBM. Based on co-expression network analysis, we identified a module (M1) that significantly overlapped with the largest number of dysregulated genes and was confirmed to be associated with GBM invasion by integrating EMT signature, experiment-validated invasive marker and pseudotime trajectory analysis. Further, we denoted invasion-associated lncRNAs which showed significant correlations with M1 and revealed their gradually increased expression levels along the tumor cell invasion trajectory, such as VIM-AS1, WWTR1-AS1, and NEAT1. We also observed the contribution of higher expression of these lncRNAs to poorer survival of GBM patients. These results were mostly recaptured in another validation data of 7930 single cells from 28 GBM patients. Our findings identified lncRNAs that played critical roles in regulating or controlling cell invasion and migration of GBM and provided new insights into the molecular mechanisms underlying GBM invasion as well as potential targets for the treatment of GBM.
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Affiliation(s)
- Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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97
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Convection Enhanced Delivery of Topotecan for Gliomas: A Single-Center Experience. Pharmaceutics 2020; 13:pharmaceutics13010039. [PMID: 33396668 PMCID: PMC7823846 DOI: 10.3390/pharmaceutics13010039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 12/24/2022] Open
Abstract
A key limitation to glioma treatment involves the blood brain barrier (BBB). Convection enhanced delivery (CED) is a technique that uses a catheter placed directly into the brain parenchyma to infuse treatments using a pressure gradient. In this manuscript, we describe the physical principles behind CED along with the common pitfalls and methods for optimizing convection. Finally, we highlight our institutional experience using topotecan CED for the treatment of malignant glioma.
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98
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Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D, Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A, Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG, Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S, Gümüş ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L, Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B, Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM, Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T, Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A, Wiznerowicz M, Schürer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI, Fenyö D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB, Rood BR, Wang P. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell 2020; 183:1962-1985.e31. [PMID: 33242424 PMCID: PMC8143193 DOI: 10.1016/j.cell.2020.10.044] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/19/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.
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Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Tignor
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mateusz Koptyra
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Antonio Colaprico
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Tatiana Omelchenko
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Richard G Ivey
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John Szpyt
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanjukta Guha Thakurta
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gonzalo Lopez
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Selim Kalayci
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jacob J Kennedy
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Lei Zhao
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brian M Ennis
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Valerie Baubet
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lamiya Tauhid
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jena V Lilly
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer L Mason
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bailey Farrow
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan Young
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sarah Leary
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Javad Nazarian
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA; Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Zürich 8032, Switzerland
| | - Nithin D Adappa
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James N Palmer
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert M Lober
- Department of Neurosurgery, Dayton Children's Hospital, Dayton, OH 45404, USA
| | - Samuel Rivero-Hinojosa
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Joshua M Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Matilda Broberg
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Neurology, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 61-203 Poznań, Poland
| | - Stephan Schürer
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Xi S Chen
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Allison P Heath
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Fenyö
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Steven P Gygi
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Brian R Rood
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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99
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Ruiz-Garcia H, Alvarado-Estrada K, Krishnan S, Quinones-Hinojosa A, Trifiletti DM. Nanoparticles for Stem Cell Therapy Bioengineering in Glioma. Front Bioeng Biotechnol 2020; 8:558375. [PMID: 33365304 PMCID: PMC7750507 DOI: 10.3389/fbioe.2020.558375] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Gliomas are a dismal disease associated with poor survival and high morbidity. Current standard treatments have reached a therapeutic plateau even after combining maximal safe resection, radiation, and chemotherapy. In this setting, stem cells (SCs) have risen as a promising therapeutic armamentarium, given their intrinsic tumor homing as well as their natural or bioengineered antitumor properties. The interplay between stem cells and other therapeutic approaches such as nanoparticles holds the potential to synergize the advantages from the combined therapeutic strategies. Nanoparticles represent a broad spectrum of synthetic and natural biomaterials that have been proven effective in expanding diagnostic and therapeutic efforts, either used alone or in combination with immune, genetic, or cellular therapies. Stem cells have been bioengineered using these biomaterials to enhance their natural properties as well as to act as their vehicle when anticancer nanoparticles need to be delivered into the tumor microenvironment in a very precise manner. Here, we describe the recent developments of this new paradigm in the treatment of malignant gliomas.
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Affiliation(s)
- Henry Ruiz-Garcia
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, FL, United States.,Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, United States
| | | | - Sunil Krishnan
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, FL, United States
| | | | - Daniel M Trifiletti
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, FL, United States.,Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, United States
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100
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Lamanna J, Scott EY, Edwards HS, Chamberlain MD, Dryden MDM, Peng J, Mair B, Lee A, Chan C, Sklavounos AA, Heffernan A, Abbas F, Lam C, Olson ME, Moffat J, Wheeler AR. Digital microfluidic isolation of single cells for -Omics. Nat Commun 2020; 11:5632. [PMID: 33177493 PMCID: PMC7658233 DOI: 10.1038/s41467-020-19394-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/02/2020] [Indexed: 11/28/2022] Open
Abstract
We introduce Digital microfluidic Isolation of Single Cells for -Omics (DISCO), a platform that allows users to select particular cells of interest from a limited initial sample size and connects single-cell sequencing data to their immunofluorescence-based phenotypes. Specifically, DISCO combines digital microfluidics, laser cell lysis, and artificial intelligence-driven image processing to collect the contents of single cells from heterogeneous populations, followed by analysis of single-cell genomes and transcriptomes by next-generation sequencing, and proteomes by nanoflow liquid chromatography and tandem mass spectrometry. The results described herein confirm the utility of DISCO for sequencing at levels that are equivalent to or enhanced relative to the state of the art, capable of identifying features at the level of single nucleotide variations. The unique levels of selectivity, context, and accountability of DISCO suggest potential utility for deep analysis of any rare cell population with contextual dependencies. Multi-Omic approaches are a powerful way for obtaining in-depth understanding of a cell’s state. Here the authors present DISCO, combining digital microfluidics, laser cell lysis, and artificial intelligence-driven image processing to analyze single-cell genomes, transcriptomes and proteomes in a mixed population.
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Affiliation(s)
- Julian Lamanna
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Erica Y Scott
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Harrison S Edwards
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
| | - M Dean Chamberlain
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Michael D M Dryden
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Barbara Mair
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Adam Lee
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
| | - Calvin Chan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Austin Heffernan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Farhana Abbas
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Charis Lam
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Maxwell E Olson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada. .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada. .,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
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